Biology subjects

Adachi, S.

Publications and source records attributed to Adachi, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Alignment-free discovery of conserved RNA structures in the human genome

Many functional RNAs were first found as conserved RNA structures, and their roles in gene regulation were identified later. In humans and other vertebrates, imperfect genome alignments have hindered the discovery of such structures. Here we present RLMHelix, which selects candidate conserved RNA structures from single sequences before any alignment by scoring helices supported by language-model dependencies and thermodynamics. Through distillation, RLMHelix rapidly scans the transcribed human genome and ranks known RNAs higher than conventional thermodynamic scanning. Two-thirds of 15,821 candidates are new to four earlier genome-wide screens, yet agree with in-cell probing, and over half retain structural signal in homologues. In eCLIP data and in exploratory pull-downs, higher RLMHelix scores were associated with more binding by double-stranded RNA-binding proteins. By linking candidates to their binding proteins, RLMHelix yields testable functional hypotheses and illuminates a path from unrecognized human RNA structures to RNA biology and therapeutic targets.

bioinformatics↗

bioRxiv2026

A positional and combinatorial regulatory code for alternative splicing

Alternative pre-mRNA splicing generates extensive transcript diversity, yet the regulatory code that determines how splicing decisions are encoded across the transcriptome remains poorly defined. Splicing outcomes are controlled by combinatorial RNA-binding protein (RBP) interactions and positional context, but how these features are integrated at the transcriptome scale remains unclear. CLIP-based approaches have mapped RBP binding, but directly comparable endogenous maps across multiple RBPs are lacking, limiting inference of global regulatory principles. Here we introduce SCALE-CLIP, an endogenous CLIP framework that integrates CRISPR-Cas9-mediated epitope tagging with long-read-guided read attribution to generate directly comparable RBP binding maps across splicing-regulatory factors. Applied to 23 RBPs, SCALE-CLIP expanded endogenous RBP coverage and, across benchmarked shared factors, increased peak recovery by a median of 12.2-fold relative to ENCODE eCLIP while preserving specificity and reproducibility. We define a transcriptome-wide positional and combinatorial code for alternative splicing, in which binding position is a primary determinant of regulatory outcome: SRSF binding within alternative exons promotes inclusion, whereas binding on flanking exons drives exon skipping. Higher-order SRSF occupancy further tunes this code, buffering exon inclusion when centered on alternative exons but reinforcing repression when distributed across flanking exons. We also show that m6A provides an epitranscriptomic layer that locally enhances SRSF binding and is associated with increased exon inclusion. Together, these results establish a multi-layered RNA-binding logic in which binding position, combinatorial RBP architecture and RNA modification jointly shape splicing outcomes, providing a framework for rational interpretation and modulation of alternative splicing.

molecular biology↗

bioRxiv2026

Natural variation in rice mitogen-activated protein kinase 4 contributes to increased photosynthetic rate under field conditions

Improving rice (Oryza sativa L.) yield requires a balanced enhancement of both sink size and source capacity. While many QTLs for sink size have been identified, only a few are known for source capacity, which is essential for achieving high yield. Here we identified qHP10 as a major QTL for increased photosynthetic rate by using chromosome segment substitution lines derived from a cross between the high-yielding indica cultivar Takanari and the average-yielding japonica cultivar Koshihikari. High-resolution mapping combined with CRISPR/Cas9-induced mutagenesis revealed that the causative gene underlying qHP10 is Mitogen-Activated Protein Kinase 4 (OsMPK4). A near-isogenic line carrying the OsMPK4Takanari allele (NIL-OsMPK4) had a 15-25% higher photosynthetic rate than Koshihikari. NIL-OsMPK4 also had higher stomatal conductance than Koshihikari but similar stomatal pore size and density, indicating that increased stomatal aperture increases photosynthetic rate. This enhancement is likely attributable to the down-regulation of OsMPK4 expression, which increases stomatal conductance and thus promotes CO2 uptake. Our findings demonstrate that OsMPK4 is a promising genetic target for increasing source capacity and, potentially, rice yield through molecular breeding. (175 words)

plant biology↗

bioRxiv2026

RIPK3-RNASE1 axis as a potential therapeutic and clinical monitoring target in VEXAS syndrome

Vacuole, E1 enzyme, X-linked, autoinflammatory, somatic (VEXAS) syndrome (VS) is a severe autoinflammatory disease driven by somatic mutations in ubiquitin-like modifier activating enzyme 1 (UBA1), for which disease activity biomarkers and therapeutic targets are needed. We conducted longitudinal deep phenotyping of patients with VS and found that ribonuclease 1 (RNASE1) expression is most strongly correlated with the disease activity score measured by the VEXAS Current Activity Form (VEXASCAF). Single-cell RNA-sequencing showed that RNASE1 was upregulated in VS monocytes. We generated human monocytic cell lines harboring UBA1 mutations (p.Met41Val, p.Met41Leu, and p.Met41Thr). These cells exhibited varying degrees of impaired ubiquitination and subsequent pathological features such as the unfolded protein response, increased pro-inflammatory cytokine production, cell death, and RNASE1 expression, mirroring the genotype-phenotype associations observed in patients with VS. Multi-omics analyses revealed that genotypes linked to greater clinical severity were enriched in pro-inflammatory, interferon, and necroptosis signatures. Notably, functional interrogation demonstrated that inhibition of receptor-interacting protein kinase 3 (RIPK3), a key regulator of necroptosis, markedly suppressed all these pathological features, including the elevated RNASE1 expression. These results identify the RIPK3-RNASE1 axis in VS, highlighting RNASE1 as a potential biomarker and RIPK3 as an attractive therapeutic target.

immunology↗

bioRxiv2025

Cytoplasmic roles of HSATIII RNAs in RNA granule assembly and production of actin cytoskeleton-associated repeat-containing proteins

HSATIII architectural lncRNAs are nuclear short-tandem repeat ncRNAs induced upon thermal stress and serve as scaffolding molecules for nuclear stress bodies (nSBs), stress-induced membraneless organelles in the nucleus. We report that HSATIII lncRNAs are exported to the cytoplasm during stress recovery, where they form novel cytoplasmic bodies with nucleocytoplasmic RNA-binding proteins, including PURA, PURB, and m6A reader proteins. Recruitment of ALYREF to nSBs promotes HSATIII RNA export. These HSATIII-based granules, named HERALDs (Heat-removal-associated scaffolds), are transported along microtubules and accumulate at distal cellular regions. We further show that cytoplasmic HSATIII RNAs are translated into MEWNG-rich proteins, which interact with actin filaments and form complexes with HSPA8 and stress granule proteins such as ZC3HAV1 and ATXN2L. Together, these findings reveal previously unrecognized cytoplasmic roles of HSATIII RNAs, functioning both as lncRNAs to scaffold RNA granules and as mRNAs to produce proteins during the late phase of thermal stress recovery.

molecular biology↗

bioRxiv2025

Thermo-Sensing Mechanisms of Splicing Control by Nuclear Stress Bodies

Nuclear stress bodies (nSBs) are stress-inducible membraneless organelles formed on HSATIII lncRNAs and regulate pre-mRNA splicing during thermal stress recovery. During stress, dephosphorylated SRSFs accumulate in nSBs, whereas upon stress removal, their kinase CLK1 is recruited to rephosphorylate SRSFs, thereby promoting intron detention in specific transcripts. However, the mechanism underlying CLK1 localization to nSBs in response to stress removal has remained unclear. Here, we identify phosphorylation of CLK1 at Ser341 as a critical determinant of its nSB localization. Ser341 is phosphorylated under normal conditions, dephosphorylated by PP1 during stress, and rephosphorylated by RIOK2 during recovery, enabling CLK1 localization to nSBs specifically during recovery. We further identify PPP1R2, an entirely intrinsically disordered PP1 inhibitory subunit, as a reversible thermosensor that dissociates under stress to activate PP1. Together, our findings reveal multilayered thermosensing mechanisms that coordinate the temporally staged localization of SRSFs and CLK1 to nSBs, thereby regulating temperature-dependent pre-mRNA splicing.

molecular biology↗

bioRxiv2025

Thalamus-cortex interactions drive cell type-specific cortical development in human pluripotent stem cell-derived assembloids

The thalamus plays a pivotal role in the development and function of neural circuits in the cerebral cortex. However, how thalamus-cortex interactions influence human cortical development remains unknown primarily because of the inaccessibility of the human embryonic brain. Here, we demonstrate thalamus-dependent gene expression, circuit organization, and neural activity during corticogenesis using human thalamocortical assembloids (hThCAs). Human cortical and thalamic organoids (hCOs and hThOs) derived from induced pluripotent stem cells exhibited region-specific gene expression and spontaneous neuronal activity. Upon the fusion of these organoids, hThCAs reconstructed reciprocal thalamus-cortex axonal projections and synaptic connections. Transcriptomic analysis revealed thalamus-dependent acceleration of cortical maturation, with upregulation of programs linked to axon development, subplate/cortical plate identity, and activity-regulated genes. Histological analysis showed expanded progenitor pools and increased deep-layer neurons within hThCAs. Wide-field Ca2+ imaging demonstrated that wave-like activity originated in the thalamic region and propagated to the cortical region. Furthermore, two-photon Ca2+ imaging of cortical neurons revealed that synchronous activity emerged exclusively in pyramidal tract (PT) and corticothalamic (CT) neurons, whereas intratelencephalic (IT) neurons remain asynchronous, highlighting cell type-specific circuit integration within hThCAs. These synchronized events were absent in isolated hCOs or in cortico-cortical assembloids, underscoring the specificity of thalamic input. Our findings suggest that diffusible thalamic cues broadly enhance progenitor expansion, while long-range thalamic input organizes cell type-specific synchronous activity. This study demonstrates the thalamus-dependent acquisition of mature cortical phenotypes in a cell type-specific manner in hThCAs, establishing developmental mechanisms linking regional interactions and cell type-specific circuit specification. Thus, hThCAs provide a tractable human platform for dissecting human-specific developmental processes and modeling neurodevelopmental disorders with disrupted thalamocortical communication at the molecular, cellular, and circuit levels. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/681772v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@95b599org.highwire.dtl.DTLVardef@c56085org.highwire.dtl.DTLVardef@43df08org.highwire.dtl.DTLVardef@1e7c4ed_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIhThCAs recapitulate the developmental sequence of reciprocal projections with synapses. C_LIO_LIhThCA cortical transcriptomes resemble the late fetal human cortex. C_LIO_LIThalamic paracrine signals promote progenitor expansion and cortical cytoarchitecture. C_LIO_LIWave-like activity originates in the thalamus and propagates across the cortex. C_LIO_LIThalamic input drives cell type-specific synchronization and circuit integration. C_LI

neuroscience↗

bioRxiv2025

A Novel In Vitro Potency Assay Demonstrating the Anti-Fibrotic Mechanism of Action of CDCs in Deramiocel

Duchenne muscular dystrophy (DMD) is characterized by progressive skeletal and cardiac muscle degeneration driven by inflammation and fibrosis, ultimately leading to cardiomyopathy and premature death. Deramiocel, an allogeneic cell therapy composed of cardiosphere-derived cells (CDCs), has demonstrated potent anti-fibrotic and immunomodulatory effects in preclinical models and clinical trials, including HOPE-2 and its open-label extension (HOPE-2 OLE), where Deramiocel treatment significantly attenuated progression of skeletal and cardiac muscle dysfunction. Here, we describe the development of a novel in vitro potency assay to quantify the anti-fibrotic activity of Deramiocel. Conditioned media (CM) from multiple Deramiocel manufacturing lots significantly suppressed expression of collagen type I alpha 1 (COL1A1) and collagen type III alpha 1 (COL3A1) in primary human dermal fibroblasts compared with non-conditioned media controls, establishing a robust, reproducible readout of anti-fibrotic activity. The effect was dose-dependent and abrogated by sequential depletion of exosomes and soluble proteins, implicating both as critical mediators of Deramiocels mechanism of action. Importantly, CDCs in deramiocel lots classified as potent by this assay were shown to exert a clinically meaningful benefit in DMD patients in the HOPE-2 and HOPE-2 OLE studies. This assay represents a mechanistically informative, therapeutically relevant, reproducible, scalable, and regulatory-compliant approach for assessing Deramiocel potency, enabling consistent manufacturing and facilitating the continued development of Deramiocel as a disease-modifying therapy for DMD.

cell biology↗

bioRxiv2025

Proteome-level robustness and the role of a histone-like protein during acute heat shock in the hyperthermophilic archaeon Pyrococcus furiosus

The hyperthermophilic archaeon Pyrococcus furiosus thrives in extreme temperatures and exhibits a complex response to heat shock. However, the regulatory dynamics of genetic information during heat shock remain poorly understood. In this study, we exposed P. furiosus (cultured at 90{degrees}C) to acute heat shock by boiling (101-102{degrees}C) and analyzed its transcriptomic and proteomic responses. The levels of 16S and 23S rRNAs and of total tRNA were decreased by approximately 50%, and pre-tRNA splicing was inhibited, indicating suppression of translation. By contrast, approximately 90% of the proteome remained stable, underscoring the robustness of existing proteins. However, the transcriptome exhibited widespread alterations with limited correlation to the proteome (correlation coefficient r = 0.32), except for a few key proteins. These proteins included PF1883 (small heat shock protein), PF1385 (uracil-DNA glycosylase), and PF1616 (inositol-1-phosphate synthase), which are involved in protein chaperoning, stress-related metabolite synthesis, and DNA repair, respectively. Additionally, PF0624, previously annotated as a hypothetical protein, was identified as a putative histone motif-containing protein. Experimental evidence suggests that PF0624 may contribute to chromatin formation via archaeal histones in P. furiosus. In summary, our findings reveal that P. furiosus responds to acute heat shock by maintaining protein stability, suppressing translation, limiting genomic damage, and potentially compacting genomic DNA into archaeal chromatin. IMPORTANCEHyperthermophilic archaea, such as Pyrococcus furiosus, thrive in extreme environments where the temperatures may reach up to 100{degrees}C. However, the precise mechanisms by which these organisms protect their genomic DNA from heat-induced damage remain incompletely understood. In this study, we propose that PF0624, a histone-like protein that is transcriptionally induced and translated in response to acute heat shock, is critical in stabilizing archaeal chromatin structure through histone-mediated mechanisms. Our results highlight the sophisticated molecular strategies employed by P. furiosus to survive extreme thermal stress.

molecular biology↗

bioRxiv2024

Conversion of silent synapses to AMPA receptor-mediated functional synapses in human cortical organoids

Despite the crucial role of synaptic connections and neural activity in the development and organization of cortical circuits, the mechanisms underlying the formation of functional synaptic connections in the developing human cerebral cortex remain unclear. We investigated the development of -amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR)-mediated synaptic transmission using human cortical organoids (hCOs) derived from induced pluripotent stem cells. Two-photon Ca2 imaging revealed an increase in the frequency and amplitude of spontaneous activity in hCOs on day 80 compared to day 50. Additionally, spontaneous neural activity in late-stage hCOs, but not in early-stage hCOs, was blocked by N-methyl-D-aspartate receptor (NMDAR) and AMPAR antagonists. However, transsynaptic circuit tracing with G-deleted rabies viral vectors indicated a similar number of synaptic connections in early- and late-stage hCOs. Notably, chemical labeling demonstrated a significant increase in AMPAR expression on the postsynaptic membrane and colocalization with NMDAR in late-stage hCOs. These results suggest that hCOs progressively organize excitatory synaptic transmission, concurrent with the transition from silent synapses lacking AMPARs to functional synapses containing NMDARs and AMPARs. This in vitro model of human cortical circuits derived from induced pluripotent stem cells reflects the developmental programs underlying physiological transitions, providing valuable insights into human corticogenesis and neurodevelopmental disorders. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/629885v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1432b6dorg.highwire.dtl.DTLVardef@d8350borg.highwire.dtl.DTLVardef@8273f8org.highwire.dtl.DTLVardef@8bbabd_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Direct Relationship between Protein Expression and Progeny Yield of Herpes Simplex Virus 1 Unveils a Rate-limiting Step for Virus Production

Although viral protein expression and progeny virus production were independently shown to be highly heterogenous in individual cells, their direct relationship, analyzed by considering their heterogeneities, has not been investigated to date. This study established a system to fractionate cells infected with a herpesvirus based on the levels of the global expression of viral late proteins, which are largely virion structural proteins, and to titrate virus yields in these fractions. This system demonstrated a direct relationship and indicated there was a threshold for the levels of viral late protein expression for progeny virus production and suggested that viral DNA cleavage/packaging was a rate-limiting step for progeny virus production. These findings, which were masked in previous studies performed at the entire population level, have uncovered a sophisticated viral strategy for efficient progeny virus production and shed new light on an effective target for the development of anti-viral drugs.

microbiology↗

bioRxiv2023

Shell protein composition specified by NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles

Many membraneless organelles (MLOs) formed through phase separation play crucial roles in various cellular processes. Although these MLOs co-exist in cells, how they maintain their independence without coalescence or engulfment remains largely unknown. Here, we investigated the molecular mechanism by which paraspeckles with core-shell architecture scaffolded by NEAT1_2 lncRNAs exist as distinct MLOs. We identified NEAT1 deletion mutants that assemble paraspeckles that are incorporated into nuclear speckles. Several paraspeckle proteins, including SFPQ, HNRNPF, and BRG1, prevent this incorporation and thus contribute to the segregation of paraspeckles from nuclear speckles. Shell localization of these proteins in the paraspeckles, which is determined by NEAT1_2 lncRNA domains, is required for this segregation process. Conversely, U2-related spliceosomal proteins are involved in internalizing the paraspeckles into nuclear speckles. This study shows that the paraspeckle shell composition dictates the independence of MLOs in the nucleus, providing insights into the importance of the shell in defining features and functions of MLOs.

cell biology↗

bioRxiv2022

RNA-triggered protein cleavage and cell death by the RNA-guided type III-E CRISPR-Cas nuclease-protease complex

The type III-E Cas7-11 effector nuclease forms a complex with a CRISPR RNA (crRNA) and the putative caspase-like protease Csx29, catalyzes crRNA-guided target RNA cleavage, and has been used for RNA targeting in eukaryotic cells. Here, we report cryo-electron microscopy structures of the Cas7-11-crRNA-Csx29 complex with and without target RNA, and demonstrate that target RNA binding induces a conformational change in Csx29 and results in the protease activation. Biochemical analysis confirmed that Cas7-11-bound Csx29 cleaves Csx30 in a target RNA-dependent manner. Reconstitution of the system in bacteria uncovered Csx30-dependent cellular toxicity regulated by Csx31, and that Csx29-mediated cleavage produces toxic Csx30 fragments, promoting cell death. We find that Csx30 can bind both Csx31 and the associated sigma factor RpoE, suggesting Csx30 can inhibit RpoE and modulate cellular stress response towards infection. Overall, the RNA-guided nuclease-protease activities of the Cas7-11-Csx29 effector complex facilitate protease-based programmed cell death.

molecular biology↗

bioRxiv2019

Induction of hierarchy and time through one-dimensional probability space with certain topologies

In a previous study, the authors utilized a single dimensional operationalization of species density that at least partially demonstrated dynamic system behavior. For completeness, a theory needs to be developed related to homology/cohomology, induction of the time dimension, and system hierarchies. The topological nature of the system is carefully examined and for testing purposes, species density data for a wild Dictyostelia community data are used in conjunction with data derived from liquid-chromatography mass spectrometry of proteins. Utilizing a Clifford algebra, a congruent zeta function, and a Weierstra{beta}[weierp] function in conjunction with a type VI Painleve equation, we confirmed the induction of hierarchy and time through one-dimensional probability space with certain topologies. This process also served to provide information concerning interactions in the model. The previously developed \"small s\" metric can characterize dynamical system hierarchy and interactions, using only abundance data along time development.

evolutionary biology↗

bioRxiv2019

LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation

A number of long noncoding RNAs (lncRNAs) are induced in response to specific stresses to construct membrane-less nuclear bodies; however, their function remains poorly understood. Here, we report the role of nuclear stress bodies (nSBs) formed on highly repetitive satellite III (HSATIII) lncRNAs derived from primate-specific satellite III repeats upon thermal stress exposure. A transcriptomic analysis revealed that depletion of HSATIII lncRNAs, resulting in elimination of nSBs, promoted splicing of 533 retained introns during thermal stress recovery. A HSATIII-Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) analysis identified multiple splicing factors in nSBs, including serine and arginine-rich pre-mRNA splicing factors (SRSFs), the phosphorylation states of which affect splicing patterns. SRSFs are rapidly dephosphorylated upon thermal stress exposure. During stress recovery, CDC like kinase 1 (CLK1) was recruited to nSBs and accelerated the re-phosphorylation of SRSF9, thereby promoting target intron retention. Our findings suggest that HSATIII-dependent nSBs serve as a conditional platform for phosphorylation of SRSFs by CLK1 to promote the rapid adaptation of gene expression through intron retention following thermal stress exposure.

molecular biology↗

bioRxiv2019

Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing

The PIWI-interacting RNA (piRNA) pathway preserves genomic integrity by repressing transposable elements (TEs) in animal germ cells. Among PIWI-clade proteins in Drosophila, Piwi transcriptionally silences its targets through interactions with cofactors, including Panoramix (Panx) and forms heterochromatin characterized by H3K9me3 and H1. Here, we identified Nxf2, a nuclear RNA export factor (NXF) variant, as a protein that forms complexes with Piwi, Panx, and p15. Panx-Nxf2-p15 complex formation is necessary in the silencing by stabilizing protein levels of Nxf2 and Panx. Notably, ectopic targeting of Nxf2 initiates co-transcriptional repression of the target reporter in a manner independent of H3K9me3 marks or H1. However, continuous silencing requires HP1a and H1. In addition, Nxf2 directly interacts with target TE transcripts in a Piwi-dependent manner. These findings suggest a model in which the Nxf2-Panx-p15 complex enforces the association of Piwi with target transcripts to trigger co-transcriptional repression, prior to heterochromatin formation in the nuclear piRNA pathway.\n\nHighlightsO_LINxf2 plays an essential role in the Piwi-piRNA pathway\nC_LIO_LIFormation of Piwi-Panx-Nxf2-p15 (PPNP) complexes stabilizes both Panx and Nxf2\nC_LIO_LIThe PPNP complex triggers transcriptional silencing before heterochromatin formation\nC_LIO_LINxf2 directly binds to target transcripts in a Piwi-dependent manner\nC_LI

molecular biology↗

bioRxiv2019

Codon Optimality Confers GC-Rich-Induced Stability to mRNAs in Humans

Codon bias has been implicated as one of the major factors contributing to mRNA stability in yeast. However, the effects of codon-bias on mRNA stability remain unclear in humans. Here we show that human cells possess a mechanism to modulate RNA stability through a unique codon bias different from that of yeast. Bioinformatics analysis showed that codons could be clustered into two distinct groups - codons with G or C at the third base position (GC3) and codons with either A or T at the third base position (AT3); the former stabilizing while the latter destabilizing mRNA. Quantification of codon bias showed that increased GC3 content entails proportionately higher GC content. Through bioinformatics, ribosome profiling and in vitro analysis, we show that decoupling of the effects of codon bias reveals two modes of mRNA regulation, GC3- and GC-content dependent. Employing an immunoprecipitation-based strategy, we identified ILF2 as an RNA binding protein that differentially regulates global mRNA abundances based on codon bias. Our results demonstrate that codon bias is a two-pronged system that governs mRNA abundance.

molecular biology↗

bioRxiv2018

Large-scale genome-wide association meta-analysis of endometriosis reveals 13 novel loci and genetically-associated comorbidity with other pain conditions

Endometriosis is a common complex inflammatory condition characterised by the presence of endometrium-like tissue outside the uterus, mainly in the pelvic area. It is associated with chronic pelvic pain and infertility, and its pathogenesis remains poorly understood. The disease is typically classified according to the revised American Fertility Society (rAFS) 4-stage surgical assessment system, although stage does not correlate well with symptomatology or prognosis. Previously identified genetic variants mainly are associated with stage III/IV disease, highlighting the need for further phenotype-stratified analysis that requires larger datasets. We conducted a meta-analysis of 15 genome-wide association studies (GWAS) and a replication analysis, including 58,115 cases and 733,480 controls in total, and sub-phenotype analyses of stage I/II, stage III/IV and infertility-associated endometriosis cases. This revealed 27 genetic loci associated with endometriosis at the genome-wide p-value threshold (P<5x10-8), 13 of which are novel and an additional 8 novel genes identified from gene-based association analyses. Of the 27 loci, 21 (78%) had greater effect sizes in stage III/IV disease compared to stage I/II, 1 (4%) had greater effect size in stage I/II compared to stage III/IV and 17 (63%) had greater effect sizes when restricted to infertility-associated endometriosis cases compared to overall endometriosis. These results suggest that specific variants may confer risk for different sub-types of endometriosis through distinct pathways. Analyses of genetic variants underlying different pain symptoms reported in the UK Biobank showed that 7/9 had positive significant (p<1.28x103) positive genetic correlations with endometriosis, suggesting a genetic basis for sensitivity to pain in general. Additional conditions with significant positive genetic correlations with endometriosis included uterine fibroids, excessive and irregular menstrual bleeding, osteoarthritis, diabetes as well as menstrual cycle length and age at menarche. These results provide a basis for fine-mapping of the causal variants at these 27 loci, and for functional follow-up to understand their contribution to endometriosis and its potential subtypes.

genomics↗