Publications by authors named "Heiko Becker"

85 Publications

Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction.

Commun Biol 2021 Feb 1;4(1):153. Epub 2021 Feb 1.

Department of Medicine I, Medical Center - University of Freiburg, Freiburg, Germany.

Single-cell multi-omics are powerful means to study cell-to-cell heterogeneity. Here, we present a single-tube, bisulfite-free method for the simultaneous, genome-wide analysis of DNA methylation and genetic variants in single cells: epigenomics and genomics of single cells analyzed by restriction (epi-gSCAR). By applying this method, we obtained DNA methylation measurements of up to 506,063 CpGs and up to 1,244,188 single-nucleotide variants from single acute myeloid leukemia-derived cells. We demonstrate that epi-gSCAR generates accurate and reproducible measurements of DNA methylation and allows to differentiate between cell lines based on the DNA methylation and genetic profiles.
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http://dx.doi.org/10.1038/s42003-021-01661-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7851132PMC
February 2021

Long-Term Survival Benefit after Allogeneic Hematopoietic Cell Transplantation for Chronic Myelomonocytic Leukemia.

Biol Blood Marrow Transplant 2020 Oct 9. Epub 2020 Oct 9.

Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. Electronic address:

The critical question in the management of chronic myelomonocytic leukemia (CMML) is which patients may benefit from allogeneic hematopoietic cell transplantation (allo-HCT). Using ad hoc statistical analysis, we designed a multicenter retrospective study to determine outcomes in 261 patients age ≤70 years at diagnosis who underwent allo-HCT (n = 119) compared with those who did not (n = 142) according to the current CMML-specific prognostic scoring system (CPSS). Categorizing patients as lower risk (CPSS low/intermediate-1) or higher risk (intermediate-2/high) showed significantly improved outcomes after transplantation in higher-risk patients, with a 37% reduced hazard for death. However, although higher CPSS was associated with worse outcomes in the nontransplantation group, the score was of limited utility for post-transplantation risk stratification. This study may provide further support for the potentially beneficial role of allo-HCT in terms of long-term survival in higher-risk patients but also underscores the need for transplantation-specific risk assessment. Recognizing limitations of retrospective comparisons, larger and prospective comparisons are needed to further refine the indication for allo-HCT and thus counseling of patients with CMML. © 2020 American Society for Transplantation and Cellular Therapy. Published by Elsevier Inc.
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http://dx.doi.org/10.1016/j.bbmt.2020.10.007DOI Listing
October 2020

Prevalence and characteristics of myeloproliferative neoplasms with concomitant monoclonal gammopathy.

Leuk Res 2020 11 15;98:106454. Epub 2020 Sep 15.

Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) Partner Site, Freiburg, Germany. Electronic address:

Of BCR-ABL negative myeloproliferative neoplasm (MPN) patients, 3-14 % display a concomitant monoclonal gammopathy (MGUS). Nonetheless, literature on co-occurring MPN and MGUS is scarce, the molecular underpinnings are unknown and it is unclear whether patients require a specific management. Here, we compared the clinical and genetic features of MPN patients with and without concomitant MGUS. Of 114 MPN patients prospectively studied by serum immunofixation (median age, 67 years; 36.0 % essential thrombocythemia [ET], 24.6 % polycythemia vera [PV], 11.4 % secondary myelofibrosis [sMF], 28.1 % primary myelofibrois [PMF]; 73.7 % JAK2 V617F positive), 10 (9 %) harbored an M-protein. No relevant clinical differences existed between MPN patients with or without M-protein. Seven additional MPN/MGUS patients were retrospectively identified in our MPN registry, yielding a total of 17 patients (7 ET, 3 PV, 3 sMF, 4 PMF). One patient developed multiple myeloma (MM) and one smoldering MM. Seven of 12 patients analyzed carried mutations (e.g. in ASXL1 or TET2) in addition to those in JAK2 or CALR, and 4 of 10 patients showed aberrant cytogenetics. M-protein was mainly IgG (12/17), followed by IgM (4/17). In the two patients that underwent allogeneic stem cell transplantation mutant JAK2 and M-protein were no longer detectable post-transplant. In conclusion, MGUS prevalence in our cohort was in the range of previous reports and at most slightly higher than expected in the general population. MGUS presence did not correlate with a specific MPN entity, clinical features or genetic alterations. Our observations suggest that there is no strong clinical or biological relationship between the occurrence of MGUS and MPN.
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http://dx.doi.org/10.1016/j.leukres.2020.106454DOI Listing
November 2020

Pattern of Recurrence and Patient Survival after Perioperative Chemotherapy with 5-FU, Leucovorin, Oxaliplatin and Docetaxel (FLOT) for Locally Advanced Esophagogastric Adenocarcinoma in Patients Treated Outside Clinical Trials.

J Clin Med 2020 Aug 16;9(8). Epub 2020 Aug 16.

Center for Surgery, Department of General and Visceral Surgery, Medical Center-University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany.

Background: The 5-FU, Leucovorin, Oxaliplatin and Docetaxel (FLOT) protocol provides superior oncologic results compared to other perioperative chemotherapeutic protocols for the treatment of non-metastatic esophagogastric cancer (EGAC). Survival and the pattern of recurrence of EGAC after FLOT and curative tumor resection are analyzed in a collective of patients treated outside clinical trials.

Methods: Two-hundred-seventy-seven patients with EGAC (cT3-4 and/or cN+) were treated with perioperative FLOT-chemotherapy plus curative surgery between 2009 and 2018. Data were analyzed retrospectively from a prospective database.

Results: Two-hundred-twenty-eight patients were included in the analysis. Postoperative in-hospital mortality was 2%. The median survival was 61-months, and median recurrence-free survival was 42 months. Multivariate analysis identified postoperative nodal status and T-stage as independent predictors of improved overall and recurrence-free survival. Administration of adjuvant chemotherapy failed to be significant for overall survival but was an independent predictor of recurrence-free survival. Recurrence occurred after a median of 9 months (range 1-46 months). Eighty-nine percent of recurrence occurred during the first 24 months. The rate of local recurrence was low. After surgery for gastric cancer, the major recurrence site was peritoneal carcinomatosis (56%), while esophageal cancer recurred mostly as metastasis to distant organs (78%). The specific site of recurrence had no impact on overall survival time.

Conclusion: Real-life application of FLOT shows oncologic results comparable to clinical trials. Recurrence after FLOT and surgery for EGAC occurs predominantly early within the first two years after surgery and in the form of distant organ metastasis for esophageal tumors or peritoneal carcinomatosis for gastric tumors.
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http://dx.doi.org/10.3390/jcm9082654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7464040PMC
August 2020

Personalized Treatment Selection and Disease Monitoring Using Circulating Tumor DNA Profiling in Real-World Cancer Patient Management.

Diagnostics (Basel) 2020 Aug 2;10(8). Epub 2020 Aug 2.

Department Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany.

Background: Circulating tumor DNA (ctDNA) in the blood plasma of cancer patients is an emerging biomarker used across oncology, facilitating noninvasive disease monitoring and genetic profiling at various disease milestones. Digital droplet PCR (ddPCR) technologies have demonstrated high sensitivity and specificity for robust ctDNA detection at relatively low costs. Yet, their value for ctDNA-based management of a broad population of cancer patients beyond clinical trials remains elusive.

Methods: We developed mutation-specific ddPCR assays that were optimized for their use in real-world cancer management, covering 12 genetic aberrations in common cancer genes, such as , , , , and . We assessed the limit of detection (LOD) and the limit of blank (LOB) for each assay and validated their performance for ctDNA detection using matched tumor sequencing.

Results: We applied our custom ddPCR assays to 352 plasma samples from 96 patients with solid tumors. Mutation detection in plasma was highly concordant with tumor sequencing, demonstrating high sensitivity and specificity across all assays. In 20 cases, radiographic cancer progression was mirrored by an increase of ctDNA concentrations or the occurrence of novel mutations in plasma. Moreover, ctDNA profiling at diagnosis and during disease progression reflected personalized treatment selection through the identification of actionable gene targets in 20 cases.

Conclusion: Collectively, our work highlights the potential of ctDNA assessment by sensitive ddPCR for accurate disease monitoring, robust identification of resistance mutations, and upfront treatment selection in patients with solid tumors. We envision an increasing future role for ctDNA profiling within personalized cancer management in daily clinical routine.
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http://dx.doi.org/10.3390/diagnostics10080550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459590PMC
August 2020

Monosomal karyotype and chromosome 17p loss or TP53 mutations in decitabine-treated patients with acute myeloid leukemia.

Ann Hematol 2020 Jul 6;99(7):1551-1560. Epub 2020 Jun 6.

Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany.

TP53 aberrations reportedly predict favorable responses to decitabine (DAC) in acute myeloid leukemia (AML). We evaluated clinical features and outcomes associated with chromosome 17p loss or TP53 gene mutations in older, unfit DAC-treated AML patients in a phase II trial. Of 178 patients, 25 had loss of 17p in metaphase cytogenetics; 24 of these had a complex (CK+) and 21 a monosomal karyotype (MK+). In analyses in all patients and restricted to CK+ and MK+ patients, 17p loss tended to associate with higher rates of complete remission (CR), partial remission (PR), or antileukemic effect (ALE). Despite favorable response rates, there was no significant OS difference between patients with or without loss of 17p in the entire cohort or in the CK+ and MK+ cohort. TP53 mutations were identified in eight of 45 patients with material available. Five of the eight TP53-mutated patients had 17p loss. TP53-mutated patients had similar rates of CR/PR/ALE but shorter OS than those with TP53 wild type (P = 0.036). Moreover, patients with a subclone based on mutation data had shorter OS than those without (P = 0.05); only one patient with TP53-mutated AML had a subclone. In conclusion, 17p loss conferred a favorable impact on response rates, even among CK+ and MK+ patients that however could not be maintained. The effect of TP53 mutations appeared to be different; however, patient numbers were low. Future research needs to further dissect the impact of the various TP53 aberrations in HMA-based combination therapies. The limited duration of favorable responses to HMA treatment in adverse-risk genetics AML should prompt physicians to advance allografting for eligible patients in a timely fashion.
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http://dx.doi.org/10.1007/s00277-020-04082-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7316846PMC
July 2020

Oncogenic Kras causes myeloproliferation via NLRP3 inflammasome activation.

Nat Commun 2020 04 3;11(1):1659. Epub 2020 Apr 3.

Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.

Oncogenic Ras mutations occur in various leukemias. It was unclear if, besides the direct transforming effect via constant RAS/MEK/ERK signaling, an inflammation-related effect of KRAS contributes to the disease. Here, we identify a functional link between oncogenic Kras and NLRP3 inflammasome activation in murine and human cells. Mice expressing active Kras in the hematopoietic system developed myeloproliferation and cytopenia, which is reversed in Kras mice lacking NLRP3 in the hematopoietic system. Therapeutic IL-1-receptor blockade or NLRP3-inhibition reduces myeloproliferation and improves hematopoiesis. Mechanistically, Kras-RAC1 activation induces reactive oxygen species (ROS) production causing NLRP3 inflammasome-activation. In agreement with our observations in mice, patient-derived myeloid leukemia cells exhibit KRAS/RAC1/ROS/NLRP3/IL-1β axis activity. Our findings indicate that oncogenic KRAS not only act via its canonical oncogenic driver function, but also enhances the activation of the pro-inflammatory RAC1/ROS/NLRP3/IL-1β axis. This paves the way for a therapeutic approach based on immune modulation via NLRP3 blockade in KRAS-mutant myeloid malignancies.
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http://dx.doi.org/10.1038/s41467-020-15497-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7125138PMC
April 2020

Valproate and Retinoic Acid in Combination With Decitabine in Elderly Nonfit Patients With Acute Myeloid Leukemia: Results of a Multicenter, Randomized, 2 × 2, Phase II Trial.

J Clin Oncol 2020 01 3;38(3):257-270. Epub 2019 Dec 3.

University Hospital of Ulm, Ulm, Germany.

Purpose: DNA-hypomethylating agents are studied in combination with other epigenetic drugs, such as histone deacetylase inhibitors or differentiation inducers (eg, retinoids), in myeloid neoplasias. A randomized, phase II trial with a 2 × 2 factorial design was conducted to investigate the effects of the histone deacetylase inhibitor valproate and all- retinoic acid (ATRA) in treatment-naive elderly patients with acute myeloid leukemia (AML).

Patients And Methods: Two hundred patients (median age, 76 years; range, 61-92 years) ineligible for induction chemotherapy received decitabine (20 mg/m intravenously, days 1 to 5) alone (n = 47) or in combination with valproate (n = 57), ATRA (n = 46), or valproate + ATRA (n = 50). The primary endpoint was objective response, defined as complete and partial remission, tested at a one-sided significance level of α = .10. Key secondary endpoints were overall survival, event-free survival, and progression-free survival and safety.

Results: The addition of ATRA resulted in a higher remission rate (21.9% with ATRA 13.5% without ATRA; odds ratio, 1.80; 95% CI, 0.86 to 3.79; one-sided = .06). For valproate, no effect was observed (17.8% with valproate 17.2% without valproate; odds ratio, 1.06; 95% CI, 0.51 to 2.21; one-sided = .44). Median overall survival was 8.2 months with ATRA 5.1 months without ATRA (hazard ratio, 0.65; 95% CI, 0.48 to 0.89; two-sided = .006). Improved survival was observed across risk groups, including patients with adverse cytogenetics, and was associated with longer response duration. With valproate, no survival difference was observed. Toxicities were predominantly hematologic, without relevant differences between the 4 arms.

Conclusion: The addition of ATRA to decitabine resulted in a higher remission rate and a clinically meaningful survival extension in these patients with difficult-to-treat disease, without added toxicity.
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http://dx.doi.org/10.1200/JCO.19.01053DOI Listing
January 2020

Water pipe smoking as a cause of secondary erythrocytosis.

Oxf Med Case Reports 2019 May 31;2019(5):omz027. Epub 2019 May 31.

Department of Medicine I, Medical Center-University of Freiburg, Freiburg, Germany.

Water pipe (WP) smoking has become very popular in European countries. A 27-year-old male patient was referred to our clinic with erythrocytosis of unknown origin. His self-reported history included almost daily WP smoking since the age of 14 years. At presentation haemoglobin, haematocrit (Hct) and carboxy-haemoglobin (CO-Hb) levels were elevated to 19.7 g/dl, 54% and 15.4%, respectively. Erythrocytosis was completely reversible upon cessation of WP smoking. Upon follow-up, haemoglobin, Hct and CO-Hb levels undulated according to the intensity of WP usage. Our report shall raise awareness among physicians for WP smoking as a possible cause of secondary erythrocytosis, particularly among younger adults, and provide guidance for the clinical management.
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http://dx.doi.org/10.1093/omcr/omz027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544420PMC
May 2019

Root system size response of bzh semi-dwarf oilseed rape hybrids to different nitrogen levels in the field.

Ann Bot 2019 11;124(6):891-901

Georg-August Universität Göttingen, Department of Crop Sciences, Göttingen, Germany.

Background And Aims: In oilseed rape (Brassica napus) semi-dwarf hybrid varieties from crosses between bzh dwarf and normal-type lines are of increasing interest. They have improved nitrogen (N) uptake, N-utilization and N-use efficiency compared to normal types. This study aimed to elucidate whether these N-related effects can be explained by the bzh shoot growth-type alone or also by differences in root traits.

Methods: Root system size was measured using root electrical capacitance (EC) in field trials with two N levels in two sets of genotypes segregating for the bzh-locus: (1) 108 doubled haploid (DH) test hybrids in two seasons, 2010-2012, and (2) 16 near-isogenic hybrids in the 2016-17 season. Quantitative trait loci (QTL) for root EC were estimated in DH test hybrids. Seedling root architecture parameters were monitored in vitro.

Key Results: In vitro root growth showed a higher root: shoot ratio in bzh semi-dwarf hybrids. Root EC in field trials was higher at high N supply than at zero N fertilization. In most trials semi-dwarf hybrids had higher EC than normal-type hybrids, but they reduced root EC in response to N limitation more than normal types. Root EC was more heritable at the end of flowering (h2 = 0.73) than at the beginning of flowering (h2 = 0.36) in near-isogenic hybrids and had a lower heritability in trials of DH test hybrids (h2 = 0.27). A QTL for root EC in the genomic region of the bzh-locus on linkage group A06 was significant at zero N fertilization.

Conclusions: Root EC proved to be a meaningful method in oilseed rape breeding programmes targeting root system size. The greater reduction of semi-dwarf root EC compared to the normal type under low N supply with simultaneous increase in N efficiency implies that in roots it is not a question of 'the more the merrier' and that the bzh root system reacts highly economically when N is scarce.
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http://dx.doi.org/10.1093/aob/mcy197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6881224PMC
November 2019

Phase I/II study on cytarabine and idarubicin combined with escalating doses of clofarabine in newly diagnosed patients with acute myeloid leukaemia and high risk for induction failure (AMLSG 17-10 CIARA trial).

Br J Haematol 2018 10;183(2):235-241

Department of Haematology, Haemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany.

This open-label, multicentre phase I/II study determined the maximum tolerated dose (MTD), safety and efficacy of clofarabine administered with cytarabine and idarubicin in newly diagnosed acute myeloid leukaemia (AML) patients lacking favourable genetic aberrations. The MTD was 30 mg/m clofarabine for patients below and above 60 years. The most frequently reported grade 3-4 non-haematological adverse events were infectious and gastrointestinal toxicities. Complete remission (CR)/CR with incomplete recovery rate was 67%. Allogeneic haematopoietic cell transplantation in first remission was feasible in a high proportion of younger AML patients and probably contributed to the favourable outcome compared to historical controls.
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http://dx.doi.org/10.1111/bjh.15546DOI Listing
October 2018

Fetal hemoglobin induction during decitabine treatment of elderly patients with high-risk myelodysplastic syndrome or acute myeloid leukemia: a potential dynamic biomarker of outcome.

Haematologica 2019 01 31;104(1):59-69. Epub 2018 Aug 31.

Department of Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine and Medical Center, University of Freiburg, Germany

Hematologic responses to hypomethylating agents are often delayed in patients with myelodysplastic syndrome or acute myeloid leukemia. Fetal hemoglobin is a potential novel bio-marker of response: recently, we demonstrated that a high fetal hemoglobin level prior to decitabine treatment was associated with superior outcome. Here we investigated whether early fetal hemoglobin induction during decitabine treatment also had prognostic value, and studied the potential of decitabine to induce erythroid differentiation and fetal hemoglobin expression Fetal hemoglobin levels were measured by high-performance liquid chromatography in patients with higher-risk myelodysplastic syndrome (n=16) and acute myeloid leukemia (n=37) before treatment and after each course of decitabine. Levels above 1.0% were considered induced. Patients achieving complete or partial remission as best response had attained a median fetal hemoglobin of 1.9% after two courses of treatment, whereas the median value in patients who did not reach complete or partial remission was 0.8% (=0.015). Fetal hemoglobin induction after two courses of decitabine treatment was associated with early platelet doubling (=0.006), and its subsequent decrease with hematologic relapse. In patients with myelodysplastic syndrome, induction of fetal hemoglobin after course 2 of treatment was associated with longer overall survival: median of 22.9 7.3 months in patients with or without induction of fetal hemoglobin, respectively [hazard ratio=0.2 (95% confidence interval: 0.1-0.9); =0.03]. decitabine treatment of two bi-potential myeloid leukemia cell lines (K562 and HEL) resulted in induction of an erythroid (not megakaryocytic) differentiation program, and of fetal hemoglobin mRNA and protein, associated with GATA1 gene demethylation and upregulation. In conclusion, fetal hemoglobin may provide a useful dynamic biomarker during hypomethylating agent therapy in patients with myelodysplastic syndrome or acute myeloid leukemia.
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http://dx.doi.org/10.3324/haematol.2017.187278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6312014PMC
January 2019

Ruxolitinib.

Recent Results Cancer Res 2018;212:119-132

Department of Hematology and Oncology, University of Freiburg Medical Center, Hugstetter Str. 55, 79106, Freiburg, Germany.

Ruxolitinib, formerly known as INCB018424 or INC424, is a potent and selective oral inhibitor of Janus kinase (JAK) 1 and JAK2. Ruxolitinib has been approved for the treatment of myelofibrosis (MF) by the US Food and Drug Administration (FDA) in 2011 and by the European Medicines Agency (EMA) in 2012, followed by the approval for the treatment of hydroxyurea (HU)-resistant or -intolerant polycythemia vera (PV) in 2014. Both MF and PV are myeloproliferative neoplasms (MPNs) which are characterized by the aberrant activation of the JAK-STAT pathway. Clinically, MF features bone marrow fibrosis, splenomegaly, abnormal blood counts, and poor quality-of-life through associated symptoms. PV is characterized by the overproduction of primarily red blood cells (RBC), risk of thrombotic complications, and development of secondary MF. Ruxolitinib treatment results in a meaningful reduction in spleen size and symptom burden in the majority of MF patients and may also have a favorable effect on survival. In PV, ruxolitinib effectively controls the hematocrit and reduces splenomegaly. Since recently, ruxolitinib is also under investigation for the treatment of graft-versus-host disease (GvHD) after allogeneic hematopoietic stem cell transplantation (HSCT). Toxicities of ruxolitinib include myelosuppression, which results in dose-limiting thrombocytopenia and anemia, and viral reactivations. The metabolization of ruxolitinib through CYP3A4 needs to be considered particularly if co-administered with potent CYP3A4 inhibitors. Several further JAK inhibitors are currently under investigation for MPNs or other immuno-inflammatory diseases.
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http://dx.doi.org/10.1007/978-3-319-91439-8_6DOI Listing
May 2019

Ten-year outcome of patients with acute myeloid leukemia not treated with allogeneic transplantation in first complete remission.

Blood Adv 2018 07;2(13):1645-1650

The Ohio State University Comprehensive Cancer Center, Columbus, OH.

The probability that adult patients with de novo acute myeloid leukemia (AML) receiving intensive chemotherapy in the absence of allogeneic hematopoietic stem cell transplantation (Allo-HCT) in first complete remission (CR1) will be disease-free at 10 years after diagnosis, a long-term surrogate of cure, is unknown. To address this question, we examined 2551 AML patients (1607 aged <60 years, and 944 aged ≥60 years) enrolled in Cancer and Leukemia Group B treatment protocols and the cytogenetics companion protocol 8461 between 1983 and 2004. At 10 years, 267 (16.6%) of patients aged <60 years and 23 (2.4%) of those aged ≥60 years were alive and disease-free. This disease-free AML group consisted predominantly of patients with core-binding factor AML with t(8;21)(q22;q22) or inv(16)(p13q22)/t(16;16)(p13;q22) and those with a normal karyotype. Occurrences of AML beyond 10 years were infrequent and associated with cytogenetic findings different from those at diagnosis. These data provide evidence that the frequency of long-term cure of AML is low among younger and especially older patients in the absence of Allo-HCT in CR1. In older patients not appropriate for Allo-HCT, these data provide further justification for early use of alternative treatments outside of intensive chemotherapy.
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http://dx.doi.org/10.1182/bloodadvances.2017015222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6039651PMC
July 2018

Gene mutations and clonal architecture in myelodysplastic syndromes and changes upon progression to acute myeloid leukaemia and under treatment.

Br J Haematol 2018 09 5;182(6):830-842. Epub 2018 Jul 5.

Department of Medicine I, Medical Centre - University of Freiburg, Freiburg, Germany.

Knowledge of the molecular and clonal characteristics in the myelodysplastic syndromes (MDS) and during progression to acute myeloid leukaemia (AML) is essential to understand the disease dynamics and optimize treatment. Sequencing serial bone marrow samples of eight patients, we observed that MDS featured a median of 3 mutations. Mutations in genes involved in RNA-splicing or epigenetic regulation were most frequent, and exclusively present in the major clone. Minor subclones were distinguishable in three patients. As the MDS progressed, a median of one mutation was gained, leading to clonal outgrowth. No AML developed genetically independent of a pre-existing clone. The gained mutation mostly affected genes encoding signalling proteins. Additional acquisition of genomic aberrations frequently occurred. Upon treatment, emergence of new clones could be observed. As confirmed by single-cell sequencing, multiple mutations in identical genes in different clones were present within individual patients. DNA-methylation profiling in patients without identification of novel mutations in AML revealed methylation changes in individual genes. In conclusion, our data complement previous observations on the mutational and clonal characteristics in MDS and at progression. Moreover, DNA-methylation changes may be associated with progression in single patients. Redundancy of mutated genes in different clones suggests fertile grounds promoting clonal selection or acquisition.
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http://dx.doi.org/10.1111/bjh.15461DOI Listing
September 2018

Cytogenetic clonal heterogeneity is not an independent prognosis factor in 15-60-year-old AML patients: results on 1291 patients included in the EORTC/GIMEMA AML-10 and AML-12 trials.

Ann Hematol 2018 Oct 20;97(10):1785-1795. Epub 2018 Jun 20.

EORTC Headquarters, Brussels, Belgium.

The presence of cytogenetic clonal heterogeneity has been associated with poor prognosis in patients with acute myeloid leukemia (AML). Here, we reassessed this association. The study cohort consisted of all patients with an abnormal karyotype randomized in the EORTC/GIMEMA AML-10 and AML-12 trials. Abnormal karyotypes were classified as no subclones present (cytogenetic abnormality in a single clone), defined subclones present (presence of one to three subclones), and composite karyotypes (CP) (clonal heterogeneity not allowing enumeration of individual subclones). The main endpoints were overall survival (OS) and disease-free survival (DFS). Among 1291 patients with an abnormal karyotype, 1026 had no subclones, 226 at least 1 subclone, and 39 a CP. Patients with defined subclones had an OS similar to those with no subclones (hazard ratio (HR) 1.05, 95% confidence interval (CI) 0.88-1.26), but CP patients had a shorter OS (HR = 1.58, 95% CI 1.11-2.26). However, in a multivariate Cox model stratified by protocol and adjusted for age, cytogenetic risk group, secondary versus primary AML, and performance status, clonal heterogeneity lost its prognostic importance (HR = 1.10, 95% CI 0.91-1.32 for defined subclones versus no subclones; HR = 0.96, 95% CI 0.67-1.38 for CP versus no subclones). Also, the impact of having a donor on DFS was similar in the three clonal subgroups. In summary, in patients with cytogenetic abnormality, presence of subclones had no impact on OS. The dismal outcome in patients with a CP was explained by the known predictors of poor prognosis.

Trial Registration: AML-10: ClinicalTrials.gov identifier: NCT00002549, retrospectively registered July 19, 2004; AML12: ClinicalTrials.gov identifier: NCT00004128, registered January 27, 2003.
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http://dx.doi.org/10.1007/s00277-018-3396-4DOI Listing
October 2018

Epigenetic regulation of NFE2 overexpression in myeloproliferative neoplasms.

Blood 2018 05 8;131(18):2065-2073. Epub 2018 Mar 8.

Division of Molecular Hematology.

The transcription factor "nuclear factor erythroid 2" (NFE2) is overexpressed in the majority of patients with myeloproliferative neoplasms (MPNs). In murine models, elevated NFE2 levels cause an MPN phenotype with spontaneous leukemic transformation. However, both the molecular mechanisms leading to NFE2 overexpression and its downstream targets remain incompletely understood. Here, we show that the histone demethylase constitutes a novel NFE2 target gene. JMJD1C levels are significantly elevated in polycythemia vera (PV) and primary myelofibrosis patients; concomitantly, global H3K9me1 and H3K9me2 levels are significantly decreased. JMJD1C binding to the promoter is increased in PV patients, decreasing both H3K9me2 levels and binding of the repressive heterochromatin protein-1α (HP1α). Hence, JMJD1C and NFE2 participate in a novel autoregulatory loop. Depleting JMJD1C expression significantly reduced cytokine-independent growth of an MPN cell line. Independently, NFE2 is regulated through the epigenetic JAK2 pathway by phosphorylation of H3Y41. This likewise inhibits HP1α binding. Treatment with decitabine lowered H3Y41ph and augmented H3K9me2 levels at the locus in HEL cells, thereby increasing HP1α binding, which normalized NFE2 expression selectively in JAK2-positive cell lines.
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http://dx.doi.org/10.1182/blood-2017-10-810622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5934799PMC
May 2018

Oncogenic JAK2 causes PD-L1 expression, mediating immune escape in myeloproliferative neoplasms.

Sci Transl Med 2018 02;10(429)

Department of Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg 79106, Germany.

Recent evidence has revealed that oncogenic mutations may confer immune escape. A better understanding of how an oncogenic mutation affects immunosuppressive programmed death ligand 1 (PD-L1) expression may help in developing new therapeutic strategies. We show that oncogenic JAK2 (Janus kinase 2) activity caused STAT3 (signal transducer and activator of transcription 3) and STAT5 phosphorylation, which enhanced PD-L1 promoter activity and PD-L1 protein expression in JAK2-mutant cells, whereas blockade of JAK2 reduced PD-L1 expression in myeloid JAK2-mutant cells. PD-L1 expression was higher on primary cells isolated from patients with JAK2-myeloproliferative neoplasms (MPNs) compared to healthy individuals and declined upon JAK2 inhibition. JAK2 mutational burden, pSTAT3, and PD-L1 expression were highest in primary MPN patient-derived monocytes, megakaryocytes, and platelets. PD-1 (programmed death receptor 1) inhibition prolonged survival in human MPN xenograft and primary murine MPN models. This effect was dependent on T cells. Mechanistically, PD-L1 surface expression in JAK2-mutant cells affected metabolism and cell cycle progression of T cells. In summary, we report that in MPN, constitutive JAK2/STAT3/STAT5 activation, mainly in monocytes, megakaryocytes, and platelets, caused PD-L1-mediated immune escape by reducing T cell activation, metabolic activity, and cell cycle progression. The susceptibility of JAK2-mutant MPN to PD-1 targeting paves the way for immunomodulatory approaches relying on PD-1 inhibition.
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http://dx.doi.org/10.1126/scitranslmed.aam7729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6034655PMC
February 2018

DArT, SNP, and SSR analyses of genetic diversity in Lolium perenne L. using bulk sampling.

BMC Genet 2018 01 22;19(1):10. Epub 2018 Jan 22.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany.

Background: Lolium perenne L. is the most important forage grass species in temperate regions. It is also considered as a sustainable source of biomass for energy production. However, improvement in biomass yield has been limited by comparison with other major crops. More efficient utilisation of genetic resources and improved breeding schemes are required to advance L. perenne breeding. In an attempt to elucidate the extent of genetic diversity in L. perenne, 1384 DArT, 182 SNP and 48 SSR markers were applied to 297 accessions (Set I) contributed by three German breeding companies and the IPK Genebank. Due to the heterogeneous nature of Lolium accessions, bulk samples were used. Apart from germplasm set I, additional set II and set III was used to determine the reproducibility of marker system and judge the feasibility of bulk strategy in this study.

Results: By assessing different bulk sizes, 24 individuals per sample were shown to be a representative number of plants to discriminate different accessions. Among the 297 accessions, all marker types revealed a high polymorphism rate; 1.99, 2.00 and 8.19 alleles, were obtained per locus on average using DArTs, SNPs and SSRs, respectively. The Jaccard distance for DArT markers ranged from 0.00 to 0.73, the Modified Roger's distance (MRD) for SNP markers ranged from 0.03 to 0.52, and for SSR markers from 0.26 to 0.76. Gene diversity for dominant DArT and co-dominant SNP and SSR markers was found to be 0.26, 0.32 and 0.45, respectively. DArT markers showed the highest consistency and reproducibility.

Conclusion: The resulting data were evaluated using a number of different classification methods, but none of the methods showed a clear differentiation into distinct genetic pools. With regard to hybrid breeding, this will possibly impede substantial progress towards increased biomass yields of L. perenne by utilising heterosis.
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http://dx.doi.org/10.1186/s12863-017-0589-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778656PMC
January 2018

Author Correction: Pancreatic cancer: Circulating Tumor Cells and Primary Tumors show Heterogeneous KRAS Mutations.

Sci Rep 2017 10 27;7(1):14631. Epub 2017 Oct 27.

Center for Surgery, Department of General and Visceral Surgery, Medical Center University of Freiburg, Freiburg, Germany.

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
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http://dx.doi.org/10.1038/s41598-017-14870-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5666001PMC
October 2017

The oligodendrocyte lineage transcription factor 2 (OLIG2) is epigenetically regulated in acute myeloid leukemia.

Exp Hematol 2017 11 28;55:76-85.e3. Epub 2017 Jul 28.

Department of Hematology/Oncology and Stem Cell Transplantation, University Medical Center, Freiburg, Germany; Department of Hematology/Oncology, Medical Center Augsburg, Augsburg, Germany. Electronic address:

DNA methylation differences between normal tissue and cancerous tissue resulting in differential expression of genes are a hallmark of acute myeloid leukemia (AML) and can provide malignant cells with a growth advantage via silencing of specific genes, for example, transcription factors. Oligodendrocyte lineage transcription factor 2 (OLIG2) was reported to be differentially methylated and associated with prognosis in AML and, as reported for acute lymphoblastic leukemia and malignant glioma, may play a role in malignant transformation. We report that DNA methylation of OLIG2 is associated with decreased expression of mRNA in AML cell lines and patients. Moreover, in cell lines, decreased mRNA expression also translated into decreased OLIG2 protein expression. Treatment of non-expressing cell lines PL-21 and U-937 with the demethylating agent decitabine resulted in robust re-expression of OLIG2 on mRNA and protein levels. Furthermore, stable overexpression of OLIG2 in non-expressing cell lines Kasumi-1 and U-937, using a lentiviral vector system, led to moderate growth inhibition after 4 days and resulted in signs of differentiation in U-937 cells. Interestingly, although CD34 + cells from healthy donors and 10 of 12 AML patients exhibited no protein expression, OLIG2 was expressed in two patients, both bearing the translocation t(15;17), corresponding to OLIG2 expression in NB-4 cells, also harboring t(15;17). In conclusion, we provide first evidence that OLIG2 is epigenetically regulated via DNA methylation and expressed in a subset of AML patients. OLIG2 may exert antiproliferative activity in leukemia cell lines, and its potential leukemia-suppressing role in AML warrants further investigation.
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http://dx.doi.org/10.1016/j.exphem.2017.07.009DOI Listing
November 2017

Evaluation of nine genotypes of oilseed rape (Brassica napus L.) for larval infestation and performance of rape stem weevil (Ceutorhynchus napi Gyll.).

PLoS One 2017 7;12(7):e0180807. Epub 2017 Jul 7.

Department for Crop Sciences, Division of Plant Pathology and Plant Protection, Section of Agricultural Entomology, Goettingen, Georg-August University, Germany.

The rape stem weevil, Ceutorhynchus napi Gyll., is a serious pest of winter oilseed rape (Brassica napus L.) crops in Europe causing severe yield loss. In currently used oilseed rape cultivars no resistance to C. napi has been identified. Resynthesized lines of B. napus have potential to broaden the genetic variability and may improve resistance to insect pests. In this study, the susceptibility to C. napi of three cultivars, one breeding line and five resynthesized lines of oilseed rape was compared in a semi-field plot experiment under multi-choice conditions. Plant acceptance for oviposition was estimated by counting the number of C. napi larvae in stems. The larval instar index and the dry body mass were assessed as indicators of larval performance. The extent of larval feeding within stems was determined by the stem injury coefficient. Morphological stem traits and stem contents of glucosinolates were assessed as potential mediators of resistance. The resynthesized line S30 had significantly fewer larvae than the cultivars Express617 and Visby and the resynthesized lines L122 and L16. The low level of larval infestation in S30 was associated with a low larval instar and stem injury index. Low numbers of larvae were not correlated with the length or diameter of stems, and the level of stem glucosinolates. As indicated by the low larval infestation and slow larval development the resistance of S30 to C. napi is based on both antixenotic and antibiotic properties of the genotypes. The resynthesized line S30 should therefore be introduced into B. napus breeding programs to enhance resistance against C. napi.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180807PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501604PMC
September 2017

Pancreatic cancer: Circulating Tumor Cells and Primary Tumors show Heterogeneous KRAS Mutations.

Sci Rep 2017 07 3;7(1):4510. Epub 2017 Jul 3.

Center for Surgery, Department of General and Visceral Surgery, Medical Center University of Freiburg, Freiburg, Germany.

Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease. Circulating tumor cells (CTC) in the blood are hypothesized as the means of systemic tumor spread. Blood obtained from healthy donors and patients with PDAC was therefore subject to size-based CTC-isolation. We additionally compared Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations in pancreatic CTC and corresponding tumors, and evaluated their significance as prognostic markers. Samples from 68 individuals (58 PDAC patients, 10 healthy donors) were analyzed; CTCs were present in patients with UICC stage IA-IV tumors and none of the controls (p < 0.001). Patients with >3 CTC/ml had a trend for worse median overall survival (OS) than patients with 0.3–3 CTC/ml (P = 0.12). Surprisingly, CTCs harbored various KRAS mutations in codon 12 and 13. Patients with a KRAS G12V mutation in their CTC (n = 14) had a trend to better median OS (24.5 months) compared to patients with other (10 months), or no detectable KRAS mutations (8 months; P = 0.04). KRAS mutations in CTC and corresponding tumor were discordant in 11 of 26 “tumor-CTC-pairs” (42%), while 15 (58%) had a matching mutation; survival was similar in both groups (P = 0.36). Genetic characterization, including mutations such as KRAS, may prove useful for prognosis and understanding of tumor biology.
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http://dx.doi.org/10.1038/s41598-017-04601-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495768PMC
July 2017

Elevated fetal haemoglobin is a predictor of better outcome in MDS/AML patients receiving 5-aza-2'-deoxycytidine (Decitabine).

Br J Haematol 2017 02 1;176(4):609-617. Epub 2016 Dec 1.

Division of Haematology, Oncology and Stem Cell Transplantation, Faculty of Medicine, University of Freiburg, Freiburg, Germany.

Although azanucleoside DNA-hypomethylating agents (HMAs) are routinely used for the treatment of myelodysplastic syndrome/acute myeloid leukaemia (MDS/AML), very few outcome predictors have been established. Expression of the β-like globin gene locus is tightly regulated by DNA methylation, is HMA-sensitive in vitro, and fetal haemoglobin (HbF) expression is under study as a potential biomarker for response of MDS patients to azacitidine. We determined HbF expression in 16 MDS and 36 AML patients receiving decitabine (DAC). Pre-treatment HbF was already elevated (>1·0% of total haemoglobin) in 7/16 and 12/36 patients, and HbF was induced by DAC in 81%/54% of MDS/AML patients, respectively. Elevated pre-treatment HbF was associated with longer median overall survival (OS): 26·6 vs. 8·6 months for MDS (hazard ratio [HR] 8·56, 95% confidence interval [CI] 1·74-42·49, P = 0·008, with similarly longer progression-free and AML-free survival), and 10·0 vs. 2·9 months OS for AML (HR 3·01, 95% CI 1·26-7·22, P = 0·014). In a multivariate analysis, the prognostic value of HbF was retained. Time-dependent Cox models revealed that the prognostic value of treatment-induced HbF induction was inferior to that of pre-treatment HbF. In conclusion, we provide first evidence for in vivo HbF induction by DAC in MDS/AML, and demonstrate prognostic value of elevated pre-treatment HbF, warranting prospective, randomized studies.
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http://dx.doi.org/10.1111/bjh.14463DOI Listing
February 2017

Molecular Genetic Characterization of Individual Cancer Cells Isolated via Single-Cell Printing.

PLoS One 2016;11(9):e0163455. Epub 2016 Sep 22.

Department of Medicine I, Medical Center - University of Freiburg, Freiburg, Germany.

Intratumoral genetic heterogeneity may impact disease outcome. Gold standard for dissecting clonal heterogeneity are single-cell analyses. Here, we present an efficient workflow based on an advanced Single-Cell Printer (SCP) device for the study of gene variants in single cancer cells. To allow for precise cell deposition into microwells the SCP was equipped with an automatic dispenser offset compensation, and the 384-microwell plates were electrostatically neutralized. The ejection efficiency was 99.7% for fluorescent beads (n = 2304) and 98.7% for human cells (U-2 OS or Kasumi-1 cancer cell line, acute myeloid leukemia [AML] patient; n = 150). Per fluorescence microscopy, 98.8% of beads were correctly delivered into the wells. A subset of single cells (n = 81) was subjected to whole genome amplification (WGA), which was successful in all cells. On empty droplets, a PCR on LINE1 retrotransposons yielded no product after WGA, verifying the absence of free-floating DNA in SCP-generated droplets. Representative gene variants identified in bulk specimens were sequenced in single-cell WGA DNA. In U-2 OS, 22 of 25 cells yielded results for both an SLC34A2 and TET2 mutation site, including cells harboring the SLC34A2 but not the TET2 mutation. In one cell, the TET2 mutation analysis was inconclusive due to allelic dropout, as assessed via polymorphisms located close to the mutation. Of Kasumi-1, 23 of 33 cells with data on both the KIT and TP53 mutation site harbored both mutations. In the AML patient, 21 of 23 cells were informative for a TP53 polymorphism; the identified alleles matched the loss of chromosome arm 17p. The advanced SCP allows efficient, precise and gentle isolation of individual cells for subsequent WGA and routine PCR/sequencing-based analyses of gene variants. This makes single-cell information readily accessible to a wide range of applications and can provide insights into clonal heterogeneity that were indeterminable solely by analyses of bulk specimens.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5033393PMC
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163455PLOS
September 2016