Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences

MOTIVATION

Local alignments of query sequences in large databases represent a core part of metagenomic studies and facilitate homology search. Following the development of NCBI Blast, many applications aimed to provide faster and equally sensitive local alignment frameworks. Most applications focus on protein alignments, while only few also facilitate DNA-based searches. None of the established programs allow searching DNA sequences from bisulfite sequencing experiments commonly used for DNA methylation profiling, for which specific alignment strategies need to be implemented.

RESULTS

Here, we introduce Lambda3, a new version of the local alignment application Lambda. Lambda3 is the first solution that enables the search of protein, nucleotide as well as bisulfite-converted nucleotide query sequences. Its protein mode achieves comparable performance to that of the highly optimized protein alignment application Diamond, while the nucleotide mode consistently outperforms established local nucleotide aligners. Combined, Lambda3 presents a universal local alignment framework that enables fast and sensitive homology searches for a wide range of use-cases.

AVAILABILITY AND IMPLEMENTATION

Lambda3 is free and open-source software publicly available at https://github.com/seqan/lambda/.

AML with complex karyotype: extreme genomic complexity revealed by combined long-read sequencing and Hi-C technology

Acute myeloid leukemia with complex karyotype (CK-AML) is associated with poor prognosis, which is only in part explained by underlying TP53 mutations. Especially in the presence of complex chromosomal rearrangements, such as chromothripsis, the outcome of CK-AML is dismal. However, this degree of complexity of genomic rearrangements contributes to the leukemogenic phenotype and treatment resistance of CK-AML remains largely unknown. Applying an integrative workflow for the detection of structural variants (SVs) based on Oxford Nanopore (ONT) genomic DNA long-read sequencing (gDNA-LRS) and high-throughput chromosome confirmation capture (Hi-C) in a well-defined cohort of CK-AML identified regions with an extreme density of SVs. These rearrangements consisted to a large degree of focal amplifications enriched in the proximity of mammalian-wide interspersed repeat elements, which often result in oncogenic fusion transcripts, such as USP7::MVD, or the deregulation of oncogenic driver genes as confirmed by RNA-seq and ONT direct complementary DNA sequencing. We termed this novel phenomenon chromocataclysm. Thus, our integrative SV detection workflow combing gDNA-LRS and Hi-C enables to unravel complex genomic rearrangements at a very high resolution in regions hard to analyze by conventional sequencing technology, thereby providing an important tool to identify novel important drivers underlying cancer with complex karyotypic changes.

Dynamic antagonism between key repressive pathways maintains the placental epigenome

DNA and Histone 3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb repressive complexes regulate the unmethylated CpG-rich promoters of developmental genes. In contrast to this general framework, the extra-embryonic lineages display non-canonical, globally intermediate DNA methylation levels, including disruption of local Polycomb domains. Here, to better understand this unusual landscape's molecular properties, we genetically and chemically perturbed major epigenetic pathways in mouse trophoblast stem cells. We find that the extra-embryonic epigenome reflects ongoing and dynamic de novo methyltransferase recruitment, which is continuously antagonized by Polycomb to maintain intermediate, locally disordered methylation. Despite its disorganized molecular appearance, our data point to a highly controlled equilibrium between counteracting repressors within extra-embryonic cells, one that can seemingly persist indefinitely without bistable features typically seen for embryonic forms of epigenetic regulation.

Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes

Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.

Acute lymphoblastic leukemia displays a distinct highly methylated genome

DNA methylation is tightly regulated during development and is stably maintained in healthy cells. In contrast, cancer cells are commonly characterized by a global loss of DNA methylation co-occurring with CpG island hypermethylation. In acute lymphoblastic leukemia (ALL), the commonest childhood cancer, perturbations of CpG methylation have been reported to be associated with genetic disease subtype and outcome, but data from large cohorts at a genome-wide scale are lacking. Here, we performed whole-genome bisulfite sequencing across ALL subtypes, leukemia cell lines and healthy hematopoietic cells, and show that unlike most cancers, ALL samples exhibit CpG island hypermethylation but minimal global loss of methylation. This was most pronounced in T cell ALL and accompanied by an exceptionally broad range of hypermethylation of CpG islands between patients, which is influenced by TET2 and DNMT3B. These findings demonstrate that ALL is characterized by an unusually highly methylated genome and provide further insights into the non-canonical regulation of methylation in cancer.

RLM: Fast and simplified extraction of Read-Level Methylation metrics from bisulfite sequencing data

 

Bisulfite sequencing data provide value beyond the straightforward methylation assessment by analyzing single-read patterns. Over the past years, various informative metrics have been established to explore this information. However, limited compatibility with alignment tools, reference genomes or the measurements they provide present a bottleneck for most groups to include this information as standard analysis. To address this, we developed RLM, a fast and scalable tool for the computation of frequently used Read-Level Methylation statistics. RLM supports several common alignment tools, works independently of the reference genome and handles all frequently used sequencing experiment designs. RLM can process large input files with a billion reads in just a few hours on common workstations.

AVAILABILITY

https://github.com/sarahet/RLM.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Cell-specific transcriptional control of mitochondrial metabolism by TIF1γ drives erythropoiesis

Transcription and metabolism both influence cell function, but dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. We discovered, using a chemical suppressor screen, that inhibition of the pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase (DHODH) rescues erythroid differentiation in bloodless zebrafish moonshine (mon) mutant embryos defective for transcriptional intermediary factor 1 gamma (tif1γ). This rescue depends on the functional link of DHODH to mitochondrial respiration. The transcription elongation factor TIF1γ directly controls coenzyme Q (CoQ) synthesis gene expression. Upon tif1γ loss, CoQ levels are reduced, and a high succinate/α-ketoglutarate ratio leads to increased histone methylation. A CoQ analog rescues mon's bloodless phenotype. These results demonstrate that mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage.

Abstract PR04: Transcriptional regulation of mitochondrial metabolism by TIF1γ drives erythroid progenitor differentiation

Understanding in-vivo mechanisms of erythropoiesis is critical for directed differentiation approaches to treat blood disorders such as leukemias. Zebrafish moonshine (mon) mutant embryos defective for the conserved transcriptional intermediary factor 1 gamma (tif1γ) do not specify enough erythroid progenitors due to a transcription elongation block characterized by aberrantly paused RNA polymerase II. To elucidate the TIF1γ-mediated mechanisms in erythroid differentiation, we performed a chemical suppressor screen using 3,100 compounds and identified inhibitors of the essential mitochondrial pyrimidine synthesis enzyme dihydroorotate dehydrogenase (DHODH). Leflunomide as well as the structurally unrelated DHODH inhibitor brequinar rescue the formation of erythroid progenitors in 61% (38/62) and 68% (50/74) of mon embryos, respectively. Beyond changes in nucleotide metabolism, in-vivo metabolic analyses revealed low levels of TCA cycle metabolites which were functionally linked to a reduced oxygen consumption rate. In addition, an increased 2HG/αKG ratio was associated with higher histone methylation states at H3K27, H3K36 and H4K20 as assessed by quantitative targeted mass spectrometry, which may contribute to the erythroid differentiation block upon tif1γ loss. DHODH is the only pyrimidine de novo synthesis enzyme located in mitochondria and its activity is coupled to that of the electron transport chain (ETC) via coenzyme Q (CoQ). Rotenone, a potent ETC complex I inhibitor reversed the rescue by DHODH inhibition in mon embryos. Through parallel genome-wide transcriptome and chromatin immunoprecipitation analyses, we found that genes encoding CoQ metabolic enzymes are direct TIF1γ targets. Treatment with the CoQ analog decylubiquinone rescued erythroid progenitors in 26% (33/126) of mon embryos. These results demonstrate a tight coordination of nucleotide and mitochondrial metabolism as a key function of tif1γ-dependent transcription and reveal that TIF1γ activity regulates a metabolic program that drives cell fate decisions in the early blood lineage. Our work highlights the importance of the plasticity achieved by transcription regulatory processes such as transcription elongation for metabolic processes during lineage differentiation and could have therapeutic potential for blood diseases.

Citation Format: Marlies P. Rossmann, Karen Hoi, Victoria Chan, Brian J. Abraham, Song Yang, James Mullahoo, Malvina Papanastasiou, Ilaria Elia, Sejal Vyas, Partha P. Nag, Lucas B. Sullivan, Julie R. Perlin, Elliott J. Hagedorn, Sara Hetzel, Raha Weigert, Curtis R. Warren, Bilguujin Dorjsuren, Eugenia Custo Greig, Chad A. Cowan, Stuart L. Schreiber, Richard A. Young, Alexander Meissner, Marcia Haigis, Steven A. Carr, Leonard I. Zon. Transcriptional regulation of mitochondrial metabolism by TIF1γ drives erythroid progenitor differentiation [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PR04.

Epigenetic regulator function through mouse gastrulation

During ontogeny, proliferating cells become restricted in their fate through the combined action of cell-type specific transcription factors and ubiquitous epigenetic machinery, which recognize universally available histone residues or nucleotides but are nonetheless deployed in a highly context-dependent manner^1,2. The molecular functions of these regulators are generally well understood, but assigning direct developmental roles is hampered by complex mutant phenotypes that often emerge following gastrulation^3,4. Recently, single-cell RNA sequencing (scRNA-seq) and analytical approaches have explored this highly conserved process across numerous model organisms^5–8, including mouse^9–18. To elaborate on these strategies, we investigated a panel of ten essential regulators using a combined zygotic perturbation, scRNA-seq platform where many mutant embryos can be assayed simultaneously to recover robust transcriptional and morphological information. Deeper analysis of central Polycomb Repressive Complex (PRC) 1 and 2 members indicate substantial cooperativity, but distinguishes a PRC2-dominant role in restricting the germline that emerges from gross molecular changes within the initial conceptus. We believe our experimental framework will eventually allow for a fully quantitative view of how cellular diversity emerges using an identical genetic template and from a single totipotent cell.

Nanopype: a modular and scalable nanopore data processing pipeline

SUMMARY

Long-read third-generation nanopore sequencing enables researchers to now address a range of questions that are difficult to tackle with short read approaches. The rapidly expanding user base and continuously increasing throughput have sparked the development of a growing number of specialized analysis tools. However, streamlined processing of nanopore datasets using reproducible and transparent workflows is still lacking. Here we present Nanopype, a nanopore data processing pipeline that integrates a diverse set of established bioinformatics software while maintaining consistent and standardized output formats. Seamless integration into compute cluster environments makes the framework suitable for high-throughput applications. As a result, Nanopype facilitates comparability of nanopore data analysis workflows and thereby should enhance the reproducibility of biological insights.

AVAILABILITY AND IMPLEMENTATION

https://github.com/giesselmann/nanopype, https://nanopype.readthedocs.io.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Comparison of the Diagnostic Utility of 4D-DSA with Conventional 2D- and 3D-DSA in the Diagnosis of Cerebrovascular Abnormalities

BACKGROUND AND PURPOSE

4D-DSA is a time-resolved technique that allows viewing of a contrast bolus at any time and from any desired viewing angle. Our hypothesis was that the information content in a 4D-DSA reconstruction was essentially equivalent to that in a combination of 2D acquisitions and a 3D-DSA reconstruction.

MATERIALS AND METHODS

Twenty-six consecutive patients who had both 2D- and 3D-DSA acquisitions were included in the study. The angiography report was used to obtain diagnoses and characteristics of abnormalities. Diagnoses included AVM/AVFs, aneurysms, stenosis, and healthy individuals. 4D-DSA reconstructions were independently reviewed by 3 experienced observers who had no part in the clinical care. Using an electronic evaluation form, these observers recorded their assessments based only on the 4D reconstructions. The clinical evaluations were then compared with the 4D evaluations for diagnosis and lesion characteristics.

RESULTS

Results showed both interrater and interclass agreements (κ = 0.813 and 0.858). Comparing the 4D diagnosis with the clinical diagnosis for the 3 observers yielded κ values of 0.906, 0.912, and 0.906. The κ values for agreement among the 3 observers for the type of abnormality were 0.949, 0.845, and 0.895. There was complete agreement on the presence of an abnormality between the clinical and 4D-DSA in 23/26 cases. In 2 cases, there were conflicting opinions.

CONCLUSIONS

In this study, the information content of 4D-DSA reconstructions was largely equivalent to that of the combined 2D/3D studies. The availability of 4D-DSA should reduce the requirement for 2D-DSA acquisitions.

Peak CSF velocities in patients with symptomatic and asymptomatic Chiari I malformation

BACKGROUND AND PURPOSE

PCMR is used to evaluate the Chiari I malformation. We compared quantitative PCMR in symptomatic and asymptomatic patients with Chiari I.

MATERIALS AND METHODS

PCMR image data in an axial section near the foramen magnum in a consecutive series of patients with Chiari I malformations were evaluated. Patients were classified as symptomatic for a Chiari I if they had apnea spells and/or exertional headaches and as asymptomatic if they had symptoms not considered specific for a Chiari I malformation. The PCMR CSF flow study was obtained with the same protocol for all patients and with the neck in neutral, flexed, and extended positions. Images were inspected for CSF flow jets and synchronous bidirectional flow. Peak CSF flow velocities were calculated with commercial software. Differences between the 2 groups were tested with mixed-effects ANOVA and Wilcoxon rank sum or Fisher exact probability tests with significance set at the .05 level.

RESULTS

Twenty-six patients with Chiari I were classified as symptomatic, and 24, as asymptomatic. Abnormal flow jets tended to occur more often in the symptomatic than in the asymptomatic patients (P = .054). Peak CSF velocities ranged from 2 to 20 cm/s in the symptomatic and the asymptomatic groups and did not differ significantly between the 2 groups or with neck position.

CONCLUSIONS

Peak CSF flow velocities near the foramen magnum did not differentiate symptomatic and asymptomatic patients with Chiari I.

Direct detection of bacterial genomic DNA using gold nanoparticle probes

The molecular probes and associated instrumentation necessary to perform genetic analyses are typically expensive, complex, and prone to error. While techniques such as real-time polymerase chain reaction (PCR) and gene expression analysis have provided a wealth of information previously unattainable, their utility in clinical diagnostics has yet to be realized due to the aforementioned limitations. Nanosphere Inc. has developed a gold nanoparticle-based platform for sequence specific DNA detection that is well-suited for clinical diagnostics due to its cost-effectiveness, simplicity, and accuracy. Thirteen nanometer gold nanoparticle probes, stabilized by a shell of oligonucleotides using proprietary attachment chemistries, enable highly sensitive and specific detection of bacterial genomic DNA sequences without synthetic amplification techniques on a glass array. After silver staining, light scattered by the nanoparticle probes is collected with robust, cost-effective instrumentation. It is the unique features of Nanosphere's detection methodology that provide the necessary steps forward to allow for genetic analyses to become part of routine clinical diagnostics.

Renal proximal tubular cell growth and differentiation are differentially modulated by renotropic growth factors and tyrosine kinase inhibitors

BACKGROUND

The renotropic growth factors (GFs), hepatocyte GF (HGF), epidermal GF (EGF), and insulin-like GF-I (IGF-I) accelerate renal regeneration in animal models after toxic or ischemic injury. These GFs initiate their biological effects on renal tubular cells by interaction with specific transmembrane receptor tyrosine kinases.

MATERIALS AND METHODS

In the proximal tubular cell line PT-1, the biological effects of HGF, EGF, and IGF-I and the growth-inhibitory effects of different tyrosine kinase inhibitors (TKIs) were investigated. Receptor binding and tyrosine kinase phosphorylation were determined by ligand binding studies and Western blot analysis.

RESULTS

HGF, EGF, and IGF-I bound with nanomolar affinity to their specific cell membrane receptor tyrosine kinases. In contrast to EGF or IGF-I, HGF induced a variety of cell morphological changes, including cell scattering, formation of tubular structures, and expression of long microvilli on the apical cell membrane. HGF was a 10-fold more potent and more effective growth promoter than EGF or IGF-I. Among the TKIs tested, the mitogenic effect of HGF could be more specifically inhibited by emodin and tyrphostin, that of EGF by methyl-2,5-dihydroxycinnamate, lavendustin A, and genistein, and that of IGF-I by geldanamycin.

CONCLUSIONS

In contrast to EGF and IGF-I, HGF stimulated both growth and differentiation of renal proximal tubular cells, demonstrating the amazing biological potency of this renotropic growth factor. Selective TKIs may be a promising approach to modulate diseases with abnormalities in protein kinase signalling pathways such as renal cell carcinoma.

Inhibitory effect of epidermal growth factor and hepatocyte growth factor on endothelin-1 release by rabbit proximal tubule cells

Several studies have demonstrated an upregulation of endothelin-1 (ET-1) synthesis in acute and chronic renal failure. Epidermal growth factor (EGF) and hepatocyte growth factor (HGF) have been shown to stimulate renal tubular cell proliferation and to accelerate renal regeneration after drug-induced and ischemia-induced renal injury. This study aimed to investigate the effect of EGF and HGF on ET-1 release, and whether the effect of EGF and HGF is antagonized by the tyrosine kinase inhibitor lavendustin A. Rabbit proximal tubule cells were incubated for 48 h with EGF or HGF (0.1-10.0 nM), lavendustin A (0.1-10.0 microM) or co-incubated with EGF or HGF (1 nM) and lavendustin A. ET-1 concentrations in the culture medium were measured with a specific enzyme-linked immunosorbent assay (ELISA). EGF and HGF exerted a significant (p < 0.001) dose-dependent inhibitory effect on ET-1 release. Lavendustin A induced a dose-dependent stimulation of ET-1 release and antagonized the inhibitory effect of EGF and HGF on ET-1 release. The inhibition of EGF and HGF receptor tyrosine kinase activity by lavendustin A was confirmed by Western blotting. These data suggest that EGF and HGF reduce ET-1 release via EGF and HGF receptor tyrosine kinase activity. The inhibitory action of EGF and HGF on ET-1 release might be involved in mediating the protective effects of EGF and HGF in renal injury.

Loss & change: new directions in death education for adolescents

The subject of this paper is Loss & change, a preventive health education school based program. The program has been developed, in conjunction with teachers, by a team of health workers from an Australian community health agency. This program is generalist in nature. It explores the losses adolescents experience within the context of healthy adolescent development. Based on a primary prevention model, it has a strong focus on life, and, as such, is a death education program which is different from those which focus on suicide prevention or bereavement support. The paper serves as an interim report on a program which is still developing, and which may provide some insight into a promising means of support for adolescent development.