Life Science Alliance

In most animals and fungi, centromere identity and function depend on the Scm3/HJURP chaperone, which deposits CENPA at centromeres. However, Scm3/HJURP orthologs appeared to be missing in insects, nematodes, many vertebrates, and other metazoans, suggesting radical chaperone replacement in these lineages. Here, we combine remote homology detection, AlphaFold-based structural modeling, and functional genetics in zebrafish and Caenorhabditis elegans to identify previously unknown Scm3/HJURP orthologs that localize to centromeres and whose loss causes catastrophic mitotic failure. We further show that Drosophila CAL1, long considered a functional analog, is instead a highly diverged Scm3/HJURP ortholog. Despite rapid primary-sequence divergence, predicted and known structures reveal a broadly conserved CENPA-H4-binding scm3 fold across fungi, vertebrates, nematodes, insects, and basally-branching metazoans. Our work demonstrates how rapid divergence can obscure the broad conservation of essential centromere machinery and provides a broadly applicable strategy to unmasking missing orthologs. Summary statementAnimals encode a rapidly evolving, essential cell cycle gene previously thought to be absent.

{gamma}-secretase is a multi-subunit enzyme complex responsible for cleaving hundreds of substrates in diverse cellular contexts. Variation in subunit composition - including the use of alternate catalytic subunits Presenilin 1 (PSEN1) and Presenilin 2 (PSEN2) - results in diverse {gamma}-secretase complexes. Point mutations in PSEN1 and PSEN2 cause familial forms of Alzheimers disease, while loss-of-function mutations in the {gamma}-secretase subunits PSEN1, PSENEN and NCSTN cause acne inversa. To advance therapeutic strategies targeting {gamma}-secretase in Alzheimers disease, a better understanding of individual {gamma}-secretase complexes is required. In this study, we used CRISPR-Cas9 genome engineering to generate PSEN2-knockout iPSCs in order to compare the consequence of PSEN2 knockout versus PSEN1 knockout in iPSC-derived brain cells. In contrast to PSEN1-knockout, PSEN2-knockout did not alter APP cleavage or A{beta} generation in iPSC-neurons, nor did it disrupt Nicastrin maturation. Similarly, PSEN2-knockout had little impact on TREM2 processing in iPSC-microglia. Instead, our data indicate that loss of PSEN2 primarily impacts the endo-lysosomal system in iPSC-neurons, causing an accumulation of early endosome markers and a reduction in lysosomal markers - phenotypes not observed in PSEN1-knockout neurons. Taken together, these findings highlight distinct and non-redundant functions of PSEN1 and PSEN2 in human brain cells, reinforcing findings in animal models and subcellular localisation studies. This work advances our understanding of distinct {gamma}-secretase complex functions and provides insights that will support future therapeutic efforts to inhibit, modulate or stabilise {gamma}-secretase.

RNF43 is best known for removing the Wnt-receptor complex from the cell surface, thereby maintaining Wnt-signaling at minimal essential levels. Recent studies reported that RNF43-mutant colorectal cancers carrying the common BRAFV600E mutation, respond more effectively to combined BRAF/EGFR inhibition. To determine whether RNF43 directly regulates EGFR or BRAF protein abundance, multiple pancreatic and colorectal cancer cell line models were generated in which RNF43 was knocked out, repaired, or stably overexpressed. Total and cell surface EGFR levels, as well as endogenous BRAF expression, were quantified. Across all models, no consistent evidence emerges that RNF43 modulates endogenous EGFR or BRAF levels. R-spondins likewise fail to alter EGFR levels or internalization. Notably, elevated EGFR expression observed in a subset of RNF43 knockout clones is induced by unintended CRISPR/Cas9 vector integration rather than the absence of RNF43 itself, highlighting a previously underappreciated artefact that can confound interpretations of EGFR regulation in genome edited lines. Overall, the data argue against a direct and general role for RNF43 in controlling EGFR or BRAF protein abundance, contradicting recent reports that propose degradation of these targets. Further studies are required to resolve these discrepancies and clarify the mechanistic basis underlying these conflicting observations.

Mitochondrial dynamics are critical for T cell activation, differentiation, and survival. The inner mitochondrial membrane ATP-dependent metalloprotease YME1L1 regulates proteostasis and the processing of optic atrophy protein 1 (OPA1), thereby shaping mitochondrial cristae architecture and respiratory function in many cell types. Whether YME1L1 fulfils similar roles in lymphocytes remains unknown. Here, we examined YME1L1 function in T cells using conditional knockout mice lacking YME1L1 in lymphocytes (YME1L1{Delta}TB). YME1L1 expression increased upon T cell activation, yet its absence did not alter thymic development, peripheral T cell homeostasis, or the proportions of naive, memory, and regulatory subsets. T cell activation and proliferation in response to anti-CD3{varepsilon} stimulation were also unaffected. Mitochondrial parameters such as mass, membrane potential, and reactive oxygen species production, were largely preserved, with only modest, transient increases in oxidative stress detected in CD4 T cells lacking YME1L1. Electron microscopy revealed no major changes in mitochondrial size or roundness but showed increased cristae branching and reduced tortuosity, indicating subtle alterations in ultrastructure. Additionally, {gamma}{delta} T cells in YME1L1{Delta}TB mice exhibited a mild shift toward interferon-{gamma}-producing phenotypes at the expense of interleukin-17-producing subsets. Collectively, our data indicate that YME1L1, despite its requirement for OPA1 cleavage, is dispensable for T cell development and acute activation but may contribute to fine-tune mitochondrial architecture and {gamma}{delta} T cell effector programming. These findings highlight cell-type-specific redundancies in mitochondrial quality control and underscore the value of negative data in refining the understanding of mitochondrial regulation in immune cells.

The multiple endocrine neoplasia type 1 (MEN1) gene encodes Menin, a nuclear scaffold protein and tumor suppressor that regulates transcription. It is frequently mutated in endocrine neoplasia. MEN1-gastrinomas are aggressive neuroendocrine tumors (NETs) that arise predominantly in the submucosal Brunners glands of the duodenum, an organelle rich in extracellular growth factors. Many duodenal NETs retain wild-type MEN1 allele and nuclear Menin, suggesting post-translational inactivation of its tumor-suppressor function. The Menin C-terminal domain (CTD) contains a conserved phosphorylation site at Ser487 within the first of three nuclear localization signals (NLS1-3). We hypothesized that extracellular signaling regulates Menin by phosphorylating the CTD at Ser487 blocking its nuclear localization. Using CTD deletion mapping, site-directed mutagenesis, and kinase activation in gastric cell lines, we show that loss of NLS1-3 reduces Menins nuclear localization, stability, and repression of GASTRIN. Cell stimulation by epiregulin, forskolin, or phorbol ester induced Menin Ser487 phosphorylation and its nuclear translocation, relieving repression of GASTRIN. The phospho-mimetic S487D mutant remained cytoplasmic and phenocopied CTD deletion of NLS1-3 sustaining de-repression of GASTRIN. These findings showed that Ser487 phosphorylation restricts nuclear accumulation of Menin and functionally links extracellular signaling to post-translational modification of Menin that ultimately contributes to transcriptional derepression and neuroendocrine tumorigenesis. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=127 HEIGHT=200 SRC="FIGDIR/small/717082v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1fbc016org.highwire.dtl.DTLVardef@fffdfdorg.highwire.dtl.DTLVardef@7bf0a2org.highwire.dtl.DTLVardef@f32422_HPS_FORMAT_FIGEXP M_FIG C_FIG

Though whole-genome duplication (WGD) contributes to cancer progression, the mechanism of post-WGD cell proliferation remains unclear. Here, using 6-day live-imaging, we analyzed the proliferation dynamics of more than 150 post-WGD HCT116 cell lineages. A quantitative comparison of mitotic patterns and cell fates between proliferative and non-proliferative lineages revealed that multipolar chromosome segregation in early mitosis is a key factor limiting the proliferative capacity of post-WGD progenies. Multipolar chromosome segregation suppressed post-WGD cell viability, particularly when accompanied by drastic chromosome loss or when it repeatedly occurred. Tracing proliferative lineages elucidated that they proliferated mainly by imposing the risk of multipolar chromosome segregation on one of two sub-lineages that formed after the first bipolar division. Meanwhile, a considerable proportion of proliferative lineages consisted entirely of progeny of early multipolar chromosome segregation events. Our results highlight key cellular events that determine the proliferation dynamics and diversity of post-WGD progenies, providing a fundamental reference for understanding WGD-associated bioprocesses. Summary statementLive image tracing of >150 cell lineages reveals the cross-generation dynamics of multipolar chromosome segregation that determine the fates of post-whole-genome duplication progeny cells.

The biogenesis of integral membrane proteins is complex, as revealed by an ever-growing number of cellular components shown to be dedicated to the insertion, folding, surveillance, rectification, or quality control of specific client membrane proteins. The zinc metalloprotease ZMPSTE24 and its yeast homolog Ste24 have well-established roles in the proteolytic maturation of the nuclear scaffold protein lamin A and yeast a-factor, respectively. Additionally, Ste24 has been implicated through yeast genetic screens in a variety of membrane processes, including ER- associated degradation (ERAD), Sec61 translocon "unclogging," the unfolded protein response (UPR), and potentially as a membrane protein topology determinant. Recently, an interaction was demonstrated between ZMPSTE24 and the antiviral interferon induced transmembrane protein IFITM3, although the functional significance of this interaction is not well-understood. IFITM3 is a tail-anchored protein with a cytoplasmic N-terminus, a single transmembrane span, and a lumenal/exocellular C-terminus. Here, we show that a catalytic-dead version of ZMPSTE24, ZMPSTE24E336A, exhibits enhanced binding to IFITM3, and this bound species of IFITM3 is hypo-palmitoylated. Using a split fluorescence topology reporter, we demonstrate that ZMPSTE24E336A "traps" and stabilizes a subpopulation of IFITM3 molecules with an atypical membrane topology, whose C-terminus is cytosolic instead of lumenal. Such inverted forms of IFITM3 are also detected in the presence of ERAD inhibitors when ZMPSTE24E336A is absent. We hypothesize the ZMPSTE24E336A trap mutant reveals a normally transient isoform of IFITM3 whose transmembrane span is inverted and that ZMPSTE24 is involved in the quality control of IFITM3 topology, either inverting, correcting or assisting in removal of aberrant IFITM3 molecules.

Guanylate-binding proteins (GBPs) are part of a family of large interferon gamma (IFN{psi})-inducible GTPases, with ascribed roles in infection control and induction of programmed cell death. While pathogen-specific functions of GBPs have been studied in detail, their broader regulation of frontline immune defences remain unexplored. Here, we analysed the global contribution of human GBP1-5 to cellular metabolism in IFN{psi}-stimulated macrophages. We found a robust role of GBP2 and GBP5 in macrophage glycolysis. Only GBP5, and not GBP2 deficiency impaired surface expression and cytokine production of classically IFN{psi}/LPS-activated macrophages. The GTPase activity of GBP5 was required for the regulation of glycolysis and cytokine production. We found that GBP5 deficiency impaired cellular glucose uptake and lactate production specifically. Isotopic tracing with [U-13C6]-Glucose confirmed a decrease in several glycolytic intermediates, including glucose 6-phosphate, pyruvate, and lactate, but stable levels of traced tricarboxylic acid cycle (TCA) intermediates. Elevated ribose-5-phosphate and glycerol levels suggest an altered cytosolic redox balance and enhanced breakdown of fatty acids. GBP5 localised predominantly to the cis-Golgi and in the absence of GBP5 we observed increased Golgi fragmentation, however the total Golgi size remained unchanged. Our results underscore the fundamental role of GBP5 in glycolytic fluxes and Golgi integrity in IFN{psi}-stimulated macrophages, highlighting its significance in immune function in general and immunometabolism specifically.

Intestinal epithelial cells are central players in mucosal barrier integrity and host-microbe interactions. Genetic studies have revealed that epithelial dysfunction is a key contributor to the pathogenesis of inflammatory bowel disease. Non-SMC condensin II complex subunit D3 (NCAPD3) is essential for chromatin organization and stability. NCAPD3 also promotes antimicrobial defense and autophagy responses in vitro. NCAPD3 expression is decreased in intestinal epithelial cells from patients with ulcerative colitis; however, it is not known whether loss of NCAPD3 expression drives intestinal barrier dysfunction or is a result of disease-associated inflammation. To investigate this relationship in vivo, a tissue-specific approach was required, as global constitutive knockout of NCAPD3 is embryonic lethal. Therefore, a transgenic mouse line with doxycycline-inducible expression of a short hairpin RNA targeting NCAPD3 restricted to villin-expressing cells was generated (NCAPD3KD mice) to enable the study of NCAPD3 function in the intestinal epithelium. Treatment of NCAPD3KD mice with 9-tert-butyl doxycycline resulted in [~]75% reduction of NCAPD3 protein in EpCAM intestinal cells. Short-term epithelial NCAPD3 knockdown did not induce spontaneous colitis but was associated with increased serum amyloid A and a trend towards increased intestinal permeability. Upon dextran sodium sulfate or Salmonella enterica serovar Typhimurium {Delta}AroA challenge, NCAPD3KD mice exhibited exacerbated weight loss, higher disease activity, increased histopathological damage, abnormal colonic cytokines and chemokines, and significantly increased intestinal permeability. These results indicate that NCAPD3 expression in the intestinal epithelium is required for optimal barrier maintenance and antimicrobial defense under chemical or microbial stress. These findings support prior in vitro observations and solidify NCAPD3 as a regulator of intestinal epithelial barrier function and mucosal host defense. Author SummaryNCAPD3 is a multifunctional protein with established roles in chromatin organization, genome stability, mitochondrial function, and antimicrobial defense. Dysregulated NCAPD3 is implicated in human diseases, such as inflammatory bowel disease (IBD) and microcephaly; however, due to its essential role in cellular division, determination of whether NCAPD3 loss drives these pathologies in vivo has been lacking. Using a new transgenic mouse model that selectively reduces NCAPD3 expression in intestinal epithelial cells, our study establishes NCAPD3 as an epithelial regulator of the mammalian intestine that enhances epithelial barrier resilience and antimicrobial defense during stress. Although dispensable for short-term basal homeostasis, NCAPD3 function becomes critical during epithelial injury and enteric infection. Reduced NCAPD3 expression may therefore lower the threshold for inflammatory disease by weakening barrier integrity, amplifying inflammatory cascades, and impairing antimicrobial defenses. These findings position NCAPD3 as a potential modulator of IBD susceptibility and highlight chromatin organization as an important, previously underappreciated layer of intestinal epithelial regulation.

Grainyhead-like 2 (GRHL2) is an epithelial transcription factor with context-dependent regulatory roles, yet the sequence rules governing its DNA recognition remain incompletely defined. In this study, a high-density genomic Specificity and Affinity for Protein (SNAP) DNA-binding array containing 772,732 tiled probes derived from GRHL2 ChIP-seq regions was used to resolve GRHL2 binding specificity at 6 base pair resolution across genomic sequences. From high-affinity probes, de novo motif analysis recovered the canonical 5-AACCGGTT-3 motif. Sequence specificity landscapes revealed a stepwise reduction in binding as mismatches were introduced, with the strongest effects at the C (position 3) and G (position 6) within the motif, greater tolerance at the central CG dinucleotide, and intermediate tolerance at the A/T bases at the motif edges. This analysis also demonstrated the influence of nearby flanking sequences. Extended motif and spacing analyses indicated dimeric binding at paired motifs, with periodic helical spacing consistent with interactions on the same face of the DNA helix. Integration of SNAP array binding with ChIP-seq data distinguished direct, motif-encoded GRHL2 occupancy from indirect, cofactor-mediated recruitment at genomic sites. These results define the sequence specificity of GRHL2 interactions with variations in the DNA consensus motif and flanking sequences within an endogenous genomic context. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/719077v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1a28904org.highwire.dtl.DTLVardef@1d197aforg.highwire.dtl.DTLVardef@13d9e97org.highwire.dtl.DTLVardef@76d55f_HPS_FORMAT_FIGEXP M_FIG C_FIG

Cell surface molecules play fundamental roles in cell-cell communication, attraction, or repulsion, and when expressed in neurons they are often implicated in neurological disorders. FAM171 is a family of three type-I transmembrane domain cell surface proteins (FAM171A1, FAM171A2, and FAM171B) expressed in several human tissues and especially enriched in the brain. Recent findings suggest that FAM171A1 transduces signals between the cell surface and the cytoskeleton. Genetic evidence links FAM171A1 to multiple cancers and FAM171A2 to neurodegenerative diseases, including Alzheimers and Parkinsons diseases. Despite multiple connections with severe human diseases, no information is currently available on their monomeric structure or oligomerization. Here we show that, structurally, the monomeric ectodomains of human FAM171A1 and FAM171A2 have a new architecture with a novel combination of two domains. Furthermore, their ectodomains oligomerize to form an equilateral trimer. In addition, the ectodomain of FAM171A1 has the propensity to form larger trimer-trimer assemblies at high concentrations. Together, these results provide novel insights into the structure and oligomerization of the extracellular domain of FAM171A1 and FAM171A2, suggesting important roles in ligand binding and signaling.

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and long COVID are complex chronic conditions that often follow infectious triggers with overlapping clinical features but poorly defined pathophysiological relationships. This study aimed to identify disease-specific immune signatures through multiparameter immunophenotyping of monocytes, dendritic cells, and T-cell subsets. A total of 207 participants were included (ME/CFS: n = 103; long COVID: n = 63; healthy controls: n = 41). Peripheral blood mononuclear cells were analyzed using multiparameter flow cytometry. Statistical analyses included non-parametric testing, age-adjusted ANCOVA, correlation network analysis, and principal component analysis (PCA). Long COVID was characterized by increased M2-like monocyte polarization, elevated CD80 expression across monocyte subsets, expansion of dendritic cells, and reduced expression of activation markers, indicating persistent immune activation with features of immune exhaustion. In contrast, ME/CFS exhibited reduced costimulatory molecule expression, impaired CCR7-mediated immune cell trafficking, and less coordinated activation patterns, consistent with a state of immune suppression. Correlation network analysis revealed more extensive and integrated immune interactions in long COVID, while PCA identified distinct immunophenotypic components and enabled moderate discrimination between the two conditions. These findings demonstrate that ME/CFS and long COVID are characterized by distinct immune profiles, supporting the concept of divergent immunopathological mechanisms. The identified signatures may contribute to biomarker development and guide targeted therapeutic approaches.

Accurate chromosome segregation relies on proper centromere and kinetochore formation and phospho-regulation. We previously demonstrated that a pluripotent state confers a low fidelity of chromosome segregation, however it is unknown how a pluripotent state impacts centromere and kinetochore function. Here, we demonstrate that both centromere and kinetochore structural organization and phosphorylation in mitosis are developmentally regulated. CENP-A, CENP-C, and HEC1 protein abundance is reduced at mitotic centromeres and kinetochores of human pluripotent stem cells (hPSCs) compared to isogenic somatic cells; however, elevating their levels does not improve chromosome segregation fidelity. Rather, we find that reduced phosphorylation of kinetochores is responsible for their low fidelity. HEC1 is hypophosphorylated at kinetochores of hPSCs compared to isogenic somatic cells at Cyclin B/Cdk1 and Aurora kinase phospho-sites. Inhibiting PP2A phosphatase activity or differentiation increases HEC1 phosphorylation at hPSC kinetochores decreasing chromosome segregation errors. Thus, mitotic fidelity in non-transformed human cells depends on the developmental regulation of the kinase and phosphatase networks controlling kinetochore phosphorylation. SummaryGalaviz Sarmiento et al show that the developmental regulation of kinetochore phosphorylation governs mitotic fidelity. HEC1 is hypophosphorylated at kinetochores of hPSCs during mitosis contributing to their high rate of chromosome segregation errors. While differentiation increases HEC1 phosphorylation improving chromosome segregation fidelity.

Intracellular calcium signaling plays a vital role in regulating various cellular processes including gene regulation, motility, metabolism and cell death. Inositol 1,4,5-trisphosphate receptors (IP3R) on the Endoplasmic Reticulum (ER) are a major cation channel that regulates stimulus-induced calcium release from the ER. While several molecular players regulate activity of IP3R, its regulation by actin filaments were uncharacterized. Here we show that actin filaments polymerized by a specific actin nucleator INF2 facilitates agonist-induced IP3R activity. Our results demonstrate that INF2-mediated actin filaments regulate formation and/or stability of IP3R clusters on the ER that have been previously shown to be hotspots of ER calcium release. Using cell-biological and biochemical techniques we further show that INF2 physically interacts with IP3R isoforms, often at IP3R clusters. While INF2-IP3R interaction is independent of INF2-activity, the ability of INF2 to mediate IP3R clusters is dependent on its actin polymerization activity. Finally, we demonstrate that in addition to its calcium mobilization activity, INF2 on ER specifically regulates IP3R cluster positioning to mediate ER-mitochondrial contacts and facilitate ER to mitochondrial calcium transfer. Overall, these results reveal an actin-dependent step in regulation of IP3R activity both in terms of ER calcium release and modulation of ER-mitochondrial contacts. HighlightsO_LIINF2-mediated actin filaments potentiate agonist-induced IP3R-mediated ER calcium release without affecting the ER calcium stores per se. C_LIO_LIER-localization of INF2 is dispensable for its role on IP3R activity. Moreover INF2-mediated actin filaments affect the activity of all IP3R isoforms. C_LIO_LIINF2 interacts with IP3R in an activity and actin filament independent manner through its C-terminal region. C_LIO_LIINF2 regulates IP3R cluster formation in actin-filament dependent manner and thereby regulates IP3R activity. C_LIO_LIFurther we show that ER-localized INF2 specifically regulate IP3R cluster positioning thereby promoting ER to mitochondrial contact and calcium transfer. C_LI

Deregulation of amyloid precursor protein (APP) metabolism leads to the production of pathological proteoforms of A{beta} peptides, which ultimately form amyloid deposits, a primary pathological feature of Alzheimers disease (AD). The accumulation of misfolded proteins and alterations in protein degradation systems, such as the ubiquitin-proteasome system, endoplasmic reticulum-associated degradation, and autophagy-lysosomal pathways, also contribute to AD development. The Valosin-Containing Protein AAA-ATPase (p97/VCP) is a crucial regulator of proteostasis, facilitating the clearance of misfolded proteins by the proteasome and other protein degradation systems. Here, we investigated whether VCP influences APP processing. Reducing VCP expression or inhibiting its ATPase activity led to the accumulation of mature, full-length APP in cells, thereby decreasing APP trafficking to the cell surface. Downstream of APP-CTFs secretase processing, p97/VCP modulates APP-CTFs cleavage and degradation via autophagy and endolysosomal-dependent mechanisms. Our findings demonstrate that VCP is involved in APP metabolism at two levels: controlling APP trafficking within the cell secretory pathway and regulating autophagy-dependent degradation of APP-CTFs, suggesting a potential role for VCP in the APP deregulation observed in AD.

SUN5 is a testis-specific SUN domain protein essential for connecting the sperm tail to the nucleus. However, until now, its precise localization, intracellular dynamics, and membrane topology during spermiogenesis have remained controversial. To address these discrepancies, we applied ultrastructure expansion microscopy (U-ExM) to systematically track SUN5 redistribution throughout spermiogenesis. This approach enabled a detailed reconstruction of SUN5 localization across developmental stages and revealed previously undescribed enrichment at the perinuclear ring (PNR) and the microtubule manchette, suggesting secondary functions at the PNR or a potential role in intra-manchette transport (IMT). Complementary immunogold labelling using the Tokuyasu method, together with biochemical assays, demonstrated that SUN5 adopts a membrane localization and topology consistent with that of classical SUN domain proteins. Quantitative measurements of the nuclear envelope architecture at the head-to-tail coupling apparatus (HTCA) further enabled us to present a refined structural model of SUN5 positioning at the head-tail junction. Overall, our findings resolve previous discrepancies in the field and provide a coherent framework for understanding SUN5 organization and its role in mammalian spermiogenesis. Summary StatementIn the presented study, we analyzed the dynamic redistribution of SUN5 during mammalian spermiogenesis and resolved its topology in developing spermatids to gain insights concerning the proteins molecular function in head-tail coupling.

Health research priorities are generally not aligned with global disease burden. Although genome-wide association studies (GWAS) are correcting a historical bias by including samples from different demographic groups, this does not necessarily translate to improved understanding of the most important causes of disease globally. We demonstrate that while in countries with high socioeconomic development index (SDI) there is some alignment between the traits being analysed in GWAS and those that contribute most to disease burden, there is almost no such alignment in countries with low SDI. Improvement in alignment between GWAS and disease burden has been seen for countries with middle SDI over time, likely due to the contributions to disease burden changing in those regions rather than GWAS responding to the needs of those regions. Low GWAS alignment with disease burden may be partially explained by lower GWAS attention to childhood health. Improving aetiological understanding of high burden neglected conditions should be a priority for emerging biobanks in order to reduce global health inequality. Short abstractWe identify some alignment between the traits being analysed in genome-wide association studies (GWAS) and disease burden in high socioeconomic development index (SDI) countries, while there is almost no such alignment in countries with low SDI, mostly due to neglecting childhood infection. Improvement in alignment between GWAS and disease burden has been seen for countries with middle SDI over time likely due to changing disease burden.

Meiotic prophase-I chromosomes are organized into linear arrays of chromatin loops anchored to proteinaceous axes that define the interaction interfaces for the pairing and synapsis of homologous chromosomes. Chromatin loop size and axial chromosome length are inversely correlated and vary widely both between and within species, including between the sexes. The molecular basis of this variation remains unclear. Here, we provide evidence that the small ubiquitin-like modifier, SUMO, regulates loop-axis organization in mouse meiosis. Our analysis shows that the longer axes of oocyte chromosomes contain more SUMO per unit length than the shorter axes of spermatocyte chromosomes. In mouse models, the loss of SUMO1 results in shorter axes and longer chromatin loops. Conversely, increased SUMO1 conjugation, caused by mutation of the SENP1 isopeptidase, produces longer axes with shorter loops. Axis length positively correlates with meiotic recombination. Accordingly, Sumo1 and Senp1 mutations respectively decrease and increase crossover frequency. These findings identify SUMO as a key regulator of meiotic chromosome architecture and suggest a molecular basis for the physiological variation in chromosome length and recombination rates seen among species, sexes, individuals, and individual meiocytes. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/710713v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@145c465org.highwire.dtl.DTLVardef@160c8aborg.highwire.dtl.DTLVardef@1165b76org.highwire.dtl.DTLVardef@ced5e0_HPS_FORMAT_FIGEXP M_FIG C_FIG

Specific interchromosomal interactions indicate direct and nonrandom physical associations between pairs of genome positions on two different chromosomes. These contact interactions can be direct communication between non-homologous chromosomes and can enable coordinated activities. It is useful to annotate these complex contact interaction patterns and render them to a property associated with a single genome position, both for a clean visualization of the patterns and for facilitating the comparison with linear genomic annotations and underpinning biological functions. We utilize abstract graphs to characterize interchromosomal interaction, as network analysis may succinctly summarize complex interaction structures. We built a graph representation of cross-chromosomal contact interactions derived from Hi-C data and implemented three network-based annotations which consistently indicate the interchromosomal interaction strength associated with specific genomic positions. Equipped with these metrics, we further investigate whether a chromosome relies on shared hot spots to communicate with other chromosomes. We found that half of the strong interaction positions of chromosome 19 are shared for interacting with chromosomes 17 and 22. We further found that lamina-associated domains (LADs) participate in fewer interchromosomal contacts. Overall, the network-based annotation framework reveals distinct chromosome regulation patches and provides insight into how chromosomes associate with each other and organize with respect to the nuclear envelope.

BackgroundThe transport of transfer RNAs (tRNAs) from the nucleus to the cytoplasm is a crucial step in the regulation of gene expression and protein synthesis. This process is mediated by specialized export molecules, among which XPOT (Exportin-t, XPO3) plays a central role by recognizing and transporting mature tRNAs through the nuclear pore complex. XPOT is not essential in RNA trafficking in the simple organisms, however the potential impact of XPOT deficiency in human health remains unresolved. MethodsWe identified eight patients from five unrelated families with rare biallelic germline variants in XPOT resulting in putative loss-of-function. Functional analyses were carried out in patient-derived fibroblasts, lymphoblastoid cells and zebrafish models. Ex vivo immunohistochemical stainings for Xpot were performed in the mouse cochlea. xpot knockout zebrafish models were generated to assess the morphology and hearing ability. ResultsAll patients presented with a uniform clinical phenotype that included increased susceptibility to infection, bronchiectasis, severe sensorineural hearing loss, developmental delay, and growth retardation. We demonstrated a complete absence of XPOT protein expression in three patient-derived cell lines. XPOT deficiency leads to disruptions in protein synthesis of the cytokine TNF pathway upon cellular stimulation. Additional XPO1 inhibition in XPOT deficient cells had little effect on cellular functions, suggesting alternative tRNA nuclear transporter pathways. Increased XPOT immunoreactivity was observed in type I spiral ganglion neurons and hair cells of the mouse cochlea, with enrichment in stereocilia. xpot knockout zebrafish model showed dysmorphic features, and reduced hearing, recapitulating key patient phenotypes. ConclusionsOur findings establish a direct connection between impaired XPOT-dependent tRNA export and human pathology. It illustrates that perturbations in nuclear export pathways lead to disease. It also raises the possibility that other nuclear transport receptors may play similarly underappreciated roles in human health and disease. The identification of XPOT as a disease-associated gene opens up new research directions and potential targets for therapeutic intervention.