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X10 Expansion Microscopy Enables 25 nm Resolution on Conventional Microscopes

Expansion microscopy is a recently introduced imaging technique that achieves super-resolution through physically expanding the specimen by ~4x, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately 4-fold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20-30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10x in each dimension, which corresponds to an expansion of the sample volume by more than 1000-fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25-30 nm on conventional epifluorescence microscopes. X10 provides multi-color images similar or even superior to those produced with more challenging methods, such as STED, STORM and iterative expansion microscopy (iExM), in both cell cultures and tissues.

cell biology

Clearance of senescent decidual cells by uterine natural killer cells drives endometrial remodeling during the window of implantation

In cycling human endometrium, menstruation is followed by rapid estrogen-dependent growth. Upon ovulation, progesterone and rising cellular cAMP levels activate the transcription factor Forkhead box O1 (FOXO1) in endometrial stromal cells (EnSCs), leading to cell cycle exit and differentiation into decidual cells that control embryo implantation. Here we show that FOXO1 also causes acute senescence of a subpopulation of decidualizing EnSCs in an IL-8 dependent manner. Selective depletion or enrichment of this subpopulation revealed that decidual senescence drives the transient inflammatory response associated with endometrial receptivity. Further, senescent cells prevent differentiation of endometrial mesenchymal stem cells in decidualizing cultures. As the cycle progresses, IL-15 activated uterine natural killer (uNK) cells selectively target and clear senescent decidual cells through granule exocytosis. Our findings reveal that acute decidual senescence governs endometrial rejuvenation and remodeling at embryo implantation, and suggest a critical role for uNK cells in maintaining homeostasis in cycling endometrium.

cell biology

Deubiquitylation and stabilization of p21 by USP11 is critical for cell cycle progression and DNA damage responses

p21WAF1/CIP1 is a broad-acting cyclin-dependent kinase inhibitor. Its stability is essential for proper cell cycle progression and cell fate decision. Ubiquitylation by the multiple E3 ubiquitin ligases complex is the major regulatory mechanism of p21, which induces p21 degradation. However, it is unclear whether ubiquitylated p21 can be recycled. In this study, we report USP11 as a deubiquitylase of p21. In the nucleus, USP11 binds to p21, catalyzes the removal of polyubiquitin chains conjugated onto p21 and stabilizes p21 protein. As a result, USP11 reverses p21 polyubiquitylation and degradation mediated by SCFSKP2, CRL4CDT2 and APC/CCDT20 in a cell cycle-independent manner. Loss of USP11 causes the destabilization of p21 and induces the G1/S transition in unperturbed cells. Furthermore, p21 accumulation mediated by DNA damage is completely abolished in cells depleted of USP11, which results in abrogation of the G2 checkpoint and induction of apoptosis. Functionally, USP11-mediated stabilization of p21 inhibits cell proliferation and tumorigenesis in vivo. These findings reveal an important mechanism by which p21 can be stabilized by direct deubiquitylation and pinpoint a crucial role of the USP11-p21 axis in regulating cell cycle progression and DNA damage responses.

cell biology

Cpk2, a catalytic subunit of cyclic AMP-PKA, regulates growth and pathogenesis in rice blast

The cAMP-Protein Kinase A signalling, anchored on CpkA, is necessary for appressorium development and host penetration, but indispensable for infectious growth in Magnaporthe oryzae. In this study, we identified and characterized the gene encoding the second catalytic subunit, CPK2, whose expression was found to be lower compared to CPKA at various stages of pathogenic growth in M. oryzae. Deletion of CPK2 caused no alterations in vegetative growth, conidiation, appressorium formation, or pathogenicity. Surprisingly, the cpkA{Delta}cpk2{Delta} double deletion strain displayed significant reduction in growth rate and conidiation compared to the single deletion mutants. Interestingly, loss of CPKA and CPK2 resulted in morphogenetic defects in germ tubes (with curled/wavy and serpentine growth pattern) on hydrophobic surfaces, and a complete failure to produce appressoria therein, thus suggesting an important role for CPK2-mediated cAMP-PKA in surface sensing and response pathway. CPKA promoter-driven CPK2 expression partially suppressed the defects in host penetration and pathogenicity in the cpkA{Delta}. Such ectopic CPK2 expressing strain successfully penetrated the rice leaves, but was unable to produce proper secondary invasive hyphae, thus underscoring the importance of CpkA in growth and differentiation in planta. The Cpk2-GFP localized to the nucleus and cytoplasmic vesicles in conidia and the germ tubes. The Cpk2-GFP colocalized with CpkA-mCherry on vesicles in the cytosol, but such overlap was not evident in the nucleus. Our studies indicate that CpkA and Cpk2 share overlapping functions, but also play distinct roles during pathogenesis-associated signalling and morphogenesis in the rice blast fungus.

cell biology

BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes

Bloom syndrome is a cancer predisposition disorder caused by mutations in the BLM helicase gene. Cells from persons with Bloom syndrome exhibit striking genomic instability characterized by excessive sister chromatid exchange events (SCEs). We applied single-cell DNA template strand-sequencing (Strand-seq) to map the genomic locations of SCEs at a resolution that is orders of magnitude better than was previously possible. Our results show that, in the absence of BLM, sister chromatid exchanges in human and murine cells do not occur randomly throughout the genome but are strikingly enriched at coding regions, specifically at sites of putative guanine quadruplex (G4) motifs in transcribed genes. We propose that BLM protects against genome instability by suppressing recombination at sites of G4 structures, particularly in transcribed regions of the genome.

cell biology

Rapid degradation and 3D CLEM of condensin reveal chromatin compaction uncoupled from chromosome architecture in mitosis

The requirement for condensin in chromosome formation in somatic cells remains unclear as imperfectly condensed chromosomes do form in conventional condensindepleted cells. Here we have dissected the role of condensin at different stages of vertebrate mitosis by combining auxin-mediated rapid depletion of condensin subunit SMC2 with chemical genetics to obtain near-synchronous mitotic entry of chicken DT40 cells. We analysed the outcomes by live and fixed-cell microscopy methods, including 3D correlative light and serial block face scanning electron microscopy. Following rapid depletion of condensin, chromosomal defects were obvious. The chromatin was compacted normally, but formed a single mass of mitotic chromosomes clustered at one side of a bent mitotic spindle. Cultures arrest at prometaphase, eventually exiting mitosis without segregating chromosomes. Experiments titrating the auxin concentration suggest a previously unsuspected dual role of condensin, as different condensin levels are required for anaphase chromosome segregation and formation of a normal chromosome architecture.

cell biology

Systematic analysis of atx-2 suppressors reveals a novel regulator of PAR-5/14-3-3sigma function during mitosis in Caenorhabditis elegans

RNA regulation plays a critical role in mitosis, yet the mechanisms remain unclear. Our lab recently identified that the conserved RNA-Binding Protein (RBP), ATX-2, regulates cytokinesis by regulating the targeting of ZEN-4 to the spindle midzone through a conserved translation regulator, PAR-5/14-3-3sigma (Gnazzo et al., 2016). While co-depletion of ATX-2 and PAR-5 restored ZEN-4 targeting to the spindle midzone, it did not rescue cell division. To identify factors that may work in concert with ATX-2 to regulate cell division, we conducted a two-part, candidate RNAi suppressor and visual screen to identify factors that are important for cell division and also mediate the targeting of ATX-2 to the centrosomes and the spindle midzone. Using this approach, we identified ten genes that suppress the embryonic lethality defect observed in atx-2 mutant embryos. These ten genes, including act-2, cgh-1, cki-1, hum-6, par-2, rnp-4, vab-3, vhl-1, vps-24, and wve-1, all have some role regulating RNA or the cell cycle. Five of these genes (cgh-1, cki-1, vab-3, vhl-1, vps-24) fail to target ATX-2 to the centrosomes and midzone when depleted. The strongest suppressor of the atx-2 phenotype is the DEAD-box RNA helicase CGH-1/DDX6, which has been implicated in cell division, RNA processing and translation, and neuronal function. Loss of CGH-1 rescued the cytokinesis defect and also restored ZEN-4 localization to the spindle midzone. ATX-2 and CGH-1 are mutually required for their localization to centrosomes and the spindle midzone. Our findings provide the first functional evidence that CGH-1/DDX6 regulates ATX-2 function during mitosis to target ZEN-4 to the spindle midzone via PAR-5/14-3-3sigma. We suggest that RNA machinery is necessary for the completion of cytokinesis.

cell biology

FLIM-based pH measurements reveal incretin-induced rejuvenation of aged insulin secretory granules.

Insulin is stored in dense-core secretory granules (SGs) and is released from beta cells in two distinct phases upon glucose stimulation. Newly synthesized insulin SGs are secreted preferentially, but the underlying mechanism of this phenomenon remains elusive. The relationship of SG age with their intraluminal pH is of particular interest: proinsulin conversion by prohormone convertases follows the acidification of immature SGs by the vacuolar proton-translocating ATPase (v-ATPase). v-ATPases may also participate in the formation of the fusion pore for SG exocytosis, with intraluminal alkalinization inhibiting membrane fusion. Previous studies examined the luminal pH of SGs on a population level only. Here we measured the pH-dependent lifetime changes of eCFP fused to the ICA512-RESP18 homology domain to assess for the first time the luminal pH of individual age-defined SGs in insulinoma INS-1 cells by fluorescence-lifetime imaging microscopy. We show that 2-4-hour-old young SGs have a pH of ~5.5, while 26-28-hour-old SGs have a pH of ~6.2. Remarkably, the GLP-1 receptor agonist Exendin-4 prompted the re-acidification of old SGs in a glutamate-dependent fashion, while it did not affect the pH of young SGs. This study demonstrates that insulin SGs change their pH over time - a change that is reversible by insulin secretagogues. Hence, it provides novel insight into the mechanisms accounting for aging and exocytosis of SGs and suggests that their rejuvenation may be exploited to enhance insulin secretion in diabetes.

cell biology

Committed hemopoietic progenitors, not stem cells, are the principal responders to Hox gene transduction

As hemopoietic stem cells differentiate, their proliferative lifespan shortens by unknown mechanisms. Homeobox cluster (Hox) genes have been implicated by their enhancement of self-renewal when transduced into hemopoietic cells, but gene deletions have been inconclusive because of functional redundancy. Here we enforced HOXB4 expression in purified precursor stages, and compared responses of early stages expressing the endogenous genes with later stages that did not. Contrary to the prevalent view that transduced Hox genes enhance the self-renewal of hemopoietic stem cells, stem cells or their multipotent progeny expressing the endogenous genes showed little response. Instead, immortalization, extensive self-renewal and acquired reconstituting potential occurred in committed erythroid and myeloid progenitors where the endogenous genes were shutting down. The results change our understanding of the stages affected by exogenous HOX proteins and point to shutdown of the endogenous genes as a principal determinant of the shortened clonal lifespans of committed progenitor cells.

cell biology

C. elegans HIF-1 is broadly required for survival in hydrogen sulfide

Hydrogen sulfide is common in the environment, and is also endogenously produced by animal cells. Although hydrogen sulfide is often toxic, exposure to low levels of hydrogen sulfide improves outcome in a variety of mammalian models of ischemia-reperfusion injury. In Caenorhabditis elegans, the initial transcriptional response to hydrogen sulfide depends on the hif-1 transcription factor, and hif-1 mutant animals die when exposed to hydrogen sulfide. In this study, we use rescue experiments to identify tissues in which hif-1 is required to survive exposure to hydrogen sulfide. We find that expression of hif-1 from the unc-14 promoter is sufficient to survive hydrogen sulfide. Although unc-14 is generally considered to be a pan-neuronal promoter, we show that it is active in many non-neuronal cells as well. Using other promoters, we show that pan-neuronal expression of hif-1 is not sufficient to survive exposure to hydrogen sulfide. Our data suggest that hif-1 is required in many different tissues to direct the essential response to hydrogen sulfide.

cell biology

Accelerated human liver progenitor generation from pluripotent stem cells by inhibiting formation of unwanted lineages

Despite decisive progress in differentiating pluripotent stem cells (PSCs) into diverse cell-types, the often-lengthy differentiation and functional immaturity of such cell-types remain pertinent issues. Here we address the first challenge of prolonged differentiation in the generation of hepatocyte-like cells from PSCs. We delineate a roadmap describing the extracellular signals controlling six sequential branching lineage choices leading from pluripotency to endoderm, foregut, and finally, liver progenitors. By blocking formation of unwanted cell-types at each lineage juncture and manipulating temporally-dynamic signals, we accelerated generation of 89.0{+/-}3.1% AFP+ human liver bud progenitors and 87.3{+/-}9.4% ALBUMIN+ hepatocyte-like cells by days 6 and 18 of PSC differentiation, respectively. 81.5{+/-}3.2% of hepatocyte-like cells expressed metabolic enzyme FAH (as assayed by a new knock-in reporter line) and improved short-term survival in the Fah-/-Rag2-/-Il2rg-/- mouse model of liver failure. Collectively the timed signaling interventions indicated by this developmental roadmap enable accelerated production of human liver progenitors from PSCs.

cell biology

Intraocular pressure elevation precedes a phagocytosis decline in a model of pigmentary glaucoma

PurposeOutflow regulation and phagocytosis are key functions of the trabecular meshwork (TM), but it is not clear how the two are related in secondary open angle glaucomas characterized by an increased particle load. We hypothesized that diminished TM phagocytosis is not the primary cause of early ocular hypertension and recreated pigment dispersion in a porcine ex vivo model.\n\nMaterials and MethodsSixteen porcine anterior chamber cultures received a continuous infusion of pigment granules (P), while 16 additional anterior chambers served as controls (C). Pressure transducers recorded the intraocular pressure (IOP). The phagocytic capacity of the trabecular meshwork was determined by fluorescent microspheres.\n\nResultsThe baseline IOPs in P and C were similar (P=0.82). A significant IOP elevation occurred in P at 48, 120, and 180 hours (all P<0.01, compared to baseline). The pigment did not cause a reduction in TM phagocytosis at 48 hours, when the earliest IOP elevation occurred, but at 120 hours onward (P=0.001 compared to C). This reduction did not result in an additional IOP increase at 120 or 180 hours compared to the first IOP elevation at 48 hours (P>0.05).\n\nConclusionIn this porcine model of pigmentary glaucoma, an IOP elevation occurs much earlier than when phagocytosis fails, suggesting that two separate mechanisms might be at work.

cell biology

Disruption of the interfacial membrane leads to Magnaporthe oryzae effector re-location and lifestyle switch during rice blast disease

The hemibiotrophic fungus Magnaporthe oryzae produces invasive hyphae enclosed in a plant-derived interfacial membrane, known as the extra-invasive hyphal membrane (EIHM), in living rice cells. Little is known about when the EIHM is disrupted and how the disruption contributes to blast disease. Here we show that EIHM disruption correlates with the hyphal growth stage in first-invaded susceptible rice cells. Our approach utilized GFP secreted from invasive hyphae as an EIHM integrity reporter. Secreted-GFP accumulated in the EIHM compartment but appeared in the rice cytoplasm when the EIHM integrity was compromised. Live-cell imaging of secreted-GFP and various fluorescent reporters revealed that EIHM disruption led to rice vacuole rupture and cell death limited to the invaded cell with closed plasmodesmata. We report that EIHM disruption and host cell death are landmarks delineating three distinct infection phases (early biotrophic, late biotrophic, and transient necrotrophic phases) within the first-invaded cell before reestablishment of biotrophy in second-invaded cells. M. oryzae effectors exhibited phase-specific localizations, including entry of the apoplastic effector Bas4 into the rice cytoplasm during the late biotrophic phase. Understanding how the phase-specific dynamics are regulated and linked to host susceptibility will offer potential targets that can be exploited to control blast disease.

cell biology

Delayed activation of the DNA replication licensing system in Lgr5(+) intestinal stem cells

During late mitosis and early G1, replication origins are licensed for replication by binding to double hexamers of MCM2-7. Here, we investigate how licensing and proliferative commitment are coupled in the small-intestinal epithelium. We developed a method for identifying cells in intact tissue containing DNA-bound MCM2-7. Interphase cells above the transit-amplifying compartment had no DNA-bound MCM2-7, but still expressed MCM2-7 protein, suggesting that licensing is inhibited immediately upon differentiation. Strikingly, we found most proliferative Lgr5(+) stem cells are in an unlicensed state. This suggests that the elongated cell-cycle of intestinal stem-cells is caused by an increased G1 length, characterised by dormant periods with unlicensed origins. Significantly, the unlicensed state is lost In Apc mutant epithelium, which lacks a functional restriction point, causing licensing immediately upon G1 entry. We propose that the unlicensed G1 of intestinal stem cells creates a temporal window when proliferative fate decisions can be made.

cell biology

Whole-tissue stretching reveals a shape-dependent mechanism of orienting the mitotic spindle and a role for mechanical stress in cueing mitosis

Distinct mechanisms involving cell shape and mechanical force are known to influence the rate and orientation of division in cultured cells. However, uncoupling the impact of shape and force in tissues remains challenging. Combining stretching of Xenopus laevis tissue with a novel method of inferring relative mechanical stress, we find separate roles for cell shape in orientating division and mechanical stress in cueing division. We demonstrate that division orientation is best predicted by an axis of cell shape defined by the position of tricellular junctions (TCJs), which aligns exactly with the principal axis of local cell stress rather than the tissue-level stress. The alignment of division to cell shape requires functional cadherin and the localisation of the spindle orientation protein, LGN, to TCJs, but is not sensitive to relative cell stress magnitude. In contrast, cell proliferation rate is more directly regulated by mechanical stress, being correlated with relative isotropic stress, and can be decoupled from cell shape when myosin II is depleted.

cell biology

Transgene-free hematopoietic stem and progenitor cells from human induced pluripotent stem cells

Introductory paragraphThe successful production of Hematopoietic Stem and Progenitor Cells (HSPCs) from human pluripotent sources is conditioned by transgene delivery1-5. We describe here a dedicated and tractable one step, GMP-grade, transgene-free and stroma-free protocol to produce HSPCs from human induced pluripotent stem cells (hiPSCs). This procedure, applied to several sources of hiPSCs with equal efficiency, is based on a directed differentiation with morphogens and cytokines to generate a cell population close to nascent HSPCs or their immediate forerunners i.e., hemogenic endothelial cells6-9. Following engraftment into immunocompromised recipients, this cell population was proved capable of a robust myeloid, lymphoid and definitive red blood cell production in sequential recipients for at least 40 weeks. Further identification of the repopulating cells show that they express the G protein-coupled receptor APELIN (APLNR) and the homing receptor CXCR4. This demonstrates that the generation of bona fide HSPCs from hiPSCs without transgenes is possible and passes through an early endo-hematopoietic intermediate. This work opens the way to the generation of clinical grade HSPCs for the treatment of hematological diseases and holds promise for the analysis of HSPC development in the human species.

cell biology

Microtubule dynamics regulates mitochondrial fission

Mitochondria are organized as tubular networks in the cell and undergo fission and fusion. While several of the molecular players involved in mediating mitochondrial dynamics have been identified, the precise cellular cues that initiate fission or fusion remain largely unknown. In fission yeast, mitochondria are organized along microtubule bundles. Here, we employed deletions of kinesin-like proteins to perturb microtubule dynamics, and determined that cells with long microtubules exhibited long, but fewer mitochondria, whereas cells with short microtubules exhibited short, but several mitochondria due to reduced mitochondrial fission in the former and elevated fission in the latter. Correspondingly, upon onset of closed mitosis in fission yeast, wherein interphase microtubules assemble to form the spindle within the nucleus, we measured increased mitochondrial fission. We determined that the consequent rise in the mitochondrial copy number was necessary to reduce partitioning errors while stochastically partitioning mitochondria between daughter cells. We discovered that the association of mitochondria with microtubules physically impeded the assembly of the fission protein Dnm1 around mitochondria, resulting in inhibition of mitochondrial fission. Taken together, we demonstrate a novel mechanism for regulation of mitochondrial fission that is dictated by the interaction between mitochondria and the microtubule cytoskeleton.

cell biology

Cryo-ET reveals nucleosome reorganization in condensed mitotic chromosomes in vivo

Chromosomes condense during mitosis in most eukaryotes. This transformation involves rearrangements at the nucleosome level and has consequences for transcription, but the details remain unclear. Here, we use cryo-electron tomography to determine the 3-D arrangement of nucleosomes and other large nuclear features in frozen-hydrated fission-yeast cells. Nucleosomes can form irregular clusters in both interphase and mitotic cells, but they are smaller than expected for Hi-C domains. The nucleosomes are co-mingled with two features: nucleosome-free pockets and megadalton-sized \"megacomplexes\". Compared to interphase, the nucleosomes in mitotic chromosomes pack into slightly larger clusters. However, nearest-neighbor distance analysis reveals that mitotic nucleosome clusters have the same internal packing density as in interphase. Furthermore, mitotic chromosomes contain fewer megacomplexes. This uneven chromosome condensation helps explain a longstanding enigma of mitosis: most genes are repressed but a subset is upregulated.

cell biology