Life Sciences Commons^™

Differential Effects Of Rasa3 Mutations On Hematopoiesis Are Profoundly Influenced By Genetic Background And Molecular Variant., Ray F. Robledo, Steven L. Ciciotte, Joel H Graber, Yue Zhao, Amy J Lambert, Babette Gwynn, Nathaniel J Maki, Elena C Brindley, Emily Hartman, Lionel Blanc, Luanne L. Peters

Faculty Research 2020

Studies of the severely pancytopenic scat mouse model first demonstrated the crucial role of RASA3, a dual RAS and RAP GTPase activating protein (GAP), in hematopoiesis. RASA3 is required for survival in utero; germline deletion is lethal at E12.5-13.5 due to severe hemorrhage. Here, conditional deletion in hematopoietic stem and progenitor cells (HSPCs) using Vav-iCre recapitulates the null phenotype demonstrating that RASA3 is required at the stem and progenitor level to maintain blood vessel development and integrity and effective blood production. In adults, bone marrow blood cell production and spleen stress erythropoiesis are suppressed significantly upon induction of RASA3 deficiency, …

Mouse Mutant Phenotyping At Scale Reveals Novel Genes Controlling Bone Mineral Density., Anna L Swan, Christine Schütt, Jan Rozman, Maria Del Mar Muñiz Moreno, Stefan Brandmaier, Michelle Simon, Stefanie Leuchtenberger, Mark Griffiths, Robert Brommage, Piia Keskivali-Bond, Harald Grallert, Thomas Werner, Raffaele Teperino, Lore Becker, Gregor Miller, Ala Moshiri, John R Seavitt, Derek D Cissell, Terrence F Meehan, Elif F Acar, Christopher J Lelliott, Ann M Flenniken, Marie-France Champy, Tania Sorg, Abdel Ayadi, Robert E Braun, Heather Cater, Mary E Dickinson, Paul Flicek, Juan Gallegos, Elena J Ghirardello, Jason D Heaney, Sylvie Jacquot, Connor Lally, John G Logan, Lydia Teboul, Jeremy Mason, Nadine Spielmann, Colin Mckerlie, Stephen A. Murray, Lauryl M J Nutter, Kristian F Odfalk, Helen Parkinson, Jan Prochazka, Corey L Reynolds, Mohammed Selloum, Frantisek Spoutil, Karen L. Svenson, Taylor S Vales, Sara E Wells, Jacqueline K White, Radislav Sedlacek, Wolfgang Wurst, Kent K C Lloyd, Peter I Croucher, Helmut Fuchs, Graham R Williams, Duncan Bassett, Valerie Gailus-Durner, Yann Herault, Ann-Marie Mallon, Steve D M Brown, Philipp Mayer-Kuckuk, Martin Hrabe De Angelis, Impc Consortium

Faculty Research 2020

The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored …

A Drosophila Screen Identifies Nkcc1 As A Modifier Of Ngly1 Deficiency, Dana M Talsness, Katie G Owings, Emily Coelho, Gaelle Mercenne, John M Pleinis, Raghavendran Partha, Kevin A Hope, Aamir Zuberi, Nathan L Clark, Cathleen Lutz, Aylin R Rodan, Clement Y Chow

Faculty Research 2020

N-Glycanase 1 (NGLY1) is a cytoplasmic deglycosylating enzyme. Loss-of-function mutations in the NGLY1 gene cause NGLY1 deficiency, which is characterized by developmental delay, seizures, and a lack of sweat and tears. To model the phenotypic variability observed among patients, we crossed a Drosophila model of NGLY1 deficiency onto a panel of genetically diverse strains. The resulting progeny showed a phenotypic spectrum from 0 to 100% lethality. Association analysis on the lethality phenotype, as well as an evolutionary rate covariation analysis, generated lists of modifying genes, providing insight into NGLY1 function and disease. The top association hit was Ncc69 (human NKCC1/2 …

Toll-Like Receptor 7 Is Required For Lacrimal Gland Autoimmunity And Type 1 Diabetes Development In Male Nonobese Diabetic Mice., Ivy L Debreceni, Michael S Chimenti, David V. Serreze, Aron M Geurts, Yi-Guang Chen, Scott M Lieberman

Faculty Research 2020

Sjögren syndrome (SS) is an immunologically complex, chronic autoimmune disease targeting lacrimal and salivary glands. Nonobese diabetic (NOD) mice spontaneously develop inflammation of lacrimal and salivary glands with histopathological features similar to SS in humans including focal lymphocytic infiltrates in the affected glands. The innate immune signals driving lymphocytic infiltration of these glands are not well-defined. Here we evaluate the role of Toll-like receptor (TLR) 7 in the development of SS-like manifestations in NOD mice. We created a Tlr7 knockout NOD mouse strain and performed histological and gene expression studies to characterize the effects of TLR7 on autoimmunity development. TLR7 …

Mass Cytometry Defines Virus-Specific Cd4 + T Cells In Influenza Vaccination, Priyanka B Subrahmanyam, Tyson H Holmes, Dongxia Lin, Laura F Su, Gerlinde Obermoser, Jacques Banchereau, Virginia Pascual, Adolfo García-Sastre, Randy A Albrecht, Karolina Palucka, Mark M Davis, Holden T Maecker

Faculty Research 2020

The antiviral response to influenza virus is complex and multifaceted, involving many immune cell subsets. There is an urgent need to understand the role of CD4+ T cells, which orchestrate an effective antiviral response, to improve vaccine design strategies. In this study, we analyzed PBMCs from human participants immunized with influenza vaccine, using high-dimensional single-cell proteomic immune profiling by mass cytometry. Data were analyzed using a novel clustering algorithm, denoised ragged pruning, to define possible influenza virus-specific clusters of CD4+ T cells. Denoised ragged pruning identified six clusters of cells. Among these, one cluster (Cluster 3) was found to increase …

Deep Learning-Based Cross-Classifications Reveal Conserved Spatial Behaviors Within Tumor Histological Images., Javad Noorbakhsh, Saman Farahmand, Ali Foroughi Pour, Sandeep Namburi, Dennis Caruana, David Rimm, Mohammad Soltanieh-Ha, Kourosh Zarringhalam, Jeffrey Chuang

Faculty Research 2020

Histopathological images are a rich but incompletely explored data type for studying cancer. Manual inspection is time consuming, making it challenging to use for image data mining. Here we show that convolutional neural networks (CNNs) can be systematically applied across cancer types, enabling comparisons to reveal shared spatial behaviors. We develop CNN architectures to analyze 27,815 hematoxylin and eosin scanned images from The Cancer Genome Atlas for tumor/normal, cancer subtype, and mutation classification. Our CNNs are able to classify TCGA pathologist-annotated tumor/normal status of whole slide images (WSIs) in 19 cancer types with consistently high AUCs (0.995 ± 0.008), as …

The Involvement Of Neuroimmune Cells In Adipose Innervation., Magdalena Blaszkiewicz, Elizabeth Wood, Sigi Koizar, Jake Willows, Ryan Anderson, Yu-Hua Tseng, James W Godwin, Kristy L Townsend

Faculty Research 2020

BACKGROUND: Innervation of adipose tissue is essential for the proper function of this critical metabolic organ. Numerous surgical and chemical denervation studies have demonstrated how maintenance of brain-adipose communication through both sympathetic efferent and sensory afferent nerves helps regulate adipocyte size, cell number, lipolysis, and 'browning' of white adipose tissue. Neurotrophic factors are growth factors that promote neuron survival, regeneration, and plasticity, including neurite outgrowth and synapse formation. Peripheral immune cells have been shown to be a source of neurotrophic factors in humans and mice. Although a number of immune cells reside in the adipose stromal vascular fraction (SVF), it …

Prd-2 Directly Regulates Casein Kinase I And Counteracts Nonsense-Mediated Decay In The Neurospora Circadian Clock., Christina M Kelliher, Randy Lambreghts, Qijun Xiang, Christopher L. Baker, Jennifer J Loros, Jay C Dunlap

Faculty Research 2020

No abstract provided.

Health Benefits Attributed To 17Α-Estradiol, A Lifespan-Extending Compound, Are Mediated Through Estrogen Receptor Α., Shivani N Mann, Niran Hadad, Molly Nelson Holte, Alicia R Rothman, Roshini Sathiaseelan, Samim Ali Mondal, Martin-Paul Agbaga, Archana Unnikrishnan, Malayannan Subramaniam, John Hawse, Derek M Huffman, Willard M Freeman, Michael B Stout

Faculty Research 2020

Metabolic dysfunction underlies several chronic diseases, many of which are exacerbated by obesity. Dietary interventions can reverse metabolic declines and slow aging, although compliance issues remain paramount. 17α-estradiol treatment improves metabolic parameters and slows aging in male mice. The mechanisms by which 17α-estradiol elicits these benefits remain unresolved. Herein, we show that 17α-estradiol elicits similar genomic binding and transcriptional activation through estrogen receptor α (ERα) to that of 17β-estradiol. In addition, we show that the ablation of ERα completely attenuates the beneficial metabolic effects of 17α-E2 in male mice. Our findings suggest that 17α-E2 may act through the liver and …

Functional Redundancy Of Type I And Type Ii Receptors In The Regulation Of Skeletal Muscle Growth By Myostatin And Activin A., Se-Jin Lee, Adam Lehar, Yewei Liu, Chi Hai Ly, Quynh-Mai Pham, Michael Michaud, Renata Rydzik, Daniel W Youngstrom, Michael M Shen, Vesa Kaartinen, Emily L Germain-Lee, Thomas A Rando

Faculty Research 2020

Myostatin (MSTN) is a transforming growth factor-β (TGF-β) family member that normally acts to limit muscle growth. The function of MSTN is partially redundant with that of another TGF-β family member, activin A. MSTN and activin A are capable of signaling through a complex of type II and type I receptors. Here, we investigated the roles of two type II receptors (ACVR2 and ACVR2B) and two type I receptors (ALK4 and ALK5) in the regulation of muscle mass by these ligands by genetically targeting these receptors either alone or in combination specifically in myofibers in mice. We show that targeting …

Deciphering Functional Redundancy In The Human Microbiome., Liang Tian, Xu-Wen Wang, Ang-Kun Wu, Yuhang Fan, Jonathan Friedman, Amber Dahlin, Matthew K Waldor, George M. Weinstock, Scott T Weiss, Yang-Yu Liu

Faculty Research 2020

Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved - implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network - a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several …

Detection Of Crispr-Mediated Genome Modifications Through Altered Methylation Patterns Of Cpg Islands., M Heath Farris, Pamela A Texter, Agustin A Mora, Michael V. Wiles, Ellen F Mac Garrigle, Sybil A Klaus, Kristine Rosfjord

Faculty Research 2020

BACKGROUND: The development and application of CRISPR technologies for the modification of the genome are rapidly expanding. Advances in the field describe new CRISPR components that are strategically engineered to improve the precision and reliability of CRISPR editing within the genome sequence. Genome modification using induced genome breaks that are targeted and mediated by CRISPR components leverage cellular mechanisms for repair like homology directed repair (HDR) to incorporate genomic edits with increased precision.

RESULTS: In this report, we describe the gain of methylation at typically hypomethylated CpG island (CGI) locations affected by the CRISPR-mediated incorporation of donor DNA using HDR …

C11orf95-Rela Reprograms 3d Epigenome In Supratentorial Ependymoma., Jacqueline Jufen Zhu, Nathaniel L. Jillette, Xiao-Nan Li, Albert Cheng, Ching C Lau

Faculty Research 2020

Supratentorial ependymoma (ST-EPN) is a type of malignant brain tumor mainly seen in children. Since 2014, it has been known that an intrachromosomal fusion C11orf95-RELA is an oncogenic driver in ST-EPN [Parker et al. Nature 506:451-455 (2014); Pietsch et al. Acta Neuropathol 127:609-611 (2014)] but the molecular mechanisms of oncogenesis are unclear. Here we show that the C11orf95 component of the fusion protein dictates DNA binding activity while the RELA component is required for driving the expression of ependymoma-associated genes. Epigenomic characterizations using ChIP-seq and HiChIP approaches reveal that C11orf95-RELA modulates chromatin states and mediates chromatin interactions, leading to transcriptional …

New Hints Towards A Precision Medicine Strategy For Idh Wild-Type Glioblastoma., K White, K Connor, J Clerkin, B M Murphy, M Salvucci, A C O'Farrell, M Rehm, D O'Brien, J H M Prehn, S P Niclou, M L M Lamfers, M Verreault, A Idbaih, Roel G W Verhaak, A Golebiewska, A T Byrne

Faculty Research 2020

Glioblastoma represents the most common primary malignancy of the central nervous system in adults and remains a largely incurable disease. The elucidation of disease subtypes based on mutational profiling, gene expression and DNA methylation has so far failed to translate into improved clinical outcomes. However, new knowledge emerging from the subtyping effort in the IDH-wild-type setting may provide directions for future precision therapies. Here, we review recent learnings in the field, and further consider how tumour microenvironment differences across subtypes may reveal novel contexts of vulnerability. We discuss recent treatment approaches and ongoing trials in the IDH-wild-type glioblastoma setting, and …

Petri Net Modelling Approach For Analysing The Behaviour Of Wnt/[Inline-Formula Removed] -Catenin And Wnt/Ca 2+ Signalling Pathways In Arrhythmogenic Right Ventricular Cardiomyopathy., Nazia Azim, Jamil Ahmad, Nadeem Iqbal, Amnah Siddiqa, Abdul Majid, Javaria Ashraf, Fazal Jalil

Faculty Research 2020

Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart muscle disease that may result in arrhythmia, heart failure and sudden death. The hallmark pathological findings are progressive myocyte loss and fibro fatty replacement, with a predilection for the right ventricle. This study focuses on the adipose tissue formation in cardiomyocyte by considering the signal transduction pathways including Wnt/[inline-formula removed]-catenin and Wnt/Ca2+ regulation system. These pathways are modelled and analysed using stochastic petri nets (SPN) in order to increase our comprehension of ARVC and in turn its treatment regimen. The Wnt/[inline-formula removed]-catenin model predicts that the dysregulation …

Investigation Of Covid-19 Comorbidities Reveals Genes And Pathways Coincident With The Sars-Cov-2 Viral Disease., Mary E. Dolan, David P. Hill, Gaurab Mukherjee, Monica Mcandrews, Elissa J Chesler, Judith A. Blake

Faculty Research 2020

The emergence of the SARS-CoV-2 virus and subsequent COVID-19 pandemic initiated intense research into the mechanisms of action for this virus. It was quickly noted that COVID-19 presents more seriously in conjunction with other human disease conditions such as hypertension, diabetes, and lung diseases. We conducted a bioinformatics analysis of COVID-19 comorbidity-associated gene sets, identifying genes and pathways shared among the comorbidities, and evaluated current knowledge about these genes and pathways as related to current information about SARS-CoV-2 infection. We performed our analysis using GeneWeaver (GW), Reactome, and several biomedical ontologies to represent and compare common COVID-19 comorbidities. Phenotypic analysis …

Model Organism Development And Evaluation For Late-Onset Alzheimer's Disease: Model-Ad., Adrian L Oblak, Stefania Forner, Paul R Territo, Michael Sasner, Gregory W. Carter, Gareth R Howell, Stacey J Sukoff-Rizzo, Benjamin A Logsdon, Lara M Mangravite, Ali Mortazavi, David Baglietto-Vargas, Kim N Green, Grant R Macgregor, Marcelo A Wood, Andrea J Tenner, Frank M Laferla, Bruce T Lamb, The Model-Ad Consortium

Faculty Research 2020

Alzheimer's disease (AD) is a major cause of dementia, disability, and death in the elderly. Despite recent advances in our understanding of the basic biological mechanisms underlying AD, we do not know how to prevent it, nor do we have an approved disease-modifying intervention. Both are essential to slow or stop the growth in dementia prevalence. While our current animal models of AD have provided novel insights into AD disease mechanisms, thus far, they have not been successfully used to predict the effectiveness of therapies that have moved into AD clinical trials. The Model Organism Development and Evaluation for Late-onset …

Molecular Estimation Of Neurodegeneration Pseudotime In Older Brains., Sumit Mukherjee, Laura Heath, Christoph Preuss, Suman Jayadev, Gwenn A Garden, Anna K Greenwood, Solveig K Sieberts, Philip L De Jager, Nilüfer Ertekin-Taner, Gregory W. Carter, Lara M Mangravite, Benjamin A Logsdon

Faculty Research 2020

The temporal molecular changes that lead to disease onset and progression in Alzheimer's disease (AD) are still unknown. Here we develop a temporal model for these unobserved molecular changes with a manifold learning method applied to RNA-Seq data collected from human postmortem brain samples collected within the ROS/MAP and Mayo Clinic RNA-Seq studies. We define an ordering across samples based on their similarity in gene expression and use this ordering to estimate the molecular disease stage-or disease pseudotime-for each sample. Disease pseudotime is strongly concordant with the burden of tau (Braak score, P = 1.0 × 10-5), Aβ (CERAD score, …

Gtpbp1 Resolves Paused Ribosomes To Maintain Neuronal Homeostasis., Markus Terrey, Scott I Adamson, Alana L Gibson, Tianda Deng, Ryuta Ishimura, Jeffrey Chuang, Susan L Ackerman

Faculty Research 2020

Ribosome-associated quality control pathways respond to defects in translational elongation to recycle arrested ribosomes and degrade aberrant polypeptides and mRNAs. Loss of a tRNA gene leads to ribosomal pausing that is resolved by the translational GTPase GTPBP2, and in its absence causes neuron death. Here, we show that loss of the homologous protein GTPBP1 during tRNA deficiency in the mouse brain also leads to codon-specific ribosome pausing and neurodegeneration, suggesting that these non-redundant GTPases function in the same pathway to mitigate ribosome pausing. As observed in

Differences In Gut Microbiome In Hospitalized Immunocompetent Vs. Immunocompromised Children, Including Those With Sickle Cell Disease., Sindhu Mohandas, Vijaya L Soma, Thi Dong Binh Tran, Erica Sodergren, Tresa Ambooken, David L Goldman, George M. Weinstock, Betsy C Herold

Faculty Research 2020

Background: Gut microbial diversity and composition play important roles in health. This cross-sectional study was designed to test the hypothesis that hospitalized children who may be relatively immunocompromised (IC), defined as those with cancer, sickle cell disease (SCD), transplantation, or receiving immunosuppressive therapy) would have decreased microbial diversity, increased Clostridioides difficile colonization and different species composition compared to non-immunocompromised (Non-IC) children admitted to the same pediatric unit. Methods: A stool sample was obtained within 72 h of admission to a single unit at The Children's Hospital at Montefiore, Bronx, NY from March 2016 to February 2017 and the microbiome assessed …

Complement Peptide C3a Receptor 1 Promotes Optic Nerve Degeneration In Dba/2j Mice., Jeffrey M. Harder, Pete A. Williams, Catherine E. Braine, Hongyuan Yang, Jocelyn M Thomas, Nicole E Foxworth, Simon W M John, Gareth R Howell

Faculty Research 2020

BACKGROUND: The risk of glaucoma increases significantly with age and exposure to elevated intraocular pressure, two factors linked with neuroinflammation. The complement cascade is a complex immune process with many bioactive end-products, including mediators of inflammation. Complement cascade activation has been shown in glaucoma patients and models of glaucoma. However, the function of complement-mediated inflammation in glaucoma is largely untested. Here, the complement peptide C3a receptor 1 was genetically disrupted in DBA/2J mice, an ocular hypertensive model of glaucoma, to test its contribution to neurodegeneration.

METHODS: A null allele of C3ar1 was backcrossed into DBA/2J mice. Development of iris disease, …

A Novel Systems Biology Approach To Evaluate Mouse Models Of Late-Onset Alzheimer's Disease., Christoph Preuss, Ravi S Pandey, Erin Piazza, Alexander D Fine, Asli Uyar, Thanneer Perumal, Dylan Garceau, Kevin P Kotredes, Harriet M. Williams, Lara M Mangravite, Bruce T Lamb, Adrian L Oblak, Gareth R Howell, Michael Sasner, Benjamin A Logsdon, Model-Ad Consortium, Gregory W. Carter

Faculty Research 2020

BACKGROUND: Late-onset Alzheimer's disease (LOAD) is the most common form of dementia worldwide. To date, animal models of Alzheimer's have focused on rare familial mutations, due to a lack of frank neuropathology from models based on common disease genes. Recent multi-cohort studies of postmortem human brain transcriptomes have identified a set of 30 gene co-expression modules associated with LOAD, providing a molecular catalog of relevant endophenotypes.

RESULTS: This resource enables precise gene-based alignment between new animal models and human molecular signatures of disease. Here, we describe a new resource to efficiently screen mouse models for LOAD relevance. A new NanoString …

Canagliflozin Extends Life Span In Genetically Heterogeneous Male But Not Female Mice., Richard A Miller, David E Harrison, David B Allison, Molly A. Bogue, Lucas Debarba, Vivian Diaz, Elizabeth Fernandez, Andrzej Galecki, W Timothy Garvey, Hashan Jayarathne, Navasuja Kumar, Martin A Javors, Warren C Ladiges, Francesca Macchiarini, James Nelson, Peter C. Reifsnyder, Nadia Rosenthal, Marianna Sadagurski, Adam B Salmon, Daniel L Smith, Jessica M Snyder, David B Lombard, Randy Strong

Faculty Research 2020

Canagliflozin (Cana) is an FDA-approved diabetes drug that protects against cardiovascular and kidney diseases. It also inhibits the sodium glucose transporter 2 by blocking renal reuptake and intestinal absorption of glucose. In the context of the mouse Interventions Testing Program, genetically heterogeneous mice were given chow containing Cana at 180 ppm at 7 months of age until their death. Cana extended median survival of male mice by 14%. Cana also increased by 9% the age for 90th percentile survival, with parallel effects seen at each of 3 test sites. Neither the distribution of inferred cause of death nor incidental pathology …

Predicting The Early Risk Of Ophthalmopathy In Graves' Disease Patients Using Tcr Repertoire., Yue Wang, Yufeng Liu, Xiaofei Yang, Hui Guo, Jiadong Lin, Jinkui Yang, Mingqian He, Jingya Wang, Xiaomei Liu, Tingting Shi, Liping Wu, Chengsheng Zhang, Kai Ye, Bingyin Shi

Faculty Research 2020

No abstract provided.

Depletion Of Clk2 Sensitizes Glioma Stem-Like Cells To Pi3k/Mtor And Fgfr Inhibitors., Soon Young Park, Sandeep Mittal, Jianwen Dong, Kangjin Jeong, Emmanuel Martinez-Ledesma, Yuji Piao, Sabbir Khan, Verlene Henry, Roel G W Verhaak, Nazanin Majd, Veerakumar Balasubramaniyan, John F De Groot

Faculty Research 2020

The Cdc2-like kinases (CLKs) regulate RNA splicing and have been shown to suppress cell growth. Knockdown of CLK2 was found to block glioma stem-like cell (GSC) growth in vivo through the AKT/FOXO3a/p27 pathway without activating mTOR and MAPK signaling, suggesting that these pathways mediate resistance to CLK2 inhibition. We identified CLK2 binding partners using immunoprecipitation assays and confirmed their interactions in vitro in GSCs. We then tested the cellular viability of several signaling inhibitors in parental and CLK2 knockdown GSCs. Our results demonstrate that CLK2 binds to 14-3-3τ isoform and prevents its ubiquitination in GSCs. Stable CLK2 knockdown increased PP2A …

Gene Selection For Optimal Prediction Of Cell Position In Tissues From Single-Cell Transcriptomics Data., Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, Ying Hu, Hoang Vv Pham, Li Xiaomei, Thuc D Le, Adi L Tarca, Gaurav Bhatti, Roberto Romero, Nestoras Karathanasis, Phillipe Loher, Yang Chen, Zhengqing Ouyang, Disheng Mao, Yuping Zhang, Maryam Zand, Jianhua Ruan, Christoph Hafemeister, Peng Qiu, Duc Tran, Tin Nguyen, Attila Gabor, Thomas Yu, Justin Guinney, Enrico Glaab, Roland Krause, Peter Banda, Dream Sctc Consortium, Gustavo Stolovitzky, Nikolaus Rajewsky, Julio Saez-Rodriguez, Pablo Meyer

Faculty Research 2020

Single-cell RNA-sequencing (scRNAseq) technologies are rapidly evolving. Although very informative, in standard scRNAseq experiments, the spatial organization of the cells in the tissue of origin is lost. Conversely, spatial RNA-seq technologies designed to maintain cell localization have limited throughput and gene coverage. Mapping scRNAseq to genes with spatial information increases coverage while providing spatial location. However, methods to perform such mapping have not yet been benchmarked. To fill this gap, we organized the DREAM Single-Cell Transcriptomics challenge focused on the spatial reconstruction of cells from the Drosophila embryo from scRNAseq data, leveraging as silver standard, genes with in situ hybridization …

Rapamycin-Mediated Mouse Lifespan Extension: Late-Life Dosage Regimes With Sex-Specific Effects., Randy Strong, Richard A Miller, Molly A. Bogue, Elizabeth Fernandez, Martin A Javors, Sergiy Libert, Paul Anthony Marinez, Michael P Murphy, Nicolas Musi, James F Nelson, Michael Petrascheck, Peter C. Reifsnyder, Arlan Richardson, Adam B Salmon, Francesca Macchiarini, David E Harrison

Faculty Research 2020

To see if variations in timing of rapamycin (Rapa), administered to middle aged mice starting at 20 months, would lead to different survival outcomes, we compared three dosing regimens. Initiation of Rapa at 42 ppm increased survival significantly in both male and female mice. Exposure to Rapa for a 3-month period led to significant longevity benefit in males only. Protocols in which each month of Rapa treatment was followed by a month without Rapa exposure were also effective in both sexes, though this approach was less effective than continuous exposure in female mice. Interpretation of these results is made more …

Cellular Taxonomy And Spatial Organization Of The Murine Ventral Posterior Hypothalamus., Laura E Mickelsen, William F Flynn, Kristen Springer, Lydia Wilson, Eric J Beltrami, Mohan Bolisetty, Paul Robson, Alexander C Jackson

Faculty Research 2020

The ventral posterior hypothalamus (VPH) is an anatomically complex brain region implicated in arousal, reproduction, energy balance, and memory processing. However, neuronal cell type diversity within the VPH is poorly understood, an impediment to deconstructing the roles of distinct VPH circuits in physiology and behavior. To address this question, we employed a droplet-based single-cell RNA sequencing (scRNA-seq) approach to systematically classify molecularly distinct cell populations in the mouse VPH. Analysis of >16,000 single cells revealed 20 neuronal and 18 non-neuronal cell populations, defined by suites of discriminatory markers. We validated differentially expressed genes in selected neuronal populations through fluorescence in …

Reduced Gabaergic Neuron Excitability, Altered Synaptic Connectivity, And Seizures In A Kcnt1 Gain-Of-Function Mouse Model Of Childhood Epilepsy., Amy N Shore, Sophie Colombo, William F Tobin, Sabrina Petri, Erin R Cullen, Soledad Dominguez, Christopher D Bostick, Michael A Beaumont, Damian Williams, Dion Khodagholy, Mu Yang, Cathleen M Lutz, Yueqing Peng, Jennifer N Gelinas, David B Goldstein, Michael J Boland, Wayne N Frankel, Matthew C Weston

Faculty Research 2020

Gain-of-function (GOF) variants in K⁺ channels cause severe childhood epilepsies, but there are no mechanisms to explain how increased K⁺ currents lead to network hyperexcitability. Here, we introduce a human Na⁺-activated K⁺ (K_Na) channel variant (KCNT1-Y796H) into mice and, using a multiplatform approach, find motor cortex hyperexcitability and early-onset seizures, phenotypes strikingly similar to those of human patients. Although the variant increases K_Na currents in cortical excitatory and inhibitory neurons, there is an increase in the K_Na current across subthreshold voltages only in inhibitory neurons, particularly in those with non-fast-spiking properties, …

Genetic Differences And Longevity-Related Phenotypes Influence Lifespan And Lifespan Variation In A Sex-Specific Manner In Mice., Rong Yuan, C J M Musters, Yun Zhu, Tracy R Evans, Yujie Sun, Elissa J Chesler, Luanne L. Peters, David E Harrison, Andrzej Bartke

Faculty Research 2020

Epidemiological studies of human longevity found two interesting features, robust advantage of female lifespan and consistent reduction of lifespan variation. To help understand the genetic aspects of these phenomena, the current study examined sex differences and variation of longevity using previously published mouse data sets including data on lifespan, age of puberty, and circulating insulin-like growth factor 1 (IGF1) levels in 31 inbred strains, data from colonies of nuclear-receptor-interacting protein 1 (Nrip1) knockout mice, and a congenic strain, B6.C3H-Igf1. Looking at the overall data for all inbred strains, the results show no significant difference in lifespan and lifespan variation between …