Genome and clonal hematopoiesis stability contrasts with immune, cfDNA, mitochondrial, and telomere length changes during short duration spaceflight

Background

The Inspiration4 (I4) mission, the first all-civilian orbital flight mission, investigated the physiological effects of short-duration spaceflight through a multi-omic approach. Despite advances, there remains much to learn about human adaptation to spaceflight's unique challenges, including microgravity, immune system perturbations, and radiation exposure.

Methods

To provide a detailed genetics analysis of the mission, we collected dried blood spots pre-, during, and post-flight for DNA extraction. Telomere length was measured by quantitative PCR, while whole genome and cfDNA sequencing provided insight into genomic stability and immune adaptations. A robust bioinformatic pipeline was used for data analysis, including variant calling to assess mutational burden.

Result

Telomere elongation occurred during spaceflight and shortened after return to Earth. Cell-free DNA analysis revealed increased immune cell signatures post-flight. No significant clonal hematopoiesis of indeterminate potential (CHIP) or whole-genome instability was observed. The long-term gene expression changes across immune cells suggested cellular adaptations to the space environment persisting months post-flight.

Conclusion

Our findings provide valuable insights into the physiological consequences of short-duration spaceflight, with telomere dynamics and immune cell gene expression adapting to spaceflight and persisting after return to Earth. CHIP sequencing data will serve as a reference point for studying the early development of CHIP in astronauts, an understudied phenomenon as previous studies have focused on career astronauts. This study will serve as a reference point for future commercial and non-commercial spaceflight, low Earth orbit (LEO) missions, and deep-space exploration.

Paired bone marrow and peripheral blood samples demonstrate lack of widespread dissemination of some CH clones

Clonal hematopoiesis (CH) represents clonal expansion of mutated hematopoietic stem cells detectable in the peripheral blood or bone marrow through next generation sequencing. The current prevailing model posits that CH mutations detected in the peripheral blood mirror bone marrow mutations with clones widely disseminated across hematopoietic compartments. We sought to test the hypothesis that all clones are disseminated throughout hematopoietic tissues by comparing CH in hip vs peripheral blood specimens collected at the time of hip replacement surgery. Here, we show that patients with osteoarthritis have a high prevalence of CH, which involve genes encoding epigenetic modifiers and DNA damage repair pathway proteins. Importantly, we illustrate that CH, including clones with variant allele frequencies >10%, can be confined to specific bone marrow spaces and may be eliminated through surgical excision. Future work will define whether clones with somatic mutations in particular genes or clonal fractions of certain sizes are either more likely to be localized or are slower to disseminate into the peripheral blood and other bony sites.

Matrix stiffness enhances cancer-macrophage interactions and M2-like macrophage accumulation in the breast tumor microenvironment

The role of intratumor heterogeneity is becoming increasingly apparent in part due to expansion in single cell technologies. Clinically, tumor heterogeneity poses several obstacles to effective cancer therapy dealing with biomarker variability and treatment responses. Matrix stiffening is known to occur during tumor progression and contribute to pathogenesis in several cancer hallmarks, including tumor angiogenesis and metastasis. However, the effects of matrix stiffening on intratumor heterogeneity have not been thoroughly studied. In this study, we applied single-cell RNA sequencing to investigate the differences in the transcriptional landscapes between stiff and compliant MMTV-PyMT mouse mammary tumors. We found similar compositions of cancer and stromal subpopulations in compliant and stiff tumors but differential intercellular communication and a significantly higher concentration of tumor-promoting, M2-like macrophages in the stiffer tumor microenvironments. Interestingly, we found that cancer cells seeded on stiffer substrates recruited more macrophages. Furthermore, elevated matrix stiffness increased Colony Stimulating Factor 1 (CSF-1) expression in breast cancer cells and reduction of CSF-1 expression on stiffer substrates reduced macrophage recruitment. Thus, our results demonstrate that tissue phenotypes were conserved between stiff and compliant tumors but matrix stiffening altered cell-cell interactions which may be responsible for shifting the phenotypic balance of macrophages residing in the tumor microenvironment towards a pro-tumor progression M2 phenotype. STATEMENT OF SIGNIFICANCE: Cells within tumors are highly heterogeneous, posing challenges with treatment and recurrence. While increased tissue stiffness can promote several hallmarks of cancer, its effects on tumor heterogeneity are unclear. We used single-cell RNA sequencing to investigate the differences in the transcriptional landscapes between stiff and compliant MMTV-PyMT mouse mammary tumors. We found similar compositions of cancer and stromal subpopulations in compliant and stiff tumors but differential intercellular communication and a significantly higher concentration of tumor-promoting, M2-like macrophages in the stiffer tumor microenvironments. Using a biomaterial-based platform, we found that cancer cells seeded on stiffer substrates recruited more macrophages, supporting our in vivo findings. Together, our results demonstrate a key role of matrix stiffness in affecting cell-cell communication and macrophage recruitment.

Mutant PPM1D- and TP53-Driven Hematopoiesis Populates the Hematopoietic Compartment in Response to Peptide Receptor Radionuclide Therapy

PURPOSE

Hematologic toxic effects of peptide receptor radionuclide therapy (PRRT) can be permanent. Patients with underlying clonal hematopoiesis (CH) may be more inclined to develop hematologic toxicity after PRRT. However, this association remains understudied.

MATERIALS AND METHODS

We evaluated pre- and post-PRRT blood samples of patients with neuroendocrine tumors. After initial screening, 13 cases of interest were selected. Serial blood samples were obtained on 4 of 13 patients. Genomic DNA was analyzed using a 100-gene panel. A variant allele frequency cutoff of 1% was used to call CH.

RESULT

Sixty-two percent of patients had CH at baseline. Persistent cytopenias were noted in 64% (7 of 11) of the patients. Serial sample analysis demonstrated that PRRT exposure resulted in clonal expansion of mutant DNA damage response genes (TP53, CHEK2, and PPM1D) and accompanying cytopenias in 75% (3 of 4) of the patients. One patient who had a normal baseline hemogram and developed persistent cytopenias after PRRT exposure showed expansion of mutant PPM1D (variant allele frequency increased to 20% after exposure from < 1% at baseline). In the other two patients, expansion of mutant TP53, CHEK2, and PPM1D clones was also noted along with cytopenia development.

CONCLUSION

The shifts in hematopoietic clonal dynamics in our study were accompanied by emergence and persistence of cytopenias. These cytopenias likely represent premalignant state, as PPM1D-, CHEK2-, and TP53-mutant clones by themselves carry a high risk for transformation to therapy-related myeloid neoplasms. Future studies should consider CH screening and longitudinal monitoring as a key risk mitigation strategy for patients with neuroendocrine tumors receiving PRRT.

Patient-Derived Bone Marrow Spheroids Reveal Leukemia-Initiating Cells Supported by Mesenchymal Hypoxic Niches in Pediatric B-ALL

B-cell acute lymphoblastic leukemia (B-ALL) results from the expansion of malignant lymphoid precursors within the bone marrow (BM), where hematopoietic niches and microenvironmental signals provide leukemia-initiating cells (LICs) the conditions to survive, proliferate, initiate disease, and relapse. Normal and malignant lymphopoiesis are highly dependent on the BM microenvironment, particularly on CXCL12-abundant Reticular (CAR) cells, which provide a niche for maintenance of primitive cells. During B-ALL, leukemic cells hijack BM niches, creating a proinflammatory milieu incompetent to support normal hematopoiesis but favoring leukemic proliferation. Although the lack of a phenotypic stem cell hierarchy is apparent in B-ALL, LICs are a rare and quiescent population potentially responsible for chemoresistance and relapse. Here, we developed novel patient-derived leukemia spheroids (PDLS), an ex vivo avatar model, from mesenchymal stromal cells (MSCs) and primary B-ALL cells, to mimic specialized niche structures and cell-to-cell intercommunication promoting normal and malignant hematopoiesis in pediatric B-ALL. 3D MSC spheroids can recapitulate CAR niche-like hypoxic structures that produce high levels of CXCL10 and CXCL11. We found that PDLS were preferentially enriched with leukemia cells displaying functional properties of LICs, such as quiescence, low reactive oxygen species, drug resistance, high engraftment in immunodeficient mice, and long-term leukemogenesis. Moreover, the combination of PDLS and patient-derived xenografts confirmed a microenvironment-driven hierarchy in their leukemic potential. Importantly, transcriptional profiles of MSC derived from primary patient samples revealed two unique signatures (1), a CXCL12low inflammatory and leukemia expansion (ILE)-like niche, that likely supports leukemic burden, and (2) a CXCL11hi immune-suppressive and leukemia-initiating cell (SLIC)-like niche, where LICs are likely sustained. Interestingly, the CXCL11+ hypoxic zones were recapitulated within the PDLS that are capable of supporting LIC functions. Taken together, we have implemented a novel PDLS system that enriches and supports leukemia cells with stem cell features driven by CXCL11+ MSCs within hypoxic microenvironments capable of recapitulating key features, such as tumor reemergence after exposure to chemotherapy and tumor initiation. This system represents a unique opportunity for designing ex vivo personalized avatars for B-ALL patients to evaluate their own LIC pathobiology and drug sensitivity in the context of the tumor microenvironment.

Targeting the epichaperome as an effective precision medicine approach in a novel PML-SYK fusion acute myeloid leukemia

The epichaperome is a new cancer target composed of hyperconnected networks of chaperome members that facilitate cell survival. Cancers with an altered chaperone configuration may be susceptible to epichaperome inhibitors. We developed a flow cytometry-based assay for evaluation and monitoring of epichaperome abundance at the single cell level, with the goal of prospectively identifying patients likely to respond to epichaperome inhibitors, to measure target engagement, and dependency during treatment. As proof of principle, we describe a patient with an unclassified myeloproliferative neoplasm harboring a novel PML-SYK fusion, who progressed to acute myeloid leukemia despite chemotherapy and allogeneic stem cell transplant. The leukemia was identified as having high epichaperome abundance. We obtained compassionate access to an investigational epichaperome inhibitor, PU-H71. After 16 doses, the patient achieved durable complete remission. These encouraging results suggest that further investigation of epichaperome inhibitors in patients with abundant baseline epichaperome levels is warranted.

Mutant PPM1D and TP53 populate the hematopoietic compartment after peptide receptor radionuclide therapy (PRRT) exposure

10605

Background: Mutations in TP53 and PPM1D are putative drivers associated with therapy related-myeloid neoplasm (T-MN) and have been identified in pre-treatment blood samples obtained at the time of primary malignancy, predating clinically evident T-MN. Genomic analysis of patients(pts) who undergo leukemogenic therapies will help understand T-MN biology and devise risk mitigation strategies. PRRT (Lu 177) for neuroendocrine tumors is associated with enhanced risk of T-MNs. The mechanism for T-MN induced by PRRT is largely elusive due to the novelty of this drug. Methods: We analyzed initial (n=13) and serial blood samples (n=4) prior to and following PRRT for clonal mutations in order to elucidate the role of PRRT in exerting selective pressures on HSCs. Genomic DNA was analyzed using a targeted myeloid 100-gene panel and a variant allele frequency (VAF) cutoff 1% was used to call clonal hematopoiesis (CH). Results: Fifty-four percent pts had CH, despite relatively young age of cohort (median age 58 years, range 41-75) and minimal chemo-radiotherapy exposure; baseline characteristics and molecular profile of cohort is published [Singh et al. Blood 2020; 136 (Supplement 1): 35–36]. Serial sample analysis in 4 pts (Table 1) demonstrates that PRRT exposure is associated with clonal evolution and accompanying cytopenias in 75% (3/4) pts. Pt-1 (age 67) with normal baseline hemogram developed persistent cytopenias after PRRT, accompanied by emergence and expansion of mutant- PPM1D (m PPM1D; VAF 20%). These data suggest that cytopenias result from repopulation of the HSC compartment by m PPM1D cells. In Pts 2 and 3 (age 74 and 75), we note expansion of m TP53 and m PPM1D clones respectively, also associated with the development of cytopenias. Pt-4 was younger (age 59) and developed no cytopenias. Exposure to PRRT was associated with loss of m TET2 and m DDX41, possibly due to lack of clonal fitness of m TET2/DDX41 clones and the relatively young HSC microenvironment. Conclusions: We conclude that mutations in PPM1D and TP53 are clinically relevant, contribute to clonal cytopenias and may increase risk of future T-MN. The temporal association of m TP53 and m PPM1D expansion with PRRT exposure in our analysis suggests selection of these clones in response to PRRT-induced stress, outcompeting wild type and less therapy-resistant HSCs. Our study along with others will inform future efforts to strategize methods of surveillance and early detection for clonality assessment and chemoprevention, to reduce adverse effects of leukemogenic therapies.[Table: see text]

Clonal Hematopoiesis Before, During, and After Human Spaceflight

Clonal hematopoiesis (CH) occurs when blood cells harboring an advantageous mutation propagate faster than others. These mutations confer a risk for hematological cancers and cardiovascular disease. Here, we analyze CH in blood samples from a pair of twin astronauts over 4 years in bulk and fractionated cell populations using a targeted CH panel, linked-read whole-genome sequencing, and deep RNA sequencing. We show CH with distinct mutational profiles and increasing allelic fraction that includes a high-risk, TET2 clone in one subject and two DNMT3A mutations on distinct alleles in the other twin. These astronauts exhibit CH almost two decades prior to the mean age at which it is typically detected and show larger shifts in clone size than age-matched controls or radiotherapy patients, based on a longitudinal cohort of 157 cancer patients. As such, longitudinal monitoring of CH may serve as an important metric for overall cancer and cardiovascular risk in astronauts.

Trinchant et al. examined twin astronauts for clonal hematopoiesis (CH). Some high-risk CH clones (TET2 and DNMT3A) were observed two decades before expected, with TET2 decreasing in spaceflight and elevating later post flight. Thus, CH is an important metric for overall cancer and cardiovascular risk in astronauts.

Plasma Cell Myeloma Presenting With Amyloid-Laden Crystal-Negative Histiocytosis

OBJECTIVES

Crystal-storing histiocytosis (CSH) is rare in plasma cell dyscrasias, with only 3 cases reported in the setting of amyloid. No cases of crystal-negative histiocytosis coincident with multiple myeloma and amyloidosis have been reported previously.

METHODS

A 58-year-old woman presented with pain due to destructive bone lesions and was found to have plasma cell myeloma (PCM) and marrow amyloid deposition associated with crystal-negative histiocytosis. Differential diagnoses included Langerhans cell histiocytosis, Erdheim-Chester disease, and Rosai Dorfman disease. BRAF mutations were negative, and there was no evidence of paraprotein crystals, arguing against typical CSH.

RESULTS

The patient was treated with bortezomib, cyclophosphamide, and dexamethasone, and she subsequently underwent autologous stem cell transplant and ixazomib maintenance. She achieved complete remission with improvement of her symptoms and preserved remission after following up at 60 months.

CONCLUSIONS

We describe a case of crystal-negative histiocytosis associated with PCM. CSH is a rare disorder associated with paraprotein-producing conditions in which immunoglobulins aggregate as intracellular crystals in the lysosomes of organ-specific phagocytic macrophages. Light chain tropism in PCM can also lead to the development of amyloid deposition in organs and, in rare cases, is associated with light chain aggregation as intracellular crystals in macrophages.

Clonal Hematopoiesis and Premalignant Diseases

Clonal hematopoiesis (CH) arises when mutations in the hematopoietic system confer a fitness advantage to specific clones, thereby favoring their disproportionate growth. The presence of CH increases with age and environmental exposures such as cytotoxic chemotherapy or radiotherapy. The most frequent mutations occur in epigenetic regulators, such as DNMT3A, TET2, and ASXL1, leading to dysregulation of tumor suppressor function, pathogen response, and inflammation. These dysregulated processes elevate risk of overall mortality, cardiovascular disease, and eventual hematologic malignancy (HM). CH is likely acting as an initiating event leading to HM when followed by cooperating mutations. However, further evidence suggests that CH exerts a bystander influence through its pro-inflammatory properties. Delineating the mechanisms that lead to the onset and expansion of CH as well as its contribution to risk of HM is crucial to defining a management and intervention strategy. In this review, we discuss the potential causes, consequences, technical considerations, and possible management strategies for CH in the context of HMs and pre-HMs.

Abstract 5681: Prediction of immunotherapy outcome by multimodal assessment of minimal residual disease and persistence of allogeneic anti-CD123 CAR T-cells (UCART123) in pre-clinical models of acute myeloid leukemia

Acute myeloid leukemia (AML) is a fatal disease. The promise of autologous T-cells expressing chimeric antigen receptors (CARs) in targeting B-cell malignancies has encouraged extension of this approach to AML. However, clinical guidance regarding infusion and re-infusion regimens for CAR-T technology is unclear for any cancer including AML. Given that studies demonstrate clear benefit for minimal residual disease (MRD) assessment in predicting relapse for AML, we thus sought to ascertain whether simultaneous molecular assessment of MRD markers and CAR-T-specific markers could inform decisions around CAR-T dosing and re-infusion. We tested this approach using patient-derived xenograft (PDX) models with allogeneic anti-CD123 CAR-T cells (UCART123). UCART123 are genetically modified allogeneic T-cells expressing an anti-CD123 CAR. These cells lack expression of the T-cell receptor (TCRabKO), in order to minimize graft vs. host disease (GvHD).

PDX were established using prognostically adverse AML (FLT3-ITD+NPM1+) and treated with 1x106 or 2.5x106 UCART123. The median overall survival (OS) of control mice injected with saline or CAR-T negative (TCRabKO) T-cells succumbed to disease was 124.5 and 126 days, respectively. In contrast, UCART123 groups survived &gt;180 days (hazard ratio 0.08, P=0.003). Clonal dynamics between disease and CAR-T were simultaneously monitored post-infusion by quantifying mutated NPM1 and CAR-T genetic markers, respectively, using digital droplet PCR (ddPCR). We found that ddPCR monitoring was more sensitive than multiparameter flow cytometry (MFC) at detecting MRD and persistence of UCART123. Using ddPCR, leukemia and UCART123 cells were detected when human cells were not evaluable using MFC in peripheral blood (PB). Mice with persistent UCART123 remained disease-free. Importantly, when mutated NPM1 levels became elevated with simultaneous loss of UCART123, relapse was evident by MFC in PB in subsequent time-points (2 out 20 mice, all at 1x106 dose, ~180 days) re-infusion of UCART123 cells resulted in effective elimination of AML.

Taken together, we have demonstrated that simultaneous monitoring of disease and UCART123 cells provides valuable insight into the kinetics and effectiveness of UCART123 cells. Currently, we have implemented the ddPCR assay in the phase I clinical trial of UCART123 in AML allowing to simultaneously detect UCART123 cells and blasts in peripheral blood of NPM1 mutant AML patients.

Citation Format: Mayumi Sugita, Nuria Mencia-Trinchant, Nathan Ewing-Crystal, Gabrielle Suppa, Roman Galetto, Agnès Gouble, Julianne Smith, Gail J. Roboz, Duane C. Hassane, Monica L. Guzman. Prediction of immunotherapy outcome by multimodal assessment of minimal residual disease and persistence of allogeneic anti-CD123 CAR T-cells (UCART123) in pre-clinical models of acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5681.

Phase I trial of plerixafor combined with decitabine in newly diagnosed older patients with acute myeloid leukemia

Acute myeloid leukemia carries a dismal prognosis in older patients. The objective of this study was to investigate the safety and efficacy of decitabine combined with the CXCR4 antagonist plerixafor in newly diagnosed older patients with acute myeloid leukemia and to evaluate the effects of plerixafor on leukemia stem cells. Patients were treated with monthly cycles of decitabine 20 mg/m² days 1–10 and escalating doses of plerixafor (320–810 mcg/kg) days 1–5. Sixty-nine patients were treated, with an overall response rate of 43%. Adverse karyotype did not predict response (P=0.31). Prior hypomethylating agent treatment was the strongest independent predictor of adverse overall survival (hazard ratio 3.1; 95%CI: 1.3–7.3; P=0.008) and response (14% in previously treated patients, 46% in treatment naïve; P=0.002). As expected, the most common toxicities were myelosuppression and infection. Plerixafor induced mobilization of leukemia stem and progenitor cells, but did not cause clinically significant hyperleukocytosis. Reduction in leukemia stem cells appeared to correlate with duration of response. Plerixafor can be safely added to decitabine in poor-prognosis, elderly acute myeloid leukemia patients. The maximum tolerated dose of the combination was 810 mcg/kg. While mobilization of leukemia stem cells was observed in some patients, the clinical benefit of adding plerixafor was uncertain. This trial was registered at clinicaltrials.gov identifier: 01352650.

CD25 expression and outcomes in older patients with acute myelogenous leukemia treated with plerixafor and decitabine

We investigated CD25 expression in older (≥60 years) patients with new acute myelogenous leukemia treated with decitabine and plerixafor. Patients resistant to therapy or survival ≤1 year had significantly higher percentages of CD25^pos myeloid blasts in baseline bone marrow. CD25^pos patients had an increased odds of resistance compared to CD25^neg patients (p = .015). In univariate analysis, we found CD25^pos patients had inferior survival compared to CD25^neg (p = .002). In patients with intermediate risk cytogenetics, CD25^pos status stratified patients associating with inferior survival (p = .002). In multivariable analysis, CD25 and TP53 mutations trended towards predicting remission to therapy but were not predictive of survival. Only remission status, ASXL1 and TET2 mutations were found to independently predict overall survival (OS). We conclude CD25 expression identifies patients at risk for resistance to hypomethylating chemotherapy but does not independently predict OS in an older AML population treated with decitabine and plerixafor.

Minimal residual disease in acute myelogenous leukemia

Treatment of acute myelogenous leukemia (AML) over the past four decades remains mostly unchanged and the prognosis for the majority of patients remains poor. Most of the significant advances that have been observed are in defining cytogenetic abnormalities, as well as the genetic and epigenetic profiles of AML patients. While new cytogenetic and genetic aberrations such as the FLT3-ITD and NPM1 mutations are able to guide prognosis for the majority of patients with AML, outcomes are still dismal and relapse rates remain high. It is thought that relapse in AML is in part driven by minimal residual disease (MRD) that remains in the patient following treatment. Thus, there is a need for sensitive and objective methodology for MRD detection. Methodologies such as multiparameter flow cytometry (MFC), quantitative real-time polymerase chain reaction (RQ-PCR), digital PCR (dPCR), or next-generation sequencing (NGS) are being employed to evaluate their utility in MRD assessment. In this review, we will provide an overview of AML and the clinical utility of MRD measurement. We will discuss optimal timing to MRD measurement, the different approaches that are available, and efforts in the standardization across laboratories.

Minimal Residual Disease Monitoring of Acute Myeloid Leukemia by Massively Multiplex Digital PCR in Patients with NPM1 Mutations

The presence of minimal residual disease (MRD) is widely recognized as a powerful predictor of therapeutic outcome in acute myeloid leukemia (AML), but methods of measurement and quantification of MRD in AML are not yet standardized in clinical practice. There is an urgent, unmet need for robust and sensitive assays that can be readily adopted as real-time tools for disease monitoring. NPM1 frameshift mutations are an established MRD marker present in half of patients with cytogenetically normal AML. However, detection is complicated by the existence of hundreds of potential frameshift insertions, clonal heterogeneity, and absence of sequence information when the NPM1 mutation is identified using capillary electrophoresis. Thus, some patients are ineligible for NPM1 MRD monitoring. Furthermore, a subset of patients with NPM1-mutated AML will have false-negative MRD results because of clonal evolution. To simplify and improve MRD testing for NPM1, we present a novel digital PCR technique composed of massively multiplex pools of insertion-specific primers that selectively detect mutated but not wild-type NPM1. By measuring reaction end points using digital PCR technology, the resulting single assay enables sensitive and specific quantification of most NPM1 exon 12 mutations in a manner that is robust to clonal heterogeneity, does not require NPM1 sequence information, and obviates the need for maintenance of hundreds of type-specific assays and associated plasmid standards.

Abstract LB-073: Epigenome evolution in relapsed acute myeloid leukemia

Acute myeloid leukemia (AML) is a predominantly fatal hematopoietic malignancy with high inter-patient and intra-patient genetic and epigenetic heterogeneity. The prognosis of relapsed AML remains dismal, yet the epigenetic basis of relapse is still unclear. Here we investigated whether and how the epigenome evolution impacts AML progression with biological and clinical relevance.

Methods: We obtained clinical annotation and AML specimens from 138 patients with paired diagnosis and relapsed samples. We used normal bone marrow (NBM) as epigenetic/transcriptomic controls and patients’ matched germline DNA as genetic controls. We then performed DNA methylation sequencing (ERRBS), RNA-seq, and Exome-seq. For one patient with 5 serial time points, we performed whole genome sequencing (WGS), ERRBS, and single cell RNA-seq. We measured the epigenetic allele burden using a compositional entropy-based approach (Methclone) and methylation heterogeneity using epipolymorphism.

Results: We found that diagnosis stage epigenetic allele burden (ΔS &lt; -90) was linked to an inferior clinical outcome (p = 0.0064, log-rank test of relapse-free survival). The higher significance in promoter regions implies the functional impact of epigenetic dynamics. Promoter epiallele shift was associated with more differential expression events (p = 3.8 × 10−6, Wilcoxon signed-rank test) and promoter epiallele diversity is significantly associated with single cell resolution transcriptional heterogeneity (p &lt; 2.2 × 10−16, ANOVA test). The global methylation heterogeneity is decreased from diagnosis to relapse, indicating a selective impact of chemotherapy on epigenetic variability (p = 0.0056, paired Wilcoxon test).

We investigated epigenetic allele burden progression from diagnosis to relapse by classifying patients into three clusters using K-means clustering: those with 1) decreased, 2) stable, or 3) increased abundance of epiallele burden. No association was seen between epigenetic clusters and patterns of genetic evolution, and the genetic abundance is higher in Cluster 3 than Cluster 1 (p = 0.048, Wilcoxon test), indicating divergent paths of genetic and epigenetic evolution. We next examined differential expression in the epigenetic cluster samples at diagnosis compared to NBM. Cluster 1 specific genes were enriched for cell cycle processes, while Cluster 3 genes were enriched for immune responses (p &lt; 0.001, gene ontology hypergeometric tests). Integrating WGS and ERRBS data showed that epiallele burden is more dynamic than somatic mutations; a significant increase in epiallele burden preceded a major increase of somatic mutational abundance.

Summary: Our results indicate that epigenetic dynamics may provide leukemia cells greater evolutionary fitness via transcriptional adaptation and is associated with clinical outcome. This provides an alternative mechanism of AML resilience during progression and a potential predictor of relapse.

Citation Format: Sheng Li, Francine E. Garrett-Bakelman, Stephen S. Chung, Todd Hricik, Franck Rapaport, Jay Patel, Richard Dillon, Priyanka Vijay, Anna L. Brown, Alexander E. Perl, Joy Connon, Mathijs A. Sanders, Peter J.M. Valk, Lars Bullinger, Selina Luger, Michael W. Becker, Ian D. Lewis, Luen Bik To, Richard J. D’Andrea, David Grimwade, Ruud Delwel, Bob Löwenberg, Hartmut Döhner, Konstanze Döhner, Monica L. Guzman, Duane C. Hassane, Gail J. Roboz, Martin Carroll, Christopher Y. Park, Donna S. Neuberg, Ross L. Levine, Ari M. Melnick, Christopher E. Mason. Epigenome evolution in relapsed acute myeloid leukemia. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-073.

Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia

Genetic heterogeneity contributes to clinical outcome and progression of most tumors. Yet, little is known regarding allelic diversity for epigenetic compartments and almost no data exists for acute myeloid leukemia (AML). Here we examined epigenetic heterogeneity as assessed by cytosine methylation within defined genomic loci with four CpGs (epigenetic alleles), somatic mutations and transcriptomes of AML patient samples at serial time points. We observe that epigenetic allele burden is linked to inferior outcome and varies considerably during disease progression. Epigenetic and genetic allelic burden and patterning follow different patterns and kinetics during disease progression. We observed a subset of AMLs with high epiallele and low somatic mutation burden at diagnosis, a subset with high somatic mutation and lower epiallele burdens at diagnosis, and a subset with a mixed profile, suggesting distinct modes of tumor heterogeneity. Genes linked to promoter-associated epiallele shifts during tumor progression display increased single-cell transcriptional variance and differential expression, suggesting functional impact on gene regulation. Thus, genetic and epigenetic heterogeneity can occur with distinct kinetics, each likely able to impact biological and clinical features of tumors.

Abstract 1158: Microtubule perturbation regulates remodeling of tumor microenvironment by modulating the composition of tumor cell secretome

Microtubules (MTs) represent one of the most effective targets in cancer chemotherapy. However, MT-targeting drugs, such as the taxanes, often fail in the metastatic setting and mechanisms underlying drug resistance are poorly elucidated. An important process during tumor development and metastasis involves the dynamic remodeling of the 3D microenvironment surrounding the tumor cells which enables them to successfully proliferate and metastasize. We hypothesized that tumor cell MTs may regulate the cellular signaling process that controls tumor-mediated remodeling of the microenvironment by paracrine activation of fibroblasts. To assess the role of MT dynamics in the secretion of factors from the tumor cells that mediate communication with the microenvironment, we collected conditioned medium (CM) from untreated or paclitaxel (PTX)-pre-treated metastatic breast cancer MDA-MB-231 cells and applied it to HMF3S human mammary fibroblasts. We observed that CM from untreated 231 cells resulted in fibroblast activation as evidenced by their increased directional 3D cell motility towards a serum gradient. CM from PTX-pretreated 231 cells, at concentrations that suppress MT dynamics, but not from the PTX-resistant β-tubulin mutation 231 clone, 231K20T cells, did not result in activation of fibroblasts' 3D motility, suggesting that MT-mediated secretion of soluble factor(s) (secretome) underlies fibroblast activation. Mass-spectrometry analysis of CM derived from untreated or PTX-pretreated 231 cells identified proteins whose secretion was diminished following suppression of MT dynamics and which are involved in cell motility, cell-cell communication, or ECM remodeling, such as TGFβ, CTGF, c-Met, fibronectin, and lysyl oxidase 2. Treatment of 231-derived CM with an anti-TGFβ blocking antibody diminished HMF3S fibroblast motility in 3D, suggesting that the presence of TGFβ in the tumor cell secretome mediated the activation of tumor associated fibroblasts. To further probe the MT-dependent regulation of TGFβ secretion we showed that PTX treatment prevented trafficking of intracellular TGFβ to the cell surface in 231 cells, likely underlying its reduced secretion. Confocal reflectance and two-photon microscopic imaging revealed that CM treatment of HMF3S fibroblasts induced significant collagen remodeling comparable to treatment with exogenous TGFβ alone. Our findings point to a novel role of interphase MTs in tumor cell secretome and raise the possibility that MTs may regulate secretion of distinct soluble factors in different types of tumor cells, which then mediate the communication between tumor cell compartment and the tumor microenvironment. These novel insights have significant implications for the mechanism of action and resistance to MT inhibitors.

Citation Format: Katsuhiro Kita, Andy Tran, Lewis M. Brown, Duane C. Hassane, Shawn Carey, Alexandre Matov, Cynthia A. Reinhart-King, Paraskevi Giannakakou. Microtubule perturbation regulates remodeling of tumor microenvironment by modulating the composition of tumor cell secretome. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1158. doi:10.1158/1538-7445.AM2014-1158

Selective activity of the histone deacetylase inhibitor AR-42 against leukemia stem cells: a novel potential strategy in acute myelogenous leukemia

Most patients with acute myelogenous leukemia (AML) relapse and die of their disease. Increasing evidence indicates that AML relapse is driven by the inability to eradicate leukemia stem cells (LSC). Thus, it is imperative to identify novel therapies that can ablate LSCs. Using an in silico gene expression-based screen for compounds evoking transcriptional effects similar to the previously described anti-LSC agent parthenolide, we identified AR-42 (OSU-HDAC42), a novel histone deacetylase inhibitor that is structurally similar to phenylbutyrate, but with improved activity at submicromolar concentrations. Here, we report that AR-42 induces NF-κB inhibition, disrupts the ability of Hsp90 to stabilize its oncogenic clients, and causes potent and specific cell death of LSCs but not normal hematopoietic stem and progenitor cells. Unlike parthenolide, the caspasedependent apoptosis caused by AR-42 occurs without activation of Nrf-2-driven cytoprotective pathways. As AR-42 is already being tested in early clinical trials, we expect that our results can be extended to the clinic.

Novel mTOR inhibitory activity of ciclopirox enhances parthenolide antileukemia activity

Ciclopirox, an antifungal agent commonly used for the dermatologic treatment of mycoses, has been shown recently to have antitumor properties. Although the exact mechanism of ciclopirox is unclear, its antitumor activity has been attributed to iron chelation and inhibition of the translation initiation factor eIF5A. In this study, we identify a novel function of ciclopirox in the inhibition of mTOR. As with other mTOR inhibitors, we show that ciclopirox significantly enhances the ability of the established preclinical antileukemia compound, parthenolide, to target acute myeloid leukemia. The combination of parthenolide and ciclopirox demonstrates greater toxicity against acute myeloid leukemia than treatment with either compound alone. We also demonstrate that the ability of ciclopirox to inhibit mTOR is specific to ciclopirox because neither iron chelators nor other eIF5A inhibitors affect mTOR activity, even at high doses. We have thus identified a novel function of ciclopirox that might be important for its antileukemic activity.

Clinical and preclinical evaluation of taxane sensitivity in gastric cancer (GC): Relevance of GC histology

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Background: Docetaxel (D) is a standard treatment for advanced gastric cancer based on the TAX-325 study (van Cutsem, JCO 2006). We asked the question, do all subtypes of GC benefit equally from D therapy? Methods: We performed a post-hoc analysis of the TAX-325 study. We classified randomized patients as diffuse or non-diffuse histology and correlated histology with clinical outcomes using a Cox proportional hazards model. Preclinical studies involved 13 GC cell lines (4 intestinal subtype, 7 diffuse subtype, 2 unknown), assessed for D sensitivity using the Sulforhodamine B (SRB) cytotoxicity assay, microtubule bundling, mitotic arrest by immunofluorescence as evidence of drug-target engagement, and apoptosis assessment by Caspase 8, Caspase 3, and PARP cleavage by Western Blot. Results: In post hoc analysis of TAX-325, patients were classified as diffuse (n=206) or non-diffuse (n=239). Non-diffuse GC showed a significant improvement in overall survival with the addition of D (12.1 v 8.8 mo, p=0.002), whereas diffuse histology was not associated with an improvement in survival (8.3 v 8.5 mo, p=0.66). Preclinical studies similarly reveal that 5/7 diffuse GC cell lines were resistant to D by SRB assay compared with 1/4 intestinal GC cell lines (IC50 > 600 nM). To examine drug target engagement, a dynamic measure of D activity, 4/6 diffuse GC cell lines showed lack of D engagement on the microtubule network at physiologic D concentrations (0-100 nM). 5/6 diffuse cell lines demonstrated no apoptosis. Additionally, we found that 0/9 GC cell lines expressed P-glycoprotein, ruling out multidrug resistance as an etiology for diffuse GC resistance to D. Conclusions: In exploratory analysis, we observed diffuse GC to be resistant to the addition of D to standard chemotherapy in a random assignment phase III clinical trial. In vitro analyses support these clinical findings and demonstrate intrinsic D resistance in diffuse GC, unrelated to multidrug resistance. Ongoing mechanistic studies focus on the molecular basis of taxane sensitivity in GC to predict treatment efficacy. These findings will inform future clinical studies aimed at individualized therapy.

Gene signature critical to cancer phenotype as a paradigm for anticancer drug discovery

Malignant cell transformation commonly results in the deregulation of thousands of cellular genes, an observation that suggests a complex biological process and an inherently challenging scenario for the development of effective cancer interventions. To better define the genes/pathways essential to regulating the malignant phenotype, we recently described a novel strategy based on the cooperative nature of carcinogenesis that focuses on genes synergistically deregulated in response to cooperating oncogenic mutations. These so-called 'cooperation response genes' (CRGs) are highly enriched for genes critical for the cancer phenotype, thereby suggesting their causal role in the malignant state. Here, we show that CRGs have an essential role in drug-mediated anticancer activity and that anticancer agents can be identified through their ability to antagonize the CRG expression profile. These findings provide proof-of-concept for the use of the CRG signature as a novel means of drug discovery with relevance to underlying anticancer drug mechanisms.

Gene sets identified with oncogene cooperativity analysis regulate in vivo growth and survival of leukemia stem cells

Leukemia stem cells (LSCs) represent a biologically distinct subpopulation of myeloid leukemias, with reduced cell cycle activity and increased resistance to therapeutic challenge. To better characterize key properties of LSCs, we employed a strategy based on identification of genes synergistically dysregulated by cooperating oncogenes. We hypothesized that such genes, termed "cooperation response genes" (CRGs), would represent regulators of LSC growth and survival. Using both a primary mouse model and human leukemia specimens, we show that CRGs comprise genes previously undescribed in leukemia pathogenesis in which multiple pathways modulate the biology of LSCs. In addition, our findings demonstrate that the CRG expression profile can be used as a drug discovery tool for identification of compounds that selectively target the LSC population. We conclude that CRG-based analyses provide a powerful means to characterize the basic biology of LSCs as well as to identify improved methods for therapeutic targeting.

Acute myelogenous leukemia stem cells: from Bench to Bedside

Despite reaching remission with traditional chemotherapy, most adult patients with acute myeloid leukemia (AML) will relapse and die of their disease. Numerous studies have identified a rare subset of leukemia cells that evade traditional chemotherapy and are capable of self-renewal and initiating leukemia. These cells are thought to be responsible for relapse and are termed leukemia stem cells (LSCs). This article will review the current LSC translational research and focus on new approaches to detect LSC burden and its prognostic implications, as well as the identification and development of therapeutic agents active against LSCs.

Abstract 1502: Microtubule stabilization alters tumor secretome and fibroblast activation

Microtubules (MTs) represent one of the most effective targets in cancer chemotherapy. However, drugs that target MTs, like the taxanes, often fail in the metastatic setting. Therefore it is of utmost importance to fully understand the roles of MTs and MT-targeting agents in tumor biology. An important process for tumor development and metastasis involves the remodeling of the 3D microenvironment surrounding tumor cells. In order to successfully proliferate and metastasize, tumor cells need to dynamically respond to, manipulate, and remodel their surrounding microenvironment. We hypothesized that MTs, as a dynamic cytoskeletal component, regulates the cellular signaling process that controls tumor-mediated remodeling of the microenvironment. To test this hypothesis, we assessed the MT-dependence of metastatic MDA-MB-231 (231) breast cancer cell activation of HMF3S human mammary fibroblasts. We collected media conditioned by vehicle- or paclitaxel (PTX)-pretreated 231 cells and then applied this conditioned media to HMF3S fibroblasts. Application of 231-derived conditioned media activated HMF3S fibroblasts as evidenced by their enhanced directional 3D motility towards a serum gradient. However, application of conditioned media from PTX-pretreated 231 cells to HMF3S fibroblasts inhibited their 3D directional motility. Importantly, we demonstrated that this effect was due to PTX-induced MT stabilization as conditioned media from PTX-treated 231 cells resistant to PTX did not inhibit fibroblasts’ 3D motility. Together, these results suggest that the composition of the tumor secretome changes upon MT stabilization by PTX, which in turn affects the ability of tumor cells to communicate with fibroblasts. In order to identify the factors responsible for this MT-dependent cell-cell communication we performed a differential proteomic analysis of the conditioned media from vehicle- and PTX-pretreated 231 cells. Using splitless nanoflow chromatography coupled with quadrupole time-of-flight mass spec, we identified a total of 2124 proteins within these tumor secretomes. Using a 2-fold change threshold, we identified 78 under-represented and 31 over-represented proteins in the secretome of PTX- versus vehicle-pretreated cells. We focused our analysis on under-represented proteins based on the hypothesis that MT stabilization would inhibit their secretion. From this analysis we have identified proteins involved in cell motility, cell-cell communication, or ECM remodeling. TGFβ, CTGF, cMet, fibronectin, and lysyl oxidase 2 were key down-regulated proteins identified in the tumor secretome upon PTX-induced MT stabilization. Currently we are investigating the mechanisms by which stabilization of the MT cytoskeleton results in the down-regulation of these factors. These findings point to a novel role of interphase MTs in tumor biology and can possibly enhance our understanding of taxane clinical efficacy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1502. doi:1538-7445.AM2012-1502

Abstract 2145: AR-42, a novel histone deacetylase inhibitor with selectivity against leukemia stem cell via apoptosis induction, inhibition of chaperone function of heat shock protein 90 in acute myeloid leukemia

AML is a fatal disease where most patients relapse and die of their disease. Increasing evidence indicates that disease relapse is driven by leukemia stem cells (LSCs). Thus, it is imperative to identify new therapies that can ablate LSCs. We have previously reported that screening the NCBI Gene Expression Omnibus (GEO) can accelerate the identification of anti-LSC compounds by searching for those mimicking the gene expression pattern of a known anti-LSC compound, parthenolide (PTL). One of our “hits” was the HDACi, AR-42 (Arno Therapeutics, Inc). This compound represents a novel class of HDACis that are structurally similar to phenylbutyrate, but with improved HDACi activity at sub-micromolar concentrations.

At first, we investigated effects of AR-42 on growth and colony forming ability by using AML cell lines and primary human AML samples. AR-42 exhibits low micromolar potency in biochemical and cellular assays. AR-42 efficiently suppressed AML cell growth at a low dosage (1 μM) after 24 hours of treatment. Just like PTL, AR-42 preferentially targets AML progenitor and stem cell populations. More than 50% cell death was induced by AR-42 in phenotypically defined AML stem / progenitor. Colony forming capability of LSCs treated with 1 μM AR-42 for 24 hours was significantly diminished. Furthermore, 1 μM AR-42 significantly impaired the potential of LSCs in a nonobese diabetic/severe combined immunodeficient (NOD/SCID) xenograft model.

Surprisingly, even though AR-42 partially mimics the gene expression pattern of PTL, it does not activate Nrf2-controlled cytoprotective responses like PTL. AR- 42 inhibits NF-κB but, unlike PTL, does not activate HMOX-1. AR-42- mediated apoptosis is associated with activation of caspase 8, PARP cleavage. Further studies found that AR-42 induced inhibition of HSP90 in conjunction with degradation of FLT3 protein. Altogether, these findings indicate that AR-42 may be a promising LSC-targeted therapeutic agent.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2145. doi:10.1158/1538-7445.AM2011-2145

An orally bioavailable parthenolide analog selectively eradicates acute myelogenous leukemia stem and progenitor cells

Leukemia stem cells (LSCs) are thought to play a central role in the pathogenesis of acute leukemia and likely contribute to both disease initiation and relapse. Therefore, identification of agents that target LSCs is an important consideration for the development of new therapies. To this end, we have previously demonstrated that the naturally occurring compound parthenolide (PTL) can induce death of human LSCs in vitro while sparing normal hematopoietic cells. However, PTL has relatively poor pharmacologic properties that limit its potential clinical use. Consequently, we generated a family of PTL analogs designed to improve solubility and bioavailability. These studies identified an analog, dimethylamino-parthenolide (DMAPT), which induces rapid death of primary human LSCs from both myeloid and lymphoid leukemias, and is also highly cytotoxic to bulk leukemic cell populations. Molecular studies indicate the prevalent activities of DMAPT include induction of oxidative stress responses, inhibition of NF-kappaB, and activation of p53. The compound has approximately 70% oral bioavailability, and pharmacologic studies using both mouse xenograft models and spontaneous acute canine leukemias demonstrate in vivo bioactivity as determined by functional assays and multiple biomarkers. Therefore, based on the collective preclinical data, we propose that the novel compound DMAPT has the potential to target human LSCs in vivo.

Interactions of Campylobacter jejuni cytolethal distending toxin subunits CdtA and CdtC with HeLa cells

Campylobacter jejuni produces a toxin, called cytolethal distending toxin (CDT), which causes direct DNA damage leading to invocation of DNA damage checkpoint pathways. The affected cells arrest in G(1) or G(2) and eventually die. CDT consists of three protein subunits, CdtA, CdtB, and CdtC, with CdtB recently identified as a nuclease. However, little is known about the functions of CdtA or CdtC. In this work, enzyme-linked immunosorbent assay-based experiments were used to show, for the first time, that both CdtA and CdtC bound with specificity to the surface of HeLa cells, whereas CdtB did not. Varying the order of the addition of subunits for reconstitution of the holotoxin had no effect on activity. In addition, mutants containing deletions of conserved regions of CdtA and CdtC were able to bind to the surface of HeLa cells but were not able to participate in holotoxin assembly. Finally, both Cdt mutant subunits were able to effectively compete with CDT holotoxin in the HeLa cell binding assay.

Campylobacter jejuni cytolethal distending toxin promotes DNA repair responses in normal human cells

Cytolethal distending toxin (CDT) is a multisubunit protein found in various gram-negative bacterial pathogens of humans which is thought to cause cell death by direct DNA damage of host cells. We sought to determine if a cellular response to DNA damage could be detected by exogenous addition of the holotoxin. Exogenous addition of the Campylobacter jejuni 81-176 CDT to primary human fibroblasts resulted in formation of Rad50 foci, which are formed around double-stranded-DNA breaks. Moreover, such foci are formed in both proliferating and nonproliferating cells that are treated with C. jejuni CDT. Fibroblasts that were intoxicated and later stimulated to proliferate failed to divide and remained arrested in the G(1) phase of the cell cycle.

Cytolethal distending toxin demonstrates genotoxic activity in a yeast model

Cytolethal distending toxins (CDTs) are multisubunit proteins produced by a variety of bacterial pathogens that cause enlargement, cell cycle arrest, and apoptosis in mammalian cells. While their function remains uncertain, recent studies suggest that they can act as intracellular DNases in mammalian cells. Here we establish a novel yeast model for understanding CDT-associated disease. Expression of the CdtB subunit in yeast causes a G2/M arrest, as seen in mammalian cells. CdtB toxicity is not circumvented in yeast genetically altered to lack DNA damage checkpoint control or that constitutively promote cell cycle progression via mutant Cdk1, because CdtB causes a permanent type of damage that results in loss of viability. Finally, we establish that CDTs are likely to be potent genotoxins, as indicated by in vivo degradation of chromosomal DNA associated with expression of CdtB-suggesting that the varied distribution of CDT in bacteria implicates many human pathogens as possessors of genotoxic activity.