Abstract: Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge 1–5 . Here we conducted a genome-wide association study (GWAS) involving 2,393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3,289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene ( DOCK2 ), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis ( n  = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target.

Abstract: The genetic make-up of an individual contributes to the susceptibility and response to viral infection. Although environmental, clinical and social factors have a role in the chance of exposure to SARS-CoV-2 and the severity of COVID-19 1,2 , host genetics may also be important. Identifying host-specific genetic factors may reveal biological mechanisms of therapeutic relevance and clarify causal relationships of modifiable environmental risk factors for SARS-CoV-2 infection and outcomes. We formed a global network of researchers to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity. Here we describe the results of three genome-wide association meta-analyses that consist of up to 49,562 patients with COVID-19 from 46 studies across 19 countries. We report 13 genome-wide significant loci that are associated with SARS-CoV-2 infection or severe manifestations of COVID-19. Several of these loci correspond to previously documented associations to lung or autoimmune and inflammatory diseases 3–7 . They also represent potentially actionable mechanisms in response to infection. Mendelian randomization analyses support a causal role for smoking and body-mass index for severe COVID-19 although not for type II diabetes. The identification of novel host genetic factors associated with COVID-19 was made possible by the community of human genetics researchers coming together to prioritize the sharing of data, results, resources and analytical frameworks. This working model of international collaboration underscores what is possible for future genetic discoveries in emerging pandemics, or indeed for any complex human disease.

Abstract: Recent studies have documented frequent evolution of clones carrying common cancer mutations in apparently normal tissues, which are implicated in cancer development 1–3 . However, our knowledge is still missing with regard to what additional driver events take place in what order, before one or more of these clones in normal tissues ultimately evolve to cancer. Here, using phylogenetic analyses of multiple microdissected samples from both cancer and non-cancer lesions, we show unique evolutionary histories of breast cancers harbouring der(1;16), a common driver alteration found in roughly 20% of breast cancers. The approximate timing of early evolutionary events was estimated from the mutation rate measured in normal epithelial cells. In der(1;16)(+) cancers, the derivative chromosome was acquired from early puberty to late adolescence, followed by the emergence of a common ancestor by the patient’s early 30s, from which both cancer and non-cancer clones evolved. Replacing the pre-existing mammary epithelium in the following years, these clones occupied a large area within the premenopausal breast tissues by the time of cancer diagnosis. Evolution of multiple independent cancer founders from the non-cancer ancestors was common, contributing to intratumour heterogeneity. The number of driver events did not correlate with histology, suggesting the role of local microenvironments and/or epigenetic driver events. A similar evolutionary pattern was also observed in another case evolving from an AKT1 -mutated founder. Taken together, our findings provide new insight into how breast cancer evolves.

Abstract: Abstract :  During food shortage, organisms activate defense mechanisms to maximize their chance of survival. At least in part, these responses are triggered by changes in hormonal status and neural status during starvation. The hypothalamus is organized as a collection of distinct autonomously active nuclei and is considered to play crucial roles in these survival responses. To isolate factors involved in these pathways, we carried out suppression subtractive hybridization analyses using complementary DNAs (cDNA) from the hypothalami of fasted and fed rats. We identified four genes, namely ubiquitin‐conjugating enzyme E2D 3 ( UBE2D3 ), cAMP‐dependent protein kinase C beta subunit ( PKC β), excitatory amino acid carrier 1 ( EAAC1 ), and ferritin heavy polypeptide 1 ( Fth1 ), that were upregulated after a 48‐h fast compared to the fed status. According to previous reports, these genes have been implicated in protection against neuronal cell death under various neurodegenerative stresses, such as hypoxia–ischemia and oxidative stress. Thus, the increased expressions of the genes identified in the present study may have protective effects against neural damage that could otherwise result in cell death.

Abstract: The present study demonstrates an epigenetic mechanism that mediates the positive feedback action of estrogen to induce GnRH/LH surges. Estrogen feedback action on GnRH release is directed to two ways, positive to stimulate and negative to inhibit GnRH release; how estrogen exerts such opposite actions on the release of a specific molecule, GnRH has been an unresolved question in reproductive biology. Our finding clarifies a mechanism for one of the two actions, the positive feedback action, which is indispensable for the induction of ovulation. This understanding may be of therapeutic importance in ovarian disorders of domestic animals and women. Taken together, the present results demonstrate that estrogen enhances the recruitment of the estrogen–ERα complex to the Kiss1 promoter region and induces histone acetylation in the promoter region. This histone acetylation enhances the chromatin loop formation of Kiss1 promoter and Kiss1 gene enhancer, resulting in an increase in AVPV-specific Kiss1 gene expression. Finally, to confirm this function of the Kiss1 gene 3′ intergenic region, we generated transgenic mice carrying DNA containing the Kiss1 locus sequence connected with a GFP with or without the candidate 3′ intergenic region. Transgenic mice carrying the intergenic region exhibited both AVPV and ARC GFP expression that colocalized with kisspeptin-immunoreactive neurons. In contrast, the deletion of the 3′ region reduced GFP expression in kisspeptin neurons in the AVPV but not in the ARC. These results suggest that the 3′ intergenic region plays an important role in mediating estrogen-dependent expression of Kiss1 in the AVPV. From these results, we hypothesized that the Kiss1 loci in the AVPV and ARC regions form different chromatin conformations. We therefore investigated the effects of estrogen on chromatin structure within the Kiss1 locus by a chromatin conformation capture (3C) analysis to identify candidate(s) for the AVPV-specific Kiss1 enhancer region. Our 3C analysis revealed that estrogen induced the formation of a gene loop between the Kiss1 promoter in the AVPV and the 3′ intergenic region, suggesting that the 3′ intergenic region functions as an enhancer for estrogen-dependent Kiss1 expression in the AVPV. We first identified the Kiss1 gene promoter region in the mouse hypothalamus by in vitro luciferase reporter assay, which is widely used to study biological processes. In this way we identified the core promoter region of the Kiss1 gene located at −180 bp 5′ of exon 1 of the Kiss1 gene. Next, to investigate if an epigenetic mechanism underlies the estrogen-dependent up-regulation of hypothalamic Kiss1 expression, we analyzed the histone acetylation and/or DNA methylation status of mouse Kiss1 gene locus in the mouse AVPV and compared it with that of the Kiss1 gene locus in the mouse ARC. ChIP using a histone H3 antibody revealed that estrogen treatment enhanced histone acetylation at the Kiss1 promoter region in the AVPV in ovariectomized mice. In contrast, histones at the Kiss1 promoter region in the ARC were deacetylated by estrogen. These findings clearly indicate that histone acetylation is a major mechanism underlying the stimulatory or inhibitory effects of estrogen on Kiss1 expression in the AVPV or ARC, respectively. This hypothesis was supported by another finding that an inhibitor of histone deacetylation, trichostatin-A (TSA), induced in vitro Kiss1 expression in the hypothalamic non– Kiss1 -expressing cells. These results indicate that histone acetylation of the Kiss1 promoter region plays a critical role in estrogen-induced up-regulation of AVPV Kiss1 expression. This notion also is supported by the results of the ChIP assay, which indicate that estrogen enhanced the recruitment of ERα at the Kiss1 promoter region in the AVPV. Unexpectedly, the Kiss1 promoter region was hypermethylated in Kiss1 -expressing cells microdissected from both AVPV and ARC regions, thereby indicating that DNA methylation at the promoter region may not be critical for the effect of estrogen on Kiss1 expression in both brain nuclei. This finding is consistent with in vitro results, which showed that 5-aza-2′-deoxycytidine, an inhibitor of DNA methylation, does not affect Kiss1 expression in mouse hypothalamic cells. The responses of kisspeptin expression to estrogen are opposite in the AVPV and ARC kisspeptin neuronal populations. Estrogen up-regulates kisspeptin expression in the AVPV but down-regulates expression in the ARC ( 4 ). Several bodies of evidence indicate that estrogen induces GnRH surges by acting on the kisspeptin neurons in the AVPV ( 4 – 6 ). The present study focused on the molecular mechanism that mediates the stimulatory action of estrogen on kisspeptin expression in the AVPV, because the mechanism is linked directly to the GnRH surge and ovulation. The kisspeptin neurons in the ARC were used consistently for reference throughout the experiment. Epigenetic modification of genomic DNA and histones has been linked tightly to chromatin organization and transcriptional regulation: Histone acetylation at gene promoter and/or enhancer regions generally is correlated with transcriptional activation ( 7 ); genomic DNA methylation is associated with gene silencing ( 8 ). Therefore this study aimed to determine whether an epigenetic regulatory mechanism underlies the effect of estrogen-positive feedback on Kiss1 gene expression in the AVPV. Ovulation is triggered by a surge-like release of estrogen from the mature ovarian follicle by a positive feedback action; this feedback action stimulates a surge in the secretion of gonadotropin-releasing hormone (GnRH)/gonadotropin to induce ovulation. Kisspeptin, a neuropeptide found in neurons of two brain areas of interest—the anteroventral periventricular nucleus (AVPV) and arcuate nucleus (ARC)—has been attracting attention as a mediator of estrogen feedback action on GnRH release in the brain. These two brain regions are considered to play a role in regulating the surge and pulse modes of GnRH/luteinizing hormone (LH) secretion, respectively. The AVPV neuronal population, in particular, is considered a candidate target of estrogen-positive feedback for many reasons. LH surges are abolished by lesion of the nucleus ( 1 ), which contains many estrogen receptors (ER). The ARC is a potential candidate for the GnRH pulse generator and a site of estrogen-negative feedback action on GnRH release, because LH pulses are not impaired by the surgical isolation of the area including the nucleus ( 2 ) and are suppressed by local implants of estrogen in this area ( 3 ). Therefore, elucidation of the molecular mechanism that mediates the estrogen-induced increase in kisspeptin expression in the AVPV is a key to unravel the effect of estrogen-positive feedback on GnRH release. In the present study, we investigated an epigenetic mechanism by which estrogen regulates the expression of the kisspeptin-encoding gene Kiss1 to mediate its positive feedback effect on GnRH release. Our results indicate that estrogen stimulates recruitment of the estrogen receptor alpha (ERα) on the Kiss1 promoter region to induce histone H3 acetylation and the formation of a chromatin loop between the Kiss1 promoter and the 3′ enhancer region. Together, these events lead to up-regulation of the Kiss1 gene in the AVPV ( Fig. P1 ).

Abstract: Oocytes mature in a specialized fluid-filled sac, the ovarian follicle, which provides signals needed for meiosis and germ cell growth. Methods have been developed to generate functional oocytes from pluripotent stem cell–derived primordial germ cell–like cells (PGCLCs) when placed in culture with embryonic ovarian somatic cells. In this study, we developed culture conditions to recreate the stepwise differentiation process from pluripotent cells to fetal ovarian somatic cell–like cells (FOSLCs). When FOSLCs were aggregated with PGCLCs derived from mouse embryonic stem cells, the PGCLCs entered meiosis to generate functional oocytes capable of fertilization and development to live offspring. Generating functional mouse oocytes in a reconstituted ovarian environment provides a method for in vitro oocyte production and follicle generation for a better understanding of mammalian reproduction.

Abstract: Realizing large-scale single-mode, high-power, high-beam-quality semiconductor lasers, which rival (or even replace) bulky gas and solid-state lasers, is one of the ultimate goals of photonics and laser physics. Conventional high-power semiconductor lasers, however, inevitably suffer from poor beam quality owing to the onset of many-mode oscillation 1,2 , and, moreover, the oscillation is destabilized by disruptive thermal effects under continuous-wave (CW) operation 3,4 . Here, we surmount these challenges by developing large-scale photonic-crystal surface-emitting lasers with controlled Hermitian and non-Hermitian couplings inside the photonic crystal and a pre-installed spatial distribution of the lattice constant, which maintains these couplings even under CW conditions. A CW output power exceeding 50 W with purely single-mode oscillation and an exceptionally narrow beam divergence of 0.05° has been achieved for photonic-crystal surface-emitting lasers with a large resonant diameter of 3 mm, corresponding to over 10,000 wavelengths in the material. The brightness, a figure of merit encapsulating both output power and beam quality, reaches 1 GW cm −2  sr −1 , which rivals those of existing bulky lasers. Our work is an important milestone toward the advent of single-mode 1-kW-class semiconductor lasers, which are expected to replace conventional, bulkier lasers in the near future.