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Despite a high clinical need for the treatment of colorectal carcinoma (CRC) as the second leading cause of cancer-related deaths, targeted therapies are still limited. The multifunctional enzyme Transglutaminase 2 (TGM2), which harbors transamidation and GTPase activity, has been implicated in the development and progression of different types of human cancers. However, the mechanism and role of TGM2 in colorectal cancer are poorly understood. Here, we present TGM2 as a promising drug target.In primary patient material of CRC patients, we detected an increased expression and enzymatic activity of TGM2 in colon cancer tissue in comparison to matched normal colon mucosa cells. The genetic ablation of TGM2 in CRC cell lines using shRNAs or CRISPR/Cas9 inhibited cell expansion and tumorsphere formation. In vivo, tumor initiation and growth were reduced upon genetic knockdown of TGM2 in xenotransplantations. TGM2 ablation led to the induction of Caspase-3-driven apoptosis in CRC cells. Functional rescue experiments with TGM2 variants revealed that the transamidation activity is critical for the pro-survival function of TGM2. Transcriptomic and protein–protein interaction analyses applying various methods including super-resolution and time-lapse microscopy showed that TGM2 directly binds to the tumor suppressor p53, leading to its inactivation and escape of apoptosis induction.We demonstrate here that TGM2 is an essential survival factor in CRC, highlighting the therapeutic potential of TGM2 inhibitors in CRC patients with high TGM2 expression. The inactivation of p53 by TGM2 binding indicates a general anti-apoptotic function, which may be relevant in cancers beyond CRC.

Autophagy is an important survival mechanism that allows recycling of nutrients and removal of damaged organelles and has been shown to contribute to the proliferation of acute myeloid leukemia (AML) cells. However, little is known about the mechanism by which autophagy- dependent AML cells can overcome dysfunctional autophagy. In our study we identified autophagy related protein 3 (ATG3) as a crucial autophagy gene for AML cell proliferation by conducting a CRISPR/Cas9 dropout screen with a library targeting around 200 autophagy-related genes. shRNA-mediated loss of ATG3 impaired autophagy function in AML cells and increased their mitochondrial activity and energy metabolism, as shown by elevated mitochondrial ROS generation and mitochondrial respiration. Using tracer-based NMR metabolomics analysis we further demonstrate that the loss of ATG3 resulted in an upregulation of glycolysis, lactate production, and oxidative phosphorylation. Additionally, loss of ATG3 strongly sensitized AML cells to the inhibition of mitochondrial metabolism. These findings highlight the metabolic vulnerabilities that AML cells acquire from autophagy inhibition and support further exploration of combination therapies targeting autophagy and mitochondrial metabolism in AML.

Simple Summary The importance of autophagy in leukemia progression and survival has been studied previously. However, little is known about the development of resistance mechanisms to autophagy inhibition in leukemia. Here, we present data on the mechanisms by which leukemia cells maintain their cell survival after inhibition of autophagy by the loss of ATG3. After the loss of ATG3, leukemia cells upregulated their energy metabolism by increasing glycolysis and mitochondrial metabolism, in particular oxidative phosphorylation, which resulted in higher ATP levels. Moreover, inhibition of mitochondrial function strongly impaired cell survival in ATG3 deficiency, thus demonstrating the importance of ATG3 in the regulation of metabolism and survival of leukemic cells. Therefore, our data provide a rationale for combining autophagy inhibitors with inhibitors targeting mitochondrial metabolism for the development of leukemia therapy to overcome the potential obstacle of emerging resistance to autophagy inhibition. Abstract Autophagy is an important survival mechanism that allows recycling of nutrients and removal of damaged organelles and has been shown to contribute to the proliferation of acute myeloid leukemia (AML) cells. However, little is known about the mechanism by which autophagy- dependent AML cells can overcome dysfunctional autophagy. In our study we identified autophagy related protein 3 (ATG3) as a crucial autophagy gene for AML cell proliferation by conducting a CRISPR/Cas9 dropout screen with a library targeting around 200 autophagy-related genes. shRNA-mediated loss of ATG3 impaired autophagy function in AML cells and increased their mitochondrial activity and energy metabolism, as shown by elevated mitochondrial ROS generation and mitochondrial respiration. Using tracer-based NMR metabolomics analysis we further demonstrate that the loss of ATG3 resulted in an upregulation of glycolysis, lactate production, and oxidative phosphorylation. Additionally, loss of ATG3 strongly sensitized AML cells to the inhibition of mitochondrial metabolism. These findings highlight the metabolic vulnerabilities that AML cells acquire from autophagy inhibition and support further exploration of combination therapies targeting autophagy and mitochondrial metabolism in AML.

We previously reported the establishment of a rare xenograft derived from a recurrent oligodendroglioma with 1p/19q codeletion. Here, we analyzed in detail the exome sequencing datasets from the recurrent oligodendroglioma (WHO grade III, recurrent O2010) and the first-generation xenograft (xenograft1). Somatic SNVs and small InDels (n = 80) with potential effects at the protein level in recurrent O2010 included variants in IDH1 (NM_005896:c.395G>A; p. Arg132His), FUBP1 (NM_003902:c.1307_1310delTAGA; p.Ile436fs), and CIC (NM_015125:c.4421T>G; p.Val1474Gly). All but 2 of these 80 variants were also present in xenograft1, along with 7 new variants. Deep sequencing of the 87 SNVs and InDels in the original tumor (WHO grade III, primary O2005) and in a second-generation xenograft (xenograft2) revealed that only 11 variants, including IDH1 (NM_005896:c.395G>A; p. Arg132His), PSKH1 (NM_006742.2:c.650G>A; p.Arg217Gln), and SNX12 (NM_001256188:c.470G>A; p.Arg157His), along with a variant in the TERT promoter (C250T, NM_198253.2: c.-146G>A), were already present in primary O2005. Allele frequencies of the 11 variants were calculated to assess their potential as putative driver genes. A missense change in NDST4 (NM_022569:c.2392C>G; p.Leu798Val) on 4q exhibited an increasing allele frequency (~ 20%, primary O2005, 80%, recurrent O2010 and 100%, xenograft1), consistent with a selection event. Sequencing of NDST4 in a cohort of 15 oligodendrogliomas, however, revealed no additional cases with potential protein disrupting variants. Our analysis illuminated a tumor evolutionary series of events, which included 1p/19q codeletion, IDH1 R132H, and TERT C250T as early events, followed by loss of function of NDST4 and mutations in FUBP1 and CIC as late events.

Aims Somatic mutations in haematopoietic stem cells can lead to the clonal expansion of mutated blood cells, known as clonal haematopoiesis (CH). Mutations in the most prevalent driver genes DNMT3A and TET2 with a variant allele frequency (VAF) ≥ 2% have been associated with atherosclerosis and chronic heart failure of ischemic origin (CHF). However, the effects of mutations in other driver genes for CH with low VAF (

Background Recurrent somatic mutations in blood stem cells cause the emergence of mutated blood cell clones, known as clonal hematopoiesis (CH). Mutations in the most prevalent driver genes DNMT3A and TET2 with a variant allele frequency (VAF)≥2% have been associated with atherosclerosis and chronic heart failure (CHF). However, the effects of mutations in other driver genes for CH with low VAF ( Purpose To assess the potential prognostic significance of mutations in distinct genes other than DNMT3A and TET2 causing CH at low VAF in patients with CHF due to post-ischemic origin. Methods We analyzed mononuclear bone marrow and peripheral blood cells from 400 CHF patients by deep error-corrected targeted amplicon sequencing allowing for the detection of very low VAF of ≥0.5% in 56 CH driver genes and associated such with the long-term mortality in these patients. Results Median age of the patients was 63 and median follow-up time was 4.8 years. We detected 1116 mutations with a VAF≥0.5% in 348 of 400 patients (87%). 21% of the patients carried 1 mutation, whereas 66% showed 2 and more mutations. Only 52 (13%) patients had no detectable mutation at all. Despite a high prevalence of mutations in the most frequently mutated driver genes DNMT3A (165 patients) and TET2 (107 pts), mutations in the genes CBL (8 pts), CEBPA (10 pts), PHF6 (22 pts), SMC1A (18 pts) and SRSF2 (14 pts) were associated with increased death compared to the average death rate of all patients (18.8%). To avoid confounding effects caused by the presence of DNMT3A and TET2 CHIP mutations, we excluded patients with DNMT3A-, TET2- and other CHIP-related mutations with a VAF≥2% for further analyses. Kaplan-Meier survival curve analyses revealed a significantly higher mortality in patients with mutations in either of the five genes, combined as the CH risk gene set for CHF (Fig. 1). Patients with mutations in the risk gene set (44 pts) did not differ from patients with mutations in other CH driver genes or without mutations with respect to age, cardiovascular risk factors, disease severity or CH clone size. By multivariate Cox proportional regression analysis, including the Seattle heart failure model (SHFM) score (as tertiles), death remained independently associated with the presence of mutations in the risk gene set (HR, 2.57; 95% CI, 1.30–5.10; p=0.007), in addition to SHFM score tertiles (tertile 2, HR, 2.36; 95% CI, 0.73–7.65 and tertile 3, HR, 7.96; 95% CI, 2.77–22.90). Conclusions Somatic mutations with low VAF in a distinct set of genes, namely in CBL, CEBPA, PHF6, SMC1A and SRSF2, are significantly associated with mortality in CHF, independently of the classical CHIP-driver mutations DNMT3A and TET2. Mutations in the CH risk gene set are prevalent in young CHF patients and comprise an independent risk factor for the outcome of CHF, potentially providing a novel tool for cardiovascular risk assessment and precision medicine in CHF. Figure 1 Funding Acknowledgement Type of funding source: Public grant(s) – National budget only. Main funding source(s): German Research Foundation (DFG)

Aims Somatic mutations of the epigenetic regulators DNMT3A and TET2 causing clonal expansion of haematopoietic cells (clonal haematopoiesis; CH) were shown to be associated with poor prognosis in chronic ischaemic heart failure (CHF). The aim of our analysis was to define a threshold of variant allele frequency (VAF) for the prognostic significance of CH in CHF. Methods and results We analysed bone marrow and peripheral blood-derived cells from 419 patients with CHF by error-corrected amplicon sequencing. Cut-off VAFs were optimized by maximizing sensitivity plus specificity from a time-dependent receiver operating characteristic (ROC) curve analysis from censored data. 56.2% of patients were carriers of a DNMT3A- (N = 173) or a TET2- (N = 113) mutation with a VAF >0.5%, with 59 patients harbouring mutations in both genes. Survival ROC analyses revealed an optimized cut-off value of 0.73% for TET2- and 1.15% for DNMT3A-CH-driver mutations. Five-year-mortality was 18% in patients without any detected DNMT3A- or TET2 mutation (VAF Conclusion The present study defines novel threshold levels for clone size caused by acquired somatic mutations in the CH-driver genes DNMT3A and TET2 that are associated with worse outcome in patients with CHF.

Somatic mutations in hematopoietic stem cells can lead to the expansion of mutated blood cells, known as clonal hematopoiesis (CH). Mutations in the most prevalent genes DNMT3A and TET2 with a variant allele frequency (VAF)≥2% (CHIP) have been associated with atherosclerosis and chronic heart failure (CHF). However, the mutational landscape in CHF and the effects in CH-driver genes other than DNMT3A and TET2 with low VAF≤2% on CHF are still unknown. Therefore we analyzed bone marrow and blood cells from 399 CHF patients by deep error-corrected targeted sequencing of 56 genes and associated mutations with the long-term mortality (3.95 years median follow-up). We detected 1113 mutations with a VAF≥0.5% in 347 patients (87%). Despite a high prevalence of mutations in the most frequently mutated genes DNMT3A and TET2, mutations in the genes CBL, CEBPA, EZH2, GNB1, PHF6, SMC1A and SRSF2 were associated with increased death compared to the average death rate of all patients (20%). To avoid confounding effects caused by the presence of DNMT3A and TET2 CHIP mutations, we excluded patients with CHIP-related mutations (VAF≥2%) for further analyses. Kaplan-Meier survival analyses revealed a significantly higher mortality in patients with mutations in the seven genes (53 patients), combined as the CH risk gene set for CHF. These patients showed no significant differences in any parameter including patient age, confounding diseases or blood parameters except for a reduced number of platelets. However, carrying a mutation in any of the risk genes remained significant after multivariate cox regression analysis (HR, 3.1; 95% CI, 1.8-5.4; p Somatic mutations with low VAF in these risk genes are prevalent in young CHF patients and comprise an independent risk factor for the outcome, potentially providing a novel tool for risk assessment in CHF.

IDH1R132H (isocitrate dehydrogenase 1) mutations play a key role in the development of low-grade gliomas. IDH1wt converts isocitrate to α-ketoglutarate while reducing nicotinamide adenine dinucleotide phosphate (NADP+), whereas IDH1R132H uses α-ketoglutarate and NADPH to generate the oncometabolite 2-hydroxyglutarate (2-HG). While the effects of 2-HG have been the subject of intense research, the 2-HG independent effects of IDH1R132H are still ambiguous. The present study demonstrates that IDH1R132H expression but not 2-HG alone leads to significantly decreased tricarboxylic acid (TCA) cycle metabolites, reduced proliferation, and enhanced sensitivity to irradiation in both glioblastoma cells and astrocytes in vitro. Glioblastoma cells, but not astrocytes, showed decreased NADPH and NAD+ levels upon IDH1R132H transduction. However, in astrocytes IDH1R132H led to elevated expression of the NAD-synthesizing enzyme nicotinamide phosphoribosyltransferase (NAMPT). These effects were not 2-HG mediated. This suggests that IDH1R132H cells utilize NAD+ to restore NADP pools, which only astrocytes could compensate via induction of NAMPT. We found that the expression of NAMPT is lower in patient-derived IDH1-mutant glioma cells and xenografts compared to IDH1-wildtype models. The Cancer Genome Atlas (TCGA) data analysis confirmed lower NAMPT expression in IDH1-mutant versus IDH1-wildtype gliomas. We show that the IDH1 mutation directly affects the energy homeostasis and redox state in a cell-type dependent manner. Targeting the impairments in metabolism and redox state might open up new avenues for treating IDH1-mutant gliomas.

Background Monocytes and macrophages have distinct roles in cardiovascular health where they may contribute to beneficial processes like wound healing and cardiac conductance or to pathological processes like inflammation, remodeling and fibrosis. Despite their importance, the specific signatures of circulating monocytes are missing. Single cell RNA sequencing (scRNA-seq) provides a novel opportunity to define subsets of monocytes mediating inflammation in humans. Purpose To detect and study the inflammatory burden driven by subsets of monocytes in healthy individuals and subjects with chronic ischemic heart failure (CHF) using scRNA-seq. Methods and results Circulating CD31+ cells of CHF patients (n=11) along with aged matched (n=3) and young healthy controls (n=5) were sorted and scRNA-seq then performed. Unsupervised clustering of present sequencing data revealed these cells to be comprised of 19 subpopulations (primarily monocytes). Many subpopulations of cells were comprised chiefly or solely by CHF subjects. Dysregulated genes in CHF subjects, relative to healthy controls included interleukin-1b, thrombospondin-1, S100A8 and matrix metalloprotease-1, which were confirmed by FACS and qRT-PCR in a validation cohort. Given the expanded, divergent and highly inflammatory transcriptional populations of monocytes in patients with CHF, we assessed whether occurrence of somatic mutations associated with clonal hematopoiesis of indeterminate potential (CHIP), recently shown to be increased in subjects with atherosclerosis and heart failure, might occur in these subjects. Indeed, we identified patients who revealed mutations in the DNA methyltransferase DNMT3A and other CHIP-driver genes. DNMT3A mutations were associated with changes in known DNMT3A target genes such as the pro-inflammatory genes CXCL1, CXCL2 and IL6 in circulating monocytic cells. Moreover, cell fate trajectory analysis showed shared fates of cells driven by pseudotime-dependent variables from subjects harboring DNMT3A mutations. Regulated genes in this fate were associated with cell survival, migration and inflammation, appropriate for this disease phenotype. Conclusions This is the first study to show scRNA-seq profiles of monocytes in patients with CHF. Healthy subjects displayed remarkable homogeneity in their transcriptional profiles. CHF subjects show changes in inflammatory gene expression. CHF subjects with clonal hematopoiesis share signature gene expression profiles driving similar cell fates. Subjects with CHF of ischemic origin harboring DNMT3A mutations have a worse prognosis than non-CHIP carrier CHF controls. Identification of early alterations in immune cell subsets recognized by single cell sequencing and genetic testing of CHIP mutations may detect subjects with a high risk and allow for a precision treatment of the immune disorders. Acknowledgement/Funding SFB834

Summary Colorectal cancer (CRC) is characterized by prominent genetic and phenotypic heterogeneity between patients. To facilitate high-throughput genetic testing and functional identification of tumor drivers, we developed a platform for pooled CRISPR-Cas9 screening in human colon organoids. Using transforming growth factor β (TGF-β) resistance as a paradigm to establish sensitivity and scalability in vitro, we identified optimal conditions and strict guide RNA (gRNA) requirements for screening in 3D organoids. We then screened a pan-cancer tumor suppressor gene (TSG) library in pre-malignant organoids with APC−/−;KRASG12D mutations, which were xenografted to study clonal advantages in context of a complex tumor microenvironment. We identified TGFBR2 as the most prevalent TSG, followed by known and previously uncharacterized mediators of CRC growth. gRNAs were validated in a secondary screen using unique molecular identifiers (UMIs) to adjust for clonal drift and to distinguish clone size and abundance. Together, these findings highlight a powerful organoid-based platform for pooled CRISPR-Cas9 screening for patient-specific functional genomics.

Summary: Clonal hematopoiesis of indeterminate potential (CHIP) is caused by recurrent somatic mutations leading to clonal blood cell expansion. However, direct evidence of the fitness of CHIP-mutated human hematopoietic stem cells (HSCs) in blood reconstitution is lacking. Because myeloablative treatment and transplantation enforce stress on HSCs, we followed 81 patients with solid tumors or lymphoid diseases undergoing autologous stem cell transplantation (ASCT) for the development of CHIP. We found a high incidence of CHIP (22%) after ASCT with a high mean variant allele frequency (VAF) of 10.7%. Most mutations were already present in the graft, albeit at lower VAFs, demonstrating a selective reconstitution advantage of mutated HSCs after ASCT. However, patients with CHIP mutations in DNA-damage response genes showed delayed neutrophil reconstitution. Thus, CHIP-mutated stem and progenitor cells largely gain on clone size upon ASCT-related blood reconstitution, leading to an increased future risk of CHIP-associated complications. : With age, human hematopoiesis becomes affected by blood cell clones with recurrent acquired mutations, resulting in clonal hematopoiesis (CHIP). Ortmann et al. show that hematopoietic stress caused by autologous stem cell transplantation and cytotoxic therapy promotes both size and number of mutant clones in 81 myeloma and lymphoma patients. Keywords: clonal hematopoiesis, CHIP, autologous stem cell transplantation, ASCT, hematopoietic stress, hematopoietic stem cells, clonal dominance, chemotherapy, somatic mutations, leukemia

LSD1 has emerged as a promising epigenetic target in the treatment of acute myeloid leukemia (AML). We used two murine AML models based on retroviral overexpression of Hoxa9/Meis1 (H9M) or MN1 to study LSD1 loss of function in AML. The conditional knockout of Lsd1 resulted in differentiation with both granulocytic and monocytic features and increased ATRA sensitivity and extended the survival of mice with H9M-driven AML. The conditional knockout led to an increased expression of multiple genes regulated by the important myeloid transcription factors GFI1 and PU.1. These include the transcription factors GFI1B and IRF8. We also compared the effect of different irreversible and reversible inhibitors of LSD1 in AML and could show that only tranylcypromine derivatives were capable of inducing a differentiation response. We employed a conditional knock-in model of inactive, mutant LSD1 to study the effect of only interfering with LSD1 enzymatic activity. While this was sufficient to initiate differentiation, it did not result in a survival benefit in mice. Hence, we believe that targeting both enzymatic and scaffolding functions of LSD1 is required to efficiently treat AML. This finding as well as the identified biomarkers may be relevant for the treatment of AML patients with LSD1 inhibitors.

Cardiovascular diseases (CVD) are one of the leading causes of death. Beside established risk factors, clonal hematopoiesis of indeterminate potential (CHIP) is associated with a higher risk of CVD. CHIP is defined as the expansion of a blood cell clone by somatic mutations in individuals without hematologic diseases. Our studies focused on the questions, whether there is a different disease progression in chronic ischemic heart failure (CHF) patients with CHIP and what the consequences on blood cell lineages and hematopoietic stem and progenitor cells (HSPC) are. Therefore, we investigated a clinically well-characterized cohort of CHF patients and correlated disease progression with CHIP-mutations and investigated alterations of peripheral blood (PB) and bone marrow (BM) cells. The most recurrent mutations occurred in DNMT3A and TET2, which both epigenetically control gene expression and regulate inflammation. We demonstrated a significant association of poor prognosis in CHF and CHIP-mutations in these genes. They may causally contribute to disease progression since there was a striking dose-response between the variant allele fraction and clinical outcome. By analyzing PB and BM in CHF patients, we detected an increase of HSPCs and BM leukocyte numbers without a bias in the distribution of leukocyte lineages in the BM of CHIP carriers. In patients harboring TET2 mutations. Surprisingly, we did not determine any alterations in HSPCs in patients with a DNMT3A mutation, which contrasts the results in knock-out mouse models, showing an increased stem cell self-renewal. Whether non-mutated HSPCs are also affected in individuals with TET2 mutations in a paracrine, cell-extrinsic fashion, caused by an inflammatory milieu due to altered cytokine production, requires further investigation.

Background The evolution of primary glioblastoma (GBM) is poorly understood. Multifocal GBM (ie, multiple synchronous lesions in one patient) could elucidate GBM development. Methods We present the first comprehensive study of 12 GBM foci from 6 patients using array-CGH, spectral karyotyping, gene expression arrays, and next-generation sequencing. Results Multifocal GBMs genetically resemble primary GBMs. Comparing foci from the same patient proved their monoclonal origin. All tumors harbored alterations in the 3 GBM core pathways: RTK/PI3K, p53, and RB regulatory pathways with aberrations of EGFR and CDKN2A/B in all (100%) patients. This unexpected high frequency reflects a distinct genetic signature of multifocal GBMs and might account for their highly malignant and invasive phenotype. Surprisingly, the types of mutations in these genes/pathways were different in tumor foci from the same patients. For example, we found distinct mutations/aberrations in PTEN, TP53, EGFR, and CDKN2A/B, which therefore must have occurred independently and late during tumor development. We also identified chromothripsis as a late event and in tumors with wild-type TP53. Only 2 events were found to be early in all patients: single copy loss of PTEN and TERT promoter point mutations. Conclusions Multifocal GBMs develop through parallel genetic evolution. The high frequency of alterations in 3 main pathways suggests that these are essential steps in GBM evolution; however, their late occurrence indicates that they are not founder events but rather subclonal drivers. This might account for the marked genetic heterogeneity seen in primary GBM and therefore has important implications for GBM therapy.

Epigallocatechin-3-gallate (EGCG) is the most abundant polyphenol molecule from green tea and is known to exhibit antioxidative as well as tumor suppressing activity. In order to examine EGCG tumor invasion and suppressing activity against adult T-cell leukemia (ATL), two HTLV-1 positive leukemia cells (HuT-102 and C91- PL) were treated with non-cytotoxic concentrations of EGCG for 2 and 4 days. Proliferation was significantly inhibited by 100 μM at 4 days, with low cell lysis or cytotoxicity. HTLV-1 oncoprotein (Tax) expression in HuT- 102 and C91-PL cells was inhibited by 25 μM and 125 μM respectively. The same concentrations of EGCG inhibited NF-kB nuclearization and stimulation of matrix metalloproteinase-9 (MMP-9) expression in both cell lines. These results indicate that EGCG can inhibit proliferation and reduce the invasive potential of HTLV-1- positive leukemia cells. It apparently exerted its effects by suppressing Tax expression, manifested by inhibiting the activation of NF-kB pathway and induction of MMP-9 transcription in HTLV-1 positive cells.

Key Points Question What is the clinical significance of clonal hematopoiesis of indeterminate potential (CHIP) for chronic heart failure (CHF) owing to ischemic origin? Findings In this cohort study, CHIP had a high prevalence in 200 investigated patients with CHF. While no clinical baseline characteristics associated with CHF were different between CHIP carriers and non-CHIP carriers, except for the mean age, harboring mutations in the most prevalent driver genes associated with CHIP, namely DNMT3A and TET2, was associated with a significant and profound increase in death and rehospitalization for heart failure. Meaning Clonal hematopoiesis of indeterminate potential is presented as a newly identified risk factor for impaired long-term survival and increased disease progression in patients with CHF that may be well targetable as a valuable approach to precision medicine in patients with CHF carrying specific mutations encoding for clonal hematopoiesis., Importance Somatic mutations causing clonal expansion of hematopoietic cells (clonal hematopoiesis of indeterminate potential [CHIP]) are increased with age and associated with atherosclerosis and inflammation. Age and inflammation are the major risk factors for heart failure, yet the association of CHIP with heart failure in humans is unknown. Objective To assess the potential prognostic significance of CHIP in patients with chronic heart failure (CHF) owing to ischemic origin. Design, Setting, and Participants We analyzed bone marrow–derived mononuclear cells from 200 patients with CHF by deep targeted amplicon sequencing to detect the presence of CHIP and associated such with long-term prognosis in patients with CHF at University Hospital Frankfurt, Frankfurt, Germany. Data were analyzed between October 2017 and April 2018. Results Median age of the patients was 65 years. Forty-seven mutations with a variant allele fraction (VAF) of at least 0.02 were found in 38 of 200 patients with CHF (18.5%). The somatic mutations most commonly occurred in the genes DNMT3A (14 patients), TET2 (9 patients), KDM6A (4 patients), and BCOR (3 patients). Patients with CHIP were older and more frequently had a history of hypertension. During a median follow-up of 4.4 years, a total of 53 patients died, and 23 patients required hospitalization for heart failure. There was a significantly worse long-term clinical outcome for patients with either DNMT3A or TET2 mutations compared with non-CHIP carriers. By multivariable Cox proportional regression analysis, the presence of somatic mutations within TET2 or DNMT3A (HR, 2.1; 95% CI, 1.1-4.0; P = .02, for death combined with heart failure hospitalization) and age (HR, 1.04; 95% CI, 1.01-1.07 per year; P = .005) but not a history of hypertension remained independently associated with adverse outcome. Importantly, there was a significant dose-response association between VAF and clinical outcome. Conclusions and Relevance Our data suggest that somatic mutations in hematopoietic cells, specifically in the most commonly mutated CHIP driver genes TET2 and DNMT3A, may be significantly associated with the progression and poor prognosis of CHF. Future studies will have to validate our findings in larger cohorts and address whether targeting specific inflammatory pathways may be valuable for precision medicine in patients with CHF carrying specific mutations encoding for CHIP., This study assesses the potential prognostic significance of clonal hematopoiesis of indeterminate potential in patients with chronic heart failure owing to ischemic origin.

Microgravity and cosmic rays as found in space are difficult to recreate on earth. However, ground-based models exist to simulate space flight experiments. In the present study, an experimental model was utilized to monitor gene expression changes in fetal skin fibroblasts of murine origin. Cells were continuously subjected for 65 h to a low dose (55 mSv) of ionizing radiation (IR), comprising a mixture of high‑linear energy transfer (LET) neutrons and low-LET gamma-rays, and/or simulated microgravity using the random positioning machine (RPM), after which microarrays were performed. The data were analyzed both by gene set enrichment analysis (GSEA) and single gene analysis (SGA). Simulated microgravity affected fetal murine fibroblasts by inducing oxidative stress responsive genes. Three of these genes are targets of the nuclear factor‑erythroid 2 p45-related factor 2 (Nrf2), which may play a role in the cell response to simulated microgravity. In addition, simulated gravity decreased the expression of genes involved in cytoskeleton remodeling, which may have been caused by the downregulation of the serum response factor (SRF), possibly through the Rho signaling pathway. Similarly, chronic exposure to low-dose IR caused the downregulation of genes involved in cytoskeleton remodeling, as well as in cell cycle regulation and DNA damage response pathways. Many of the genes or gene sets that were altered in the individual treatments (RPM or IR) were not altered in the combined treatment (RPM and IR), indicating a complex interaction between RPM and IR.

IDH1 R132H mutations are considered to play a key role in the development of low grade gliomas and therefrom derived secondary glioblastomas (GBM). Wild type IDH1 converts isocitrate to α-ketoglutarate (a-KG) while reducing NADP+. IDH1R132H has a neomorphic enzymatic function using a-KG to generate high amounts of the oncometabolite D-2-hydroxyglutarate (D-2-HG). While the effects of D-2-HG have been subject to intense research, D-2-HG independent effects of IDH1R132H on energy homeostasis and redox status are not well studied. Here we demonstrate that IDH1R132H transduction but not D-2-HG alone leads to significantly decreased Krebs cycle metabolite concentrations and proliferation in U87 and the primary GBM cell line HT7606 as well as in immortalized astrocytes SVGp12. Furthermore, IDH1R132H mutation, but not D-2-HG treatment, resulted in a significant drop in NADPH levels in tumor cells (U87 and HT7606), whereas immortalized astrocytes retained normal NADPH levels. Since NAPDH levels can be restored via the reaction of the NAD-kinase, we analyzed NAD levels and enzymes involved in NAD-synthesis in our cell lines. Indeed we found a significant drop of NAD levels and in the activity of the NAD-dependent enzyme sirtuin in IDH1R132H mutant U87 and HT7606 but not in NADPH stable SVGp12-IDH1R132H. Interestingly, there were marked differences in expression of NAD-synthesis enzymes between the different cell-lines. In particular, NAMPT-levels were much higher in U87 and HT7606 then in astrocytes (SVGp12) and significantly decreased in U87-IDH1R132H and HT7606-IDH1R132H. Importantly, we also found decreased levels of NAMPT in primary tumor tissues and patient derived glioma cell lines with IDH1 R132H compared to wild type gliomas. Altogether our results for the first time show that the IDH1 mutation directly affects energy homeostasis and redox status in a cell-type dependent manner. We hypothesize that this leads to a drop in NADPH and NAD-levels during malignant progression, resulting in a disadvantage for proliferating tumor cells. This is in line with the favorable prognosis and good response to chemo- and radiation therapy clinically observed in IDH-mutated gliomas. Our findings suggest that the impaired metabolism in IDH1-mutant tumors might be a promising target for future therapies. Citation Format: Evelin Schrock, Julia Biedermann, Khalil Abou-El-Ardat, Matthias Lehmann, Marina Conde, Mirko Peitzsch, Susan Richter, Ralf Wiedemuth, Matthias Meinhardt, William P. J. Leenders, Christel Herold-Mende, Graeme Eisenhofer, Simone P. Niclou, Leoni Kunz-Schughart, Achim Temme, Barbara Klink. Effects of the IDH1 R132H mutation on redox status and metabolism are cell type dependent but independent from D-2-hydroxyglutarate accumulation. [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-308.

Background: In the thyroid, iodine deficiency (ID) induces angiogenesis via a tightly controlled reactive oxygen species (ROS)-hypoxia inducible factor-1 (HIF-1)-vascular endothelial growth factor (VEGF) dependent pathway (ROS-HIF-VEGF). Deficient iodine intake may be associated with increased thyroid cancer incidence. The hypothesis of this work is to test whether ID affects the angiogenic processes in thyroid malignant cells by altering the ROS-HIF-VEGF pathway. Methods: Goiters were obtained in RET/PTC3 transgenic and wild-type (wt) mice and ID was induced in three thyroid carcinoma cell lines (TPC-1, 8305c, and R082-w1). Thyroid blood flow, VEGF mRNA and protein, and HIF-1α protein expression were measured. The role of HIF-1 and of ROS was assessed using echinomycin and N-acetylcysteine (NAC), respectively. Results: The goitrogen treatment increased the thyroid blood flow in wt and RET/PTC3 mice. Compared with wt mice, basal VEGF expression was higher in RET/PTC3 mice and increased with goitrogen treatment. In the three cell lines, ID induced marked increases in VEGF mRNA, and moderate increases in HIF-1α protein expression that were not transient as in normal cells. ID-induced VEGF mRNA expression was fully (8305c), partially (TPC-1), or not (R082-w1) blocked by echinomycin. NAC had no effect on ID-induced VEGF mRNA and HIF-1α protein expression in the three cell lines. Conclusions: ID induces a long lasting angiogenic phenotype in thyroid cancer cells that occurs through VEGF induction via a pathway partially mediated by HIF-1, but not by ROS. These results suggest that, in contrast with normal cells, ID-induced angiogenesis in cancer cells occurs via alternative and likely less controlled routes, thereby leading to uncontrolled growth.

The high doses of radiation received in the wake of the Chernobyl incident and the atomic bombing of Hiroshima and Nagasaki have been linked to the increased appearance of thyroid cancer in the children living in the vicinity of the site. However, the data gathered on the effect of low doses of radiation on the thyroid remain limited. We have examined the genome wide transcriptional response of a culture of TPC-1 human cell line of papillary thyroid carcinoma origin with a RET/PTC1 translocation to various doses (0.0625, 0.5, and 4 Gy) of X-rays and compared it to response of thyroids with a RET/PTC3 translocation and against wild-type mouse thyroids irradiated with the same doses using Affymetrix microarrays. We have found considerable overlap at a high dose of 4 Gy in both RET/PTC-positive systems but no common genes at 62.5 mGy. In addition, the response of RET/PTC-positive system at all doses was distinct from the response of wild-type thyroids with both systems signaling down different pathways. Analysis of the response of microRNAs in TPC-1 cells revealed a radiation-responsive signature of microRNAs in addition to dose-responsive microRNAs. Our results point to the fact that a low dose of X-rays seems to have a significant proliferative effect on normal thyroids. This observation should be studied further as opposed to its effect on RET/PTC-positive thyroids which was subtle, anti-proliferative and system-dependent.

The link between high doses of radiation and thyroid cancer has been well established in various studies, as opposed to the effects of low doses. In this study, we investi-gated the effects of low-dose X-ray irradiation in a papillary thyroid carcinoma model with wild-type and mutated p53. A low dose of 62.5 mGy was enough to cause an upregulation of p16 and a decrease in the number of TPC-1 cells in the S phase, but not in the number of BCPAP p53-mutant cells. At a dose of 0.5 Gy, visible signs of senescence appeared only in the TPC-1 cells. We conclude that low doses of X-rays are enough to cause a change in cell cycle distribution, possibly p53-dependent p16 activation, but no significant apoptosis. Senescence requires higher doses of X-irradiation via a mechanism involving both p16 and p21.

Lower grade gliomas can be histologically classified into astrocytomas, oligoastrocytomas, or oligodendrogliomas. The latter have come into focus because of their interesting characteristics: they have a more favorable outcome and better response to chemo/radiotherapy. This is correlated with a unique unbalanced translocation der(1;19)(q10;p10) causing a codeletion of the short arm of chromosome 1 and the long arm of chromosome 19. Like the other lower grade gliomas, a large percentage of oligodendrogliomas carry the IDH1 R132 mutation and this is associated with the presence of the codeletion. We identified a high number of mutations in the remaining alleles of the Capicua homolog gene (CIC) and in the far upstream element binding protein (FUBP1) in 1p/19q codeleted oligodendrogliomas (Eisenreich et al. 2013, doi:10.1371/journal.pone.0076623). Both genes are suspected to act as tumor suppressor genes. We then analyzed the expression profiles of 13 oligodendrogliomas and oligoastrocytomas both with the 1p/19q codeletion (nine samples) and without (four samples) using a combination of expression microarrays and transcriptome sequencing (RNA-Seq). Our results showed that all nine samples with the 1p/19q codeletion carried the heterozygous IDH1 R132H mutation while only one tumor without the codeletion carried said mutation. There was a high concordance between the results of RNA-Seq and the microarray experiments and both showed a distinctive expression signature between samples with the 1p/19q codeletion and those without. Using MSigDB, we found that the genes whose expression was altered in in tumors with the 1p/19q codeletion showed significant overlap with those involved in stemness and differentiation and genes that had CpG-rich promoters. Furthermore, there was an overlap with genes with altered expression in chronic myelogenous leukemia (CML). When we compared the expression of genes located on 1p and 19q between the tumors with the 1p/19q codeletion and those without, we found that only 82% of genes on 1p and 19q were downregulated significantly. When we ran the upregulated genes in PathScan, we found enrichment in GA binding protein alpha (GABPA)binding sites. GABPA expression levels were increased in our glioma samples with and without the 1p/19q codeletion. Investigating the expression levels of GABPA in the Cancer Genome Atlas (TCGA) GBM dataset also revealed an upregulation of this transcription factor. An increase in GABPA-mediated transcription was recently reported in CML but has not been yet reported in gliomas. We therefore propose that GABPA is an important transcription factor in gliomas. We are currently evaluating the function of GABPA in glioma what will also be presented. Acknowledgements: This project was partially supported by a MeDDrive grant of the Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden. Citation Format: Barbara Klink, Karol Szafranski, Jaime Campos-Valenzuela, Sophie Eisenreich, Dietmar Krex, Eva-Maria Gerlach, Karl Hackmann, Andreas Rump, Gabriele Schackert, Matthias Platzer, Lars Kaderali, Evelin Schröck, Khalil Abou-El-Ardat. Upregulation of gene expression in oligodendrogliomas is linked to an increase in GA binding protein alpha transcription. [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 3387. doi:10.1158/1538-7445.AM2014-3387

Glioblastoma (GBM) is the most common and malignant type of brain tumor in adults with an average survival time of less than a year. A hallmark of GBM is its infiltrating growth hampering successful surgical treatment and precluding curative therapy. Multifocal GBMs - multiple synchronous lesions in the same patient - represent approximately 8-10% of all gliomas and generally have a poor prognosis. There are two theories as to the nature of these multifocal GBMs: they could either have originated from one main GBM or they can be independent tumors. Genetic studies of multifocal GBMs are very rare and such studies could elucidate the nature of these tumors. We have analyzed eleven tumor foci of six patients with multifocal GBMs using array comparative genome hybridization (aCGH), spectral karyotyping (SKY), and Sanger sequencing of PTEN, TP53, and IDH1/2. Array CGH analysis of ten of the tumors revealed multiple genetic aberrations. The most frequent were gain of chromosome 7 (9/10), amplification of EGFR (10/10), loss of chromosome 10 (10/10), and partial loss of chromosome 9 (7/10). SKY analysis identified multiple translocations including complex rearrangements. None of the tumors carried a mutation in IDH1/2 and they were genetically similar to primary GBMs although they exhibited unique characteristics; e.g. all carried an EGFR amplification, indicating that it is important for the multifocal phenotype. Tumor foci derived from the same patient always shared identical aberrations, proving monoclonal origin of these tumors but also exhibited additional aberrations, which were specific for each focus and therefore must have occurred later in tumor development. Moreover, our results show that events important for gliomagenesis could occur at different time points in tumor evolution: for example, the region involved in the EGFR amplification was different in both foci from three patients and identical in two foci from one patient. The same can be said of point mutations in TP53 and PTEN; TP53 mutations were identical in the different foci from one patient and different in another patient while PTEN mutations were different in the foci from two patients and similar in those of one. Interestingly, in each patient one focus always contained more aberrations than the other, highlighting the possibility that one derived from the other; this would further support the hypothesis that multifocal GBMs are of monoclonal origin and then develop independently of each other by clonal evolution. Taken together, multifocal GBM provide an excellent model for investigating tumor progression and invasion and might help to distinguish between driver and passenger alterations in GBM. Acknowledgements: This work was partially supported by a grant (MeDDrive program) of the Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden. Citation Format: Khalil Abou-El-Ardat, Dietmar Krex, Michael Seifert, Kerstin Becker, Morten Hillmer, Sophie Eisenreich, Arleta Käßner-Frensel, Petra Freitag, Eva-Maria Gerlach, Karl Hackmann, Andreas Rump, Gabriele Schackert, Evelin Schröck, Barbara Klink. Genetic analysis of multifocal glioblastoma multiforme foci points to their monoclonal evolution and highlights early and late events in their development. [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 3415. doi:10.1158/1538-7445.AM2014-3415

Glioblastoma multiforme (GBM) is the most prevalent malignant primary brain tumor in adults. GBM is classified as primary if it is assumed to have arisen de novo or as secondary if it progressed from lower grade astrocytoma. Previous studies have found that primary and secondary GBMs have distinct molecular and mutational profiles. Both have a grim prognosis with survival times of about a year with therapy. Although much progress in delineating the temporal order of mutations and copy number aberrations in the progression of lower grade gliomas was made in the past years, none of the studies have actively followed individual tumors through their progression. Whereas this method can detect aberrations that are prevalent in gliomas, it can miss events that are important in a subset of gliomas or are necessary for progression. The GlioMath-DD consortium is an interdisciplinary collaboration of several groups at the Technische Universität Dresden (TU-Dresden) aiming to study the progression of gliomas and to come up with a mathematical model for gliomagenesis. The work involves analyzing pairs of gliomas obtained from patients who had presented with a low grade glioma and who later had a recurrence of a higher grade glioma. All tumors were checked by pathologists and then high quality DNA and RNA material extracted and used for analysis. The tumors are analyzed for copy number variations (CNV) by array comparative genome hybridization (aCGH), while gene expression changes and small mutations are analyzed using high-throughput sequencing (RNA- and Exome-seq). The data gleaned from these experiments and from in vitro models of cell growth and spheroid formation will be used by bioinformaticians and mathematicians to infer key signaling networks and formulate a mathematical model of glioma progression. The ultimate aim of this work that spans two and a half years is to create a comprehensive model of glioma promotion and progression. Furthermore, it will pinpoint driver mutations and aberrations that contribute to this progression and eventually isolate biomarkers for diagnosis and therapy. During the conference, we will present preliminary genetic data of our ongoing study. Acknowledgements: The GlioMath-DD project (coordinator: Andreas Deutsch; SAB-Number 100098214) is funded by the European Social Fund (ESF) and the Free State of Saxony Citation Format: Evelin Schröck, Khalil Abou-El-Ardat, Ralf Wiedemuth, Michael Seifert, Alvaro Köhn-Luque, Mirjam Ingargiola, Kristin Stirnnagel, Alexander Krüger, Wolfgang Nagel, Kathrin Geiger, Andreas Beyer, Leoni A. Kunz-Schughart, Gabriele Schackert, Achim Temme, Barbara Klink, Andreas Deutsch. GlioMath-DD: A multidisciplinary approach to study glioma evolution and identify targets for individualized therapies. [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 5341. doi:10.1158/1538-7445.AM2014-5341

Several lines of evidence have linked limb teratogenesis to radiation-induced apoptosis and to the p53 status in murine fetuses. In previous reports, we studied the occurrence of various malformations after intrauterine irradiation and showed that these malformations were modulated by p53-deficiency as well as by the developmental stage at which embryos were irradiated. In this new study, we focused onto one particular phenotype namely forelimb defects to further unravel the cellular and molecular mechanisms underlying this malformation. We measured various parameters expected to be directly or indirectly influenced by irradiation damage. The mouse fetuses were irradiated at day 12 p.c. (post conception) and examined for forelimb defects on gestational days 15, 16, 17 and 19 of development. The release of inflammatory cytokines was determined in the amniotic fluid on day 16 p.c. and the mean telomere lengths assessed at days 12, 13 and 19 p.c. Differential gene expression within the forelimb bud tissues was determined using Real Time quantitative PCR (RTqPCR) 24 h following irradiation. Apoptosis was investigated in the normal and malformed fetuses using the TUNEL assay and RTqPCR. First, we found that irradiated fetuses with forelimb defects displayed excessive apoptosis in the predigital regions. Besides, overexpression of the pro-apoptotic Bax gene indicates a mitochondrial-mediated cell death. Secondly, our results showed overexpression of MKK3 and MKK7 (members of the stress-activated MAP kinase family) within the malformed fetuses. The latter could be involved in radiation-induced apoptosis through activation of the p38 and JNK pathways. Thirdly, we found that irradiated fetuses exhibiting forelimb defects showed a marked telomere shortening. Interestingly, telomere shortening was observed as the malformations became apparent. Fourthly, we measured cytokine levels in the amniotic fluid and detected a considerable inflammatory reaction among the irradiated fetuses as evidenced by the increase in pro-inflammatory cytokine levels. Altogether, our data suggest that transcriptional modulations of apoptotic, inflammation, stress, and DNA damage players are early events in radiation-induced forelimb defects. These changes resulted in harsh developmental conditions as indicated by a marked increase in cytokine levels in the amniotic fluid and telomere shortening, two features concomitant with the onset of the forelimb defect phenotype in our study.