Biology subjects

Murakami, Y.

Publications and source records attributed to Murakami, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2021

Combined landscape of single-nucleotide variants and copy-number alterations in clonal hematopoiesis

Implicated in the development of hematological malignancies (HM) and cardiovascular mortality, clonal hematopoiesis (CH) in apparently healthy individuals has been investigated by detecting either single-nucleotide variants and indels (SNVs/indels) or copy number alterations (CNAs), but not both. Here by combining targeted sequencing of 23 CH-related genes and array-based CNA detection of blood-derived DNA, we have delineated the landscape of CH-related SNVs/indels and CNAs in a general population of 11,234 individuals, including 672 with subsequent HM development. Both CH-related lesions significantly co-occurred, which combined, affected blood count, hypertension, and the mortality from HM and cardiovascular diseases depending on the total number of both lesions, highlighting the importance of detecting both lesions in the evaluation of CH.

cancer biology↗

bioRxiv2020

Ethanolamine phosphate on the second mannose as bridge in GPI anchored proteins: Towards understanding inherited PIGG deficiency

Glycosylphosphatidylinositols (GPIs) are glycolipids that anchor many proteins (GPI-APs) on the cell surface. The core glycan of GPI precursor has three mannoses, which in mammals, are all modified by ethanolamine-phosphate (EthN-P). It is postulated that EthN-P on the third mannose (EthN-P-Man3) is the bridge between GPI to the protein and the second (EthN-P-Man2) is removed after GPI-protein attachment. However, EthN-P-Man2 may not be always transient, as mutations of PIGG, the enzyme that transfers EthN-P to Man2, result in inherited GPI deficiencies (IGDs), characterized by neuronal dysfunctions. Here, we show EthN-P on Man2 is the preferential bridge in some GPI-APs, among them, the ect-5-nucleotidase and netrin G2. We found that CD59, a GPI-AP, is attached via EthN-P-Man2 both in PIGB-knockout cells, in which GPI lacks Man3 and with a small fraction, in wild type cells. Our findings modify the current view of GPI anchoring and provide mechanistic bases of IGDs caused by PIGG mutations.

molecular biology↗

bioRxiv2020

Involvement of I-BAR protein IRSp53 in tumor cell growth via extracellular microvesicle secretion

Cellular protrusions mediated by the membrane-deforming I-BAR domain protein IRSp53 are involved in cell migration, including metastasis. However, the role of IRSp53 in cell proliferation remains unclear. Here, we examined the role of IRSp53 in cell proliferation and found that it acts through secretion. Coculture of gingiva squamous carcinoma Ca9-22 cells and their IRSp53-knockout cells restored proliferation to parental Ca9-22 cell levels, suggesting possible secretion dependent on IRSp53. Notably, the amounts of microvesicle fraction proteins that were secreted into the culture medium were reduced in the IRSp53-knockout cells. The IRSp53-knockout cells exhibited decreased phosphorylation of mitogen-activated protein kinase, suggesting the decrease in the proliferation signals. The phosphorylation was restored by the addition of the microvesicles. In mice xenograft Ca9-22 cells, IRSp53-containing particles were secreted around the xenograft, indicating that IRSp53-dependent secretion occurs in vivo. In a tumor mice model, IRSp53 deficiency elongated lifespan. In some human cancers, the higher levels of IRSp53 mRNA expression was found to be correlated with shorter survival years. Therefore, IRSp53 is involved in tumor progression and secretion for cellular proliferation.

cell biology↗

bioRxiv2020

Population-wide Screening for Germline Variants of Hereditary Cancer Genes in 12K Unselected Japanese Colorectal Cancers and 27K Controls

Background & AimsColorectal cancer (CRC) is one of the most common cancers in Western countries and Japan. Currently, a few % of CRCs can be attributed to recognizable hereditary germline variants of known CRC susceptibility genes, predominantly the DNA mismatch repair genes. To establish a universal screening strategy for hereditary CRCs, it is necessary to explore the prevalence of hereditary CRC and pathogenic variants of multiple cancer-predisposing genes in non-European populations. MethodsWe analyzed the coding regions of 27 cancer-predisposing genes, including mismatch repair genes, APC, and BRCA1/2, in 12,503 unselected Japanese CRC patients and 23,705 controls aged [≥] 60 years without any personal or family history of cancer by target sequencing and genome-wide SNP chip data. Their clinical significance was assessed using ClinVar and the guidelines by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP). ResultsWe identified 4,804 variants in the 27 genes and annotated them as 397 pathogenic variants, 941 benign variants, and 3,466 variants of uncertain significance, of which 43.6% were registered in neither ClinVar nor dbSNP. In total, 3.3% of the unselected CRC patients and 1.5% of the controls had a pathogenic variant of the 27 genes. The pathogenic variants of MSH2 (odds ratio (OR) =18.1), MLH1 (OR=8.6), MSH6 (OR=4.9), APC (OR=49.4), BRIP1 (OR=3.6), BRCA1 (OR=2.6), BRCA2 (OR=1.9), and TP53 (OR=1.7) were significantly associated with CRC development in the Japanese population (P-values < 0.01, FDR<0.05). Furthermore, we confirmed copy number variants (CNVs) of MSH2/EPCAM, MLH1, and APC by multiplex ligation-dependent probe amplification (MLPA) and quantitative PCR in this cohort (n = 23), including whole gene duplications of MSH2 and APC. These pathogenic variants were significantly associated with the diagnostic age and personal/family history of other types of cancer. In total, at least 3.5% of the Japanese CRC population had a pathogenic variant or CNV of the 27 cancer-predisposing genes. ConclusionsThis is the largest study of CRC heredity in the Asian population and would contribute to the development of guidelines for genetic testing and variant interpretation for heritable CRCs. Universal screening for CRC risk should be assessed in multiple genes, including BRCA1/2 and BRIP1. These data would facilitate risk assessment of cancer and optimize the screening strategy.

genetics↗

bioRxiv2020

In silico integration of thousands of epigenetic datasets into 707 cell type regulatory annotations improves the trans-ethnic portability of polygenic risk scores

Poor trans-ethnic portability of polygenic risk score (PRS) models is a critical issue that may be partially due to limited knowledge of causal variants shared among populations. Hence, leveraging noncoding regulatory annotations that capture genetic variation across populations has the potential to enhance the trans-ethnic portability of PRS. To this end, we constructed a unique resource of 707 cell-type-specific IMPACT regulatory annotations by aggregating 5,345 public epigenetic datasets to predict binding patterns of 142 cell-type-regulating transcription factors across 245 cell types. With this resource, we partitioned the common SNP heritability of diverse polygenic traits and diseases from 111 GWAS summary statistics of European (EUR, average N=180K) and East Asian (EAS, average N=157K) origin. For 95 traits, we were able to identify a single IMPACT annotation most strongly enriched for trait heritability. Across traits, these annotations captured an average of 43.3% of heritability (se = 13.8%) with the top 5% of SNPs. Strikingly, we observed highly concordant polygenic trait regulation between populations: the same regulatory annotations captured statistically indistinguishable SNP heritability (fitted slope = 0.98, se = 0.04). Since IMPACT annotations capture both large and consistent proportions of heritability across populations, prioritizing variants in IMPACT regulatory elements may improve the trans-ethnic portability of PRS. Indeed, we observed that EUR PRS models more accurately predicted 21 tested phenotypes of EAS individuals when variants were prioritized by key IMPACT tracks (49.9% mean relative increase in R2). Notably, the improvement afforded by IMPACT was greater in the trans-ethnic EUR-to-EAS PRS application than in the EAS-to-EAS application (47.3% vs 20.9%, P < 1.7e-4). Overall, our study identifies a crucial role for functional annotations such as IMPACT to improve the trans-ethnic portability of genetic data, and this has important implications for future risk prediction models that work across populations.

genetics↗

bioRxiv2019

Endogenization and excision of human herpesvirus 6 in human genomes

The genome of human herpesvirus 6 (HHV-6) is integrated within the nuclear genome of about 1% of humans, but how this came about is not clear. HHV-6 integrates into telomeres, and this has recently been associated with polymorphisms affecting MOV10L1. MOV10L1 is located on the subtelomere of chromosome 22q (chr22q) and is required to make PIWI-interacting RNAs (piRNAs). piRNAs block integration of transposons in the germline, so piRNA-mediated repression of HHV-6 integration has been suspected. Whether integrated HHV-6 can reactive into an infectious virus is also uncertain. In vitro, recombination of the viral genome along its terminal direct repeats (DRs) leads to excision from the telomere and viral reactivation, but the expected single DR "scar" has not been described in vivo. We analyzed whole-genome sequencing (WGS) data from 13,040 subjects, including 7,485 from Japan. We found an association between integrated HHV-6 and polymorphisms on chr22q in Japanese subjects. However, association with the reported MOV10L1 polymorphism was driven by physical linkage to a single ancient endogenous HHV-6A variant integrated into the telomere of chr22q in East Asians. We resolved the junction of the human chromosome with this viral genome using long read sequencing. Unexpectedly, an HHV-6B variant has also endogenized in chr22q; two endogenous HHV-6 variants at this locus thus account for 72% of all integrated HHV-6 in Japan. We also report human genomes carrying only one portion of the HHV-6B genome, a single DR, supporting in vivo excision and viral reactivation. Using WGS data from North American families, we show that the incidence of HHV-6 integration into the germline is lower than its prevalence, and that integrated HHV-6 is not associated with the reported variant in MOV10L1. Together these results explain the recently reported association between integrated HHV-6 and MOV10L1/piRNAs, suggest exaptation of HHV-6 in its coevolution with human chr22q, and clarify the evolution and risk of reactivation of the only intact non-retroviral genome known to be present in human germlines. SIGNIFICANCE STATEMENT Human herpesvirus 6 (HHV-6) infects most people during childhood, usually only causing fever and rash. Reactivation of HHV-6 has been linked to a number of neurological diseases including encephalitis, Alzheimers disease and multiple sclerosis. However, about 1% of people are born with the HHV-6 genome present within their genome, included in the end "cap" of one of their 46 chromosomes. Little is known about how and when HHV-6 genomes entered human genomes, whether or not they still do, and whether or not this poses risk for virus reactivation. We looked for HHV-6 in genome sequences from over 13,000 people. Most HHV-6 variants present in human genomes have been co-evolving with human chromosomes for many generations, and new integration events are rare. Surprisingly, in almost three fourths of Japanese people with HHV-6 in their genome, HHV-6 integrated in the same end of the same chromosome - 22q. Persistence of the HHV-6 genome within the short "cap" that preserves the end of chromosome 22q suggests that the integrated viral sequence may have taken on a useful function for this chromosome. We also found that some human genomes harbor only one part of the HHV-6 genome. This part is the same part that remains after experimental viral reactivation, during which most of the virus is cut out of the genome. This warrants assessment of the risk that integration of HHV-6 into inherited human genomes is not irreversible, and possibly leads to production of infectious virus.

genetics↗

bioRxiv2019

Nucleosides drive histiocytosis in SLC29A3 disorders by activating TLR7

A lysosomal transmembrane protein SLC29A3 transports nucleosides from lysosomes to the cytoplasm. Loss-of-function mutations of the SLC29A3 gene cause lysosomal nucleoside storage in monocyte/macrophages, leading to their accumulation called histiocytosis in humans and mice. Little is known, however, about a mechanism behind nucleoside-dependent histiocytosis. TLR7, an innate immune sensors for single stranded RNA, bind and respond to nucleosides. We here show that they drive nucleoside-mediated histiocytosis. Patrolling monocyte/macrophages accumulate in the spleen of Slc29a3-/- mice but not Slc29a3-/- Tlr7-/- mice. Accumulated patrolling monocyte/macrophages stored nucleosides derived from cell corpse. TLR7 was recruited to phagosomes and activated as evidenced by TLR7-dependent phagosomal maturation. TLR7 induced hyper-responsiveness to M-CSF in Slc29a3-/- monocyte/macrophages. These results suggest that TLR7 drives histiocytosis in SLC29A3 disorders. One Sentence SummarySLC29A3 disorders are caused by activation of TLR7 with accumulated nucleosides in lysosomes.

immunology↗

bioRxiv2019

Trans-biobank analysis with 676,000 individuals elucidates the association of polygenic risk scores of complex traits with human lifespan

Human genetics seeks a way to improve human health on a global scale. Expectations are running high for polygenic risk scores (PRSs) to be translated into clinical practice to predict an inborn susceptibility to health risks. While risk stratification based on PRS is one way to promote population health, a strategy to utilize genetics to prioritize modifiable risk factors and biomarkers driving heath outcome is also warranted. To this end, here we utilized PRSs to comprehensively investigate the association of the genetic susceptibility to complex traits with human lifespan in collaboration with three worldwide biobanks (ntotal = 675,898). First, we conducted genome-wide association studies for 45 quantitative clinical phenotypes, constructed the individual PRSs, and associated them with the age at death of 179,066 participants in BioBank Japan. The PRSs revealed that the genetic susceptibility of high systolic blood pressure (sBP) was strongly associated with a shorter lifespan (hazard ratio [HR] = 1.03, P = 1.4x10-7). Next, we sought to replicate these associations in individuals of European ancestry in UK Biobank (n = 361,194) and FinnGen (n = 135,638). Among the investigated traits, the individuals with higher blood pressure-related PRSs were trans-ethnically associated with a shorter lifespan (HR = 1.03, Pmeta = 3.9x10-13 for sBP) and parental lifespan (HR = 1.06, PUKBB = 2.0x10-86 for sBP). Further, our trans-biobank study identified additional complex traits associated with lifespan (e.g., obesity, height, serum lipids, and platelet counts). Of them, obesity-related traits showed strikingly heterogeneous effects on lifespan between Japanese and European populations (Pheterogeneity = 9.5x10-8 for body mass index). Through trans-ethnic biobank collaboration, we elucidated the novel value of the PRS study in genetics-driven prioritization of risk factors and biomarkers which can be medically intervened to improve population health.

genetics↗

bioRxiv2019

Population-specific and transethnic genome-wide analyses reveal distinct and shared genetic risks of coronary artery disease

To elucidate the genetics of coronary artery disease (CAD) in the Japanese population, we conducted a large-scale genome-wide association study (GWAS) of 168,228 Japanese (25,892 cases and 142,336 controls) with genotype imputation using a newly developed reference panel of Japanese haplotypes including 1,782 CAD cases and 3,148 controls. We detected 9 novel disease-susceptibility loci and Japanese-specific rare variants contributing to disease severity and increased cardiovascular mortality. We then conducted a transethnic meta-analysis and discovered 37 additional novel loci. Using the result of the meta-analysis, we derived a polygenic risk score (PRS) for CAD, which outperformed those derived from either Japanese or European GWAS. The PRS prioritized risk factors among various clinical parameters and segregated individuals with increased risk of long-term cardiovascular mortality. Our data improves clinical characterization of CAD genetics and suggests the utility of transethnic meta-analysis for PRS derivation in non-European populations.

genetics↗

bioRxiv2019

Cross-talks of glycosylphosphatidylinositol biosynthesis with glycosphingolipid biosynthesis and ER-associated degradation

Glycosylphosphatidylinositol (GPI)-anchored proteins and glycosphingolipids interact with each other in the mammalian plasma membranes, forming dynamic microdomains. How their interaction starts in the cells has been unclear. Here, based on a genome-wide CRISPR-Cas9 genetic screen for genes required for GPI side-chain modification by galactose in the Golgi apparatus, we report that {beta}1,3-galactosyltransferase 4 (B3GALT4), also called GM1 ganglioside synthase, additionally functions in transferring galactose to the N-acetylgalactosamine side-chain of GPI. Furthermore, B3GALT4 requires lactosylceramide for the efficient GPI side-chain galactosylation. Thus, our work demonstrates previously unexpected evolutionary and functional relationships between GPI-anchored proteins and glycosphingolipids in the Golgi. Through the same screening, we also show that GPI biosynthesis in the endoplasmic reticulum (ER) is severely suppressed by ER-associated degradation to prevent GPI accumulation when the transfer of synthesized GPI to proteins is defective. Our data demonstrates cross-talks of GPI biosynthesis with glycosphingolipid biosynthesis and the ER quality control system.

cell biology↗

bioRxiv2019

RIP1 kinase mediates angiogenesis by modulating macrophages in experimental neovascularization

Inflammation plays an important role in pathologic angiogenesis. Receptor-interacting protein 1 (RIP1) is highly expressed in inflammatory cells and is known to play an important role in the regulation of apoptosis, necroptosis, and inflammation, however its role in angiogenesis remains elusive. Here, we show that RIP1 is abundantly expressed in infiltrating macrophages during angiogenesis, and genetic or pharmacological inhibition of RIP1 kinase activity using kinase-inactive RIP1K45A/K45A mice or necrostatin-1 attenuates angiogenesis in laser-induced choroidal neovascularization (CNV), Matrigel plug angiogenesis, and alkali injury-induced corneal neovascularization in mice. The inhibitory effect on angiogenesis was mediated by caspase activation through a kinase-independent function of RIP1 and RIP3, and simultaneous caspase inhibition with RIP1 kinase inhibition abrogated the effects of RIP1 kinase inhibition on angiogenesis in vivo. Mechanistically, infiltrating macrophages are the key target for RIP1 kinase inhibition to attenuate pathological angiogenesis, and we observed that the inhibition of RIP1 kinase activity is associated with caspase activation in infiltrating macrophages and decreased expression of pro-angiogenic M2-like markers while M1 marker expressions were sustained. Similarly, in vitro, catalytic inhibition of RIP1 down-regulated M2 marker expressions in IL-4-activated bone marrow-derived macrophages, which was blocked by simultaneous caspase inhibition. Taken together, these results suggest a novel, non-necrotic function of RIP1 kinase activity and suggest that RIP1-mediated modulation of macrophage activation may represent a therapeutic target for the control of angiogenesis-related diseases.\n\nSignificancePathological angiogenesis has been implicated in diverse pathologies. Infiltrating macrophages, especially those activated to M2-like phenotype are critically important to support angiogenesis. Whereas the role of RIP1 kinase in the regulation of apoptosis, necroptosis, and inflammation have been well established, its role in angiogenesis remains elusive despite being abundantly expressed in angiogenesis-related infiltrating macrophages. This study demonstrated for the first time that RIP1 kinase inhibition attenuates angiogenesis in multiple mouse models of pathological angiogenesis in vivo. Mechanistically, the inhibitory effect on angiogenesis depends on RIP kinase inhibition-mediated caspase activation in infiltrating macrophages that suppresses M2-like polarization, thereby attenuating pathological angiogenesis.

molecular biology↗

bioRxiv2019

Transethnic meta-analysis of genome-wide association studies identifies three new loci and characterizes population-specific differences for coronary artery disease

BackgroundGenome-wide association studies (GWAS) provided many biological insights into coronary artery disease (CAD), but these studies were mainly performed in Europeans. GWAS in diverse populations have the potential to advance our understanding of CAD.\n\nMethods and ResultsWe conducted two GWAS for CAD in the Japanese population, which included 12,494 cases and 28,879 controls, and 2,808 cases and 7,261 controls, respectively. Then, we performed transethnic meta-analysis using the results of the CARDIoGRAMplusC4D 1000 Genomes meta-analysis with UK Biobank. We identified 3 new loci on chromosome 1q21 (CTSS), 10q26 (WDR11-FGFR2), and 11q22 (RDX-FDX1). Quantitative trait locus analyses suggested the association of CTSS and RDX-FDX1 with atherosclerotic immune cells. Tissue/cell type enrichment analysis showed the involvement of arteries, adrenal glands and fat tissues in the development of CAD. Finally, we performed tissue/cell type enrichment analysis using East Asian-frequent and European-frequent variants according to the risk allele frequencies, and identified significant enrichment of adrenal glands in the East Asian-frequent group while the enrichment of arteries and fat tissues was found in the European-frequent group. These findings indicate biological differences in CAD susceptibility between Japanese and Europeans.\n\nConclusionsWe identified 3 new loci for CAD and highlighted the genetic differences between the Japanese and European populations. Moreover, our transethnic analyses showed both shared and unique genetic architectures between the Japanese and Europeans. While most of the underlying genetic bases for CAD are shared, further analyses in diverse populations will be needed to elucidate variations fully.

genetics↗

bioRxiv2019

An annotation dataset facilitates automatic annotation of whole-brain activity imaging of C. elegans

Annotation of cell identity is an essential process in neuroscience that allows for comparing neural activities across different animals. In C. elegans, although unique identities have been assigned to all neurons, the number of annotatable neurons in an intact animal is limited in practice and comprehensive methods for cell annotation are required. Here we propose an efficient annotation method that can be integrated with the whole-brain imaging technique. We systematically identified neurons in the head region of 311 adult worms using 35 cell-specific promoters and created a dataset of the expression patterns and the positions of the neurons. The large positional variations illustrated the difficulty of the annotation task. We investigated multiple combinations of cell-specific promoters to tackle this problem. We also developed an automatic annotation method with human interaction functionality that facilitates annotation for whole-brain imaging.

neuroscience↗

bioRxiv2019

The genomic landscape of clonal hematopoiesis in Japan

Cancer and aging are widely assumed to involve similar biological trajectories in different populations, though such biology has not been systematically characterized on a population scale. Clonal hematopoiesis with acquired mutations is a pre-cancerous condition that becomes common with advancing age. Here we describe shared and population-specific patterns of genomic mutation revealed by 33,250 autosomal mosaic chromosomal alterations (mCAs) we ascertained from 179,417 Japanese participants in the BioBank Japan cohort and compared to analogous analyses of UK Biobank. In this long-lived Japanese population, mCAs were detected in more than 35.0% (s.e. 1.4%) of individuals older than 90 years, suggesting that such clones trend toward inevitability with aging. Japanese and Europeans exhibited key differences in the genomic locations of mutations in their respective hematopoietic clones, which anticipated the populations relative rates of CLL (more common among Europeans) and T-cell lymphoma (more common among Japanese). Multiple mutational precursors of CLL (including trisomy 12, 13q loss, and 13q CNN-LOH) were also 2-6x less common among the Japanese, suggesting that these populations differ in selective pressures on clones long before the development of clinically apparent CLL. Japanese and UK populations also exhibited very different rates of clones arising from B- and T-cell lineages, anticipating the relative rates of B- and T-cell cancers in these populations. We identified six new loci at which inherited variants predispose to mCAs that duplicate or remove inherited risk alleles, including large-effect rare variants at NBN, MRE11, and CTU2 (OR=28-91). Our results motivate further exploration of the global genomic landscape of clonal hematopoiesis and cancer, and point to population-specific selective pressures on hematopoietic clones.

genetics↗

bioRxiv2019

Complement- and inflammasome-mediated autoinflammation-paroxysmal nocturnal hemoglobinuria

Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired hematopoietic stem cell disorder characterized by complement-mediated hemolysis and thrombosis, and bone marrow failure. Affected cells harbor somatic mutation in X-linked PIGA gene, essential for the initial step in glycosylphosphatidylinositol (GPI) biosynthesis. Loss of GPI biosynthesis results in defective cell-surface expression of GPI-anchored complement regulators CD59 and DAF. The affected stem cells generate many abnormal blood cells after clonal expansion, which occurs under bone marrow failure. Here, we report the mechanistic basis of a disease entity, autoinflammation-paroxysmal nocturnal hemoglobinuria (AIF-PNH), caused by germline mutation plus somatic loss of PIGT on chromosome 20q. A region containing maternally imprinted genes implicated in clonal expansion in 20q-myeloproliferative syndromes was lost together with normal PIGT from paternal chromosome 20. Taking these findings together with a lack of bone marrow failure, the mechanisms of clonal expansion in AIF-PNH appear to differ from those in PNH. AIF-PNH is characterized by intravascular hemolysis and recurrent autoinflammation, such as urticaria, arthralgia, fever and aseptic meningitis. Consistent with PIGTs essential role in synthesized GPIs attachment to precursor proteins, non-protein-linked free GPIs appeared on the surface of PIGT-defective cells. PIGT-defective THP-1 cells accumulated higher levels of C3 fragments and C5b-9 complexes, and secreted more IL-1{beta} than PIGA-defective cells after activation of the complement alternative pathway. IL-1{beta} secretion was dependent upon C5b-9 complexes, accounting for the effectiveness of the anti-C5 drug eculizumab for both intravascular hemolysis and autoinflammation. These results suggest that free GPIs enhance complement activation and inflammasome-mediated IL-1{beta} secretion.

immunology↗

bioRxiv2019

A transcription factor Abf1 facilitates ORC binding onto the Saccharomyces cerevisiae replication origin via histone acetylase Gcn5

Chromatin structure has been implicated in the regulation of DNA replication but the molecular mechanism involved is unclear. In this study, we observed that binding of the transcription factor Abf1 to the replication origin ARS1 facilitated the association of the origin recognition complex (ORC) with ARS1 using genetic interaction analysis and ChIP assay. The histone acetyltransferases (HATs), Gcn5 and Esa1, were also loaded onto ARS1 in an Abf1 site-dependent manner, where they were then responsible for acetylating histone H3 lysine 18 (H3K18) and histone H4 lysine 12 (H4K12), respectively. Interestingly, Abf1 interacted with Gcn5, while ORC interacted with Esa1. Indeed the B3 element showed genetic interaction with Gcn5 and Rpd3 not with Esa1, Act3 and Tra1.\n\nThese data suggest that Gcn5, which is recruited by Abf1, alters chromatin structure via histone acetylation and facilitates the loading of ORC. We therefore propose that transcription factors regulate chromatin structure at replication origins by recruiting chromatin-modifying proteins, such as HATs, to load the initiator.

genetics↗

bioRxiv2019

GWAS identifies nine nephrolithiasis susceptibility loci related with metabolic and crystallization pathways

Nephrolithiasis is a common urological trait disorder with acute pain. Although previous studies have identified various genetic variations associated with nephrolithiasis, the host genetic factors remain largely unidentified. To identify novel nephrolithiasis loci in the Japanese population, we performed large-scale GWAS (Genome wide association study) using 11,130 cases and 187,639 controls, followed by a replication analysis using 2,289 cases and 3,817 controls. The analysis identified 14 significant loci, including 9 novel loci on 2p23.2-3, 6p21.2, 6p12.3, 6q23.2, 16p12.3, 16q12.2, 17q23.2, 19p13.12, and 20q13.2. Interestingly, 10 of the 14 regions showed a significant association with any of 16 quantitative traits, including metabolic, kidney-related, and electrolyte traits, suggesting a common genetic background among nephrolithiasis patients and these quantitative traits. Four novel loci are related to the metabolic pathway, while the remaining 10 loci are associated with the crystallization pathway. Our findings demonstrate the crucial roles of genetic variations in the development of nephrolithiasis.\n\nSIGNIFICANCE STATEMENTNephrolithiasis is a common urothelial disorders with frequent recurrence rate, but its genetic background is largely remained unidentified. Previous GWAS identified 6 genetic factors in total. Here we performed a GWAS using more than 200,000 samples in the Japanese populations, and identified 14 significant loci and nine of them are novel. We also found that 10 of the 14 loci showed a significant association with any of 16 quantitative traits, including metabolic, kidney-related, and electrolyte traits (BMI, eGFR, UA, Ca etc). All 14 significant loci are associate with either metabolic or crystallization pathways. Thus, our findings elucidated the underlying molecular pathogenesis of nephrolithiasis.

genetics↗

bioRxiv2019

Genetic predisposition to mosaic Y chromosome loss in blood is associated with genomic instability in other tissues and susceptibility to non-haematological cancers

Mosaic loss of chromosome Y (LOY) in circulating white blood cells is the most common form of clonal mosaicism, yet our knowledge of the causes and consequences of this is limited. Using a newly developed approach, we estimate that 20% of the UK Biobank male population (N=205,011) has detectable LOY. We identify 156 autosomal genetic determinants of LOY, which we replicate in 757,114 men of European and Japanese ancestry. These loci highlight genes involved in cell-cycle regulation, cancer susceptibility, somatic drivers of tumour growth and cancer therapy targets. Genetic susceptibility to LOY is associated with non-haematological health outcomes in both men and women, supporting the hypothesis that clonal haematopoiesis is a biomarker of genome instability in other tissues. Single-cell RNA sequencing identifies dysregulated autosomal gene expression in leukocytes with LOY, providing insights into how LOY may confer cellular growth advantage. Collectively, these data highlight the utility of studying clonal mosaicism to uncover fundamental mechanisms underlying cancer and other ageing-related diseases.

genetics↗