Predictive value of DNA methylation patterns in AML patients treated with an azacytidine containing induction regimen.

BACKGROUND: Acute myeloid leukemia (AML) is a heterogeneous disease with a poor prognosis. Dysregulation of the epigenetic machinery is a significant contributor to disease development. Some AML patients benefit from treatment with hypomethylating agents (HMAs), but no predictive biomarkers for therapy response exist. Here, we investigated whether unbiased genome-wide assessment of pre-treatment DNA-methylation profiles in AML bone marrow blasts can help to identify patients who will achieve a remission after an azacytidine-containing induction regimen. RESULTS: A total of n = 155 patients with newly diagnosed AML treated in the AMLSG 12-09 trial were randomly assigned to a screening and a refinement and validation cohort. The cohorts were divided according to azacytidine-containing induction regimens and response status. Methylation status was assessed for 664,227 500-bp-regions using methyl-CpG immunoprecipitation-seq, resulting in 1755 differentially methylated regions (DMRs). Top regions were distilled and included genes such as WNT10A and GATA3. 80% of regions identified as a hit were represented on HumanMethlyation 450k Bead Chips. Quantitative methylation analysis confirmed 90% of these regions (36 of 40 DMRs). A classifier was trained using penalized logistic regression and fivefold cross validation containing 17 CpGs. Validation based on mass spectra generated by MALDI-TOF failed (AUC 0.59). However, discriminative ability was maintained by adding neighboring CpGs. A recomposed classifier with 12 CpGs resulted in an AUC of 0.77. When evaluated in the non-azacytidine containing group, the AUC was 0.76. CONCLUSIONS: Our analysis evaluated the value of a whole genome methyl-CpG screening assay for the identification of informative methylation changes. We also compared the informative content and discriminatory power of regions and single CpGs for predicting response to therapy. The relevance of the identified DMRs is supported by their association with key regulatory processes of oncogenic transformation and support the idea of relevant DMRs being enriched at distinct loci rather than evenly distribution across the genome. Predictive response to therapy could be established but lacked specificity for treatment with azacytidine. Our results suggest that a predictive epigenotype carries its methylation information at a complex, genome-wide level, that is confined to regions, rather than to single CpGs. With increasing application of combinatorial regimens, response prediction may become even more complicated.

DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts.

Immunotherapies targeting cancer-specific neoantigens have revolutionized the treatment of cancer patients. Recent evidence suggests that epigenetic therapies synergize with immunotherapies, mediated by the de-repression of endogenous retroviral element (ERV)-encoded promoters, and the initiation of transcription. Here, we use deep RNA sequencing from cancer cell lines treated with DNA methyltransferase inhibitor (DNMTi) and/or Histone deacetylase inhibitor (HDACi), to assemble a de novo transcriptome and identify several thousand ERV-derived, treatment-induced novel polyadenylated transcripts (TINPATs). Using immunopeptidomics, we demonstrate the human leukocyte antigen (HLA) presentation of 45 spectra-validated treatment-induced neopeptides (t-neopeptides) arising from TINPATs. We illustrate the potential of the identified t-neopeptides to elicit a T-cell response to effectively target cancer cells. We further verify the presence of t-neopeptides in AML patient samples after in vivo treatment with the DNMT inhibitor Decitabine. Our findings highlight the potential of ERV-derived neoantigens in epigenetic and immune therapies.

Global hypomethylation in childhood asthma identified by genome-wide DNA-methylation sequencing preferentially affects enhancer regions.

BACKGROUND: Childhood asthma is a result of a complex interaction of genetic and environmental components causing epigenetic and immune dysregulation, airway inflammation and impaired lung function. Although different microarray based EWAS studies have been conducted, the impact of epigenetic regulation in asthma development is still widely unknown. We have therefore applied unbiased whole genome bisulfite sequencing (WGBS) to characterize global DNA-methylation profiles of asthmatic children compared to healthy controls. METHODS: Peripheral blood samples of 40 asthmatic and 42 control children aged 5-15 years from three birth cohorts were sequenced together with paired cord blood samples. Identified differentially methylated regions (DMRs) were categorized in genotype-associated, cell-type-dependent, or prenatally primed. Network analysis and subsequent natural language processing of DMR-associated genes was complemented by targeted analysis of functional translation of epigenetic regulation on the transcriptional and protein level. RESULTS: In total, 158 DMRs were identified in asthmatic children compared to controls of which 37% were related to the eosinophil content. A global hypomethylation was identified affecting predominantly enhancer regions and regulating key immune genes such as IL4, IL5RA, and EPX. These DMRs were confirmed in n = 267 samples and could be linked to aberrant gene expression. Out of the 158 DMRs identified in the established phenotype, 56 were perturbed already at birth and linked, at least in part, to prenatal influences such as tobacco smoke exposure or phthalate exposure. CONCLUSION: This is the first epigenetic study based on whole genome sequencing to identify marked dysregulation of enhancer regions as a hallmark of childhood asthma.

TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer.

T-cell acute lymphocytic leukemia protein 1 (TAL1) is one of the most frequently deregulated oncogenes in T-cell acute lymphoblastic leukemia (T-ALL). Its deregulation can occur through diverse cis-alterations, including SIL-TAL1 microdeletions, translocations with T-cell Receptor loci, and more recently described upstream intergenic non-coding mutations. These mutations consist of recurrent focal microinsertions that create an oncogenic neo-enhancer accompanied by activating epigenetic marks. This observation laid the groundwork for an innovative paradigm concerning the activation of proto-oncogenes via genomic alterations of non-coding intergenic regions. However, for the majority of T-ALL expressing TAL1 (TAL1+), the deregulation mechanism remains 'unresolved'. We took advantage of H3K27ac and H3K4me3 chromatin immunoprecipitation sequencing data of eight cases of T-ALL, including five TAL1+ cases. We identified a putative novel oncogenic neo-enhancer downstream of TAL1 in an unresolved monoallelic TAL1+ case. A rare but recurrent somatic heterozygous microinsertion within this region creates a de novo binding site for MYB transcription factor. Here we demonstrate that this mutation leads to increased enhancer activity, gain of active epigenetic marks, and TAL1 activation via recruitment of MYB. These results highlight the diversity of non-coding mutations that can drive oncogene activation.

Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients.

Mutations in splicing factor genes have a severe impact on the survival of cancer patients. Splicing factor 3b subunit 1 (SF3B1) is one of the most frequently mutated genes in chronic lymphocytic leukemia (CLL); patients carrying these mutations have a poor prognosis. Since the splicing machinery and the epigenome are closely interconnected, we investigated whether these alterations may affect the epigenomes of CLL patients. While an overall hypomethylation during CLL carcinogenesis has been observed, the interplay between the epigenetic stage of the originating B cells and SF3B1 mutations, and the subsequent effect of the mutations on methylation alterations in CLL, have not been investigated. We profiled the genome-wide DNA methylation patterns of 27 CLL patients with and without SF3B1 mutations and identified local decreases in methylation levels in SF3B1mut CLL patients at 67 genomic regions, mostly in proximity to telomeric regions. These differentially methylated regions (DMRs) were enriched in gene bodies of cancer-related signaling genes, e.g., NOTCH1, HTRA3, and BCL9L. In our study, SF3B1 mutations exclusively emerged in two out of three epigenetic stages of the originating B cells. However, not all the DMRs could be associated with the methylation programming of B cells during development, suggesting that mutations in SF3B1 cause additional epigenetic aberrations during carcinogenesis.

Fully stabilized multi-TW optical waveform synthesizer: Toward gigawatt isolated attosecond pulses.

A stable 50-mJ three-channel optical waveform synthesizer is demonstrated and used to reproducibly generate a high-order harmonic supercontinuum in the soft x-ray region. This synthesizer is composed of pump pulses from a 10-Hz repetition-rate Ti:sapphire pump laser and signal and idler pulses from an infrared two-stage optical parametric amplifier driven by this pump laser. With full active stabilization of all relative time delays, relative phases, and the carrier-envelope phase, a shot-to-shot stable intense continuum harmonic spectrum is obtained around 60 eV with pulse energy above 0.24 µJ. The peak power of the soft x-ray continuum is evaluated to be beyond 1 GW with a 170-as transform limit duration. We found a characteristic delay dependence of the multicycle waveform synthesizer and established its control scheme. Compared with the one-color case, we experimentally observe an enhancement of the cutoff spectrum intensity by one to two orders of magnitude using three-color waveform synthesis.

Method for direct observation of Bloch oscillations in semiconductors.

We propose a scheme for real-time observations of Bloch oscillations in semiconductors using time-resolved band gap emission spectroscopy. By solving the time-dependent Schrödinger equation, we find one remarkable band gap emission besides the normal high harmonics generated in the interaction of a mid-infrared laser pulse and a semiconductor. It is shown that the band gap emission yield is directly connected to the population in the conduction band (CB). By adopting a pump-probe scheme, the time-dependent population in the CB, that is the dynamical Bloch oscillation, can be probed by measuring the band gap emission signal versus pump-probe delay. We also present a model based on accelerated Bloch states to explain the time-resolved measurement of dynamical Bloch oscillation.

Molecular polarizability anisotropy of liquid water revealed by terahertz-induced transient orientation.

Reaction pathways of biochemical processes are influenced by the dissipative electrostatic interaction of the reagents with solvent water molecules. The simulation of these interactions requires a parametrization of the permanent and induced dipole moments. However, the underlying molecular polarizability of water and its dependence on ions are partially unknown. Here, we apply intense terahertz pulses to liquid water, whose oscillations match the timescale of orientational relaxation. Using a combination of terahertz pump / optical probe experiments, molecular dynamics simulations, and a Langevin dynamics model, we demonstrate a transient orientation of their dipole moments, not possible by optical excitation. The resulting birefringence reveals that the polarizability of water is lower along its dipole moment than the average value perpendicular to it. This anisotropy, also observed in heavy water and alcohols, increases with the concentration of sodium iodide dissolved in water. Our results enable a more accurate parametrization and a benchmarking of existing and future water models.

Near- and Extended-Edge X-Ray-Absorption Fine-Structure Spectroscopy Using Ultrafast Coherent High-Order Harmonic Supercontinua.

Recent advances in high-order harmonic generation have made it possible to use a tabletop-scale setup to produce spatially and temporally coherent beams of light with bandwidth spanning 12 octaves, from the ultraviolet up to x-ray photon energies >1.6 keV. Here we demonstrate the use of this light for x-ray-absorption spectroscopy at the K- and L-absorption edges of solids at photon energies near 1 keV. We also report x-ray-absorption spectroscopy in the water window spectral region (284-543 eV) using a high flux high-order harmonic generation x-ray supercontinuum with 10^{9} photons/s in 1% bandwidth, 3 orders of magnitude larger than has previously been possible using tabletop sources. Since this x-ray radiation emerges as a single attosecond-to-femtosecond pulse with peak brightness exceeding 10^{26} photons/s/mrad^{2}/mm^{2}/1% bandwidth, these novel coherent x-ray sources are ideal for probing the fastest molecular and materials processes on femtosecond-to-attosecond time scales and picometer length scales.

Publisher Correction: Ellipticity dependence of high-harmonic generation in solids originating from coupled intraband and interband dynamics.

The published version of this Article contained an error in the second sentence of the fourth paragraph of the subheaded section "Ellipticity and helicity of the emitted harmonics". The final exponent in this sentence should read: inπ/2. This has now been corrected in the PDF and HTML versions of the Article.

Ellipticity dependence of high-harmonic generation in solids originating from coupled intraband and interband dynamics.

The strong ellipticity dependence of high-harmonic generation (HHG) in gases enables numerous experimental techniques that are nowadays routinely used, for instance, to create isolated attosecond pulses. Extending such techniques to solids requires a fundamental understanding of the microscopic mechanism of HHG. Here we use first-principles simulations within a time-dependent density-functional framework and show how intraband and interband mechanisms are strongly and differently affected by the ellipticity of the driving laser field. The complex interplay between intraband and interband effects can be used to tune and improve harmonic emission in solids. In particular, we show that the high-harmonic plateau can be extended by as much as 30% using a finite ellipticity of the driving field. We furthermore demonstrate the possibility to generate, from single circularly polarized drivers, circularly polarized harmonics. Our work shows that ellipticity provides an additional knob to experimentally optimize HHG in solids.The mechanisms of high-order harmonic generation in bulk system and dilute gas are different. Here the authors use first-principle methods to explore the ellipticity dependence and control of the HHG in periodic solids by involving the interband and intraband dynamics in Si and MgO.

Epigenetic dysregulation of the erythropoietic transcription factor KLF1 and the ß-like globin locus in juvenile myelomonocytic leukemia.

Increased levels of fetal hemoglobin (HbF) are a hallmark of more than half of the children diagnosed with juvenile myelomonocytic leukemia (JMML). Elevated HbF levels in JMML are associated with DNA hypermethylation of distinct gene promoter regions in leukemic cells. Since the regulation of globin gene transcription is known to be under epigenetic control, we set out to study the relation of DNA methylation patterns at ß-/γ-globin promoters, mRNA and protein expression of globins, and epigenetic modifications of genes encoding the globin-regulatory transcription factors BCL11A and KLF1 in nucleated erythropoietic precursor cells of patients with JMML. We describe several altered epigenetic components resulting in disordered globin synthesis in JMML. We identify a cis-regulatory upstream KLF1 enhancer sequence as highly sensitive to DNA methylation and frequently hypermethylated in JMML. The data indicate that the dysregulation of ß-like globin genes is a genuine attribute of the leukemic cell clone in JMML and involves mechanisms not taking part in the normal fetal-to-adult hemoglobin switch.

High-dynamic-range arrival time control for flexible, accurate and precise parametric sub-cycle waveform synthesis.

We introduce a simple all-inline variation of a balanced optical cross-correlator (BOC) that allows to measure the arrival time difference (ATD), over the full Nyquist bandwidth, with increased common-mode rejection and long-term stability. An FPGA-based signal processing unit allows for real-time signal normalization and enables locking to any setpoint with an unprecedented accuracy of 0.07 % within an increased ATD range of more than 400 fs, resulting in attosecond resolution locking. The setup precision is verified with an out-of-loop measurement to be less than 80 as residual jitter paving the way for highly demanding applications such as parametric waveform synthesizers.

Suppression of indoleamine-2,3-dioxygenase 1 expression by promoter hypermethylation in ER-positive breast cancer.

Kynurenine formation by tryptophan-catabolic indoleamine-2,3-dioxygenase 1 (IDO1) plays a key role in tumor immune evasion and inhibition of IDO1 is efficacious in preclinical models of breast cancer. As the response of breast cancer to immune checkpoint inhibitors may be limited, a better understanding of the expression of additional targetable immunomodulatory pathways is of importance. We therefore investigated the regulation of IDO1 expression in different breast cancer subtypes. We identified estrogen receptor α (ER) as a negative regulator of IDO1 expression. Serum kynurenine levels as well as tumoral IDO1 expression were lower in patients with ER-positive than ER-negative tumors and an inverse relationship between IDO1 and estrogen receptor mRNA was observed across 14 breast cancer data sets. Analysis of whole genome bisulfite sequencing, 450k, MassARRAY and pyrosequencing data revealed that the IDO1 promoter is hypermethylated in ER-positive compared with ER-negative breast cancer. Reduced induction of IDO1 was also observed in human ER-positive breast cancer cell lines. IDO1 induction was enhanced upon DNA demethylation in ER-positive but not in ER-negative cells and methylation of an IDO1 promoter construct reduced IDO1 expression, suggesting that enhanced methylation of the IDO1 promoter suppresses IDO1 in ER-positive breast cancer. The association of ER overexpression with epigenetic downregulation of IDO1 appears to be a particular feature of breast cancer as IDO1 was not suppressed by IDO1 promoter hypermethylation in the presence of high ER expression in cervical or endometrial cancer.

Impact of the Electronic Band Structure in High-Harmonic Generation Spectra of Solids.

An accurate analytic model describing the microscopic mechanism of high-harmonic generation (HHG) in solids is derived. Extensive first-principles simulations within a time-dependent density-functional framework corroborate the conclusions of the model. Our results reveal that (i) the emitted HHG spectra are highly anisotropic and laser-polarization dependent even for cubic crystals; (ii) the harmonic emission is enhanced by the inhomogeneity of the electron-nuclei potential; the yield is increased for heavier atoms; and (iii) the cutoff photon energy is driver-wavelength independent. Moreover, we show that it is possible to predict the laser polarization for optimal HHG in bulk crystals solely from the knowledge of their electronic band structure. Our results pave the way to better control and optimize HHG in solids by engineering their band structure.

Attosecond precision multi-kilometer laser-microwave network.

Synchronous laser-microwave networks delivering attosecond timing precision are highly desirable in many advanced applications, such as geodesy, very-long-baseline interferometry, high-precision navigation and multi-telescope arrays. In particular, rapidly expanding photon-science facilities like X-ray free-electron lasers and intense laser beamlines require system-wide attosecond-level synchronization of dozens of optical and microwave signals up to kilometer distances. Once equipped with such precision, these facilities will initiate radically new science by shedding light on molecular and atomic processes happening on the attosecond timescale, such as intramolecular charge transfer, Auger processes and their impacts on X-ray imaging. Here we present for the first time a complete synchronous laser-microwave network with attosecond precision, which is achieved through new metrological devices and careful balancing of fiber nonlinearities and fundamental noise contributions. We demonstrate timing stabilization of a 4.7-km fiber network and remote optical-optical synchronization across a 3.5-km fiber link with an overall timing jitter of 580 and 680 attoseconds root-mean-square, respectively, for over 40 h. Ultimately, we realize a complete laser-microwave network with 950-attosecond timing jitter for 18 h. This work can enable next-generation attosecond photon-science facilities to revolutionize many research fields from structural biology to material science and chemistry to fundamental physics.

40-µJ passively CEP-stable seed source for ytterbium-based high-energy optical waveform synthesizers.

We demonstrate experimentally for the first time a ~40-µJ two-octave-wide passively carrier-envelope phase (CEP)-stable parametric front-end for seeding an ytterbium (Yb)-pump-based, few-optical-cycle, high-energy optical parametric waveform synthesizer. The system includes a CEP-stable white-light continuum and two-channel optical parametric chirped pulse amplifiers (OPCPAs) in the near- and mid-infrared spectral regions spanning altogether a two-octave-wide spectrum driven by a regenerative amplifier. The output pulses are compressed and fully characterized to demonstrate the well-behaved spectral phase of this seed source.

Jitter analysis of timing-distribution and remote-laser synchronization systems.

We present a powerful jitter analysis method for timing-distribution and remote-laser synchronization systems based on feedback flow between setup elements. We synchronize two different mode-locked lasers in a master-slave configuration locally and remotely over a timing-stabilized fiber link network. Local synchronization reveals the inherent jitter of the slave laser as 2.1 fs RMS (>20 kHz), whereas remote synchronization exhibits an out-of-loop jitter of 8.55 fs RMS integrated for 1 Hz - 1 MHz. Our comprehensive feedback model yields excellent agreement with the experimental results and identifies seven uncorrelated noise sources, out of which the slave laser's jitter dominates with 8.19 fs RMS.