Clueless/CLUH regulates mitochondrial fission by promoting recruitment of Drp1 to mitochondria

Nature communications

2022 Mar 24

Yang, H;Sibilla, C;Liu, R;Yun, J;Hay, BA;Blackstone, C;Chan, DC;Harvey, RJ;Guo, M;
PMID: 35332133 | DOI: 10.1038/s41467-022-29071-4

Mitochondrial fission is critically important for controlling mitochondrial morphology, function, quality and transport. Drp1 is the master regulator driving mitochondrial fission, but exactly how Drp1 is regulated remains unclear. Here, we identified Drosophila Clueless and its mammalian orthologue CLUH as key regulators of Drp1. As with loss of drp1, depletion of clueless or CLUH results in mitochondrial elongation, while as with drp1 overexpression, clueless or CLUH overexpression leads to mitochondrial fragmentation. Importantly, drp1 overexpression rescues adult lethality, tissue disintegration and mitochondrial defects of clueless null mutants in Drosophila. Mechanistically, Clueless and CLUH promote recruitment of Drp1 to mitochondria from the cytosol. This involves CLUH binding to mRNAs encoding Drp1 receptors MiD49 and Mff, and regulation of their translation. Our findings identify a crucial role of Clueless and CLUH in controlling mitochondrial fission through regulation of Drp1.

A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes

Nature communications

2022 Feb 24

Dos Santos, M;Backer, S;Auradé, F;Wong, MM;Wurmser, M;Pierre, R;Langa, F;Do Cruzeiro, M;Schmitt, A;Concordet, JP;Sotiropoulos, A;Jeffrey Dilworth, F;Noordermeer, D;Relaix, F;Sakakibara, I;Maire, P;
PMID: 35210422 | DOI: 10.1038/s41467-022-28666-1

The contractile properties of adult myofibers are shaped by their Myosin heavy chain isoform content. Here, we identify by snATAC-seq a 42 kb super-enhancer at the locus regrouping the fast Myosin genes. By 4C-seq we show that active fast Myosin promoters interact with this super-enhancer by DNA looping, leading to the activation of a single promoter per nucleus. A rainbow mouse transgenic model of the locus including the super-enhancer recapitulates the endogenous spatio-temporal expression of adult fast Myosin genes. In situ deletion of the super-enhancer by CRISPR/Cas9 editing demonstrates its major role in the control of associated fast Myosin genes, and deletion of two fast Myosin genes at the locus reveals an active competition of the promoters for the shared super-enhancer. Last, by disrupting the organization of fast Myosin, we uncover positional heterogeneity within limb skeletal muscles that may underlie selective muscle susceptibility to damage in certain myopathies.

Cell adhesion molecule KIRREL1 is a feedback regulator of Hippo signaling recruiting SAV1 to cell-cell contact sites

Nature communications

2022 Feb 17

Paul, A;Annunziato, S;Lu, B;Sun, T;Evrova, O;Planas-Paz, L;Orsini, V;Terracciano, LM;Charlat, O;Loureiro, ZY;Ji, L;Zamponi, R;Sigoillot, F;Lei, H;Lindeman, A;Russ, C;Reece-Hoyes, JS;Nicholson, TB;Tchorz, JS;Cong, F;
PMID: 35177623 | DOI: 10.1038/s41467-022-28567-3

The Hippo/YAP pathway controls cell proliferation through sensing physical and spatial organization of cells. How cell-cell contact is sensed by Hippo signaling is poorly understood. Here, we identified the cell adhesion molecule KIRREL1 as an upstream positive regulator of the mammalian Hippo pathway. KIRREL1 physically interacts with SAV1 and recruits SAV1 to cell-cell contact sites. Consistent with the hypothesis that KIRREL1-mediated cell adhesion suppresses YAP activity, knockout of KIRREL1 increases YAP activity in neighboring cells. Analyzing pan-cancer CRISPR proliferation screen data reveals KIRREL1 as the top plasma membrane protein showing strong correlation with known Hippo regulators, highlighting a critical role of KIRREL1 in regulating Hippo signaling and cell proliferation. During liver regeneration in mice, KIRREL1 is upregulated, and its genetic ablation enhances hepatic YAP activity, hepatocyte reprogramming and biliary epithelial cell proliferation. Our data suggest that KIRREL1 functions as a feedback regulator of the mammalian Hippo pathway through sensing cell-cell interaction and recruiting SAV1 to cell-cell contact sites.

Generation of the organotypic kidney structure by integrating pluripotent stem cell-derived renal stroma

Nature communications

2022 Feb 01

Tanigawa, S;Tanaka, E;Miike, K;Ohmori, T;Inoue, D;Cai, CL;Taguchi, A;Kobayashi, A;Nishinakamura, R;
PMID: 35105870 | DOI: 10.1038/s41467-022-28226-7

Organs consist of the parenchyma and stroma, the latter of which coordinates the generation of organotypic structures. Despite recent advances in organoid technology, induction of organ-specific stroma and recapitulation of complex organ configurations from pluripotent stem cells (PSCs) have remained challenging. By elucidating the in vivo molecular features of the renal stromal lineage at a single-cell resolution level, we herein establish an in vitro induction protocol for stromal progenitors (SPs) from mouse PSCs. When the induced SPs are assembled with two differentially induced parenchymal progenitors (nephron progenitors and ureteric buds), the completely PSC-derived organoids reproduce the complex kidney structure, with multiple types of stromal cells distributed along differentiating nephrons and branching ureteric buds. Thus, integration of PSC-derived lineage-specific stroma into parenchymal organoids will pave the way toward recapitulation of the organotypic architecture and functions.

The EDA deficient mouse has Zymbal's gland hypoplasia and acute otitis externa

Disease models & mechanisms

2022 Feb 02

Del-Pozo, J;Headon, DJ;Glover, JD;Azar, A;Schuepbach-Mallepell, S;Bhutta, MF;Riddell, J;Maxwell, S;Milne, E;Schneider, P;Cheeseman, M;
PMID: 35107126 | DOI: 10.1242/dmm.049034

In mice, rats, dogs and humans the growth and function of sebaceous glands and eyelid Meibomian glands depend on the ectodysplasin signalling pathway. Mutation of genes encoding the ligand EDA, its transmembrane receptor EDAR, and the intracellular signal transducer EDARADD leads to Hypohidrotic Ectodermal Dysplasia characterised by impaired development of teeth and hair as well as cutaneous glands. The rodent ear canal has a large auditory sebaceous gland, the Zymbal's gland, whose function in the health of the ear canal and tympanic membrane has not been determined. We report that the EDA deficient Tabby (EdaTa) mouse, the EDAR deficient mouse (EdarOVE1B/OVE1B) and the EDARADD deficient sparse and wavy hair rat (Edaraddswh/swh) have Zymbal's gland hypoplasia. EdaTa mice also have ear canal hypotrichosis and a 25% prevalence of otitis externa at P21. Treatment with agonist anti-EDAR antibodies rescues Zymbal's glands and ear canal pilosebaceous units. The aetiopathogenesis of otitis externa involves infection with Gram-positive cocci and dosing pregnant and lactating EdaTa females and pups with Enrofloxacin reduces the prevalence of otitis externa. We infer the deficit of sebum is the principal factor in predisposition to bacterial infection and the EdaTa mouse is a potentially useful microbial challenge model for human acute otitis externa, commonly known as swimmer's ear.

Co-emergence of cardiac and gut tissues promotes cardiomyocyte maturation within human iPSC-derived organoids

Cell stem cell

2021 Dec 02

Silva, AC;Matthys, OB;Joy, DA;Kauss, MA;Natarajan, V;Lai, MH;Turaga, D;Blair, AP;Alexanian, M;Bruneau, BG;McDevitt, TC;
PMID: 34861147 | DOI: 10.1016/j.stem.2021.11.007

During embryogenesis, paracrine signaling between tissues in close proximity contributes to the determination of their respective cell fate(s) and development into functional organs. Organoids are in vitro models that mimic organ formation and cellular heterogeneity, but lack the paracrine input of surrounding tissues. Here, we describe a human multilineage iPSC-derived organoid that recapitulates cooperative cardiac and gut development and maturation, with extensive cellular and structural complexity in both tissues. We demonstrate that the presence of endoderm tissue (gut/intestine) in the organoids contributed to the development of cardiac tissue features characteristic of stages after heart tube formation, including cardiomyocyte expansion, compartmentalization, enrichment of atrial/nodal cells, myocardial compaction, and fetal-like functional maturation. Overall, this study demonstrates the ability to generate and mature cooperative tissues originating from different germ lineages within a single organoid model, an advance that will further the examination of multi-tissue interactions during development, physiological maturation, and disease.

Coordinated repression of pro-differentiation genes via P-bodies and transcription maintains Drosophila intestinal stem cell identity

Current biology : CB

2021 Dec 01

Buddika, K;Huang, YT;Ariyapala, IS;Butrum-Griffith, A;Norrell, SA;O'Connor, AM;Patel, VK;Rector, SA;Slovan, M;Sokolowski, M;Kato, Y;Nakamura, A;Sokol, NS;
PMID: 34875230 | DOI: 10.1016/j.cub.2021.11.032

The role of processing bodies (P-bodies), key sites of post-transcriptional control, in adult stem cells remains poorly understood. Here, we report that adult Drosophila intestinal stem cells, but not surrounding differentiated cells such as absorptive enterocytes (ECs), harbor P-bodies that contain Drosophila orthologs of mammalian P-body components DDX6, EDC3, EDC4, and LSM14A/B. A targeted RNAi screen in intestinal progenitor cells identified 39 previously known and 64 novel P-body regulators, including Patr-1, a gene necessary for P-body assembly. Loss of Patr-1-dependent P-bodies leads to a loss of stem cells that is associated with inappropriate expression of EC-fate gene nubbin. Transcriptomic analysis of progenitor cells identifies a cadre of such weakly transcribed pro-differentiation transcripts that are elevated after P-body loss. Altogether, this study identifies a P-body-dependent repression activity that coordinates with known transcriptional repression programs to maintain a population of in vivo stem cells in a state primed for differentiation.

Metabolic nuclear receptors coordinate energy metabolism to regulate Sox9+ hepatocyte fate

iScience

2021 Sep 01

Liu, S;Qin, D;Yan, Y;Wu, J;Meng, L;Huang, W;Wang, L;Chen, X;Zhang, L;
| DOI: 10.1016/j.isci.2021.103003

Recent research has indicated the adult liver Sox9+ cells located in the portal triads contribute to the physiological maintenance of liver mass and injury repair. However, the physiology and pathology regulation mechanisms of adult liver Sox9+ cells remain unknown. Here, PPARα and FXR bound to the shared site in Sox9 promoter with opposite transcriptional outputs. PPARα activation enhanced the fatty acid β-oxidation, oxidative phosphorylation (OXPHOS), and adenosine triphosphate (ATP) production, thus promoting proliferation and differentiation of Sox9+ hepatocytes along periportal (PP)-perivenous (PV) axis. However, FXR activation increased glycolysis but decreased OXPHOS and ATP production, therefore preventing proliferation of Sox9+ hepatocytes along PP-PV axis by promoting Sox9+ hepatocyte self-renewal. Our research indicates that metabolic nuclear receptors play critical roles in liver progenitor Sox9+ hepatocyte homeostasis to initiate or terminate liver injury-induced cell proliferation and differentiation, suggesting that PPARα and FXR are potential therapeutic targets for modulating liver regeneration.

The retinal ipRGC-preoptic circuit mediates the acute effect of light on sleep

Nature communications

2021 Aug 25

Zhang, Z;Beier, C;Weil, T;Hattar, S;
PMID: 34433830 | DOI: 10.1038/s41467-021-25378-w

Light regulates daily sleep rhythms by a neural circuit that connects intrinsically photosensitive retinal ganglion cells (ipRGCs) to the circadian pacemaker, the suprachiasmatic nucleus. Light, however, also acutely affects sleep in a circadian-independent manner. The neural circuits involving the acute effect of light on sleep remain unknown. Here we uncovered a neural circuit that drives this acute light response, independent of the suprachiasmatic nucleus, but still through ipRGCs. We show that ipRGCs substantially innervate the preoptic area (POA) to mediate the acute light effect on sleep in mice. Consistently, activation of either the POA projecting ipRGCs or the light-responsive POA neurons increased non-rapid eye movement (NREM) sleep without influencing REM sleep. In addition, inhibition of the light-responsive POA neurons blocked the acute light effects on NREM sleep. The predominant light-responsive POA neurons that receive ipRGC input belong to the corticotropin-releasing hormone subpopulation. Remarkably, the light-responsive POA neurons are inhibitory and project to well-known wakefulness-promoting brain regions, such as the tuberomammillary nucleus and the lateral hypothalamus. Therefore, activation of the ipRGC-POA circuit inhibits arousal brain regions to drive light-induced NREM sleep. Our findings reveal a functional retina-brain circuit that is both necessary and sufficient for the acute effect of light on sleep.

Mechanical load regulates bone growth via periosteal Osteocrin

Cell reports

2021 Jul 13

Watanabe-Takano, H;Ochi, H;Chiba, A;Matsuo, A;Kanai, Y;Fukuhara, S;Ito, N;Sako, K;Miyazaki, T;Tainaka, K;Harada, I;Sato, S;Sawada, Y;Minamino, N;Takeda, S;Ueda, HR;Yasoda, A;Mochizuki, N;
PMID: 34260913 | DOI: 10.1016/j.celrep.2021.109380

Mechanical stimuli including loading after birth promote bone growth. However, little is known about how mechanical force triggers biochemical signals to regulate bone growth. Here, we identified a periosteal-osteoblast-derived secretory peptide, Osteocrin (OSTN), as a mechanotransducer involved in load-induced long bone growth. OSTN produced by periosteal osteoblasts regulates growth plate growth by enhancing C-type natriuretic peptide (CNP)-dependent proliferation and maturation of chondrocytes, leading to elongation of long bones. Additionally, OSTN cooperates with CNP to regulate bone formation. CNP stimulates osteogenic differentiation of periosteal osteoprogenitors to induce bone formation. OSTN binds to natriuretic peptide receptor 3 (NPR3) in periosteal osteoprogenitors, thereby preventing NPR3-mediated clearance of CNP and consequently facilitating CNP-signal-mediated bone growth. Importantly, physiological loading induces Ostn expression in periosteal osteoblasts by suppressing Forkhead box protein O1 (FoxO1) transcription factor. Thus, this study reveals a crucial role of OSTN as a mechanotransducer converting mechanical loading to CNP-dependent bone formation.

Coordination of endothelial cell positioning and fate specification by the epicardium

Nature communications

2021 Jul 06

Quijada, P;Trembley, MA;Misra, A;Myers, JA;Baker, CD;Pérez-Hernández, M;Myers, JR;Dirkx, RA;Cohen, ED;Delmar, M;Ashton, JM;Small, EM;
PMID: 34230480 | DOI: 10.1038/s41467-021-24414-z

The organization of an integrated coronary vasculature requires the specification of immature endothelial cells (ECs) into arterial and venous fates based on their localization within the heart. It remains unclear how spatial information controls EC identity and behavior. Here we use single-cell RNA sequencing at key developmental timepoints to interrogate cellular contributions to coronary vessel patterning and maturation. We perform transcriptional profiling to define a heterogenous population of epicardium-derived cells (EPDCs) that express unique chemokine signatures. We identify a population of Slit2+ EPDCs that emerge following epithelial-to-mesenchymal transition (EMT), which we term vascular guidepost cells. We show that the expression of guidepost-derived chemokines such as Slit2 are induced in epicardial cells undergoing EMT, while mesothelium-derived chemokines are silenced. We demonstrate that epicardium-specific deletion of myocardin-related transcription factors in mouse embryos disrupts the expression of key guidance cues and alters EPDC-EC signaling, leading to the persistence of an immature angiogenic EC identity and inappropriate accumulation of ECs on the epicardial surface. Our study suggests that EC pathfinding and fate specification is controlled by a common mechanism and guided by paracrine signaling from EPDCs linking epicardial EMT to EC localization and fate specification in the developing heart.

Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell

Cell reports

2021 Jun 23

Puray-Chavez, M;LaPak, KM;Schrank, TP;Elliott, JL;Bhatt, DP;Agajanian, MJ;Jasuja, R;Lawson, DQ;Davis, K;Rothlauf, PW;Liu, Z;Jo, H;Lee, N;Tenneti, K;Eschbach, JE;Shema Mugisha, C;Cousins, EM;Cloer, EW;Vuong, HR;VanBlargan, LA;Bailey, AL;Gilchuk, P;Crowe, JE;Diamond, MS;Hayes, DN;Whelan, SPJ;Horani, A;Brody, SL;Goldfarb, D;Major, MB;Kutluay, SB;
PMID: 34214467 | DOI: 10.1016/j.celrep.2021.109364

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) variants govern transmissibility, responsiveness to vaccination, and disease severity. In a screen for new models of SARS-CoV-2 infection, we identify human H522 lung adenocarcinoma cells as naturally permissive to SARS-CoV-2 infection despite complete absence of angiotensin-converting enzyme 2 (ACE2) expression. Remarkably, H522 infection requires the E484D S variant; viruses expressing wild-type S are not infectious. Anti-S monoclonal antibodies differentially neutralize SARS-CoV-2 E484D S in H522 cells as compared to ACE2-expressing cells. Sera from vaccinated individuals block this alternative entry mechanism, whereas convalescent sera are less effective. Although the H522 receptor remains unknown, depletion of surface heparan sulfates block H522 infection. Temporally resolved transcriptomic and proteomic profiling reveal alterations in cell cycle and the antiviral host cell response, including MDA5-dependent activation of type I interferon signaling. These findings establish an alternative SARS-CoV-2 host cell receptor for the E484D SARS-CoV-2 variant, which may impact tropism of SARS-CoV-2 and consequently human disease pathogenesis.

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	Description
sense Example: Hs-LAG3-sense	Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe.
Intron# Example: Mm-Htt-intron2	Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection
Pool/Pan Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G)	A mixture of multiple probe sets targeting multiple genes or transcripts
No-XSp Example: Hs-PDGFB-No-XMm	Does not cross detect with the species (Sp)
XSp Example: Rn-Pde9a-XMm	designed to cross detect with the species (Sp)
O# Example: Mm-Islr-O1	Alternative design targeting different regions of the same transcript or isoforms
CDS Example: Hs-SLC31A-CDS	Probe targets the protein-coding sequence only
EnEm	Probe targets exons n and m
En-Em	Probe targets region from exon n to exon m
Retired Nomenclature
tvn Example: Hs-LEPR-tv1	Designed to target transcript variant n
ORF Example: Hs-ACVRL1-ORF	Probe targets open reading frame
UTR Example: Hs-HTT-UTR-C3	Probe targets the untranslated region (non-protein-coding region) only
5UTR Example: Hs-GNRHR-5UTR	Probe targets the 5' untranslated region only
3UTR Example: Rn-Npy1r-3UTR	Probe targets the 3' untranslated region only
Pan Example: Pool	A mixture of multiple probe sets targeting multiple genes or transcripts

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