Rare and common genetic determinants of mitochondrial function determine severity but not risk of amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving selective vulnerability of energy-intensive motor neurons (MNs). It has been unclear whether mitochondrial function is an upstream driver or a downstream modifier of neurotoxicity. We separated upstream genetic determinants of mitochondrial function, including genetic variation within the mitochondrial genome or autosomes; from downstream changeable factors including mitochondrial DNA copy number (mtCN). Across three cohorts including 6,437 ALS patients, we discovered that a set of mitochondrial haplotypes, chosen because they are linked to measurements of mitochondrial function, are a determinant of ALS survival following disease onset, but do not modify ALS risk. One particular haplotype appeared to be neuroprotective and was significantly over-represented in two cohorts of long-surviving ALS patients. Causal inference for mitochondrial function was achievable using mitochondrial haplotypes, but not autosomal SNPs in traditional Mendelian randomization (MR). Furthermore, rare loss-of-function genetic variants within, and reduced MN expression of, ACADM and DNA2 lead to ∼50 % shorter ALS survival; both proteins are implicated in mitochondrial function. Both mtCN and cellular vulnerability are linked to DNA2 function in ALS patient-derived neurons. Finally, MtCN responds dynamically to the onset of ALS independently of mitochondrial haplotype, and is correlated with disease severity. We conclude that, based on the genetic measures we have employed, mitochondrial function is a therapeutic target for amelioration of disease severity but not prevention of ALS.

Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality

Mitochondria carry their own circular genome and disruption of the mitochondrial genome is associated with various aging-related diseases. Unlike the nuclear genome, mitochondrial DNA (mtDNA) can be present at 1000 s to 10,000 s copies in somatic cells and variants may exist in a state of heteroplasmy, where only a fraction of the DNA molecules harbors a particular variant. We quantify mtDNA heteroplasmy in 194,871 participants in the UK Biobank and find that heteroplasmy is associated with a 1.5-fold increased risk of all-cause mortality. Additionally, we functionally characterize mtDNA single nucleotide variants (SNVs) using a constraint-based score, mitochondrial local constraint score sum (MSS) and find it associated with all-cause mortality, and with the prevalence and incidence of cancer and cancer-related mortality, particularly leukemia. These results indicate that mitochondria may have a functional role in certain cancers, and mitochondrial heteroplasmic SNVs may serve as a prognostic marker for cancer, especially for leukemia.

A bioinformatics pipeline for estimating mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data

Mitochondrial diseases are a heterogeneous group of disorders that can be caused by mutations in the nuclear or mitochondrial genome. Mitochondrial DNA (mtDNA) variants may exist in a state of heteroplasmy, where a percentage of DNA molecules harbor a variant, or homoplasmy, where all DNA molecules have the same variant. The relative quantity of mtDNA in a cell, or copy number (mtDNA-CN), is associated with mitochondrial function, human disease, and mortality. To facilitate accurate identification of heteroplasmy and quantify mtDNA-CN, we built a bioinformatics pipeline that takes whole genome sequencing data and outputs mitochondrial variants, and mtDNA-CN. We incorporate variant annotations to facilitate determination of variant significance. Our pipeline yields uniform coverage by remapping to a circularized chrM and by recovering reads falsely mapped to nuclear-encoded mitochondrial sequences. Notably, we construct a consensus chrM sequence for each sample and recall heteroplasmy against the sample's unique mitochondrial genome. We observe an approximately 3-fold increased association with age for heteroplasmic variants in non-homopolymer regions and, are better able to capture genetic variation in the D-loop of chrM compared to existing software. Our bioinformatics pipeline more accurately captures features of mitochondrial genetics than existing pipelines that are important in understanding how mitochondrial dysfunction contributes to disease.

Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation

Oocyte maturation is a coordinated process that is tightly linked to reproductive potential. A better understanding of gene regulation during human oocyte maturation will not only answer an important question in biology, but also facilitate the development of in vitro maturation technology as a fertility treatment. We generated single-cell transcriptome and used our previously published single-cell methylome data from human oocytes at different maturation stages to investigate how genes are regulated during oocyte maturation, focusing on the potential regulatory role of non-CpG methylation. DNMT3B, a gene encoding a key non-CpG methylation enzyme, is one of the 1,077 genes upregulated in mature oocytes, which may be at least partially responsible for the increased non-CpG methylation as oocytes mature. Non-CpG differentially methylated regions (DMRs) between mature and immature oocytes have multiple binding motifs for transcription factors, some of which bind with DNMT3B and may be important regulators of oocyte maturation through non-CpG methylation. Over 98% of non-CpG DMRs locate in transposable elements, and these DMRs are correlated with expression changes of the nearby genes. Taken together, this data indicates that global non-CpG hypermethylation during oocyte maturation may play an active role in gene expression regulation, potentially through the interaction with transcription factors.

Superovulation alters global DNA methylation in early mouse embryo development

Assisted reproductive technologies are known to alter the developmental environment of gametes and early embryos during the most dynamic period of establishing the epigenome. This may result in the introduction of errors during active DNA methylation reprogramming. Controlled ovarian hyperstimulation, or superovulation, is a ubiquitously used intervention which has been demonstrated to alter the methylation of certain imprinted genes. The objective of this study was to investigate whether ovarian hyperstimulation results in genome-wide DNA methylation changes in mouse early embryos. Ovarian hyperstimulation was induced by treating mice with either low doses (5 IU) or high doses (10 IU) of PMSG and hCG. Natural mating (NM) control mice received no treatment. Zygotes and 8-cell embryos were collected from each group and DNA methylomes were generated by whole-genome bisulfite sequencing. In the NM group, mean CpG methylation levels slightly decreased from zygote to 8-cell stage, whereas a large decrease in mean CpG methylation level was observed in both superovulated groups. A separate analysis of the mean CpG methylation levels within each developmental stage confirmed that significant genome-wide erasure of CpG methylation from the zygote to 8-cell stage only occurred in the superovulation groups. Our results suggest that superovulation alters the genome-wide DNA methylation erasure process in mouse early pre-implantation embryos. It is not clear whether these changes are transient or persistent. Further studies are ongoing to investigate the impact of ovarian hyperstimulation on DNA methylation re-establishment in later stages of embryo development.

Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States

During mammalian embryogenesis, changes in morphology and gene expression are concurrent with epigenomic reprogramming. Using human embryonic stem cells representing the preimplantation blastocyst (naive) and postimplantation epiblast (primed), our data in 2iL/I/F naive cells demonstrate that a substantial portion of known human enhancers are premarked by H3K4me1, providing an enhanced open chromatin state in naive pluripotency. The 2iL/I/F enhancer repertoire occupies 9% of the genome, three times that of primed cells, and can exist in broad chromatin domains over 50 kb. Enhancer chromatin states are largely poised. Seventy-seven percent of 2iL/I/F enhancers are decommissioned in a stepwise manner as cells become primed. While primed topologically associating domains are largely unaltered upon differentiation, naive 2iL/I/F domains expand across primed boundaries, affecting three-dimensional genome architecture. Differential topologically associating domain edges coincide with 2iL/I/F H3K4me1 enrichment. Our results suggest that naive-derived 2iL/I/F cells have a unique chromatin landscape, which may reflect early embryogenesis.

Methylome Analysis of Human Bone Marrow MSCs Reveals Extensive Age- and Culture-Induced Changes at Distal Regulatory Elements

Human bone marrow stromal cells, or mesenchymal stem cells (BM-MSCs), need expansion prior to use as cell-based therapies in immunological and tissue repair applications. Aging and expansion of BM-MSCs induce epigenetic changes that can impact therapeutic outcomes. By applying sequencing-based methods, we reveal that the breadth of DNA methylation dynamics associated with aging and expansion is greater than previously reported. Methylation changes are enriched at known distal transcription factor binding sites such as enhancer elements, instead of CpG-rich regions, and are associated with changes in gene expression. From this, we constructed hypo- and hypermethylation-specific regulatory networks, including a sub-network of BM-MSC master regulators and their predicted target genes, and identified putatively disrupted signaling pathways. Our genome-wide analyses provide a broader overview of age- and expansion-induced DNA methylation changes and a better understanding of the extent to which these changes alter gene expression and functionality of human BM-MSCs.

cChIP-seq: a robust small-scale method for investigation of histone modifications

BACKGROUND

ChIP-seq is highly utilized for mapping histone modifications that are informative about gene regulation and genome annotations. For example, applying ChIP-seq to histone modifications such as H3K4me1 has facilitated generating epigenomic maps of putative enhancers. This powerful technology, however, is limited in its application by the large number of cells required. ChIP-seq involves extensive manipulation of sample material and multiple reactions with limited quality control at each step, therefore, scaling down the number of cells required has proven challenging. Recently, several methods have been proposed to overcome this limit but most of these methods require extensive optimization to tailor the protocol to the specific antibody used or number of cells being profiled.

RESULTS

Here we describe a robust, yet facile method, which we named carrier ChIP-seq (cChIP-seq), for use on limited cell amounts. cChIP-seq employs a DNA-free histone carrier in order to maintain the working ChIP reaction scale, removing the need to tailor reactions to specific amounts of cells or histone modifications to be assayed. We have applied our method to three different histone modifications, H3K4me3, H3K4me1 and H3K27me3 in the K562 cell line, and H3K4me1 in H1 hESCs. We successfully obtained epigenomic maps for these histone modifications starting with as few as 10,000 cells. We compared cChIP-seq data to data generated as part of the ENCODE project. ENCODE data are the reference standard in the field and have been generated starting from tens of million of cells. Our results show that cChIP-seq successfully recapitulates bulk data. Furthermore, we showed that the differences observed between small-scale ChIP-seq data and ENCODE data are largely to be due to lab-to-lab variability rather than operating on a reduced scale.

CONCLUSIONS

Data generated using cChIP-seq are equivalent to reference epigenomic maps from three orders of magnitude more cells. Our method offers a robust and straightforward approach to scale down ChIP-seq to as low as 10,000 cells. The underlying principle of our strategy makes it suitable for being applied to a vast range of chromatin modifications without requiring expensive optimization. Furthermore, our strategy of a DNA-free carrier can be adapted to most ChIP-seq protocols.

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

For nearly a century developmental biologists have recognized that cells from embryos can differ in their potential to differentiate into distinct cell types. Recently, it has been recognized that embryonic stem cells derived from both mice and humans exhibit two stable yet epigenetically distinct states of pluripotency: naive and primed. We now show that nicotinamide N-methyltransferase (NNMT) and the metabolic state regulate pluripotency in human embryonic stem cells (hESCs).  Specifically, in naive hESCs, NNMT and its enzymatic product 1-methylnicotinamide are highly upregulated, and NNMT is required for low S-adenosyl methionine (SAM) levels and the H3K27me3 repressive state. NNMT consumes SAM in naive cells, making it unavailable for histone methylation that represses Wnt and activates the HIF pathway in primed hESCs. These data support the hypothesis that the metabolome regulates the epigenetic landscape of the earliest steps in human development.

Abstract AS04: Epigenomic characterization of gene regulatory networks in human ovarian cancer stem cells

Ovarian cancer is the fifth leading cause of cancer mortality among women in the United States. Despite aggressive surgery and chemotherapy, most patients relapse and develop drug-resistant tumors, leading to the <40% chance of 5 year survival in ovarian cancer patients. Evidence suggests that a small subpopulation of cells in the tumor, ovarian cancer stem cells (OvCSCs), are responsible for tumor relapse and drug resistance. OvCSCs have enhanced tumorigenicity, inherent chemoresistance, and stem-like properties such as the ability to self-renew or divide asymmetrically. These latter characteristics give CSCs an analogous role in tumors that healthy stem cells have in developing organs (adult stem cells) or entire organisms (embryonic stem cells).The goal of this study is to determine how the cancer stem cell state is regulated by annotating the gene regulatory network of OvCSCs. In doing so, we will uncover commonalities that exist between OvCSCs and embryonic or progenitor stem cells.

The epigenome provides the structural framework for cell-type specific gene regulation. Chromatin modifications that uniquely mark gene regulatory elements, like promoters and enhancers, are easily identified throughout the genome using ChIP-seq. ChIP-seq performed in pluripotent stem cells has revealed many epigenetic features that distinguish them from differentiated cells. In an effort to better understand CSC gene regulatory networks, we are generating comprehensive transcriptomic maps and globally identifying enhancers marked by histone 3, lysine 4 monomethylation (via RNAseq and H3K4me1 ChIP-seq respectively) in OvCSCs and their daughter tumor cells. We are also comparing OvCSCs to previously generated data in human embryonic stem cells (hESCs) to identify shared stemness traits. OvCSCs were acquired from patient biopsies and detailed characterization identified a CD133+ CSC population within the tumor. We are using a mouse xenograft model to expand tumors in vivo. Harvested tumors are depleted of blood lineage cells and CD133+ cells (CSCs) are isolated from the remaining cells in the tumor.

Our analysis of RNA-seq and enhancer maps have revealed OvCSC signatures that are absent in tumor cells but present in embryonic stem cells. Many important embryonic stem cell transcription factors are expressed in OvCSCs and have almost identical chromatin enhancer profiles. We identified over 7000 H1 hESC enhancers that have at least 95% overlap with OvCSC enhancers implying a shared regulatory network in these cell types. Motif analysis of nucleosome-free regions within enhancers reveals enrichment for many ESC transcription factors that are also expressed in OvCSCs. Our integrative analysis indicates that OvCSCs share common features of the ESC regulatory network and is beginning to provide novel insight on why CSCs have stem cell properties. We are continuing to build maps for additional histone modifications and genome-wide DNA methylation in OvCSCs to gain a comprehensive view of how the epigenome regulates the cancer stem cell state.

Citation Format: Stephanie L. Battle, Antti Larjo, Joling Liao, Harri Lähdesmäki, Andre Lieber, R. David Hawkins. Epigenomic characterization of gene regulatory networks in human ovarian cancer stem cells [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr AS04.

Circadian clock-regulated phosphate transporter PHT4;1 plays an important role in Arabidopsis defense

The Arabidopsis accelerated cell death 6-1 (acd6-1) mutant shows constitutive defense, cell death, and extreme dwarf phenotypes. In a screen for acd6-1 suppressors, we identified a mutant that was disrupted by a T-DNA in the PHOSPHATE TRANSPORTER 4;1 (PHT4;1) gene. The suppressor mutant pht4;1-1 is dominant, expresses truncated PHT4;1 transcripts, and is more susceptible to virulent Pseudomonas syringae strains but not to several avirulent strains. Treatment with a salicylic acid (SA) agonist induced a similar level of resistance in Col-0 and pht4;1-1, suggesting that PHT4;1 acts upstream of the SA pathway. Genetic analysis further indicates that PHT4;1 contributes to SID2-dependent and -independent pathways. Transgenic expression of the DNA fragment containing the PHT4;1-1 region or the full-length PHT4;1 gene in wild-type conferred enhanced susceptibility to Pseudomonas infection. Interestingly, expression of PHT4;1 is regulated by the circadian clock. Together, these data suggest that the phosphate transporter PHT4;1 is critical for basal defense and also implicate a potential role of the circadian clock in regulating innate immunity of Arabidopsis.

Synthesis and characterization of 8-(dimethylamino)-1-naphthyl derivatives of aluminum, gallium, and indium

The group 13 dichlorides of formula Ar'MCl2 [Ar' = 8-(dimethylamino)-1-naphthyl (8-(Me2N)C10H6)], M = Al (1), Ga (2), and In (3), have been prepared via the salt elimination reaction of 1 equiv of Ar'Li with MCl3 in toluene solution at -78 degrees C. The reaction of 1 with LiAlH4 in diethyl ether solution at -78 degrees C produced the dihydride [Ar'AlH2]2 (4). The X-ray crystal structures of 1-4 have been determined and show that 1 and 2 are monomeric while 3 and 4 are dimeric in the solid state. The reaction of 1 with RLi in toluene solution at -78 degrees C results in ligand redistribution and formation of Ar'2AlR (R = Me (5), t-Bu (6)). The chloride analogue of 5 and 6, Ar'2AlCl (7), can be prepared directly from the reaction of 2 equiv of Ar'Li with AlCl3 in toluene solution at -78 degrees C. The homoleptic derivative Ar'3Al (8) was obtained when 3 equiv of Ar'Li was employed. Crystal data for 1: monoclinic, space group P2(1), a = 6.534(1) A, b = 10.801(1) A, c = 9.631(2) A, beta = 105.57(2) degrees, V = 654.8(2) A3, Z = 2, R = 0.0453. Crystal data for 2: monoclinic, space group P2(1), a = 6.552(2) A, b = 10.833(2) A, c = 9.601(2) A, beta = 106.05(2) degrees, V = 654.9(3) A3, Z = 2, R = 0.0609. Crystal data for 3: monoclinic, space group P2(1)/c, a = 7.401(2) A, b = 15.746 A, c = 10.801(4) A, beta = 92.37(3) degrees, V = 1257.6(7) A3, Z = 2, R = 0.0712. Crystal data for 4: monoclinic, space group P2(1)/c, a = 13.343(2) A, b = 11.228(2) A, c = 7.505(1) A, beta = 100.64(1) degrees, V = 1105.0(4) A3, Z = 4, R = 0.0560.

Synthesis of Linear Acetylenic Carbon: The "sp" Carbon Allotrope

A carbon allotrope based on "sp" hybridization containing alternating triple and single bonds (an acetylenic or linear carbon allotrope) has been prepared. Studies of small (8 to 28 carbon atoms) acetylenic carbon model compounds show that such species are quite stable (130 degrees to 140 degrees C) provided that nonreactive terminal groups or end caps (such as tert-butyl or trifluoromethyl) are present to stabilize these molecules against further reactions. In the presence of end capping groups, laser-based synthetic techniques similar to those normally used to generate fullerenes, produce thermally stable acetylenic carbon species capped with trifluoromethyl or nitrile groups with chain lengths in excess of 300 carbon atoms. Under these conditions, only a negligible quantity of fullerenes is produced. Acetylenic carbon compounds are not particularly moisture or oxygen sensitive but are moderately light sensitive.