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Table of Contents

December 2022 | Volume 5, No. 12

Research Articles

  • <em>Drosophila</em> insulator proteins exhibit in vivo liquid–liquid phase separation properties
    Open Access
    Drosophila insulator proteins exhibit in vivo liquid–liquid phase separation properties

    Bright Amankwaa, Todd Schoborg, Mariano Labrador

    Bright Amankwaa ... Mariano Labrador

    Published 19 July 2022

    Drosophila insulator proteins and the cohesin subunit Rad21 coalesce in vivo to form liquid-droplet condensates, suggesting that liquid–liquid phase separation mediates their function in 3D genome organization.

  • RFWD3 and translesion DNA polymerases contribute to PCNA modification–dependent DNA damage tolerance
    Open Access
    RFWD3 and translesion DNA polymerases contribute to PCNA modification–dependent DNA damage tolerance

    Rie Kanao, Hidehiko Kawai, Toshiyasu Taniguchi, Minoru Takata, Chikahide Masutani

    Rie Kanao ... Chikahide Masutani

    Published 29 July 2022

    RFWD3 and the translesion DNA polymerases Polκ and Polη, for illudin S and UV DNA lesions, respectively, contribute to PCNA ubiquitination–dependent DNA damage tolerance in human cells.

  • Dimerization of kringle 1 domain from hepatocyte growth factor/scatter factor provides a potent MET receptor agonist
    Open Access
    Dimerization of kringle 1 domain from hepatocyte growth factor/scatter factor provides a potent MET receptor agonist

    Giovanni de Nola, Bérénice Leclercq, Alexandra Mougel, Solenne Taront, Claire Simonneau, Federico Forneris, Eric Adriaenssens, Hervé Drobecq, Luisa Iamele, Laurent Dubuquoy, Oleg Melnyk, Ermanno Gherardi, Hugo de Jonge, Jérôme Vicogne

    Giovanni de Nola ... Jérôme Vicogne

    Published 29 July 2022

    We designed and characterized a potent full MET receptor agonist consisting of two recombinantly linked HGF/SF kringle 1 domains and demonstrated its potential in epithelial tissue regeneration.

  • Chr21 protein–protein interactions: enrichment in proteins involved in intellectual disability, autism, and late-onset Alzheimer’s disease
    Open Access
    Chr21 protein–protein interactions: enrichment in proteins involved in intellectual disability, autism, and late-onset Alzheimer’s disease

    Julia Viard, Yann Loe-Mie, Rachel Daudin, Malik Khelfaoui, Christine Plancon, Anne Boland, Francisco Tejedor, Richard L Huganir, Eunjoon Kim, Makoto Kinoshita, Guofa Liu, Volker Haucke, Thomas Moncion, Eugene Yu, Valérie Hindie, Henri Bléhaut, Clotilde Mircher, Yann Herault, Jean-François Deleuze, Jean-Christophe Rain, Michel Simonneau, Aude-Marie Lepagnol-Bestel

    Julia Viard ... Aude-Marie Lepagnol-Bestel

    Published 1 August 2022

    A large-scale (82) yeast two-hybrid screen focusing on chromosome 21 proteins and their direct interactors revealed enrichment in proteins linked to synapse plasticity, autism, and Alzheimer’s disease.

  • Novel <em>DNM1L</em> variants impair mitochondrial dynamics through divergent mechanisms
    Open Access
    Novel DNM1L variants impair mitochondrial dynamics through divergent mechanisms

    Kelsey A Nolden, John M Egner, Jack J Collier, Oliver M Russell, Charlotte L Alston, Megan C Harwig, Michael E Widlansky, Souphatta Sasorith, Inês A Barbosa, Andrew GL Douglas, Julia Baptista, Mark Walker, Deirdre E Donnelly, Andrew A Morris, Hui Jeen Tan, Manju A Kurian, Kathleen Gorman, Santosh Mordekar, Charu Deshpande, Rajib Samanta, Robert McFarland, R Blake Hill, Robert W Taylor, Monika Oláhová

    Kelsey A Nolden ... Monika Oláhová

    Published 1 August 2022

    Novel DNM1L variants underlie a spectrum of clinical phenotypes and impair mitochondrial and peroxisomal dynamics via divergent mechanisms, with effects on DRP1 protein stability, GTPase activity, and oligomerisation in vitro.

  • PFKFB4 interacts with ICMT and activates RAS/AKT signaling-dependent cell migration in melanoma
    Open Access
    PFKFB4 interacts with ICMT and activates RAS/AKT signaling-dependent cell migration in melanoma

    Méghane Sittewelle, Vincent Kappès, Chenxi Zhou, Déborah Lécuyer, Anne H Monsoro-Burq

    Méghane Sittewelle ... Anne H Monsoro-Burq

    Published 1 August 2022

    Glycolysis regulator PFKFB4 promotes cell migration in metastatic melanoma and normal melanocytes by a non-conventional glycolysis-independent function involving ICMT, RAS, and AKT signaling.

  • Insight into the mechanism of DNA synthesis by human terminal deoxynucleotidyltransferase
    Open Access
    Insight into the mechanism of DNA synthesis by human terminal deoxynucleotidyltransferase

    Aleksandra A Kuznetsova, Timofey E Tyugashev, Irina V Alekseeva, Nadezhda A Timofeyeva, Olga S Fedorova, Nikita A Kuznetsov

    Aleksandra A Kuznetsova ... Nikita A Kuznetsov

    Published 1 August 2022

    The role of metal ions and specific interactions of dNTP with active-site amino acid residues in the mechanisms underlying the recognition of nucleoside triphosphates by human terminal deoxynucleotidyltransferase were revealed by pre–steady-state kinetics and molecular dynamics approaches.

  • RNA-sequencing of single cholangiocyte-derived organoids reveals high organoid-to organoid variability
    Open Access
    RNA-sequencing of single cholangiocyte-derived organoids reveals high organoid-to organoid variability

    Kristin Gehling, Swati Parekh, Farina Schneider, Marcel Kirchner, Vangelis Kondylis, Chrysa Nikopoulou, Peter Tessarz

    Kristin Gehling ... Peter Tessarz

    Published 1 August 2022

    Whereas batch variation between organoid cultures is low, inter-culture heterogeneity can be large, even within one well, which might stem from microenvironmental differences within the culture.

  • A protective role for <em>Drosophila</em> Filamin in nephrocytes via Yorkie mediated hypertrophy
    Open Access
    A protective role for Drosophila Filamin in nephrocytes via Yorkie mediated hypertrophy

    Sybille Koehler, Tobias B Huber, Barry Denholm

    Sybille Koehler ... Barry Denholm

    Published 3 August 2022

    Nephrocytes lacking key components of the filtration barrier respond by increasing Drosophila Filamin expression, which accumulates at the cell cortex to elicit a protective role.

  • Human milk inhibits some enveloped virus infections, including SARS-CoV-2, in an intestinal model
    Open Access
    Human milk inhibits some enveloped virus infections, including SARS-CoV-2, in an intestinal model

    Ikrame Aknouch, Adithya Sridhar, Eline Freeze, Francesca Paola Giugliano, Britt J van Keulen, Michelle Romijn, Carlemi Calitz, Inés García-Rodríguez, Lance Mulder, Manon E Wildenberg, Vanesa Muncan, Marit J van Gils, Johannes B van Goudoever, Koert J Stittelaar, Katja C Wolthers, Dasja Pajkrt

    Ikrame Aknouch ... Dasja Pajkrt

    Published 4 August 2022

    Human milk blocks some enveloped, but not non-enveloped, virus infections in a primary human fetal intestinal model and the transcriptomic data points towards inhibition of entry mediated by ATP1A1.

  • Ubiquitome profiling reveals a regulatory pattern of UPL3 with UBP12 on metabolic-leaf senescence
    Open Access
    Ubiquitome profiling reveals a regulatory pattern of UPL3 with UBP12 on metabolic-leaf senescence

    Wei Lan, Weibo Ma, Shuai Zheng, Yuhao Qiu, Han Zhang, Haisen Lu, Yu Zhang, Ying Miao

    Wei Lan ... Ying Miao

    Published 4 August 2022

    A landscape of UPL3-ubiquitinated proteins by ubiquitome profile indicates UPL3 interacting with UBP12 as a hub of regulator on proteolysis-independent regulation and proteolysis-dependent degradation.

  • The L-NAME mouse model of preeclampsia and impact to long-term maternal cardiovascular health
    Open Access
    The L-NAME mouse model of preeclampsia and impact to long-term maternal cardiovascular health

    Natasha de Alwis, Natalie K Binder, Sally Beard, Yeukai TM Mangwiro, Elif Kadife, James SM Cuffe, Emerson Keenan, Bianca R Fato, Tu’uhevaha J Kaitu’u-Lino, Fiona C Brownfoot, Sarah A Marshall, Natalie J Hannan

    Natasha de Alwis ... Natalie J Hannan

    Published 5 August 2022

    The L-NAME mouse model of preeclampsia mimics key aspects of disease in pregnancy, but does not demonstrate the increased long-term risk of cardiovascular disease seen in individuals following preeclampsia.

  • The conserved Pelado/ZSWIM8 protein regulates actin dynamics by promoting linear actin filament polymerization
    Open Access
    The conserved Pelado/ZSWIM8 protein regulates actin dynamics by promoting linear actin filament polymerization

    Claudia Molina-Pelayo, Patricio Olguin, Marek Mlodzik, Alvaro Glavic

    Claudia Molina-Pelayo ... Alvaro Glavic

    Published 8 August 2022

    Pldo/ZSWIM8 is a conserved protein that promotes linear actin polymerization at the expense of branched actin in several contexts, ranging from Drosophila morphogenesis to human cell migration.

  • Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis
    Open Access
    Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis

    Yusuke Imoto, Tomonori Nakamura, Emerson G Escolar, Michio Yoshiwaki, Yoji Kojima, Yukihiro Yabuta, Yoshitaka Katou, Takuya Yamamoto, Yasuaki Hiraoka, Mitinori Saitou

    Yusuke Imoto ... Mitinori Saitou

    Published 9 August 2022

    This work formulates a noise reduction method, RECODE, which resolves the curse of dimensionality in noisy high-dimensional data, including scRNA-seq data, for effective downstream analyses.

  • Bivalent binding of p14ARF to MDM2 RING and acidic domains inhibits E3 ligase function
    Open Access
    Bivalent binding of p14ARF to MDM2 RING and acidic domains inhibits E3 ligase function

    Dominika Kowalczyk, Mark A Nakasone, Brian O Smith, Danny T Huang

    Dominika Kowalczyk ... Danny T Huang

    Published 9 August 2022

    This study shows that MDM2 acidic and zinc finger regions weakly interact with the RING domain and a fragment of p14ARF strengthens this interaction to inhibit MDM2 ubiquitin ligase activity.

  • Efficacy of SARS-CoV-2 vaccination in patients with monoclonal gammopathies: A cross sectional study
    Open Access
    Efficacy of SARS-CoV-2 vaccination in patients with monoclonal gammopathies: A cross sectional study

    Eugenia Abella, Macedonia Trigueros, Edwards Pradenas, Francisco Muñoz-Lopez, Francesc Garcia-Pallarols, Randa Ben Azaiz Ben Lahsen, Benjamin Trinité, Victor Urrea, Silvia Marfil, Carla Rovirosa, Teresa Puig, Eulàlia Grau, Anna Chamorro, Ruth Toledo, Marta Font, Dolors Palacín, Francesc Lopez-Segui, Jorge Carrillo, Nuria Prat, Lourdes Mateu, Bonaventura Clotet, Julià Blanco, Marta Massanella, VAC-COV-GM-HMAR, KING Cohort Extension and CoronAVI@S studies

    Eugenia Abella ... KING Cohort Extension and CoronAVI@S studies

    Published 12 August 2022

    Uninfected multiple myeloma patients do not develop adequate immunity after SARS-COV-2 vaccination and will clearly benefit from tailored monitoring of immune responses after booster vaccine doses.

  • Telescoping bimodal latent Dirichlet allocation to identify expression QTLs across tissues
    Open Access
    Telescoping bimodal latent Dirichlet allocation to identify expression QTLs across tissues

    Ariel DH Gewirtz, F William Townes, Barbara E Engelhardt

    Ariel DH Gewirtz ... Barbara E Engelhardt

    Published 17 August 2022

    We present telescoping bimodal LDA, a method to identify complex associations across high-dimensional count data, and we show TBLDA’s behavior for expression QTL mapping for bulk RNA-seq data from 10 tissues in the GTEx data.

  • Methionine uptake via the SLC43A2 transporter is essential for regulatory T-cell survival
    Open Access
    Methionine uptake via the SLC43A2 transporter is essential for regulatory T-cell survival

    Neetu Saini, Afsana Naaz, Shree Padma Metur, Pinki Gahlot, Adhish Walvekar, Anupam Dutta, Umamaheswari Davathamizhan, Apurva Sarin, Sunil Laxman

    Neetu Saini ... Sunil Laxman

    Published 9 September 2022

    Regulatory T cells survive after IL-2 withdrawal by taking up and using methionine through the SLC43A2 transporter in a Notch1-dependent manner.

  • Emetine blocks DNA replication via proteosynthesis inhibition not by targeting Okazaki fragments
    Open Access
    Emetine blocks DNA replication via proteosynthesis inhibition not by targeting Okazaki fragments

    David Lukac, Zuzana Machacova, Pavel Moudry

    David Lukac ... Pavel Moudry

    Published 9 September 2022

    This study clarifies the long-standing misuse of emetine as a lagging strand synthesis-specific inhibitor. Emetine blocks the synthesis of both DNA strands by the inhibition of protein biosynthesis.

  • Cross talk between glucose metabolism and immunosuppression in IFN-γ–primed mesenchymal stem cells
    Open Access
    Cross talk between glucose metabolism and immunosuppression in IFN-γ–primed mesenchymal stem cells

    Mengwei Yao, Zhuo Chen, Xiao He, Jiaoyue Long, Xuewei Xia, Zhan Li, Yu Yang, Luoquan Ao, Wei Xing, Qizhou Lian, Huaping Liang, Xiang Xu

    Mengwei Yao ... Xiang Xu

    Published 9 September 2022

    This study reveals a novel relationship between mesenchymal stem cell immunomodulation and metabolism and provides a new strategy to improve their therapeutic efficacy in inflammatory diseases.

  • Mitochondrial impairment and intracellular reactive oxygen species alter primary cilia morphology
    Open Access
    Mitochondrial impairment and intracellular reactive oxygen species alter primary cilia morphology

    Noah Moruzzi, Ismael Valladolid-Acebes, Sukanya A Kannabiran, Sara Bulgaro, Ingo Burtscher, Barbara Leibiger, Ingo B Leibiger, Per-Olof Berggren, Kerstin Brismar

    Noah Moruzzi ... Kerstin Brismar

    Published 14 September 2022

    This work shows how altering energetic status and promoting intracellular/mitochondrial ROS induces cell-dependent ciliary impairments, which is relevant in diseases characterized by these features.

  • Mesenchymal stem cells derived from patients with premature aging syndromes display hallmarks of physiological aging
    Open Access
    Mesenchymal stem cells derived from patients with premature aging syndromes display hallmarks of physiological aging

    Jean Philippe Trani, Raphaël Chevalier, Leslie Caron, Claire El Yazidi, Natacha Broucqsault, Léa Toury, Morgane Thomas, Karima Annab, Bernard Binetruy, Annachiara De Sandre-Giovannoli, Nicolas Levy, Frédérique Magdinier, Jérôme D Robin

    Jean Philippe Trani ... Jérôme D Robin

    Published 14 September 2022

    Using of genome-wide approaches on models from laminopathies with or without progerin accumulation (HGPS, HGPS-L, APS), this study provides new insights on pathways altered during early stages of mesenchymal stem cells differentiation.

  • ALS-linked loss of Cyclin-F function affects HSP90
    Open Access
    ALS-linked loss of Cyclin-F function affects HSP90

    Alexander Siebert, Vanessa Gattringer, Jochen H Weishaupt, Christian Behrends

    Alexander Siebert ... Christian Behrends

    Published 16 September 2022

    Analysis of ALS patient cell lines and cyclin-F overexpression and knockout cells identified HSP90AB1 as novel SCFcyclin-F substrate pointing to a loss-of-function mechanism for ALS CCNF mutations.

  • Ataxin-2, Twenty-four, and Dicer-2 are components of a noncanonical cytoplasmic polyadenylation complex
    Open Access
    Ataxin-2, Twenty-four, and Dicer-2 are components of a noncanonical cytoplasmic polyadenylation complex

    Hima Priyanka Nadimpalli, Tanit Guitart, Olga Coll, Fátima Gebauer

    Hima Priyanka Nadimpalli ... Fátima Gebauer

    Published 16 September 2022

    Identification of components of a noncanonical cytoplasmic polyadenylation machinery in Drosophila expands the diversity of RNA-binding proteins involved in poly(A) tail length control.

  • RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription
    Open Access
    RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription

    Andrew CK Wu, Claudia Vivori, Harshil Patel, Theodora Sideri, Fabien Moretto, Folkert J van Werven

    Andrew CK Wu ... Folkert J van Werven

    Published 16 September 2022

    We show that the chromatin remodelling complex RSC and general regulatory factors (GRFs) limit transcription in the noncoding divergent direction, thereby increasing the directionality of promoters.

  • A critique of the hypothesis that CA repeats are primary targets of neuronal MeCP2
    Open Access
    A critique of the hypothesis that CA repeats are primary targets of neuronal MeCP2

    Kashyap Chhatbar, John Connelly, Shaun Webb, Skirmantas Kriaucionis, Adrian Bird

    Kashyap Chhatbar ... Adrian Bird

    Published 19 September 2022

    Using relevant neuronal datasets and in vitro experiments, we show that MeCP2 function depends on methylated CAC (mCAC) sites regardless of their occurrence in CA repeats or elsewhere in the genome.

  • miR-329– and miR-495–mediated Prr7 down-regulation is required for homeostatic synaptic depression in rat hippocampal neurons
    Open Access
    miR-329– and miR-495–mediated Prr7 down-regulation is required for homeostatic synaptic depression in rat hippocampal neurons

    Michiko O Inouye, David Colameo, Irina Ammann, Jochen Winterer, Gerhard Schratt

    Michiko O Inouye ... Gerhard Schratt

    Published 23 September 2022

    In rat hippocampal neurons, miRNA-dependent regulation of the synaptic Prr7 protein is required for the homeostatic synaptic depression of excitatory synapses upstream of the CDK5-SPAR pathway.

  • Timapiprant, a prostaglandin D2 receptor antagonist, ameliorates pathology in a rat Alzheimer’s model
    Open Access
    Timapiprant, a prostaglandin D2 receptor antagonist, ameliorates pathology in a rat Alzheimer’s model

    Charles H Wallace, Giovanni Oliveros, Peter A Serrano, Patricia Rockwell, Lei Xie, Maria Figueiredo-Pereira

    Charles H Wallace ... Maria Figueiredo-Pereira

    Published 27 September 2022

    PGD2 is a major brain prostaglandin and we report that timapiprant that is an antagonist for the PGD2 receptor DP2 reduces pathology and cognitive deficits in a transgenic rat model of Alzheimer’s.

  • Synthetic evolution of herbicide resistance using a T7 RNAP–based random DNA base editor
    Open Access
    Synthetic evolution of herbicide resistance using a T7 RNAP–based random DNA base editor

    Haroon Butt, Jose Luis Moreno Ramirez, Magdy Mahfouz

    Haroon Butt ... Magdy Mahfouz

    Published 28 September 2022

    A chimeric fusion of T7 RNAP and deaminase edits the DNA under the T7 promoter in plant cells. It directs the continuous synthetic evolution of OsALS to produce variants with herbicide resistance.

  • Nodal and <em>churchill1</em> position the expression of a notch ligand during <em>Xenopus</em> germ layer segregation
    Open Access
    Nodal and churchill1 position the expression of a notch ligand during Xenopus germ layer segregation

    María Belén Favarolo, Diego R Revinski, Matías J Garavaglia, Silvia L López

    María Belén Favarolo ... Silvia L López

    Published 30 September 2022

    Churchill and Nodal signaling, which participate in vertebrates’ germ layer induction, position a domain of Delta/Notch activity, which refines germ layer boundaries during frog gastrulation.

  • Non-canonical miRNA-RNA base-pairing impedes tumor suppressor activity of miR-16
    Open Access
    Non-canonical miRNA-RNA base-pairing impedes tumor suppressor activity of miR-16

    Anaïs M Quéméner, Laura Bachelot, Marc Aubry, Stéphane Avner, Delphine Leclerc, Gilles Salbert, Florian Cabillic, Didier Decaudin, Bernard Mari, Frédéric Mouriaux, Marie-Dominique Galibert, David Gilot

    Anaïs M Quéméner ... David Gilot

    Published 6 October 2022

    In uveal melanoma tumors, the RNA decay activity of the tumor suppressor miR-16 is impaired by sponge RNAs. These RNAs defined a powerful signature to predict overall survival.

  • Direct CD32 T-cell cytotoxicity: implications for breast cancer prognosis and treatment
    Open Access
    Direct CD32 T-cell cytotoxicity: implications for breast cancer prognosis and treatment

    Giuseppe Sconocchia, Giulia Lanzilli, Valeriana Cesarini, Domenico A Silvestris, Katayoun Rezvani, Roberto Arriga, Sara Caratelli, Ken Chen, Jinzhuang Dou, Carlo Cenciarelli, Gabriele Toietta, Silvia Baldari, Tommaso Sconocchia, Francesca De Paolis, Anna Aureli, Giandomenica Iezzi, Maria Irno Consalvo, Francesco Buccisano, Maria I del Principe, Luca Maurillo, Adriano Venditti, Alessio Ottaviani, Giulio C Spagnoli

    Giuseppe Sconocchia ... Giulio C Spagnoli

    Published 14 October 2022

    CD32-chimeric receptor T cell identifies CD32 cell surface ligand(s), on breast cancer (BC) cells, leading to BC cell elimination in vitro and in vivo and allowing detection of genes prognostically relevant.

  • VEGFR3 modulates brain microvessel branching in a mouse model of 22q11.2 deletion syndrome
    Open Access
    VEGFR3 modulates brain microvessel branching in a mouse model of 22q11.2 deletion syndrome

    Sara Cioffi, Gemma Flore, Stefania Martucciello, Marchesa Bilio, Maria Giuseppina Turturo, Elizabeth Illingworth

    Sara Cioffi ... Elizabeth Illingworth

    Published 10 October 2022

    This study provides genetic evidence that VEGFR3 regulates vessel branching and filopodia formation in the embryonic mouse brain and is a likely mediator of brain vessel anomalies in Tbx1 mutant mice.

  • Aerocyte specification and lung adaptation to breathing is dependent on alternative splicing changes
    Open Access
    Aerocyte specification and lung adaptation to breathing is dependent on alternative splicing changes

    Marta F Fidalgo, Catarina G Fonseca, Paulo Caldas, Alexandre ASF Raposo, Tania Balboni, Lenka Henao-Mišíková, Ana R Grosso, Francisca F Vasconcelos, Cláudio A Franco

    Marta F Fidalgo ... Cláudio A Franco

    Published 11 October 2022

    Perinatal cell type–specific alternative splicing changes modulate the intercellular communication between alveolar epithelial AT1 and endothelial cells, leading to the specification of aerocytes, a specialized type of alveolar capillary ECs critical for gas exchanges.

  • High-resolution structure of a fish aquaporin reveals a novel extracellular fold
    Open Access
    High-resolution structure of a fish aquaporin reveals a novel extracellular fold

    Jiao Zeng, Florian Schmitz, Simon Isaksson, Jessica Glas, Olivia Arbab, Martin Andersson, Kristina Sundell, Leif A Eriksson, Kunchithapadam Swaminathan, Susanna Törnroth-Horsefield, Kristina Hedfalk

    Jiao Zeng ... Kristina Hedfalk

    Published 13 October 2022

    The structural and functional characterization of a fish AQP reveals a water-specific AQP with unique structural features that may have implications for channel gating in response to osmotic changes.

  • Autoimmune RNA dysregulation and seizures: therapeutic prospects in neuropsychiatric lupus
    Open Access
    Autoimmune RNA dysregulation and seizures: therapeutic prospects in neuropsychiatric lupus

    Ilham A Muslimov, Valerio Berardi, Stacy Stephenson, Ellen M Ginzler, John G Hanly, Henri Tiedge

    Ilham A Muslimov ... Henri Tiedge

    Published 13 October 2022

    Lupus autoantibodies directed at neuroregulatory BC200 RNA cause seizure susceptibility in mice, but sequestration with antigen prevents seizures, indicating utility in therapeutic interventions.

  • Whole-exome sequencing of epithelial ovarian carcinomas differing in resistance to platinum therapy
    Open Access
    Whole-exome sequencing of epithelial ovarian carcinomas differing in resistance to platinum therapy

    Viktor Hlaváč, Petr Holý, Radka Václavíková, Lukáš Rob, Martin Hruda, Marcela Mrhalová, Petr Černaj, Jiří Bouda, Pavel Souček

    Viktor Hlaváč ... Pavel Souček

    Published 13 October 2022

    Exploration of the prognostic and predictive significance of exome variation in epithelial ovarian carcinoma patients, with TP53, Hippo, homologous recombination genes, and the SBS6 signature as the most interesting results.

Methods

  • Measuring cystic fibrosis drug responses in organoids derived from 2D differentiated nasal epithelia
    Open Access
    Measuring cystic fibrosis drug responses in organoids derived from 2D differentiated nasal epithelia

    Gimano D Amatngalim, Lisa W Rodenburg, Bente L Aalbers, Henriette HM Raeven, Ellen M Aarts, Dounia Sarhane, Sacha Spelier, Juliet W Lefferts, Iris AL Silva, Wilco Nijenhuis, Sacha Vrendenbarg, Evelien Kruisselbrink, Jesse E Brunsveld, Cornelis M van Drunen, Sabine Michel, Karin M de Winter-de Groot, Harry G Heijerman, Lukas C Kapitein, Magarida D Amaral, Cornelis K van der Ent, Jeffrey M Beekman

    Gimano D Amatngalim ... Jeffrey M Beekman

    Published 3 August 2022

    This work describes an optimized assay to determine CFTR drug responses in people with cystic fibrosis, using nasal-airway organoids that are generated from 2D differentiated epithelial monolayers.

Resources

  • Improving the computation efficiency of polygenic risk score modeling: faster in Julia
    Open Access
    Improving the computation efficiency of polygenic risk score modeling: faster in Julia

    Annika Faucon, Julian Samaroo, Tian Ge, Lea K Davis, Nancy J Cox, Ran Tao, Megan M Shuey

    Annika Faucon ... Megan M Shuey

    Published 18 July 2022

    To enable computationally efficient polygenic risk score (PRS) calculations, PRS.jl translates a field standard PRS construction method, PRS-CS, to the Julia programming language.

  • Islet Gene View—a tool to facilitate islet research
    Open Access
    Islet Gene View—a tool to facilitate islet research

    Olof Asplund, Petter Storm, Vikash Chandra, Gad Hatem, Emilia Ottosson-Laakso, Dina Mansour-Aly, Ulrika Krus, Hazem Ibrahim, Emma Ahlqvist, Tiinamaija Tuomi, Erik Renström, Olle Korsgren, Nils Wierup, Mark Ibberson, Michele Solimena, Piero Marchetti, Claes Wollheim, Isabella Artner, Hindrik Mulder, Ola Hansson, Timo Otonkoski, Leif Groop, Rashmi B Prasad

    Olof Asplund ... Rashmi B Prasad

    Published 10 August 2022

    Islet Gene View (IGW) is a web resource that makes information on gene expression in human islets from donors easily accessible to the scientific community. The relationship of global RNA expression from 188 donor-islets with islet phenotypes is explored.

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Volume 5, No. 12
December 2022
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