Life Sciences Commons^™

Nuclear Pore Protein Nup210 Depletion Suppresses Metastasis Through Heterochromatin-Mediated Disruption Of Tumor Cell Mechanical Response., Ruhul Amin, Anjali Shukla, Jacqueline Jufen Zhu, Sohyoung Kim, Ping Wang, Simon Zhongyuan Tian, Andy D Tran, Debasish Paul, Steven D Cappell, Sandra Burkett, Huaitian Liu, Maxwell P Lee, Michael J Kruhlak, Jennifer E Dwyer, R Mark Simpson, Gordon L Hager, Yijun Ruan, Kent W Hunter

Faculty Research 2021

Mechanical signals from the extracellular microenvironment have been implicated in tumor and metastatic progression. Here, we identify nucleoporin NUP210 as a metastasis susceptibility gene for human estrogen receptor positive (ER+) breast cancer and a cellular mechanosensor. Nup210 depletion suppresses lung metastasis in mouse models of breast cancer. Mechanistically, NUP210 interacts with LINC complex protein SUN2 which connects the nucleus to the cytoskeleton. In addition, the NUP210/SUN2 complex interacts with chromatin via the short isoform of BRD4 and histone H3.1/H3.2 at the nuclear periphery. In Nup210 knockout cells, mechanosensitive genes accumulate H3K27me3 heterochromatin modification, mediated by the polycomb repressive complex 2 …

Core-Atac: A Deep Learning Model For The Functional Classification Of Regulatory Elements From Single Cell And Bulk Atac-Seq Data., Asa Thibodeau, Shubham Khetan, Alper Eroglu, Ryan Tewhey, Michael L. Stitzel, Duygu Ucar

Faculty Research 2021

Cis-Regulatory elements (cis-REs) include promoters, enhancers, and insulators that regulate gene expression programs via binding of transcription factors. ATAC-seq technology effectively identifies active cis-REs in a given cell type (including from single cells) by mapping accessible chromatin at base-pair resolution. However, these maps are not immediately useful for inferring specific functions of cis-REs. For this purpose, we developed a deep learning framework (CoRE-ATAC) with novel data encoders that integrate DNA sequence (reference or personal genotypes) with ATAC-seq cut sites and read pileups. CoRE-ATAC was trained on 4 cell types (n = 6 samples/replicates) and accurately predicted known cis-RE functions from …

Abdominal Computed Tomography Imaging Findings In Hospitalized Covid-19 Patients: A Year-Long Experience And Associations Revealed By Explainable Artificial Intelligence., Alice Scarabelli, Massimo Zilocchi, Elena Casiraghi, Pierangelo Fasani, Guido Giovanni Plensich, Andrea Alessandro Esposito, Elvira Stellato, Alessandro Petrini, Justin Reese, Peter N Robinson, Giorgio Valentini, Gianpaolo Carrafiello

Faculty Research 2021

The aim of this retrospective study is to assess any association between abdominal CT findings and the radiological stage of COVID-19 pneumonia, pulmonary embolism and patient outcomes. We included 158 adult hospitalized COVID-19 patients between 1 March 2020 and 1 March 2021 who underwent 206 abdominal CTs. Two radiologists reviewed all CT images. Pathological findings were classified as acute or not. A subset of patients with inflammatory pathology in ACE2 organs (bowel, biliary tract, pancreas, urinary system) was identified. The radiological stage of COVID pneumonia, pulmonary embolism, overall days of hospitalization, ICU admission and outcome were registered. Univariate statistical analysis …

Human Macrophage Polarization In The Response To, Alberto Marin, Kristopher Van Huss, John Corbett, Sangjin Kim, Jonathon Mohl, Bo-Young Hong, Jorge Cervantes

Faculty Research 2021

Infection with Mycobacterium leprae, the causative organism of leprosy, is still endemic in numerous parts of the world including the southwestern United States. The broad variation of symptoms in the leprosy disease spectrum range from the milder tuberculoid leprosy (paucibacillary) to the more severe and disfiguring lepromatous leprosy (multibacillary). The established thinking in the health community is that host response, rather than M. leprae strain variation, is the reason for the range of disease severity. More recent discoveries suggest that macrophage polarization also plays a significant role in the spectrum of leprosy disease but to what degree it contributes is …

Spatial Concordance Of Dna Methylation Classification In Diffuse Glioma., Niels Verburg, Floris P Barthel, Kevin J Anderson, Kevin C Johnson, Thomas Koopman, Maqsood M Yaqub, Otto S Hoekstra, Adriaan A Lammertsma, Frederik Barkhof, Petra J W Pouwels, Jaap C Reijneveld, Annemieke J M Rozemuller, Jeroen A M Beliën, Ronald Boellaard, Michael D Taylor, Sunit Das, Joseph F Costello, William Peter Vandertop, Pieter Wesseling, Philip C De Witt Hamer, Roel G W Verhaak

Faculty Research 2021

BACKGROUND: Intratumoral heterogeneity is a hallmark of diffuse gliomas. DNA methylation profiling is an emerging approach in the clinical classification of brain tumors. The goal of this study is to investigate the effects of intratumoral heterogeneity on classification confidence.

METHODS: We used neuronavigation to acquire 133 image-guided and spatially separated stereotactic biopsy samples from 16 adult patients with a diffuse glioma (7 IDH-wildtype and 2 IDH-mutant glioblastoma, 6 diffuse astrocytoma, IDH-mutant and 1 oligodendroglioma, IDH-mutant and 1p19q codeleted), which we characterized using DNA methylation arrays. Samples were obtained from regions with and without abnormalities on contrast-enhanced T1-weighted and fluid-attenuated inversion …

Characterizing Long Covid: Deep Phenotype Of A Complex Condition., Rachel R Deer, Madeline A Rock, Nicole Vasilevsky, Leigh Carmody, Halie Rando, Alfred J Anzalone, Marc D Basson, Tellen D Bennett, Timothy Bergquist, Eilis A Boudreau, Carolyn T Bramante, James Brian Byrd, Tiffany J Callahan, Lauren E Chan, Haitao Chu, Christopher G Chute, Ben D Coleman, Hannah E Davis, Joel Gagnier, Casey S Greene, William B Hillegass, Ramakanth Kavuluru, Wesley D Kimble, Farrukh M Koraishy, Sebastian Köhler, Chen Liang, Feifan Liu, Hongfang Liu, Vithal Madhira, Charisse R Madlock-Brown, Nicolas Matentzoglu, Diego R Mazzotti, Julie A Mcmurry, Douglas S Mcnair, Richard A Moffitt, Teshamae S Monteith, Ann M Parker, Mallory A Perry, Emily Pfaff, Justin T Reese, Joel Saltz, Robert A Schuff, Anthony E Solomonides, Julian Solway, Heidi Spratt, Gary S Stein, Anupam A Sule, Umit Topaloglu, George D Vavougios, Liwei Wang, Melissa A Haendel, Peter N Robinson

Faculty Research 2021

BACKGROUND: Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 (PASC or "long COVID"), but they are difficult to integrate because of heterogeneous methods and the lack of a standard for denoting the many phenotypic manifestations. Patient-led studies are of particular importance for understanding the natural history of COVID-19, but integration is hampered because they often use different terms to describe the same symptom or condition. This significant disparity in patient versus clinical characterization motivated the proposed ontological approach to specifying manifestations, which will improve capture and integration of future long COVID studies.

METHODS: The Human Phenotype Ontology …

Community Oncologists' Perceptions And Utilization Of Large-Panel Genomic Tumor Testing., Eric C Anderson, Alexandra C Hinton, Christine W Lary, Anny T H R Fenton, Andrey Antov, Emily A Edelman, Petra Helbig, Kate Reed, Susan Miesfeldt, Christian A Thomas, Michael J Hall, J Scott Roberts, Jens Rueter, Paul K J Han, Mcgi Working Group

Faculty Research 2021

PURPOSE: Large-panel genomic tumor testing (GTT) is an emerging technology with great promise but uncertain clinical value. Previous research has documented variability in academic oncologists' perceptions and use of GTT, but little is known about community oncologists' perceptions of GTT and how perceptions relate to clinicians' intentions to use GTT.

METHODS: Community oncology physicians (N = 58) participating in a statewide initiative aimed at improving access to large-panel GTT completed surveys assessing their confidence in using GTT, attitudes regarding the value of GTT, perceptions of barriers to GTT implementation, and future intentions to use GTTs. Descriptive and multivariable regression analyses …

Immuno-Transcriptomic Profiling Of Extracranial Pediatric Solid Malignancies., Andrew S Brohl, Sivasish Sindiri, Jun S Wei, David Milewski, Hsien-Chao Chou, Young K Song, Xinyu Wen, Jeetendra Kumar, Hue V Reardon, Uma S Mudunuri, Jack R Collins, Sushma Nagaraj, Vineela Gangalapudi, Manoj Tyagi, Yuelin J Zhu, Katherine E Masih, Marielle E Yohe, Jack F Shern, Yue Qi, Udayan Guha, Daniel Catchpoole, Rimas J Orentas, Igor B Kuznetsov, Nicolas J Llosa, John A Ligon, Brian K Turpin, Daniel G Leino, Shintaro Iwata, Irene L Andrulis, Jay S Wunder, Silvia R C Toledo, Paul S Meltzer, Ching C Lau, Beverly A Teicher, Heather Magnan, Marc Ladanyi, Javed Khan

Faculty Research 2021

We perform an immunogenomics analysis utilizing whole-transcriptome sequencing of 657 pediatric extracranial solid cancer samples representing 14 diagnoses, and additionally utilize transcriptomes of 131 pediatric cancer cell lines and 147 normal tissue samples for comparison. We describe patterns of infiltrating immune cells, T cell receptor (TCR) clonal expansion, and translationally relevant immune checkpoints. We find that tumor-infiltrating lymphocytes and TCR counts vary widely across cancer types and within each diagnosis, and notably are significantly predictive of survival in osteosarcoma patients. We identify potential cancer-specific immunotherapeutic targets for adoptive cell therapies including cell-surface proteins, tumor germline antigens, and lineage-specific transcription factors. …

An Asp To Strike Out Cancer? Therapeutic Possibilities Arising From Aspartate's Emerging Roles In Cell Proliferation And Survival., Iiro Taneli Helenius, Hanumantha Rao Madala, Jing-Ruey Joanna Yeh

Faculty Research 2021

A better understanding of the metabolic constraints of a tumor may lead to more effective anticancer treatments. Evidence has emerged in recent years shedding light on a crucial aspartate dependency of many tumor types. As a precursor for nucleotide synthesis, aspartate is indispensable for cell proliferation. Moreover, the malate-aspartate shuttle plays a key role in redox balance, and a deficit in aspartate can lead to oxidative stress. It is now recognized that aspartate biosynthesis is largely governed by mitochondrial metabolism, including respiration and glutaminolysis in cancer cells. Therefore, under conditions that suppress mitochondrial metabolism, including mutations, hypoxia, or chemical inhibitors, …

Ga4gh: International Policies And Standards For Data Sharing Across Genomic Research And Healthcare., Heidi L Rehm, Angela J H Page, Lindsay Smith, Jeremy B Adams, Gil Alterovitz, Lawrence J Babb, Maxmillian P Barkley, Michael Baudis, Michael J S Beauvais, Tim Beck, Jacques S Beckmann, Sergi Beltran, David Bernick, Alexander Bernier, James K Bonfield, Tiffany F Boughtwood, Guillaume Bourque, Sarion R Bowers, Anthony J Brookes, Michael Brudno, Matthew H Brush, David Bujold, Tony Burdett, Orion J Buske, Moran N Cabili, Daniel L Cameron, Robert J Carroll, Esmeralda Casas-Silva, Debyani Chakravarty, Bimal P Chaudhari, Shu Hui Chen, J Michael Cherry, Justina Chung, Melissa Cline, Hayley L Clissold, Robert M Cook-Deegan, Mélanie Courtot, Fiona Cunningham, Miro Cupak, Robert M Davies, Danielle Denisko, Megan J Doerr, Lena I Dolman, Edward S Dove, L Jonathan Dursi, Stephanie O M Dyke, James A Eddy, Karen Eilbeck, Kyle P Ellrott, Susan Fairley, Khalid A Fakhro, Helen V Firth, Michael S Fitzsimons, Marc Fiume, Paul Flicek, Ian M Fore, Mallory A Freeberg, Robert R Freimuth, Lauren A Fromont, Jonathan Fuerth, Clara L Gaff, Weiniu Gan, Elena M Ghanaim, David Glazer, Robert C Green, Malachi Griffith, Obi L Griffith, Robert L Grossman, Tudor Groza, Jaime M Guidry Auvil, Roderic Guigó, Dipayan Gupta, Melissa A Haendel, Ada Hamosh, David P Hansen, Reece K Hart, Dean Mitchell Hartley, David Haussler, Rachele M Hendricks-Sturrup, Calvin W L Ho, Ashley E Hobb, Michael M Hoffman, Oliver M Hofmann, Petr Holub, Jacob Shujui Hsu, Jean-Pierre Hubaux, Sarah E Hunt, Ammar Husami, Julius O Jacobsen, Saumya S Jamuar, Elizabeth L Janes, Francis Jeanson, Aina Jené, Amber L Johns, Yann Joly, Steven J M Jones, Alexander Kanitz, Kazuto Kato, Thomas M Keane, Kristina Kekesi-Lafrance, Jerome Kelleher, Giselle Kerry, Seik-Soon Khor, Bartha M Knoppers, Melissa A Konopko, Kenjiro Kosaki, Martin Kuba, Jonathan Lawson, Rasko Leinonen, Stephanie Li, Michael F Lin, Mikael Linden, Xianglin Liu, Isuru Udara Liyanage, Javier Lopez, Anneke M Lucassen, Michael Lukowski, Alice L Mann, John Marshall, Michele Mattioni, Alejandro Metke-Jimenez, Anna Middleton, Richard J Milne, Fruzsina Molnár-Gábor, Nicola Mulder, Monica C Munoz-Torres, Rishi Nag, Hidewaki Nakagawa, Jamal Nasir, Arcadi Navarro, Tristan H Nelson, Ania Niewielska, Amy Nisselle, Jeffrey Niu, Tommi H Nyrönen, Brian D O'Connor, Sabine Oesterle, Soichi Ogishima, Vivian Ota Wang, Laura A D Paglione, Emilio Palumbo, Helen E Parkinson, Anthony A Philippakis, Angel D Pizarro, Andreas Prlic, Jordi Rambla, Augusto Rendon, Renee A Rider, Peter N Robinson, Kurt W Rodarmer, Laura Lyman Rodriguez, Alan F Rubin, Manuel Rueda, Gregory A Rushton, Rosalyn S Ryan, Gary I Saunders, Helen Schuilenburg, Torsten Schwede, Serena Scollen, Alexander Senf, Nathan C Sheffield, Neerjah Skantharajah, Albert V Smith, Heidi J Sofia, Dylan Spalding, Amanda B Spurdle, Zornitza Stark, Lincoln D Stein, Makoto Suematsu, Patrick Tan, Jonathan A Tedds, Alastair A Thomson, Adrian Thorogood, Timothy L Tickle, Katsushi Tokunaga, Juha Törnroos, David Torrents, Sean Upchurch, Alfonso Valencia, Roman Valls Guimera, Jessica Vamathevan, Susheel Varma, Danya F Vears, Coby Viner, Craig Voisin, Alex H Wagner, Susan E Wallace, Brian P Walsh, Marc S Williams, Eva C Winkler, Barbara J Wold, Grant M Wood, J Patrick Woolley, Chisato Yamasaki, Andrew D Yates, Christina K Yung, Lyndon J Zass, Ksenia Zaytseva, Junjun Zhang, Peter Goodhand, Kathryn North, Ewan Birney

Faculty Research 2021

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight …

Three Decades Of The Human Genome Organization., Charles Lee, Stylianos E Antonarakis, Ada Hamosh, John Burn

Faculty Research 2021

The Human Genome Organization (HUGO) was initially established in 1988 to help integrate international scientific genomic activity and to accelerate the diffusion of knowledge from the efforts of the human genome project. Its founding President was Victor McKusick. During the late 1980s and 1990s, HUGO organized lively gene mapping meetings to accurately place genes on the genome as chromosomes were being sequenced. With the completion of the Human Genome Project, HUGO went through some transitions and self-reflection. In 2020, HUGO (which hosts a large annual scientific meeting and comprises the renowned HUGO Gene Nomenclature Committee [HGNC], responsible for naming genes, …

Dna Methylation-Calling Tools For Oxford Nanopore Sequencing: A Survey And Human Epigenome-Wide Evaluation., Yang Liu, Wojciech Rosikiewicz, Ziwei Pan, Nathaniel L. Jillette, Ping Wang, Aziz Taghbalout, Jonathan Foox, Christopher Mason, Martin Carroll, Albert Cheng, Sheng Li

Faculty Research 2021

BACKGROUND: Nanopore long-read sequencing technology greatly expands the capacity of long-range, single-molecule DNA-modification detection. A growing number of analytical tools have been developed to detect DNA methylation from nanopore sequencing reads. Here, we assess the performance of different methylation-calling tools to provide a systematic evaluation to guide researchers performing human epigenome-wide studies.

RESULTS: We compare seven analytic tools for detecting DNA methylation from nanopore long-read sequencing data generated from human natural DNA at a whole-genome scale. We evaluate the per-read and per-site performance of CpG methylation prediction across different genomic contexts, CpG site coverage, and computational resources consumed by each …

Cultivation Of Common Bacterial Species And Strains From Human Skin, Oral, And Gut Microbiota., Elizabeth Fleming, Victor Pabst, Zoe Scholar, Ruoyun Xiong, Anita Y Voigt, Wei Zhou, Amelia Hoyt, Rachel Hardy, Anna Peterson, Ryan Beach, Yvette Ondouah-Nzutchi, Jinhong Dong, Lucinda Bateman, Suzanne D Vernon, Julia Oh

Faculty Research 2021

BACKGROUND: Genomics-driven discoveries of microbial species have provided extraordinary insights into the biodiversity of human microbiota. In addition, a significant portion of genetic variation between microbiota exists at the subspecies, or strain, level. High-resolution genomics to investigate species- and strain-level diversity and mechanistic studies, however, rely on the availability of individual microbes from a complex microbial consortia. High-throughput approaches are needed to acquire and identify the significant species- and strain-level diversity present in the oral, skin, and gut microbiome. Here, we describe and validate a streamlined workflow for cultivating dominant bacterial species and strains from the skin, oral, and gut …

Dti2vec: Drug-Target Interaction Prediction Using Network Embedding And Ensemble Learning., Maha A Thafar, Rawan S Olayan, Somayah Albaradei, Vladimir B Bajic, Takashi Gojobori, Magbubah Essack, Xin Gao

Faculty Research 2021

Drug-target interaction (DTI) prediction is a crucial step in drug discovery and repositioning as it reduces experimental validation costs if done right. Thus, developing in-silico methods to predict potential DTI has become a competitive research niche, with one of its main focuses being improving the prediction accuracy. Using machine learning (ML) models for this task, specifically network-based approaches, is effective and has shown great advantages over the other computational methods. However, ML model development involves upstream hand-crafted feature extraction and other processes that impact prediction accuracy. Thus, network-based representation learning techniques that provide automated feature extraction combined with traditional ML …

Large Scale Enzyme Based Xenobiotic Identification For Exposomics., Ken H Liu, Choon M Lee, Grant Singer, Preeti Bais, Francisco Castellanos, Michael H Woodworth, Thomas R Ziegler, Colleen S Kraft, Gary W Miller, Shuzhao Li, Young-Mi Go, Edward T Morgan, Dean P Jones

Faculty Research 2021

Advances in genomics have revealed many of the genetic underpinnings of human disease, but exposomics methods are currently inadequate to obtain a similar level of understanding of environmental contributions to human disease. Exposomics methods are limited by low abundance of xenobiotic metabolites and lack of authentic standards, which precludes identification using solely mass spectrometry-based criteria. Here, we develop and validate a method for enzymatic generation of xenobiotic metabolites for use with high-resolution mass spectrometry (HRMS) for chemical identification. Generated xenobiotic metabolites were used to confirm identities of respective metabolites in mice and human samples based upon accurate mass, retention time …

Functional Characterization Of T2d-Associated Snp Effects On Baseline And Er Stress-Responsive Β Cell Transcriptional Activation., Shubham Khetan, Susan Kales, Romy Kursawe, Alexandria Jillette, Jacob C Ulirsch, Steven K Reilly, Duygu Ucar, Ryan Tewhey, Michael L. Stitzel

Faculty Research 2021

Genome-wide association studies (GWAS) have linked single nucleotide polymorphisms (SNPs) at >250 loci in the human genome to type 2 diabetes (T2D) risk. For each locus, identifying the functional variant(s) among multiple SNPs in high linkage disequilibrium is critical to understand molecular mechanisms underlying T2D genetic risk. Using massively parallel reporter assays (MPRA), we test the cis-regulatory effects of SNPs associated with T2D and altered in vivo islet chromatin accessibility in MIN6 β cells under steady state and pathophysiologic endoplasmic reticulum (ER) stress conditions. We identify 1,982/6,621 (29.9%) SNP-containing elements that activate transcription in MIN6 and 879 SNP alleles that …

Solving Patients With Rare Diseases Through Programmatic Reanalysis Of Genome-Phenome Data., Leslie Matalonga, Carles Hernández-Ferrer, Davide Piscia, Rebecca Schüle, Matthis Synofzik, Ana Töpf, Lisenka E L M Vissers, Richarda De Voer, Raul Tonda, Steven Laurie, Marcos Fernandez-Callejo, Daniel Picó, Carles Garcia-Linares, Anastasios Papakonstantinou, Alberto Corvó, Ricky Joshi, Hector Diez, Ivo Gut, Alexander Hoischen, Holm Graessner, Sergi Beltran, Solve-Rd Consortia, Peter N Robinson

Faculty Research 2021

Reanalysis of inconclusive exome/genome sequencing data increases the diagnosis yield of patients with rare diseases. However, the cost and efforts required for reanalysis prevent its routine implementation in research and clinical environments. The Solve-RD project aims to reveal the molecular causes underlying undiagnosed rare diseases. One of the goals is to implement innovative approaches to reanalyse the exomes and genomes from thousands of well-studied undiagnosed cases. The raw genomic data is submitted to Solve-RD through the RD-Connect Genome-Phenome Analysis Platform (GPAP) together with standardised phenotypic and pedigree data. We have developed a programmatic workflow to reanalyse genome-phenome data. It uses …

Solve-Rd: Systematic Pan-European Data Sharing And Collaborative Analysis To Solve Rare Diseases., Birte Zurek, Kornelia Ellwanger, Lisenka E L M Vissers, Rebecca Schüle, Matthis Synofzik, Ana Töpf, Richarda M De Voer, Steven Laurie, Leslie Matalonga, Christian Gilissen, Stephan Ossowski, Peter A C 'T Hoen, Antonio Vitobello, Julia M Schulze-Hentrich, Olaf Riess, Han G Brunner, Anthony J Brookes, Ana Rath, Gisèle Bonne, Gulcin Gumus, Alain Verloes, Nicoline Hoogerbrugge, Teresinha Evangelista, Tina Harmuth, Morris Swertz, Dylan Spalding, Alexander Hoischen, Sergi Beltran, Holm Graessner, Peter N Robinson

Faculty Research 2021

For the first time in Europe hundreds of rare disease (RD) experts team up to actively share and jointly analyse existing patient's data. Solve-RD is a Horizon 2020-supported EU flagship project bringing together >300 clinicians, scientists, and patient representatives of 51 sites from 15 countries. Solve-RD is built upon a core group of four European Reference Networks (ERNs; ERN-ITHACA, ERN-RND, ERN-Euro NMD, ERN-GENTURIS) which annually see more than 270,000 RD patients with respective pathologies. The main ambition is to solve unsolved rare diseases for which a molecular cause is not yet known. This is achieved through an innovative clinical research …

Amulet: A Novel Read Count-Based Method For Effective Multiplet Detection From Single Nucleus Atac-Seq Data., Asa Thibodeau, Alper Eroglu, Christopher S Mcginnis, Nathan Lawlor, Djamel Nehar-Belaid, Romy Kursawe, Radu Marches, Daniel N Conrad, George A Kuchel, Zev J Gartner, Jacques Banchereau, Michael L. Stitzel, A Ercument Cicek, Duygu Ucar

Faculty Research 2021

Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned reads across the genome to effectively detect multiplets. We evaluate the method by generating snATAC-seq data in the human blood and pancreatic islet samples. AMULET has high precision, estimated via donor-based multiplexing, and high recall, estimated via simulated multiplets, compared to alternatives and identifies multiplets most effectively when a certain read depth of 25K median valid reads per nucleus is achieved.

Solving Unsolved Rare Neurological Diseases-A Solve-Rd Viewpoint., Rebecca Schüle, Dagmar Timmann, Corrie E Erasmus, Jennifer Reichbauer, Melanie Wayand, Bart Van De Warrenburg, Ludger Schöls, Carlo Wilke, Andrea Bevot, Stephan Zuchner, Sergi Beltran, Steven Laurie, Leslie Matalonga, Holm Graessner, Matthis Synofzik, Solve-Rd Consortium, Peter N Robinson

Faculty Research 2021

No abstract provided.

Tet2 Controls The Responses Of Β Cells To Inflammation In Autoimmune Diabetes., Jinxiu Rui, Songyan Deng, Ana Luisa Perdigoto, Gerald Ponath, Romy Kursawe, Nathan Lawlor, Tomokazu Sumida, Maya Levine-Ritterman, Michael L. Stitzel, David Pitt, Jun Lu, Kevan C Herold

Faculty Research 2021

β cells may participate and contribute to their own demise during Type 1 diabetes (T1D). Here we report a role of their expression of Tet2 in regulating immune killing. Tet2 is induced in murine and human β cells with inflammation but its expression is reduced in surviving β cells. Tet2-KO mice that receive WT bone marrow transplants develop insulitis but not diabetes and islet infiltrates do not eliminate β cells even though immune cells from the mice can transfer diabetes to NOD/scid recipients. Tet2-KO recipients are protected from transfer of disease by diabetogenic immune cells.Tet2-KO β cells show reduced expression …

Local Versus Systemic Control Of Bone And Skeletal Muscle Mass By Components Of The Transforming Growth Factor-Β Signaling Pathway., Yewei Liu, Adam Lehar, Renata Rydzik, Harshpreet Chandok, Yun-Sil Lee, Daniel W Youngstrom, Joshy George, Martin M Matzuk, Emily L Germain-Lee, Se-Jin Lee

Faculty Research 2021

Skeletal muscle and bone homeostasis are regulated by members of the myostatin/GDF-11/activin branch of the transforming growth factor-β superfamily, which share many regulatory components, including inhibitory extracellular binding proteins and receptors that mediate signaling. Here, we present the results of genetic studies demonstrating a critical role for the binding protein follistatin (FST) in regulating both skeletal muscle and bone. Using an allelic series corresponding to varying expression levels of endogenous Fst, we show that FST acts in an exquisitely dose-dependent manner to regulate both muscle mass and bone density. Moreover, by employing a genetic strategy to target Fst expression …

A Novel Treatment Strategy For Lapatinib Resistance In A Subset Of Her2-Amplified Gastric Cancer., Gang Ning, Qihui Zhu, Wonyoung Kang, Hamin Lee, Leigh Maher, Yun-Suhk Suh, Michael Michaud, Mayerlin Silva, Jee Young Kwon, Chengsheng Zhang, Charles Lee

Faculty Research 2021

BACKGROUND: Gastric cancer (GC) is one of the leading causes of cancer-related deaths worldwide. Human epidermal growth factor receptor 2 (HER2) amplification occurs in approximately 13-23% of all GC cases and patients with HER2 overexpression exhibit a poor prognosis. Lapatinib, a dual EGFR/HER2 tyrosine kinase inhibitor, is an effective agent to treat HER2-amplified breast cancer but it failed in gastric cancer (GC) clinical trials. However, the molecular mechanism of lapatinib resistance in HER2-amplified GC is not well studied.

METHODS: We employed an unbiased, genome-scale screening with pooled CRISPR library on HER2-amplified GC cell lines to identify genes that are associated …

Actinin Bioid Reveals Sarcomere Crosstalk With Oxidative Metabolism Through Interactions With Igf2bp2., Feria A Ladha, Ketan Thakar, Anthony M Pettinato, Nicholas Legere, Shahnaz Ghahremani, Rachel Cohn, Robert Romano, Emily Meredith, Yu-Sheng Chen, J Travis Hinson

Faculty Research 2021

Actinins are strain-sensing actin cross-linkers that are ubiquitously expressed and harbor mutations in human diseases. We utilize CRISPR, pluripotent stem cells, and BioID to study actinin interactomes in human cardiomyocytes. We identify 324 actinin proximity partners, including those that are dependent on sarcomere assembly. We confirm 19 known interactors and identify a network of RNA-binding proteins, including those with RNA localization functions. In vivo and biochemical interaction studies support that IGF2BP2 localizes electron transport chain transcripts to actinin neighborhoods through interactions between its K homology (KH) domain and actinin's rod domain. We combine alanine scanning mutagenesis and metabolic assays to …

Host Genetic Control Of Gut Microbiome Composition., Jason A. Bubier, Elissa J Chesler, George M. Weinstock

Faculty Research 2021

The gut microbiome plays a significant role in health and disease, and there is mounting evidence indicating that the microbial composition is regulated in part by host genetics. Heritability estimates for microbial abundance in mice and humans range from (0.05-0.45), indicating that 5-45% of inter-individual variation can be explained by genetics. Through twin studies, genetic association studies, systems genetics, and genome-wide association studies (GWAS), hundreds of specific host genetic loci have been shown to associate with the abundance of discrete gut microbes. Using genetically engineered knock-out mice, at least 30 specific genes have now been validated as having specific effects …

In Situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing., Ping Wang, Yuliang Feng, Kun Zhu, Haoxi Chai, Ya-Ting Chang, Xiaofei Yang, Xiyuan Liu, Chen Shen, Eva Gega, Byoungkoo Lee, Minji Kim, Xiaoan Ruan, Yijun Ruan

Faculty Research 2021

Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET) is an established method to map protein-mediated chromatin interactions. A limitation, however, is that it requires a hundred million cells per experiment, which hampers its broad application in biomedical research, particularly in studies in which it is impractical to obtain a large number of cells from rare samples. To reduce the required input cell number while retaining high data quality, we developed an in situ ChIA-PET protocol, which requires as few as 1 million cells. Here, we describe detailed step-by-step procedures for performing in situ ChIA-PET from cultured cells, including both an …

Comprehensive Evaluation Of The 5xfad Mouse Model For Preclinical Testing Applications: A Model-Ad Study., Adrian L Oblak, Peter B Lin, Kevin P Kotredes, Ravi S Pandey, Dylan Garceau, Harriet M. Jackson, Asli Uyar, Rita O'Rourke, Sarah O'Rourke, Cynthia Ingraham, Daria Bednarczyk, Melisa Belanger, Zackary A Cope, Gabriela J Little, Sean-Paul G Williams, Carl Ash, Adam Bleckert, Tim Ragan, Benjamin A Logsdon, Lara M Mangravite, Stacey J Sukoff Rizzo, Paul R Territo, Gregory W. Carter, Gareth R Howell, Michael Sasner, Bruce T Lamb

Faculty Research 2021

The ability to investigate therapeutic interventions in animal models of neurodegenerative diseases depends on extensive characterization of the model(s) being used. There are numerous models that have been generated to study Alzheimer's disease (AD) and the underlying pathogenesis of the disease. While transgenic models have been instrumental in understanding AD mechanisms and risk factors, they are limited in the degree of characteristics displayed in comparison with AD in humans, and the full spectrum of AD effects has yet to be recapitulated in a single mouse model. The Model Organism Development and Evaluation for Late-Onset Alzheimer's Disease (MODEL-AD) consortium was assembled …

Reprogramming Of Bivalent Chromatin States In Nras Mutant Melanoma Suggests Prc2 Inhibition As A Therapeutic Strategy., Christopher J Terranova, Ming Tang, Mayinuer Maitituoheti, Ayush T Raman, Archit K Ghosh, Jonathan Schulz, Samirkumar B Amin, Elias Orouji, Katarzyna Tomczak, Sharmistha Sarkar, Junna Oba, Caitlin Creasy, Chang-Jiun Wu, Samia Khan, Rossana Lazcano, Khalida Wani, Anand Singh, Praveen Barrodia, Dongyu Zhao, Kaifu Chen, Lauren E Haydu, Wei-Lien Wang, Alexander J Lazar, Scott E Woodman, Chantale Bernatchez, Kunal Rai

Faculty Research 2021

The dynamic evolution of chromatin state patterns during metastasis, their relationship with bona fide genetic drivers, and their therapeutic vulnerabilities are not completely understood. Combinatorial chromatin state profiling of 46 melanoma samples reveals an association of NRAS mutants with bivalent histone H3 lysine 27 trimethylation (H3K27me3) and Polycomb repressive complex 2. Reprogramming of bivalent domains during metastasis occurs on master transcription factors of a mesenchymal phenotype, including ZEB1, TWIST1, and CDH1. Resolution of bivalency using pharmacological inhibition of EZH2 decreases invasive capacity of melanoma cells and markedly reduces tumor burden in vivo, specifically in NRAS mutants. Coincident with bivalent reprogramming, …

Fos Rescues Neuronal Differentiation Of Sox2-Deleted Neural Stem Cells By Genome-Wide Regulation Of Common Sox2 And Ap1(Fos-Jun) Target Genes., Miriam Pagin, Mattias Pernebrink, Mattia Pitasi, Federica Malighetti, Chew Yee Ngan, Sergio Ottolenghi, Giulio Pavesi, Claudio Cantù, Silvia K Nicolis

Faculty Research 2021

The transcription factor SOX2 is important for brain development and for neural stem cells (NSC) maintenance. Sox2-deleted (Sox2-del) NSC from neonatal mouse brain are lost after few passages in culture. Two highly expressed genes, Fos and Socs3, are strongly downregulated in Sox2-del NSC; we previously showed that Fos or Socs3 overexpression by lentiviral transduction fully rescues NSC's long-term maintenance in culture. Sox2-del NSC are severely defective in neuronal production when induced to differentiate. NSC rescued by Sox2 reintroduction correctly differentiate into neurons. Similarly, Fos transduction rescues normal or even increased numbers of immature neurons expressing beta-tubulinIII, but not …

Homozygous Mtap Deletion In Primary Human Glioblastoma Is Not Associated With Elevation Of Methylthioadenosine., Yasaman Barekatain, Jeffrey J Ackroyd, Victoria C Yan, Sunada Khadka, Lin Wang, Ko-Chien Chen, Anton H Poral, Theresa Tran, Dimitra K Georgiou, Kenisha Arthur, Yu-Hsi Lin, Nikunj Satani, Elliot S Ballato, Eliot I Behr, Ana C Decarvalho, Roel G W Verhaak, John De Groot, Jason T Huse, John M Asara, Raghu Kalluri, Florian L Muller

Faculty Research 2021

Homozygous deletion of methylthioadenosine phosphorylase (MTAP) in cancers such as glioblastoma represents a potentially targetable vulnerability. Homozygous MTAP-deleted cell lines in culture show elevation of MTAP's substrate metabolite, methylthioadenosine (MTA). High levels of MTA inhibit protein arginine methyltransferase 5 (PRMT5), which sensitizes MTAP-deleted cells to PRMT5 and methionine adenosyltransferase 2A (MAT2A) inhibition. While this concept has been extensively corroborated in vitro, the clinical relevance relies on exhibiting significant MTA accumulation in human glioblastoma. In this work, using comprehensive metabolomic profiling, we show that MTA secreted by MTAP-deleted cells in vitro results in high levels of extracellular MTA. We further demonstrate …