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Additional file 1. Supplementary Figures S1 ��� S8

Mitochondrial dysfunction plays a critical role in metabolic associated fatty liver disease (MAFLD). This study aims to characterize mitochondrial dysfunctions in a human MAFLD Huh7 cell model triggered by free fatty acid (FFA) (palmitate and oleate) overload for 24 hours. We investigate its impact on cellular energy metabolism and identify potential targets for MAFLD treatment. FFA-treated cells displayed an accumulation of lipid droplets and slightly decreased viability but no significant changes in mitochondrial superoxide levels. Bioenergetic analysis showed a shift to more respiration and less glycolytic fermentation. Comprehensive transcriptomics and proteomics analyses identified changes in the expression of genes prominently involved in fatty acid handling and metabolism. The expressions of seven genes were consistently and significantly (p < 0.05) altered (4 upregulated and 3 downregulated genes) in both proteomics and transcriptomics. The FFA-treated Huh7 cell model is an appropriate in vitro model to study fatty acid metabolism and suitable to investigate the role of mitochondria, glycolysis, and multiple metabolic pathways in MAFLD. Our comprehensive analyses form a basis for drug discovery and screening using this model.

Genes in the major histocompatibility complex (MHC, also known as HLA) play a critical role in the immune response and variation within the extended 4-Mb region shows association with major risks of many diseases. Yet, deciphering the underlying causes of these associations is difficult because the MHC is the most polymorphic region of the genome with a complex linkage disequilibrium structure. Here, we reconstruct full MHC haplotypes from de novo assembled trios without relying on a reference genome and perform evolutionary analyses. We report 100 full MHC haplotypes and call a large set of structural variants in the regions for future use in imputation with GWAS data. We also present the first complete analysis of the recombination landscape in the entire region and show how balancing selection at classical genes have linked effects on the frequency of variants throughout the region.

Summary The truncated mutant form of the charged multivesicular body protein 2B (CHMP2B) is causative for frontotemporal dementia linked to chromosome 3 (FTD3). CHMP2B is a constituent of the endosomal sorting complex required for transport (ESCRT) and, when mutated, disrupts endosome-to-lysosome trafficking and substrate degradation. To understand the underlying molecular pathology, FTD3 patient induced pluripotent stem cells (iPSCs) were differentiated into forebrain-type cortical neurons. FTD3 neurons exhibited abnormal endosomes, as previously shown in patients. Moreover, mitochondria of FTD3 neurons displayed defective cristae formation, accompanied by deficiencies in mitochondrial respiration and increased levels of reactive oxygen. In addition, we provide evidence for perturbed iron homeostasis, presenting an in vitro patient-specific model to study the effects of iron accumulation in neurodegenerative diseases. All phenotypes observed in FTD3 neurons were rescued in CRISPR/Cas9-edited isogenic controls. These findings illustrate the relevance of our patient-specific in vitro models and open up possibilities for drug target development., Graphical Abstract, Highlights • FTD3 neurons show abnormalities in endosomes and mitochondria • Parkinson's and Alzheimer's disease core genes are altered in FTD3 neurons • Iron homeostasis is perturbed in FTD3 neurons • Impairments in FTD3 neurons are rescued in CRISPR/Cas9-edited isogenic controls, In this article, Freude, Zhang, and colleagues describe a patient iPSC-derived neuronal model for FTD3. This cellular model shows endosome abnormalities previously reported in patients. Furthermore, it provides insights into the role of impaired mitochondria function and imbalanced iron homeostasis in FTD3 pathology. All observed phenotypes were rescued in CRISPR/Cas9-edited isogenic controls.

BACKGROUND: The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advances in next-generation sequencing (NGS) methodologies, have increased the need for precise computational typing methods.RESULTS: We tested two widespread HLA typing methods using high quality full genome sequencing data from 150 individuals in 50 family trios from the Genome Denmark project. First, we computed descendant accuracies assessing the agreement in the inheritance of alleles from parents to offspring. Second, we compared the locus-specific homozygosity rates as well as the allele frequencies; and we compared those to the observed values in related populations. We provide guidelines for testing the accuracy of HLA typing methods by comparing family information, which is independent of the availability of curated alleles.CONCLUSIONS: Although current computational methods for HLA typing generally provide satisfactory results, our benchmark - using data with ultra-high sequencing depth - demonstrates the incompleteness of current reference databases, and highlights the importance of providing genomic databases addressing current sequencing standards, a problem yet to be resolved before benefiting fully from personalised medicine approaches HLA phenotyping is essential.

The human Y-chromosome does not recombine across its male-specific part and is therefore an excellent marker of human migrations. It also plays an important role in male fertility. However, its evolution is difficult to fully understand because of repetitive sequences, inverted repeats and the potentially large role of gene conversion. Here we perform an evolutionary analysis of 62 Y-chromosomes of Danish descent sequenced using a wide range of library insert sizes and high coverage, thus allowing large regions of these chromosomes to be well assembled. These include 17 father-son pairs, which we use to validate variation calling. Using a recent method that can integrate variants based on both mapping and de novo assembly, we genotype 10898 SNVs and 2903 indels (max length of 27241 bp) in our sample and show by father-son concordance and experimental validation that the non-recurrent SNP and indel variation on the Y chromosome tree is called very accurately. This includes variation called in a 0.9 Mb centromeric heterochromatic region, which is by far the most variable in the Y chromosome. Among the variation is also longer sequence-stretches not present in the reference genome but shared with the chimpanzee Y chromosome. We analyzed 2.7 Mb of large inverted repeats (palindromes) for variation patterns among the two palindrome arms and identified 603 mutation and 416 gene conversions events. We find clear evidence for GC-biased gene conversion in the palindromes (and a balancing AT mutation bias), but irrespective of this, also a strong bias towards gene conversion towards the ancestral state, suggesting that palindromic gene conversion may alleviate Muller’s ratchet. Finally, we also find a large number of large-scale gene duplications and deletions in the palindromic regions (at least 24) and find that such events can consist of complex combinations of simultaneous insertions and deletions of long stretches of the Y chromosome., Author summary The Y chromosome is extraordinary in many respects; it is non-recombining along most of its length, it carries many testis-expressed genes that are often found in palindromes and thus in several copies, and it is generally highly repetitive with very few unique genes. Its evolutionary process is not well understood in general because short-read mapping in such complex sequence is difficult. We combine de novo assembly and mapping to investigate evolution in more than 60% of the length of 62 Y chromosomes of Danish descent. We find that Y chromosome evolution is very dynamic even among the set of closely related Y chromosomes in Denmark with many cases of complex duplications and deletions of large regions including whole genes, clear evidence of GC-biased gene conversion in the palindromes and a tendency for gene conversion to revert mutations to their ancestral state.

Derivation and stable maintenance of porcine induced pluripotent stem cells (piPSCs) is challenging. We herein systematically analyzed two piPSC lines, derived by lentiviral transduction and cultured under either leukemia inhibitory factor (LIF) or fibroblast growth factor (FGF) conditions, to shed more light on the underlying biological mechanisms of porcine pluripotency. LIF-derived piPSCs were more successful than their FGF-derived counterparts in the generation of in vitro chimeras and in teratoma formation. When LIF piPSCs chimeras were transferred into surrogate sows and allowed to develop, only their prescence within the embryonic membranes could be detected. Whole transcriptome analysis of the piPSCs and porcine neonatal fibroblasts showed that they clustered together, but apart from the two pluripotent cell populations of early porcine embryos, indicating incomplete reprogramming. Indeed, bioinformatic analysis of the pluripotency-related gene network of the LIF- versus FGF-derived piPSCs revealed that ZFP42 (REX1) expression was absent in both piPSC-like cells, whereas it was expressed in the porcine inner cell mass at Day 7/8. A second striking difference was the expression of ATOH1 in piPSC-like cells, which was absent in the inner cell mass. Moreover, our gene expression analyses plus correlation analyses of known pluripotency genes identified unique relationships between pluripotency genes in the inner cell mass, which are to some extend, in the piPSC-like cells. This deficiency in downstream gene activation and divergent gene expression may be underlie the inability to derive germ line-transmitting piPSCs, and provides unique insight into which genes are necessary to achieve fully reprogrammed piPSCs. This article is protected by copyright. All rights reserved.

Production of transgenic animals via somatic cell nuclear transfer (SCNT) has been widely used worldwide. However, the application of SCNT is impeded by overall high costs and low efficiency. Here, we reported a modification of the existing technology in order to overcome some of the disadvantages associated with SCNT. Firstly, a marker gene, enhanced green fluorescent gene (EGFP), was transfected into pig fetal fibroblast cells, and was subsequently screened by fluorescent expression to ensure donor cells expressing EGFP. Porcine embryos expressing EGFP were then produced by a method called handmade cloning (HMC), a simplified method for micromanipulation. To demonstrate the concept, we collected a total of 378 fresh swine oocytes, from which 266 with the nucleus removed, obtained a total of 127 viable recombinant oocytes after fusion with EGFP-expressing cells. In vitro incubation of the 127 recombinant oocytes for approximately 144 hours resulted in successful generation of 65 viable embryos, with an average success rate of 52.1±8.3%. Compared with the traditional SCNT, the method of HMC is not only easy to operate, but also increases the rate of recombinant embryo significantly. Furthermore, the modified method no longer relies on expensive instrument like micromanipulator, facilitating the industrialization of transgenic animal production.

Mesenchymal stem cells (MSCs) are adult stem cells with the capacity of self-renewal and multilineage differentiation, and can be isolated from several adult tissues. However, isolating MSCs from adult tissues for cell therapy is hampered by the invasive procedure, the rarity of the cells and their attenuated proliferation capacity when cultivated and expanded in vitro. Human MSCs derived from induced pluripotent stem cells (iPSC-MSCs) have now evolved as a promising alternative cell source for MSCs and regenerative medicine. Several groups, including ours, have reported successful derivation of functional iPSC-MSCs and applied these cells in MSC-based therapeutic testing. Still, the current experience and understanding of iPSC-MSCs with respect to production methods, safety and efficacy are primitive. In this review, we highlight the methodological progress in iPSC-MSC research, describing the importance of choosing the right sources of iPSCs, iPSC reprogramming methods, iPSC culture systems, embryoid body intermediates, pathway inhibitors, basal medium, serum, growth factors and culture surface coating. We also highlight some progress in the application of iPSC-MSCs in direct cell therapy, tissue engineering and gene therapy.

Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analysis by the web based software ChIP-Enrich of FUS and EWS ChIP-seq peaks [51]. (DOCX 19 kb)

Background Comprehensive recognition of genomic variation in one individual is important for understanding disease and developing personalized medication and treatment. Many tools based on DNA re-sequencing exist for identification of single nucleotide polymorphisms, small insertions and deletions (indels) as well as large deletions. However, these approaches consistently display a substantial bias against the recovery of complex structural variants and novel sequence in individual genomes and do not provide interpretation information such as the annotation of ancestral state and formation mechanism. Findings We present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variation and novel sequence from population-scale de novo genome assemblies up to nucleotide resolution. Application of AsmVar to several human de novo genome assemblies captures a wide spectrum of structural variants and novel sequences present in the human population in high sensitivity and specificity. Conclusions Our method provides a direct solution for investigating structural variants and novel sequences from de novo genome assemblies, facilitating the construction of population-scale pan-genomes. Our study also highlights the usefulness of the de novo assembly strategy for definition of genome structure. Electronic supplementary material The online version of this article (doi:10.1186/s13742-015-0103-4) contains supplementary material, which is available to authorized users.

qPCR validation of enrichment peaks identified by FUS and EWS ChIP-seq. The enrichment of DNA was quantified as percentage of the amount in the input sample and the p-values for enrichment of FUS and EWS were calculated. IFG28 was used as a negative control for enrichment. A control ChIP experiment was also performed with inclusion of pre-immune antiserum added to the AG beads used for chromatin purification (AG) instead of FUS and EWS antibodies. Data represents three independent experiments and standard deviation shown by error bars. A. C19orf48 and ACPT; B. RCC1 and SNHG3; C. HNRNPK. (PDF 23 kb)

Analysis of ChIP-seq FUS and EWS enrichment peaks in the RCC1 and SNHG3 gene complex, including SNORA73A and SNORA73B genes. A. Graphic distribution of ChIP-seq reads aligned to the RCC1 and SNHG3 genes from the input, FUS, EWS and Ac-H3K9 ChIP-seq samples. The number of reads is shown on the scale to the left of each figure. The transcripts from the genes in the UCSC hg19 genomic database are shown in the bottom. The arrows beneath peaks illustrate location of the several qPCR amplicons used. The arrows above the transcripts illustrate location of RT-qPCR amplicons. Numbers above arrows denotes target exon numbers. B-C. FUS and EWS effect for RCC1, SNHG3 and snoRNA expression. The expression levels were determined by qPCR from HEK-293 cells transfected with siRNA for FUS and EWS or control siRNA. Three independent experiments were performed and error bars indicate standard deviation. In B., simultaneous depletion of FUS and EWS was performed, whereas in C. FUS and EWS were individually depleted. (PDF 552 kb)

Consequences of siRNA mediated depletion of FUS and EWS for gene expression. HEK-293 cells were double-transfected with specific siRNAs for FUS, EWS and FUS plus EWS, and as well as with a control siRNA (siControl). A. siRNA-depleted cells were used for relative mRNA quantification of FUS and EWS by qPCR. FUS and EWS expression was normalized to reference gene TBP. Experiments were performed in triplicates. Data presented as mean + SEM. Similar qPCR expression analyses showed a 1.5 to 2 fold increase in TAF15 mRNA by EWS and FUS depletion (not shown). B. Protein quantification by western blot of FUS and EWS from siRNA and control transfected cells. 4 F4 antibody recognizing HNRNP C1 + C2 was used as a loading control. (PDF 276 kb)

Comparison of the distribution of FindPeaks called ChIP-seq peaks across a model gene using data from this study or the study by Schwarts et al. [30]. For A. and B. legend details see Additional file 16. (DOCX 693 kb)

Genes co-identified in the hereby presented ChIP-seq data and RNA-CLIP from Hoell et al. [26]. (DOCX 37 kb)

Building a population-specific catalogue of single nucleotide variants (SNVs), indels and structural variants (SVs) with frequencies, termed a national pan-genome, is critical for further advancing clinical and public health genetics in large cohorts. Here we report a Danish pan-genome obtained from sequencing 10 trios to high depth (50 × ). We report 536k novel SNVs and 283k novel short indels from mapping approaches and develop a population-wide de novo assembly approach to identify 132k novel indels larger than 10 nucleotides with low false discovery rates. We identify a higher proportion of indels and SVs than previous efforts showing the merits of high coverage and de novo assembly approaches. In addition, we use trio information to identify de novo mutations and use a probabilistic method to provide direct estimates of 1.27e−8 and 1.5e−9 per nucleotide per generation for SNVs and indels, respectively., The generation of a national pan-genome, a population-specific catalogue of genetic variation, may advance the impact of clinical genetics studies. Here the Besenbacher et al. carry out deep sequencing and de novo assembly of 10 parent–child trios to generate a Danish pan-genome that provides insight into structural variation, de novo mutation rates and variant calling.

Comparative analysis and alignment to the human genome (UCSC hg19) of raw FUS ChIP-seq reads from this study and recalculated from the few data files presented in the study by Schwartz et al. [30]. (DOCX 16 kb)

Comparative distribution of p-values for ChIP-seq peaks called by FindPeaks and MACS of data from this study and the study by Schwarts et al. [30]. A. Distribution of p-values for ChIP-seq peaks called by FindPeaks (F). Most of the ChIP-seq peaks from the hereby presented FUS ChIP-seq data (unFUS_JB) have a low p-value. Most of the ChIP-seq peaks from Schwartz’s et al. (unFUS_ref) have a high P-value. B. Distribution of p-values for ChIP-seq peaks called by MACS. A lower number of ChIP-seq peaks were identified compared to with usage of FindPeaks and the p-value distribution is more comparable between the two datasets. (DOCX 106 kb)

Annotated genes overlapping the significant enrichment peaks determined from FUS, EWS and Ac-H3K9 ChIP-seq analysis. Chromosome (CH): the peak start and end in base pairs; Length: the peak length in base pairs; Tags: the number of sequences included in the peak; p-value: p-value on log2 scale; fold-change (fc): relative to input sample; FDR: false discovery rate in percentage; ENS ID: gene ID in the ensemble database; gene location: location of the enrichment in the gene (upstream, downstream, intron, exon); and T: number of known transcript variants produced from the given gene. (PDF 1497 kb)

Cross-comparison of the genes identified to be associated with FUS, EWS or Ac-H3K9 by ChIP-seq analysis. The displayed overlap categories are FUS and EWS, FUS and Ac-H3K9, EWS and Ac-H3K9, FUS and EWS and Ac-H3K9, FUS and EWS. Chromosome (CH): the peak start and end in base pairs; Length: the peak length in base pairs; Tags: the number of sequences included in the peak; p-value: p-value on log2 scale; fold-change (fc): relative to input sample; FDR: false discovery rate in percent; ENS ID: gene ID in the ensemble database; gene location: location of the enrichment in the gene (upstream, downstream, intron, exon); and T: number of known transcript variants produced from the given gene. (DOCX 325 kb)

Analysis of ChIP-seq FUS and EWS enrichment peaks in the ACPT and C19orf48 gene complex. A. Graphic distribution of ChIP-seq reads aligned to the ACPT and C19orf48 genes from the input, FUS, EWS and Ac-H3K9 ChIP-seq samples. The number of reads is shown on the scale to the left of each figure. The transcripts from the genes in the UCSC hg19 genomic database are shown in the bottom. The arrows beneath peaks illustrate location of the several qPCR amplicons used. The arrows above the transcripts illustrate location of RT-qPCR amplicons. Numbers above arrows denotes target exon numbers. B-C. FUS and EWS effect in ACPT and C19orf48 expression. The expression levels of C19orf48 transcripts were determined by qPCR from HEK-293 cells transfected with siRNA for FUS and EWS or control siRNA. Three independent experiments were performed and error bars indicate standard deviation. In B. simultaneous depletion of FUS and EWS was performed, whereas in C. FUS and EWS were individually depleted. (PDF 483 kb)

FUS and EWS regulate RNA processing in the 3’-end of HNRNPK . A. Graphic distribution of ChIP-seq reads aligned to HNRNPK. The number of reads is shown on the scale to the left of each figure. The transcripts from the genes in the UCSC hg19 genomic database are shown in the bottom. The arrows beneath peaks illustrate location of qPCR amplicons. The arrows above the transcripts illustrate location of RT-qPCR amplicons. Numbers above arrows denote target exon numbers. B-C. The expression levels were determined by qPCR from HEK-293 cells transfected with siRNA for FUS and EWS or control siRNA. In B, simultaneous depletion of FUS and EWS was performed, whereas in C FUS and EWS were individually depleted. All values were normalized to reference gene TBP. All experiments were performed in triplicates. *P

List of primer sequences for PCR. (DOCX 20 kb)

In this paper, we mine full mtDNA sequences from an exome capture data set of 2000 Danes, showing that it is possible to get high-quality full-genome sequences of the mitochondrion from this resource. The sample includes 1000 individuals with type 2 diabetes and 1000 controls. We characterise the variation found in the mtDNA sequence in Danes and relate the variation to diabetes risk as well as to several blood phenotypes of the controls but find no significant associations. We report 2025 polymorphisms, of which 393 have not been reported previously. These 393 mutations are both very rare and estimated to be caused by very recent mutations but individuals with type 2 diabetes do not possess more of these variants. Population genetics analysis using Bayesian skyline plot shows a recent history of rapid population growth in the Danish population in accordance with the fact that >40% of variable sites are observed as singletons.

Logistic regression analysis based on data from 822 Han Chinese oldest old aged 92+ demonstrated that interactions between carrying FOXO1A-266 or FOXO3-310 or FOXO3-292 and tea drinking at around age 60 or at present time were significantly associated with lower risk of cognitive disability at advanced ages. Associations between tea drinking and reduced cognitive disability were much stronger among carriers of the genotypes of FOXO1A-266 or FOXO3-310 or FOXO3-292 compared with noncarriers, and it was reconfirmed by analysis of three-way interactions across FOXO genotypes, tea drinking at around age 60, and at present time. Based on prior findings from animal and human cell models, we postulate that intake of tea compounds may activate FOXO gene expression, which in turn may positively affect cognitive function in the oldest old population. Our empirical findings imply that the health benefits of particular nutritional interventions, including tea drinking, may, in part, depend upon individual genetic profiles.

The health status of the oldest old, the fastest increasing population segment worldwide, progressively becomes more heterogeneous, and this peculiarity represents a major obstacle to their classification. We compared the effectiveness of four previously proposed criteria (Franceschi et al., 2000; Evert et al., 2003; Gondo et al., 2006; Andersen-Ranberg et al., 2001) in 1160 phenotypically fully characterized Italian siblings of 90 years of age and older (90+, mean age: 93 years; age range: 90-106 years) belonging to 552 sib-ships, recruited in Northern, Central and Southern Italy within the EU-funded project GEHA, followed for a six-year-survival. Main findings were: (i) "healthy" subjects varied within a large range, i.e. 5.2% (Gondo), 8.7% (Evert), 17.7% (Franceschi), and 28.5% (Andersen-Ranberg); (ii) Central Italy subjects showed better health than those from Northern and Southern Italy; (iii) mortality risk was correlated with health status independently of geographical areas; and (iv) 90+ males, although fewer in number, were healthier than females, but with no survival advantage. In conclusion, we identified a modified version of Andersen-Ranberg criteria, based on the concomitant assessment of two basic domains (cognitive, SMMSE; physical, ADL), called "Simple Model of Functional Status" (SMFS), as the most effective proxy to distinguish healthy from not-healthy subjects. This model showed that health status was correlated within sib-ships, suggesting a familial/genetic component. The health status of the oldest old, the fastest increasing population segment worldwide, progressively becomes more heterogeneous, and this peculiarity represents a major obstacle to their classification. We compared the effectiveness of four previously proposed criteria (Franceschi et al., 2000; Evert et al., 2003; Gondo et al., 2006; Andersen-Ranberg et al., 2001) in 1160 phenotypically fully characterized Italian siblings of 90 years of age and older (90+, mean age: 93 years; age range: 90-106 years) belonging to 552 sib-ships, recruited in Northern, Central and Southern Italy within the EU-funded project GEHA, followed for a six-year-survival. Main findings were: (i) "healthy" subjects varied within a large range, i.e. 5.2% (Gondo), 8.7% (Evert), 17.7% (Franceschi), and 28.5% (Andersen-Ranberg); (ii) Central Italy subjects showed better health than those from Northern and Southern Italy; (iii) mortality risk was correlated with health status independently of geographical areas; and (iv) 90+ males, although fewer in number, were healthier than females, but with no survival advantage. In conclusion, we identified a modified version of Andersen-Ranberg criteria, based on the concomitant assessment of two basic domains (cognitive, SMMSE; physical, ADL), called "Simple Model of Functional Status" (SMFS), as the most effective proxy to distinguish healthy from not-healthy subjects. This model showed that health status was correlated within sib-ships, suggesting a familial/genetic component.

Production of transgenic animals via somatic cell nuclear transfer (SCNT) has been widely used worldwide. However, the application of SCNT is impeded by overall high costs and low efficiency. Here, we reported a modification of the existing technology in order to overcome some of the disadvantages associated with SCNT. Firstly, a marker gene, enhanced green fluorescent gene (EGFP), was transfected into pig fetal fibroblast cells, and was subsequently screened by fluorescent expression to ensure donor cells expressing EGFP. Porcine embryos expressing EGFP were then produced by a method called handmade cloning (HMC), a simplified method for micromanipulation. To demonstrate the concept, we collected a total of 378 fresh swine oocytes, from which 266 with the nucleus removed, obtained a total of 127 viable recombinant oocytes after fusion with EGFP-expressing cells. In vitro incubation of the 127 recombinant oocytes for approximately 144 hours resulted in successful generation of 65 viable embryos, with an average success rate of 52.1±8.3%. Compared with the traditional SCNT, the method of HMC is not only easy to operate, but also increases the rate of recombinant embryo significantly. Furthermore, the modified method no longer relies on expensive instrument like micromanipulator, facilitating the industrialization of transgenic animal production.

Massively parallel sequencing technology opens new possibilities for epigenetic research. Many methods have been developed based on the new sequencing platforms, allowing an ultra-deep mapping of epigenetic variants in a fast and cost-effective way. However, handling millions of short reads produced by these sequencing platforms is a huge challenge for many laboratories. Thus, there is a need for the development of accurate and fast computational tools for epigenetic studies in the new era of genomic sequencing.Modified methylation-specific digital karyotyping (MMSDK) is an improved method for genome-wide DNA methylation profiling based on the combination of traditional MSDK and Illumina/Solexa sequencing. Here, we introduce our computational tools used in the MMSDK analysis process from the experimental design to statistical analysis. We have developed a mapping process based on the in silico simulation of combined enzyme cutting and tag extraction of the reference genome. Subsequently, the 20-21 nucleotides (nt) long tags obtained by sequencing are mapped to the simulated library using an open source software Mapping and Assembly with Qualities. Our computational methods include trimming, annotation, normalization, and counting the reads to obtain digital DNA methylation profiles. We present the complete protocol and discuss some important issues that should be considered by readers, such as handling of repeat sequences, SNPs, and normalization. The core part of this protocol (mapping and annotation of tags) is suitable for any tag profiling-based methods, and it could also be modified to analyze results from other types of epigenetic studies based on massively parallel sequencing.

Udgivelsesdato: 2010-Jun-10 In vitro culture, storage and manipulation of gametes and embryos require meticulously adjusted conditions to avoid or minimize the harmful effects of uncontrolled stress. However, recent work indicates that a well-defined and properly applied stress may induce general adaptation and increase tolerance to various in vitro procedures. The aim of this review is to summarize reports on the effects of stress on gametes and embryos of several species. Treatment with sublethal doses of high hydrostatic pressure (HHP), osmotic, heat, or oxidative stress resulted in increased morphological survival, fertilizing ability or developmental potential after various in vitro or in vivo procedures. HHP treatment of spermatozoa, oocytes, embryos and embryonic stem cells increased fertilizing ability, developmental competence and differentiation and improved results after cryopreservation, parthenogenetic activation, intracytoplasmic sperm injection and somatic cell nuclear transfer. Osmotic stress of oocytes resulted in higher developmental rates after cryopreservation, parthenogenetic activation and somatic cell nuclear transfer. Heat shock was reported to increase developmental competence of parthenogenetically activated oocytes. Although cellular and subcellular mechanisms supposedly contributing in these processes require further research, the new principle, i.e. to improve the stress tolerance by a defined sublethal stress may outline a completely new strategy in mammalian embryology, as well as cryopreservation of other cells and tissues with remarkable theoretical and practical consequences.

Modified environmental stress was reported to improve the developmental competence and cryotolerance of porcine oocytes, such as high hydrostatic pressure (HHP; Du et al. 2008 Cloning Stem Cells, Epub ahead of print) and osmotic stress (Lin et al. 2008 Reprod. Biomed. Online, in press). HHP also improved the cryotolerance of bovine and murine blastocysts (Pribenszky et al. 2005a Reprod. Dom. Anim. 40, 338-344; Pribenszky et al. 2005b Anim. Reprod. Sci. 87, 143-150). In the present study we compared the effects of NaCl with that of concentrated solutions of two non-permeable osmotic agents, sucrose and trehalose on in vitro maturated oocytes. A total of 2050 slaughterhouse-derived porcine cumulus-oocyte complexes (COCs) were matured for 41-42 h, and then put into 800 μL T2 (HEPES-buffered TCM-199 [Earle's salts] with 2% cattle serum) supplemented with additional NaCl, sucrose or trehalose with the same osmotic level (588 mOsmol) in 4-well dishes and incubated for 1 h at 38.5°C in air. COCs incubated in T2 under the same conditions without supplementation were used as controls. Subsequently COCs were incubated in IVM medium for 1 h at 38.5°C in 5% CO2 with maximum humidity. After this recovery period cumulus cells were removed with 1 mg mL-1 hyaluronidase and pipetting, and oocytes were used as recipients for somatic nuclear transfer with handmade cloning (HMC) method. Porcine fetal fibroblasts were used as nuclear donor cells. Embryo culture was performed in PZM-3 medium (Yoshioka et al. 2002 Biol. Reprod. 66, 112-119) in 5% CO2, 5% O2 and 90% N2 and maximum humidity. Cleavage and blastocyst rates were checked on Day 1 and Day 6, respectively. Cell numbers were counted after fixation in glycerol containing 20 μg mL-1 Hoechst 33342 fluorochrome on Day 6. t-test was performed for statistical calculations with SPSS 11.0 program (SPSS, Chicago, IL, USA). Results are shown in Table 1. Osmotic stress with both permeable and non-permeable agents increased developmental competence of porcine IVM oocytes. NaCl seems to be more appropriate for the purpose, as the other two components resulted in decreased cell number in blastocysts after somatic cell nuclear transfer (SCNT). In conclusion, a simple NaCl pre-treatment of oocytes has improved the in vitro efficiency of porcine SCNT Modified environmental stress was reported to improve the developmental competence and cryotolerance of porcine oocytes, such as high hydrostatic pressure (HHP; Du et al. 2008 Cloning Stem Cells, Epub ahead of print) and osmotic stress (Lin et al. 2008 Reprod. Biomed. Online, in press). HHP also improved the cryotolerance of bovine and murine blastocysts (Pribenszky et al. 2005a Reprod. Dom. Anim. 40, 338-344; Pribenszky et al. 2005b Anim. Reprod. Sci. 87, 143-150). In the present study we compared the effects of NaCl with that of concentrated solutions of two non-permeable osmotic agents, sucrose and trehalose on in vitro maturated oocytes. A total of 2050 slaughterhouse-derived porcine cumulus-oocyte complexes (COCs) were matured for 41-42 h, and then put into 800 μL T2 (HEPES-buffered TCM-199 [Earle's salts] with 2% cattle serum) supplemented with additional NaCl, sucrose or trehalose with the same osmotic level (588 mOsmol) in 4-well dishes and incubated for 1 h at 38.5°C in air. COCs incubated in T2 under the same conditions without supplementation were used as controls. Subsequently COCs were incubated in IVM medium for 1 h at 38.5°C in 5% CO2 with maximum humidity. After this recovery period cumulus cells were removed with 1 mg mL-1 hyaluronidase and pipetting, and oocytes were used as recipients for somatic nuclear transfer with handmade cloning (HMC) method. Porcine fetal fibroblasts were used as nuclear donor cells. Embryo culture was performed in PZM-3 medium (Yoshioka et al. 2002 Biol. Reprod. 66, 112-119) in 5% CO2, 5% O2 and 90% N2 and maximum humidity. Cleavage and blastocyst rates were checked on Day 1 and Day 6, respectively. Cell numbers were counted after fixation in glycerol containing 20 μg mL-1 Hoechst 33342 fluorochrome on Day 6. t-test was performed for statistical calculations with SPSS 11.0 program (SPSS, Chicago, IL, USA). Results are shown in Table 1. Osmotic stress with both permeable and non-permeable agents increased developmental competence of porcine IVM oocytes. NaCl seems to be more appropriate for the purpose, as the other two components resulted in decreased cell number in blastocysts after somatic cell nuclear transfer (SCNT). In conclusion, a simple NaCl pre-treatment of oocytes has improved the in vitro efficiency of porcine SCNT

High hydrostatic pressure has been reported to improve the fertilizing or developmental ability of mammalian spermatozoa, oocytes and embryos. This study investigated the effect of another stress, temporarily increased NaCl concentration, on cryotolerance and developmental competence of porcine oocytes. In Experiment 1, survival rates were compared after 1 h exposure to seven elevated NaCl concentrations and 1 h recovery time. In Experiment 2, oocytes were exposed to 593 and 1306 mOsmol NaCl, subsequently recovered, vitrified, then subjected to parthenogenetic activation. Both cleavage and blastocyst rates increased after NaCl treatment compared with untreated controls. In Experiment 3, oocytes were treated with 593 mOsmol NaCl followed by 1 and 2 h recovery, respectively, then used as recipients for somatic cell nuclear transfer (SCNT). Cleavage rates were not different from those in untreated controls, but blastocyst rates increased in both NaCl-treated groups. In conclusion, treatment of porcine oocytes with elevated NaCl concentrations improved their developmental competence after vitrification and parthenogenetic activation or SCNT. Further experiments are required to investigate in-vivo consequences, and the effect on gametes and embryos of different mammalian species. Udgivelsesdato: March High hydrostatic pressure has been reported to improve the fertilizing or developmental ability of mammalian spermatozoa, oocytes and embryos. This study investigated the effect of another stress, temporarily increased NaCl concentration, on cryotolerance and developmental competence of porcine oocytes. In Experiment 1, survival rates were compared after 1 h exposure to seven elevated NaCl concentrations and 1 h recovery time. In Experiment 2, oocytes were exposed to 593 and 1306 mOsmol NaCl, subsequently recovered, vitrified, then subjected to parthenogenetic activation. Both cleavage and blastocyst rates increased after NaCl treatment compared with untreated controls. In Experiment 3, oocytes were treated with 593 mOsmol NaCl followed by 1 and 2 h recovery, respectively, then used as recipients for somatic cell nuclear transfer (SCNT). Cleavage rates were not different from those in untreated controls, but blastocyst rates increased in both NaCl-treated groups. In conclusion, treatment of porcine oocytes with elevated NaCl concentrations improved their developmental competence after vitrification and parthenogenetic activation or SCNT. Further experiments are required to investigate in-vivo consequences, and the effect on gametes and embryos of different mammalian species.

Somatic cell nuclear transfer (SCNT) offers the possibility of pig transgenesis. Importantly, specific genetic manipulations can be performed in donor cells before SCNT to derive pig models for specific human genetic diseases, including the neurodegenerative disorder Alzheimer's disease (AD). In the present study, we established pregnancies after transfer of SCNT blastocysts produced by the handmade cloning (HMC) technique. The blastocysts were transgenic for a human gene, amyloid precursor protein gene with the 'Swedish mutation' (APPsw), causing AD. For transgenesis, minipig fibroblasts were transfected by lipofection with a vector containing the APPsw gene under control of the platelet-derived growth factor β promoter (PDGF-APPsw) and a neomycin-resistance selection gene. Neomycin-resistant colonies were isolated, expanded, analyzed, and used for HMC. Cumulus-oocyte complexes were aspirated from ovaries of slaughtered sows and matured for 41 h. Subsequently, the cumulus cells were removed in hyaluronidase, and zonae pellucidae were partially digested by incubation in pronase. Oocytes with a visible polar body (PB) were subjected to oriented bisection. Less than half of the cytoplasm adjacent to the PB was removed with a microblade. The cytoplasts were used as recipients for embryo reconstruction. Reconstructed embryos were produced by a 2-step fusion procedure. At the first step, 1 cytoplast was fused with 1 fibroblast in the absence of Ca2+. After 1 h, the cytoplast-fibroblast pair and another cytoplast were fused and activated simultaneously in the presence of Ca2+, incubated in cytochalasin B and cycloheximide for 4 h, and then cultured in PZM-3 medium. The development of reconstructed embryos to the blastocysts stage was determined after 5, 6, or 7 days of in vitro culture. To investigate the in vivo developmental capacity, blastocysts were transferred surgically to synchronized recipients. When using PDGF-APPsw-transgenic minipig fibroblasts, the rate of blastocyst formation (mean ± SEM) was 39 ± 3% (164/424). In comparison, non-transgenic fibroblasts resulted in a blastocyst development of 36 ± 7% (36/102). In 4 recipients that received an average of 54 Day 5, 6, and 7 PDGF-APPsw-transgenic blastocysts, 2 ongoing pregnancies were confirmed by ultrasonography, 1 pregnancy was lost, and 1 returned to estrus. The results show a high in vivo developmental competence of blastocysts produced after SCNT of PDGF-APPsw-transgenic minipig fibroblasts Somatic cell nuclear transfer (SCNT) offers the possibility of pig transgenesis. Importantly, specific genetic manipulations can be performed in donor cells before SCNT to derive pig models for specific human genetic diseases, including the neurodegenerative disorder Alzheimer's disease (AD). In the present study, we established pregnancies after transfer of SCNT blastocysts produced by the handmade cloning (HMC) technique. The blastocysts were transgenic for a human gene, amyloid precursor protein gene with the 'Swedish mutation' (APPsw), causing AD. For transgenesis, minipig fibroblasts were transfected by lipofection with a vector containing the APPsw gene under control of the platelet-derived growth factor β promoter (PDGF-APPsw) and a neomycin-resistance selection gene. Neomycin-resistant colonies were isolated, expanded, analyzed, and used for HMC. Cumulus-oocyte complexes were aspirated from ovaries of slaughtered sows and matured for 41 h. Subsequently, the cumulus cells were removed in hyaluronidase, and zonae pellucidae were partially digested by incubation in pronase. Oocytes with a visible polar body (PB) were subjected to oriented bisection. Less than half of the cytoplasm adjacent to the PB was removed with a microblade. The cytoplasts were used as recipients for embryo reconstruction. Reconstructed embryos were produced by a 2-step fusion procedure. At the first step, 1 cytoplast was fused with 1 fibroblast in the absence of Ca2+. After 1 h, the cytoplast-fibroblast pair and another cytoplast were fused and activated simultaneously in the presence of Ca2+, incubated in cytochalasin B and cycloheximide for 4 h, and then cultured in PZM-3 medium. The development of reconstructed embryos to the blastocysts stage was determined after 5, 6, or 7 days of in vitro culture. To investigate the in vivo developmental capacity, blastocysts were transferred surgically to synchronized recipients. When using PDGF-APPsw-transgenic minipig fibroblasts, the rate of blastocyst formation (mean ± SEM) was 39 ± 3% (164/424). In comparison, non-transgenic fibroblasts resulted in a blastocyst development of 36 ± 7% (36/102). In 4 recipients that received an average of 54 Day 5, 6, and 7 PDGF-APPsw-transgenic blastocysts, 2 ongoing pregnancies were confirmed by ultrasonography, 1 pregnancy was lost, and 1 returned to estrus. The results show a high in vivo developmental competence of blastocysts produced after SCNT of PDGF-APPsw-transgenic minipig fibroblasts

Background: Previous results have suggested an association of the region of 19q13.3 with several forms of cancer. In the present study, we investigated 27 public markers within a previously identified 69 kb stretch of chromosome 19q for association with breast cancer by using linkage disequilibrium mapping. The study groups included 434 postmenopausal breast cancer cases and an identical number of individually matched controls. Methods and Results: Studying one marker at a time, we found a region spanning the gene RAI ( alias PPP1R13L or iASPP) and the 5' portion of XPD to be associated with this cancer. The region corresponds to a haplotype block, in which there seems to be very limited recombination in the Danish population. Studying combinations of markers, we found that two to four neighboring markers gave the most consistent and strongest result. The haplotypes with strongest association with cancers were located in the gene RAI and just 3' to the gene. Coinciding peaks were seen in the region of RAI in groups of women of different age. In a follow-up to these results we sequenced 10 cases and 10 controls in a 44 kb region spanning the peaks of association. This revealed 106 polymorphisms, many of which were not in the public databases. We tested an additional 44 of these for association with disease and found a new tandem repeat marker, called RAI-3' d1, located downstream of the transcribed region of RAI, which was more strongly associated with breast cancer than any other marker we have tested (RR = 2.44 (1.41 - 4.23, p = 0.0008, all cases; RR = 6.29 (1.49 - 26.6), p = 0.01, cases up to 55 years of age). Conclusion: We expect the marker RAI-3' d1 to be (part of) the cause for the association of the chromosome 19q13.3 region's association with cancer.

During the past few years vitrification has been acknowledged as a viable alternative to traditional slow-rate freezing in both animal and human embryology. However, few data are available regarding the comparative efficiency of published and commercially available vitrification methods. The purpose of our work was to compare the OPS and Cryotop technology for cryopreservation of porcine in vitro matured oocytes. In a 2 x 2 factorial experiment, OPS and Cryotop devices and solutions were used for vitrification and warming. Two hours after warming oocytes were parthenogenetically activated and cultured in vitro. In 6 replicates a total of 1153 oocytes were vitrified. The cleavage rate after vitrification with Cryotop device and Cryotop solution (34.7 percent) were higher than those after vitrification with Cryotop device and OPS solution, or OPS device with both OPS and Cryotop solution (11.5, 5.1 and 11.3 percent, respectively). Further embryo development has shown a similar difference: Cryotop device applied with Cryotop solution resulted in 11.6 percent blastocyst/oocyte rates, higher than those achieved with Cryotop device and OPS solutions, or OPS device with both Cryotop and OPS solution (1.6, 1,65 and 0.6 percent, respectively). Our results indicate that for cryopreservation of some highly sensitive biological specimen including porcine oocytes Cryotop vitrification is superior to the OPS technique.