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Maldonado H, Savage BD, Barker HR, May U, Vähätupa M, Badiani RK, Wolanska KI, Turner CMJ, Pemmari T, Ketomäki T, Prince S, Humphries MJ, Ruoslahti E, Morgan MR, Järvinen TAH. Systemically administered wound-homing peptide accelerates wound healing by modulating syndecan-4 function. Nat Commun 2023; 14:8069. [PMID: 38057316 PMCID: PMC10700342 DOI: 10.1038/s41467-023-43848-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 11/19/2023] [Indexed: 12/08/2023] Open
Abstract
CAR (CARSKNKDC) is a wound-homing peptide that recognises angiogenic neovessels. Here we discover that systemically administered CAR peptide has inherent ability to promote wound healing: wounds close and re-epithelialise faster in CAR-treated male mice. CAR promotes keratinocyte migration in vitro. The heparan sulfate proteoglycan syndecan-4 regulates cell migration and is crucial for wound healing. We report that syndecan-4 expression is restricted to epidermis and blood vessels in mice skin wounds. Syndecan-4 regulates binding and internalisation of CAR peptide and CAR-mediated cytoskeletal remodelling. CAR induces syndecan-4-dependent activation of the small GTPase ARF6, via the guanine nucleotide exchange factor cytohesin-2, and promotes syndecan-4-, ARF6- and Cytohesin-2-mediated keratinocyte migration. Finally, we show that genetic ablation of syndecan-4 in male mice eliminates CAR-induced wound re-epithelialisation following systemic administration. We propose that CAR peptide activates syndecan-4 functions to selectively promote re-epithelialisation. Thus, CAR peptide provides a therapeutic approach to enhance wound healing in mice; systemic, yet target organ- and cell-specific.
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52
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Zhao B, Shi X, Khakalo S, Meng Y, Miettinen A, Turpeinen T, Mi S, Sun Z, Khakalo A, Rojas OJ, Mattos BD. Wood-based superblack. Nat Commun 2023; 14:7875. [PMID: 38052773 DOI: 10.1038/s41467-023-43594-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023] Open
Abstract
Light is a powerful and sustainable resource, but it can be detrimental to the performance and longevity of optical devices. Materials with near-zero light reflectance, i.e. superblack materials, are sought to improve the performance of several light-centered technologies. Here we report a simple top-down strategy, guided by computational methods, to develop robust superblack materials following metal-free wood delignification and carbonization (1500 °C). Subwavelength severed cells evolve under shrinkage stresses, yielding vertically aligned carbon microfiber arrays with a thickness of ~100 µm and light reflectance as low as 0.36% and independent of the incidence angle. The formation of such structures is rationalized based on delignification method, lignin content, carbonization temperature and wood density. Moreover, our measurements indicate a laser beam reflectivity lower than commercial light stoppers in current use. Overall, the wood-based superblack material is introduced as a mechanically robust surrogate for microfabricated carbon nanotube arrays.
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53
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Meinander O, Kouznetsov R, Uppstu A, Sofiev M, Kaakinen A, Salminen J, Rontu L, Welti A, Francis D, Piedehierro AA, Heikkilä P, Heikkinen E, Laaksonen A. African dust transport and deposition modelling verified through a citizen science campaign in Finland. Sci Rep 2023; 13:21379. [PMID: 38049489 PMCID: PMC10695925 DOI: 10.1038/s41598-023-46321-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023] Open
Abstract
African desert dust is emitted and long-range transported with multiple effects on climate, air quality, cryosphere, and ecosystems. On 21-23 February 2021, dust from a sand and dust storm in northern Africa was transported to Finland, north of 60°N. The episode was predicted 5 days in advance by the global operational SILAM forecast, and its key features were confirmed and detailed by a retrospective analysis. The scavenging of dust by snowfall and freezing rain in Finland resulted in a rare case of substantial mineral dust contamination of snow surfaces over a large area in the southern part of the country. A citizen science campaign was set up to collect contaminated snow samples prepared according to the scientists' instructions. The campaign gained wide national interest in television, radio, newspapers and social media, and dust samples were received from 525 locations in Finland, up to 64.3°N. The samples were utilised in investigating the ability of an atmospheric dispersion model to simulate the dust episode. The analysis confirmed that dust came from a wide Sahara and Sahel area from 5000 km away. Our results reveal the features of this rare event and demonstrate how deposition samples can be used to evaluate the skills and limitations of current atmospheric models in simulating transport of African dust towards northern Europe.
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54
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Ahvo A, Heino M, Sandström V, Chrisendo D, Jalava M, Kummu M. Agricultural input shocks affect crop yields more in the high-yielding areas of the world. NATURE FOOD 2023; 4:1037-1046. [PMID: 37945784 PMCID: PMC10727984 DOI: 10.1038/s43016-023-00873-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 10/05/2023] [Indexed: 11/12/2023]
Abstract
The industrialization of agriculture has led to an increasing dependence on non-locally sourced agricultural inputs. Hence, shocks in the availability of agricultural inputs can be devastating to food crop production. There is also a pressure to decrease the use of synthetic fertilizers and pesticides in many areas. However, the combined impact of the agricultural input shocks on crop yields has not yet been systematically assessed globally. Here we modelled the effects of agricultural input shocks using a random forest machine learning algorithm. We show that shocks in fertilizers cause the most drastic yield losses. Under the scenario of 50% shock in all studied agricultural inputs, global maize production could decrease up to 26%, and global wheat production up to 21%, impacting particularly the high-yielding 'breadbasket' areas of the world. Our study provides insights into global food system resilience and can be useful for preparing for potential future shocks or agricultural input availability decreases at local and global scales.
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55
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De Franco E, Owens NDL, Montaser H, Wakeling MN, Saarimäki-Vire J, Triantou A, Ibrahim H, Balboa D, Caswell RC, Jennings RE, Kvist JA, Johnson MB, Muralidharan S, Ellard S, Wright CF, Maddirevula S, Alkuraya FS, Hanley NA, Flanagan SE, Otonkoski T, Hattersley AT, Imbeault M. Primate-specific ZNF808 is essential for pancreatic development in humans. Nat Genet 2023; 55:2075-2081. [PMID: 37973953 PMCID: PMC10703691 DOI: 10.1038/s41588-023-01565-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023]
Abstract
Identifying genes linked to extreme phenotypes in humans has the potential to highlight biological processes not shared with all other mammals. Here, we report the identification of homozygous loss-of-function variants in the primate-specific gene ZNF808 as a cause of pancreatic agenesis. ZNF808 is a member of the KRAB zinc finger protein family, a large and rapidly evolving group of epigenetic silencers which target transposable elements. We show that loss of ZNF808 in vitro results in aberrant activation of regulatory potential contained in the primate-specific transposable elements it represses during early pancreas development. This leads to inappropriate specification of cell fate with induction of genes associated with liver identity. Our results highlight the essential role of ZNF808 in pancreatic development in humans and the contribution of primate-specific regions of the human genome to congenital developmental disease.
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56
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Laine RF, Heil HS, Coelho S, Nixon-Abell J, Jimenez A, Wiesner T, Martínez D, Galgani T, Régnier L, Stubb A, Follain G, Webster S, Goyette J, Dauphin A, Salles A, Culley S, Jacquemet G, Hajj B, Leterrier C, Henriques R. High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation. Nat Methods 2023; 20:1949-1956. [PMID: 37957430 PMCID: PMC10703683 DOI: 10.1038/s41592-023-02057-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/29/2023] [Indexed: 11/15/2023]
Abstract
Live-cell super-resolution microscopy enables the imaging of biological structure dynamics below the diffraction limit. Here we present enhanced super-resolution radial fluctuations (eSRRF), substantially improving image fidelity and resolution compared to the original SRRF method. eSRRF incorporates automated parameter optimization based on the data itself, giving insight into the trade-off between resolution and fidelity. We demonstrate eSRRF across a range of imaging modalities and biological systems. Notably, we extend eSRRF to three dimensions by combining it with multifocus microscopy. This realizes live-cell volumetric super-resolution imaging with an acquisition speed of ~1 volume per second. eSRRF provides an accessible super-resolution approach, maximizing information extraction across varied experimental conditions while minimizing artifacts. Its optimal parameter prediction strategy is generalizable, moving toward unbiased and optimized analyses in super-resolution microscopy.
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57
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Subero D, Maillet O, Golubev DS, Thomas G, Peltonen JT, Karimi B, Marín-Suárez M, Yeyati AL, Sánchez R, Park S, Pekola JP. Bolometric detection of Josephson inductance in a highly resistive environment. Nat Commun 2023; 14:7924. [PMID: 38040683 PMCID: PMC10692220 DOI: 10.1038/s41467-023-43668-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/10/2023] [Indexed: 12/03/2023] Open
Abstract
The Josephson junction is a building block of quantum circuits. Its behavior, well understood when treated as an isolated entity, is strongly affected by coupling to an electromagnetic environment. In 1983, Schmid predicted that a Josephson junction shunted by a resistance exceeding the resistance quantum RQ = h/4e2 ≈ 6.45 kΩ for Cooper pairs would become insulating since the phase fluctuations would destroy the coherent Josephson coupling. However, recent microwave measurements have questioned this interpretation. Here, we insert a small Josephson junction in a Johnson-Nyquist-type setup where it is driven by weak current noise arising from thermal fluctuations. Our heat probe minimally perturbs the junction's equilibrium, shedding light on features not visible in charge transport. We find that the Josephson critical current completely vanishes in DC charge transport measurement, and the junction demonstrates Coulomb blockade in agreement with the theory. Surprisingly, thermal transport measurements show that the Josephson junction acts as an inductor at high frequencies, unambiguously demonstrating that a supercurrent survives despite the Coulomb blockade observed in DC measurements.
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58
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Qin X, Hansen HA, Honkala K, Melander MM. Cation-induced changes in the inner- and outer-sphere mechanisms of electrocatalytic CO 2 reduction. Nat Commun 2023; 14:7607. [PMID: 37993426 PMCID: PMC10665450 DOI: 10.1038/s41467-023-43300-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
The underlying mechanism of cation effects on CO2RR remains debated. Herein, we study cation effects by simulating both outer-sphere electron transfer (OS-ET) and inner-sphere electron transfer (IS-ET) pathways during CO2RR via constrained density functional theory molecular dynamics (cDFT-MD) and slow-growth DFT-MD (SG-DFT-MD), respectively. Our results show without any cations, only OS-ET is feasible with a barrier of 1.21 eV. In the presence of K+ (Li+), OS-ET shows a very high barrier of 2.93 eV (4.15 eV) thus being prohibited. However, cations promote CO2 activation through IS-ET with the barrier of only 0.61 eV (K+) and 0.91 eV (Li+), generating the key intermediate (adsorbed CO[Formula: see text]). Without cations, CO2-to-CO[Formula: see text](ads) conversion cannot proceed. Our findings reveal cation effects arise from short-range Coulomb interactions with reaction intermediates. These results disclose that cations modulate the inner- and outer-sphere pathways of CO2RR, offering substantial insights on the cation specificity in the initial CO2RR steps.
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Lin J, Moradi E, Salenius K, Lehtipuro S, Häkkinen T, Laiho JE, Oikarinen S, Randelin S, Parikh HM, Krischer JP, Toppari J, Lernmark Å, Petrosino JF, Ajami NJ, She JX, Hagopian WA, Rewers MJ, Lloyd RE, Rautajoki KJ, Hyöty H, Nykter M. Distinct transcriptomic profiles in children prior to the appearance of type 1 diabetes-linked islet autoantibodies and following enterovirus infection. Nat Commun 2023; 14:7630. [PMID: 37993433 PMCID: PMC10665402 DOI: 10.1038/s41467-023-42763-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 10/17/2023] [Indexed: 11/24/2023] Open
Abstract
Although the genetic basis and pathogenesis of type 1 diabetes have been studied extensively, how host responses to environmental factors might contribute to autoantibody development remains largely unknown. Here, we use longitudinal blood transcriptome sequencing data to characterize host responses in children within 12 months prior to the appearance of type 1 diabetes-linked islet autoantibodies, as well as matched control children. We report that children who present with insulin-specific autoantibodies first have distinct transcriptional profiles from those who develop GADA autoantibodies first. In particular, gene dosage-driven expression of GSTM1 is associated with GADA autoantibody positivity. Moreover, compared with controls, we observe increased monocyte and decreased B cell proportions 9-12 months prior to autoantibody positivity, especially in children who developed antibodies against insulin first. Lastly, we show that control children present transcriptional signatures consistent with robust immune responses to enterovirus infection, whereas children who later developed islet autoimmunity do not. These findings highlight distinct immune-related transcriptomic differences between case and control children prior to case progression to islet autoimmunity and uncover deficient antiviral response in children who later develop islet autoimmunity.
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Grants
- U01 DK063821 NIDDK NIH HHS
- UC4 DK063863 NIDDK NIH HHS
- UL1 TR002535 NCATS NIH HHS
- U01 DK128847 NIDDK NIH HHS
- U01 DK063790 NIDDK NIH HHS
- UL1 TR000064 NCATS NIH HHS
- HHSN267200700014C NLM NIH HHS
- U01 DK063836 NIDDK NIH HHS
- U01 DK063829 NIDDK NIH HHS
- U01 DK063865 NIDDK NIH HHS
- UC4 DK095300 NIDDK NIH HHS
- UC4 DK063861 NIDDK NIH HHS
- UC4 DK063829 NIDDK NIH HHS
- UC4 DK063821 NIDDK NIH HHS
- UC4 DK117483 NIDDK NIH HHS
- UC4 DK063836 NIDDK NIH HHS
- UC4 DK112243 NIDDK NIH HHS
- U01 DK124166 NIDDK NIH HHS
- U01 DK063861 NIDDK NIH HHS
- UC4 DK063865 NIDDK NIH HHS
- U01 DK063863 NIDDK NIH HHS
- UC4 DK106955 NIDDK NIH HHS
- UC4 DK100238 NIDDK NIH HHS
- Academy of Finland (Suomen Akatemia)
- Sigrid Juséliuksen Säätiö (Sigrid Jusélius Foundation)
- U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- The TEDDY Study is funded by U01 DK63829, U01 DK63861, U01 DK63821, U01 DK63865, U01 DK63863, U01 DK63836, U01 DK63790, UC4 DK63829, UC4 DK63861, UC4 DK63821, UC4 DK63865, UC4 DK63863, UC4 DK63836, UC4 DK95300, UC4 DK100238, UC4 DK106955, UC4 DK112243, UC4 DK117483, U01 DK124166, U01 DK128847, and Contract No. HHSN267200700014C from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of Allergy and Infectious Diseases (NIAID), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institute of Environmental Health Sciences (NIEHS), Centers for Disease Control and Prevention (CDC), and JDRF. This work is supported in part by the NIH/NCATS Clinical and Translational Science Awards to the University of Florida (UL1 TR000064) and the University of Colorado (UL1 TR002535).
- Päivikki and Sakari Sohlberg's Foundation
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60
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Vihervaara A, Versluis P, Himanen SV, Lis JT. PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution. Nat Commun 2023; 14:7039. [PMID: 37923726 PMCID: PMC10624850 DOI: 10.1038/s41467-023-42715-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
RNA Polymerase II (Pol II) is a multi-subunit complex that undergoes covalent modifications as transcription proceeds through genes and enhancers. Rate-limiting steps of transcription control Pol II recruitment, site and degree of initiation, pausing duration, productive elongation, nascent transcript processing, transcription termination, and Pol II recycling. Here, we develop Precision Run-On coupled to Immuno-Precipitation sequencing (PRO-IP-seq), which double-selects nascent RNAs and transcription complexes, and track phosphorylation of Pol II C-terminal domain (CTD) at nucleotide-resolution. We uncover precise positional control of Pol II CTD phosphorylation as transcription proceeds from the initiating nucleotide (+1 nt), through early (+18 to +30 nt) and late (+31 to +60 nt) promoter-proximal pause, and into productive elongation. Pol II CTD is predominantly unphosphorylated from initiation until the early pause-region, whereas serine-2- and serine-5-phosphorylations are preferentially deposited in the later pause-region. Upon pause-release, serine-7-phosphorylation rapidly increases and dominates over the region where Pol II assembles elongation factors and accelerates to its full elongational speed. Interestingly, tracking CTD modifications upon heat-induced transcriptional reprogramming demonstrates that Pol II with phosphorylated CTD remains paused on thousands of heat-repressed genes. These results uncover dynamic Pol II regulation at rate-limiting steps of transcription and provide a nucleotide-resolution technique for tracking composition of engaged transcription complexes.
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Niva V, Horton A, Virkki V, Heino M, Kosonen M, Kallio M, Kinnunen P, Abel GJ, Muttarak R, Taka M, Varis O, Kummu M. World's human migration patterns in 2000-2019 unveiled by high-resolution data. Nat Hum Behav 2023; 7:2023-2037. [PMID: 37679443 PMCID: PMC10663150 DOI: 10.1038/s41562-023-01689-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/01/2023] [Indexed: 09/09/2023]
Abstract
Despite being a topical issue in public debate and on the political agenda for many countries, a global-scale, high-resolution quantification of migration and its major drivers for the recent decades remained missing. We created a global dataset of annual net migration between 2000 and 2019 (~10 km grid, covering the areas of 216 countries or sovereign states), based on reported and downscaled subnational birth (2,555 administrative units) and death (2,067 administrative units) rates. We show that, globally, around 50% of the world's urban population lived in areas where migration accelerated urban population growth, while a third of the global population lived in provinces where rural areas experienced positive net migration. Finally, we show that, globally, socioeconomic factors are more strongly associated with migration patterns than climatic factors. While our method is dependent on census data, incurring notable uncertainties in regions where census data coverage or quality is low, we were able to capture migration patterns not only between but also within countries, as well as by socioeconomic and geophysical zonings. Our results highlight the importance of subnational analysis of migration-a necessity for policy design, international cooperation and shared responsibility for managing internal and international migration.
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62
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Beaumont RN, Flatley C, Vaudel M, Wu X, Chen J, Moen GH, Skotte L, Helgeland Ø, Solé-Navais P, Banasik K, Albiñana C, Ronkainen J, Fadista J, Stinson SE, Trajanoska K, Wang CA, Westergaard D, Srinivasan S, Sánchez-Soriano C, Bilbao JR, Allard C, Groleau M, Kuulasmaa T, Leirer DJ, White F, Jacques PÉ, Cheng H, Hao K, Andreassen OA, Åsvold BO, Atalay M, Bhatta L, Bouchard L, Brumpton BM, Brunak S, Bybjerg-Grauholm J, Ebbing C, Elliott P, Engelbrechtsen L, Erikstrup C, Estarlich M, Franks S, Gaillard R, Geller F, Grove J, Hougaard DM, Kajantie E, Morgen CS, Nohr EA, Nyegaard M, Palmer CNA, Pedersen OB, Rivadeneira F, Sebert S, Shields BM, Stoltenberg C, Surakka I, Thørner LW, Ullum H, Vaarasmaki M, Vilhjalmsson BJ, Willer CJ, Lakka TA, Gybel-Brask D, Bustamante M, Hansen T, Pearson ER, Reynolds RM, Ostrowski SR, Pennell CE, Jaddoe VWV, Felix JF, Hattersley AT, Melbye M, Lawlor DA, Hveem K, Werge T, Nielsen HS, Magnus P, Evans DM, Jacobsson B, Järvelin MR, Zhang G, Hivert MF, Johansson S, Freathy RM, Feenstra B, Njølstad PR. Genome-wide association study of placental weight identifies distinct and shared genetic influences between placental and fetal growth. Nat Genet 2023; 55:1807-1819. [PMID: 37798380 PMCID: PMC10632150 DOI: 10.1038/s41588-023-01520-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 08/31/2023] [Indexed: 10/07/2023]
Abstract
A well-functioning placenta is essential for fetal and maternal health throughout pregnancy. Using placental weight as a proxy for placental growth, we report genome-wide association analyses in the fetal (n = 65,405), maternal (n = 61,228) and paternal (n = 52,392) genomes, yielding 40 independent association signals. Twenty-six signals are classified as fetal, four maternal and three fetal and maternal. A maternal parent-of-origin effect is seen near KCNQ1. Genetic correlation and colocalization analyses reveal overlap with birth weight genetics, but 12 loci are classified as predominantly or only affecting placental weight, with connections to placental development and morphology, and transport of antibodies and amino acids. Mendelian randomization analyses indicate that fetal genetically mediated higher placental weight is causally associated with preeclampsia risk and shorter gestational duration. Moreover, these analyses support the role of fetal insulin in regulating placental weight, providing a key link between fetal and placental growth.
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63
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Herzon I, Mazac R, Erkkola M, Garnett T, Hansson H, Kaljonen M, Kortetmäki T, Lonkila A, Jonell M, Niva M, Pajari AM, Tribaldos T, Toivonen M, Tuomisto HL, Koppelmäki K, Röös E. A rebalanced discussion of the roles of livestock in society. NATURE FOOD 2023; 4:926-927. [PMID: 37821624 DOI: 10.1038/s43016-023-00866-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
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64
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Ottensmann L, Tabassum R, Ruotsalainen SE, Gerl MJ, Klose C, Widén E, Simons K, Ripatti S, Pirinen M. Genome-wide association analysis of plasma lipidome identifies 495 genetic associations. Nat Commun 2023; 14:6934. [PMID: 37907536 PMCID: PMC10618167 DOI: 10.1038/s41467-023-42532-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023] Open
Abstract
The human plasma lipidome captures risk for cardiometabolic diseases. To discover new lipid-associated variants and understand the link between lipid species and cardiometabolic disorders, we perform univariate and multivariate genome-wide analyses of 179 lipid species in 7174 Finnish individuals. We fine-map the associated loci, prioritize genes, and examine their disease links in 377,277 FinnGen participants. We identify 495 genome-trait associations in 56 genetic loci including 8 novel loci, with a considerable boost provided by the multivariate analysis. For 26 loci, fine-mapping identifies variants with a high causal probability, including 14 coding variants indicating likely causal genes. A phenome-wide analysis across 953 disease endpoints reveals disease associations for 40 lipid loci. For 11 coronary artery disease risk variants, we detect strong associations with lipid species. Our study demonstrates the power of multivariate genetic analysis in correlated lipidomics data and reveals genetic links between diseases and lipid species beyond the standard lipids.
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65
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Yan J, Ma X, Liang D, Ran M, Zheng D, Chen X, Zhou S, Sun W, Shen X, Zhang H. An autocatalytic multicomponent DNAzyme nanomachine for tumor-specific photothermal therapy sensitization in pancreatic cancer. Nat Commun 2023; 14:6905. [PMID: 37903795 PMCID: PMC10616286 DOI: 10.1038/s41467-023-42740-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023] Open
Abstract
Multicomponent deoxyribozymes (MNAzymes) have great potential in gene therapy, but their ability to recognize disease tissue and further achieve synergistic gene regulation has rarely been studied. Herein, Arginylglycylaspartic acid (RGD)-modified Distearyl acylphosphatidyl ethanolamine (DSPE)-polyethylene glycol (PEG) (DSPE-PEG-RGD) micelle is prepared with a DSPE hydrophobic core to load the photothermal therapy (PTT) dye IR780 and the calcium efflux pump inhibitor curcumin. Then, the MNAzyme is distributed into the hydrophilic PEG layer and sealed with calcium phosphate through biomineralization. Moreover, RGD is attached to the outer tail of PEG for tumor targeting. The constructed nanomachine can release MNAzyme and the cofactor Ca2+ under acidic conditions and self-assemble into an active mode to cleave heat shock protein (HSP) mRNA by consuming the oncogene miRNA-21. Silencing miRNA-21 enhances the expression of the tumor suppressor gene PTEN, leading to PTT sensitization. Meanwhile, curcumin maintains high intracellular Ca2+ to further suppress HSP-chaperone ATP by disrupting mitochondrial Ca2+ homeostasis. Therefore, pancreatic cancer is triple-sensitized to IR780-mediated PTT. The in vitro and in vivo results show that the MNAzyme-based nanomachine can strongly regulate HSP and PTEN expression and lead to significant pancreatic tumor inhibition under laser irradiation.
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Sokolovskii I, Tichauer RH, Morozov D, Feist J, Groenhof G. Multi-scale molecular dynamics simulations of enhanced energy transfer in organic molecules under strong coupling. Nat Commun 2023; 14:6613. [PMID: 37857599 PMCID: PMC10587084 DOI: 10.1038/s41467-023-42067-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Exciton transport can be enhanced in the strong coupling regime where excitons hybridize with confined light modes to form polaritons. Because polaritons have group velocity, their propagation should be ballistic and long-ranged. However, experiments indicate that organic polaritons propagate in a diffusive manner and more slowly than their group velocity. Here, we resolve this controversy by means of molecular dynamics simulations of Rhodamine molecules in a Fabry-Pérot cavity. Our results suggest that polariton propagation is limited by the cavity lifetime and appears diffusive due to reversible population transfers between polaritonic states that propagate ballistically at their group velocity, and dark states that are stationary. Furthermore, because long-lived dark states transiently trap the excitation, propagation is observed on timescales beyond the intrinsic polariton lifetime. These insights not only help to better understand and interpret experimental observations, but also pave the way towards rational design of molecule-cavity systems for coherent exciton transport.
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Heutte B, Bergner N, Beck I, Angot H, Dada L, Quéléver LLJ, Laurila T, Boyer M, Brasseur Z, Daellenbach KR, Henning S, Kuang C, Kulmala M, Lampilahti J, Lampimäki M, Petäjä T, Shupe MD, Sipilä M, Uin J, Jokinen T, Schmale J. Measurements of aerosol microphysical and chemical properties in the central Arctic atmosphere during MOSAiC. Sci Data 2023; 10:690. [PMID: 37821470 PMCID: PMC10567811 DOI: 10.1038/s41597-023-02586-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023] Open
Abstract
The Arctic environment is transforming rapidly due to climate change. Aerosols' abundance and physicochemical characteristics play a crucial, yet uncertain, role in these changes due to their influence on the surface energy budget through direct interaction with solar radiation and indirectly via cloud formation. Importantly, Arctic aerosol properties are also changing in response to climate change. Despite their importance, year-round measurements of their characteristics are sparse in the Arctic and often confined to lower latitudes at Arctic land-based stations and/or short high-latitude summertime campaigns. Here, we present unique aerosol microphysics and chemical composition datasets collected during the year-long Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition, in the central Arctic. These datasets, which include aerosol particle number concentrations, size distributions, cloud condensation nuclei concentrations, fluorescent aerosol concentrations and properties, and aerosol bulk chemical composition (black carbon, sulfate, nitrate, ammonium, chloride, and organics) will serve to improve our understanding of high-Arctic aerosol processes, with relevance towards improved modelling of the future Arctic (and global) climate.
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Grants
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- AWI_PS122_00 Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Alfred-Wegener- Institute, Helmholtz Centre for Polar and Marine Research)
- 1010003826 EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- 101003826 EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- 101003826 EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- 101003826 EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- DE-SC0022046 DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)
- DE-SC0022046 DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)
- DE-SC0022046 DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)
- DE-SC0019251 DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)
- DE-SC0019251 DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)
- DE-SC0019251 DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)
- DE-SC0022046 DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)
- 200021_188478 Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)
- 200021_188478 Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)
- 200021_188478 Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)
- 337552 Academy of Finland (Suomen Akatemia)
- 333397 Academy of Finland (Suomen Akatemia)
- 337549 Academy of Finland (Suomen Akatemia)
- 337552 Academy of Finland (Suomen Akatemia)
- 333397 Academy of Finland (Suomen Akatemia)
- 337549 Academy of Finland (Suomen Akatemia)
- 337552 Academy of Finland (Suomen Akatemia)
- 333397 Academy of Finland (Suomen Akatemia)
- 337549 Academy of Finland (Suomen Akatemia)
- 337552 Academy of Finland (Suomen Akatemia)
- 333397 Academy of Finland (Suomen Akatemia)
- 337549 Academy of Finland (Suomen Akatemia)
- 337552 Academy of Finland (Suomen Akatemia)
- 333397 Academy of Finland (Suomen Akatemia)
- 337549 Academy of Finland (Suomen Akatemia)
- 337552 Academy of Finland (Suomen Akatemia)
- 333397 Academy of Finland (Suomen Akatemia)
- 337549 Academy of Finland (Suomen Akatemia)
- 333397 Academy of Finland (Suomen Akatemia)
- 337549 Academy of Finland (Suomen Akatemia)
- 337552 Academy of Finland (Suomen Akatemia)
- 337552 Academy of Finland (Suomen Akatemia)
- 333397 Academy of Finland (Suomen Akatemia)
- 337549 Academy of Finland (Suomen Akatemia)
- 337552 Academy of Finland (Suomen Akatemia)
- 333397 Academy of Finland (Suomen Akatemia)
- 337552 Academy of Finland (Suomen Akatemia)
- 333397 Academy of Finland (Suomen Akatemia)
- 337549 Academy of Finland (Suomen Akatemia)
- Swiss Polar Institute (grant no. DIRCR-2018-004) Ferring Pharmaceuticals (sponsor)
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Wang MM, Coupland SE, Aittokallio T, Figueiredo CR. Resistance to immune checkpoint therapies by tumour-induced T-cell desertification and exclusion: key mechanisms, prognostication and new therapeutic opportunities. Br J Cancer 2023; 129:1212-1224. [PMID: 37454231 PMCID: PMC10575907 DOI: 10.1038/s41416-023-02361-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Immune checkpoint therapies (ICT) can reinvigorate the effector functions of anti-tumour T cells, improving cancer patient outcomes. Anti-tumour T cells are initially formed during their first contact (priming) with tumour antigens by antigen-presenting cells (APCs). Unfortunately, many patients are refractory to ICT because their tumours are considered to be 'cold' tumours-i.e., they do not allow the generation of T cells (so-called 'desert' tumours) or the infiltration of existing anti-tumour T cells (T-cell-excluded tumours). Desert tumours disturb antigen processing and priming of T cells by targeting APCs with suppressive tumour factors derived from their genetic instabilities. In contrast, T-cell-excluded tumours are characterised by blocking effective anti-tumour T lymphocytes infiltrating cancer masses by obstacles, such as fibrosis and tumour-cell-induced immunosuppression. This review delves into critical mechanisms by which cancer cells induce T-cell 'desertification' and 'exclusion' in ICT refractory tumours. Filling the gaps in our knowledge regarding these pro-tumoral mechanisms will aid researchers in developing novel class immunotherapies that aim at restoring T-cell generation with more efficient priming by APCs and leukocyte tumour trafficking. Such developments are expected to unleash the clinical benefit of ICT in refractory patients.
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69
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Hirvonen MK, Lietzén N, Moulder R, Bhosale SD, Koskenniemi J, Vähä-Mäkilä M, Nurmio M, Orešič M, Ilonen J, Toppari J, Veijola R, Hyöty H, Lähdesmäki H, Knip M, Cheng L, Lahesmaa R. Serum APOC1 levels are decreased in young autoantibody positive children who rapidly progress to type 1 diabetes. Sci Rep 2023; 13:15941. [PMID: 37743383 PMCID: PMC10518308 DOI: 10.1038/s41598-023-43039-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023] Open
Abstract
Better understanding of the early events in the development of type 1 diabetes is needed to improve prediction and monitoring of the disease progression during the substantially heterogeneous presymptomatic period of the beta cell damaging process. To address this concern, we used mass spectrometry-based proteomics to analyse longitudinal pre-onset plasma sample series from children positive for multiple islet autoantibodies who had rapidly progressed to type 1 diabetes before 4 years of age (n = 10) and compared these with similar measurements from matched children who were either positive for a single autoantibody (n = 10) or autoantibody negative (n = 10). Following statistical analysis of the longitudinal data, targeted serum proteomics was used to verify 11 proteins putatively associated with the disease development in a similar yet independent and larger cohort of children who progressed to the disease within 5 years of age (n = 31) and matched autoantibody negative children (n = 31). These data reiterated extensive age-related trends for protein levels in young children. Further, these analyses demonstrated that the serum levels of two peptides unique for apolipoprotein C1 (APOC1) were decreased after the appearance of the first islet autoantibody and remained relatively less abundant in children who progressed to type 1 diabetes, in comparison to autoantibody negative children.
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70
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Pajanoja C, Hsin J, Olinger B, Schiffmacher A, Yazejian R, Abrams S, Dapkunas A, Zainul Z, Doyle AD, Martin D, Kerosuo L. Maintenance of pluripotency-like signature in the entire ectoderm leads to neural crest stem cell potential. Nat Commun 2023; 14:5941. [PMID: 37741818 PMCID: PMC10518019 DOI: 10.1038/s41467-023-41384-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 09/01/2023] [Indexed: 09/25/2023] Open
Abstract
The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like derivatives is obtained. Here, we monitor transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. We show maintenance of pluripotency-like signature (Nanog, Oct4/PouV, Klf4-positive) in undecided pan-ectodermal stem-cells spanning the entire ectoderm late during neurulation with ectodermal patterning completed only at the end of neurulation when the pluripotency-like signature becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency-like signature is found at multiple axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond "ectodermal-capacity" in chick and mouse embryos.
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71
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Uçar MC, Hannezo E, Tiilikainen E, Liaqat I, Jakobsson E, Nurmi H, Vaahtomeri K. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nat Commun 2023; 14:5878. [PMID: 37735168 PMCID: PMC10514270 DOI: 10.1038/s41467-023-41456-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
Branching morphogenesis is a ubiquitous process that gives rise to high exchange surfaces in the vasculature and epithelial organs. Lymphatic capillaries form branched networks, which play a key role in the circulation of tissue fluid and immune cells. Although mouse models and correlative patient data indicate that the lymphatic capillary density directly correlates with functional output, i.e., tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms ensuring efficient tissue coverage remain poorly understood. Here, we use the mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing, genetic perturbations, whole-organ reconstructions and theoretical modeling to show that the dermal lymphatic capillaries tile space in an optimal, space-filling manner. This coverage is achieved by two complementary mechanisms: initial tissue invasion provides a non-optimal global scaffold via self-organized branching morphogenesis, while VEGF-C dependent side-branching from existing capillaries rapidly optimizes local coverage by directionally targeting low-density regions. With these two ingredients, we show that a minimal biophysical model can reproduce quantitatively whole-network reconstructions, across development and perturbations. Our results show that lymphatic capillary networks can exploit local self-organizing mechanisms to achieve tissue-scale optimization.
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Lee J, Jukarainen S, Karvanen A, Dixon P, Davies NM, Smith GD, Natarajan P, Ganna A. Quantifying the causal impact of biological risk factors on healthcare costs. Nat Commun 2023; 14:5672. [PMID: 37704630 PMCID: PMC10499912 DOI: 10.1038/s41467-023-41394-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 08/29/2023] [Indexed: 09/15/2023] Open
Abstract
Understanding the causal impact that clinical risk factors have on healthcare-related costs is critical to evaluate healthcare interventions. Here, we used a genetically-informed design, Mendelian Randomization (MR), to infer the causal impact of 15 risk factors on annual total healthcare costs. We calculated healthcare costs for 373,160 participants from the FinnGen Study and replicated our results in 323,774 individuals from the United Kingdom and Netherlands. Robust causal effects were observed for waist circumference (WC), adult body mass index, and systolic blood pressure, in which a standard deviation increase corresponded to 22.78% [95% CI: 18.75-26.95], 13.64% [10.26-17.12], and 13.08% [8.84-17.48] increased healthcare costs, respectively. A lack of causal effects was observed for certain clinically relevant biomarkers, such as albumin, C-reactive protein, and vitamin D. Our results indicated that increased WC is a major contributor to annual total healthcare costs and more attention may be given to WC screening, surveillance, and mitigation.
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Santangeli A, Weigel B, Antão LH, Kaarlejärvi E, Hällfors M, Lehikoinen A, Lindén A, Salemaa M, Tonteri T, Merilä P, Vuorio K, Ovaskainen O, Vanhatalo J, Roslin T, Saastamoinen M. Mixed effects of a national protected area network on terrestrial and freshwater biodiversity. Nat Commun 2023; 14:5426. [PMID: 37704608 PMCID: PMC10499833 DOI: 10.1038/s41467-023-41073-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023] Open
Abstract
Protected areas are considered fundamental to counter biodiversity loss. However, evidence for their effectiveness in averting local extinctions remains scarce and taxonomically biased. We employ a robust counterfactual multi-taxon approach to compare occupancy patterns of 638 species, including birds (150), mammals (23), plants (39) and phytoplankton (426) between protected and unprotected sites across four decades in Finland. We find mixed impacts of protected areas, with only a small proportion of species explicitly benefiting from protection-mainly through slower rates of decline inside protected areas. The benefits of protection are enhanced for larger protected areas and are traceable to when the sites were protected, but are mostly unrelated to species conservation status or traits (size, climatic niche and threat status). Our results suggest that the current protected area network can partly contribute to slow down declines in occupancy rates, but alone will not suffice to halt the biodiversity crisis. Efforts aimed at improving coverage, connectivity and management will be key to enhance the effectiveness of protected areas towards bending the curve of biodiversity loss.
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Åberg F, Färkkilä M, Salomaa V, Jula A, Männistö S, Perola M, Lundqvist A, Männistö V. Waist-hip ratio is superior to BMI in predicting liver-related outcomes and synergizes with harmful alcohol use. COMMUNICATIONS MEDICINE 2023; 3:119. [PMID: 37674006 PMCID: PMC10482890 DOI: 10.1038/s43856-023-00353-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Obesity is associated with liver disease, but the best obesity-related predictor remains undefined. Controversy exists regarding possible synergism between obesity and alcohol use for liver-related outcomes (LRO). We assessed the predictive performance for LROs, and synergism with alcohol use, of abdominal obesity (waist-hip ratio, WHR), and compared it to overall obesity (body mass index, BMI). METHODS Forty-thousand nine-hundred twenty-two adults attending the Finnish health-examination surveys, FINRISK 1992-2012 and Health 2000 studies, were followed through linkage with electronic healthcare registries for LROs (hospitalizations, cancers, and deaths). Predictive performance of obesity measures (WHR, waist circumference [WC], and BMI) were assessed by Fine-Gray models and time-dependent area-under-the-curve (AUC). RESULTS There are 355 LROs during a median follow-up of 12.9 years (509047.8 person-years). WHR and WC emerge as more powerful predictors of LROs than BMI. WHR shows significantly better 10-year AUC values for LROs (0.714, 95% CI 0.685-0.743) than WC (0.648, 95% CI 0.617-0.679) or BMI (0.550, 95% CI 0.514-0.585) both overall and separately among men and women. WHR is predictive also in BMI strata. Absolute 10-year risks of LROs are more dependent on WHR than BMI. Moreover, WHR shows a significant supra-additive interaction effect with harmful alcohol use for liver-related outcomes (excess 10-year cumulative incidence of 2.8% from the interaction), which is not seen between BMI and harmful alcohol use. CONCLUSIONS WHR is a better predictor than BMI or WC for LROs, and WHR better reflects the synergism with harmful alcohol use. WHR should be included in clinical assessment when evaluating obesity-related risks for liver outcomes.
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Karttunen K, Patel D, Xia J, Fei L, Palin K, Aaltonen L, Sahu B. Transposable elements as tissue-specific enhancers in cancers of endodermal lineage. Nat Commun 2023; 14:5313. [PMID: 37658059 PMCID: PMC10474299 DOI: 10.1038/s41467-023-41081-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
Transposable elements (TE) are repetitive genomic elements that harbor binding sites for human transcription factors (TF). A regulatory role for TEs has been suggested in embryonal development and diseases such as cancer but systematic investigation of their functions has been limited by their widespread silencing in the genome. Here, we utilize unbiased massively parallel reporter assay data using a whole human genome library to identify TEs with functional enhancer activity in two human cancer types of endodermal lineage, colorectal and liver cancers. We show that the identified TE enhancers are characterized by genomic features associated with active enhancers, such as epigenetic marks and TF binding. Importantly, we identify distinct TE subfamilies that function as tissue-specific enhancers, namely MER11- and LTR12-elements in colon and liver cancers, respectively. These elements are bound by distinct TFs in each cell type, and they have predicted associations to differentially expressed genes. In conclusion, these data demonstrate how different cancer types can utilize distinct TEs as tissue-specific enhancers, paving the way for comprehensive understanding of the role of TEs as bona fide enhancers in the cancer genomes.
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