title: RNA sequencing of HAP1 WT and MED13 KO clones

city: Trondheim

first: Barbara

last: van Loon

address: Erling Skjalgssons gt 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Norwegian University of Science and Technology

summary:
Purpose: The aim of the experiment was to eludicate differentialy expressed genes (DEGs) upon treatment with alkylating agent MMS between WT and MED13 deficient HAP1 cells.
Results: After bioinformatic processing, at ≥2-fold change and an FDR≤0.1, 446 DEGs were identified in MED13 KO cells when compared to WT. Upon the MMS treatment 394 DEGs were identified in MED13 KO cells, of which 229 were common with untreated MED13 KO cells.
Conclusions: Common DEGs represented genes directly regulated by MED13.

overall_design: Each genotype were analysed in 3 biological replicates for both MMS treated and untreated conditions. Control sample were represented by HAP1 WT untreated replicates.

first: Milosz

last: Rolinski

first: Sarah

middle: L

last: Fordyce Martin

first: Nicola

last: Montaldo


title: CDK2-mediated TNFa Upregulation as a Mechanism of Cytotoxicity in Acute Leukemia

status: Public on Dec 28 2020

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

country: USA

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

summary: Although inhibitors of the kinases CHK1, ATR and WEE1 are undergoing clinical testing, it remains unclear how these three classes of agents kill susceptible cells and whether they utilize the same cytotoxic mechanism. Here we observed that CHK1 inhibition induces apoptosis in a subset of acute leukemia cell lines, including TP53 null acute myeloid leukemia (AML) and BCR/ABL-positive acute lymphoid leukemia (ALL), in vitro and inhibits leukemic colony formation in clinical AML samples ex vivo. In further studies, CHK1 downregulation or CHK1 inhibitor treatment triggered signaling in sensitive human acute leukemia cell lines that involved CDK2 activation followed by AP1-dependent TNF transactivation, TNF production and engagement of a TNFR1- and BID-dependent apoptotic pathway. AML lines that were intrinsically CHK1 inhibitor resistant exhibited high CHK1 expression and were sensitized by CHK1 downregulation. Signaling through this same CDK2  AP1  TNF cytotoxic pathway was also initiated by ATR or WEE1 inhibitors in vitro and during CHK1 inhibitor treatment of AML xenografts in vivo. Collectively, these observations not only identify new contributors to antileukemic cell action of CHK1, ATR and WEE1 inhibitors, but also delineate a previously undescribed pathway leading from aberrant CDK2 activation to death ligand-induced killing that can potentially be exploited for acute leukemia treatment.

overall_design: Compare RNAseq data from ML1 or U937 in different treatments to check significant mRNA change for potential TNFa transcription factors

first: Scott

last: Kaufmann


title: Urinary miRNA biomarkers of the rat kidney nephron

status: Public on Dec 25 2020

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

type: Non-coding RNA profiling by high throughput sequencing

summary: The Health and Environmental Sciences Institute initiated a cross-laboratory program to identify and characterize microRNA (miRNA) patterns reflecting nephron-specific localization in naïve adult male Sprague-Dawley rats.

overall_design: Kidneys from 3 naïve adult male Sprague-Dawley rats, 6 months old, were collected and laser capture dissection was used to sample the proximal tubules, glomeruli,  the thick ascending limb (TAL) of the loop of Henle, and collecting duct (CD). Samples were measured for microRNAs using small RNA sequencing on an Illumina HiSeq 2000.

middle: N

first: Alison

middle: H

last: Harrill


title: RNAseq data from intravascular vs parenchymal cells during Mtb infection

status: Public on Dec 29 2020

city: Seattle

first: Benjamin

middle: Henry

last: Gern

state: WA

address: 307 Westlake Ave N

department: Center for Global Infectious Diseases Research

institute: Seattle Children's Research Institute

summary: Bulk RNAseq data looking at transcriptional differences between Mtb-specific T cells in the lung, vs those in the vasculature (with naive, CD44low controls) during Mycobacterium tuberculosis infection. Allowing us an unbiased way to discern differentially expressed genes in the two tissue spaces.

overall_design: We compared bulk RNAseq data across 3 cell types

first: Moguche

last: Albanus

first: Gern

last: Ben

first: Shehata

last: Laila

first: Urdahl

last: Kevin


title: EPIC-HPS

status: Public on Dec 26 2020

city: Barcelona

first: Nuria

last: Mendoza

address: C/Casanova 143, cellex 2 A

country: Spain

institute: IDIBAPS

summary: EPIC methylation array from liver DNA obtained from liver tissue preserved in paraffin, from individuals with or without HEPATOPULMONARY SYNDROME (HPS)

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina EPIC 850K array

first: Rosa

last: Faner


title: Multipathogen analysis of IgA and IgG antigen specificity for selected pathogens in milk produced by women from diverse geographical regions: The INSPIRE Study

city: Irvine

first: Joseph

middle: John

last: Campo

state: CA

address: 1 Technology Dr., STE E309

institute: Antigen Discovery, Inc.

summary: This SuperSeries is composed of the SubSeries listed below.

platform_organism:
Bordetella pertussis
Staphylococcus aureus
Streptococcus sp. 'group B'
Mycobacterium tuberculosis
Plasmodium falciparum
Onchocerca volvulus
Yellow fever virus
Dengue virus
Human immunodeficiency virus
Respiratory syncytial virus
Chikungunya virus
Zika virus

overall_design: Refer to individual Series


title: BRD9 is a regulator of androgen receptor signaling and prostate cancer progression - ChIP-Seq

city: West Lafayette

first: Emily

last: Dykhuizen

state: IN

address: 201 S. University

department: medicinal chemistry and molecular pharmacology

institute: Purdue University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: BRD9 and BRD4 ChIP-Seq in LNCaP prostate cancer cells

overall_design: Examination of BRD9 and BRD4 localization in LNCaP cells with and without BRD9 bromodomain inhibition. Further analysis of BRD9 localization in LNCaP cells with knockout of GLTSCR1 and GLTSCR1L.

first: Sagar

last: Utturkar


title: Proprioception is governed by highly diverse and versatile sensory neuron types

city: Stockholm

first: Francois

last: Lallemend

state: Stockholm

address: Tomtebodavägen 16

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Proprioceptive neurons (PNs) are essential for the proper execution of all our movements by providing muscle sensory feedback to the central motor network. Here, using deep single cell RNAseq of adult PNs coupled with advanced virus- and genetic tracings, we have molecularly identified the 3 main types of PNs (Ia, Ib and II) and unexpectedly found that they segregate into 8 subgroups. Our data further reveal a highly sophisticated organization of PNs into discrete sensory input channels with distinct spatial distribution, innervation patterns and molecular profiles, that together contribute to the sensory monitoring of complex motor behavior. Moreover, while Ib- and II-PN subtypes are specified around birth, Ia-PN subtypes diversify later along with increased motor activity and show versatility in the adult following exercise training, suggesting adaptive proprioceptive function.

overall_design: Exploring the molecular heterogeneity of mouse proprioceptors at different developmental stages (E16.5, P5 and P54)

first: Haohao

last: Wu

first: Charles

last: Petitpré

first: Paula

last: Fontanet

first: Anil

last: Sharma

first: Carmelo

last: Bellardita

first: Rolen

middle: M

last: Quadros

first: Paulo

last: Jannig

first: Yiqiao

last: Wang

first: J

middle: A

last: Heimel

first: Kylie

middle: K

last: Cheung

first: Simone

last: Wanderoy

first: Yang

last: Xuan

first: Konstantinos

last: Meletis

first: Jorge

last: Ruas

first: Channabasavaiah

middle: B

last: Gurumurthy

first: Ole

last: Kiehn

first: Saida

last: Hadjab

first: François


title: microRNA regulation related to the protective effects of environmental enrichment against cocaine-seeking behavior

city: Tempe

first: Janet

last: Neisewander

state: AZ

address: 427 E Tyler Mall

department: SOLS

institute: Arizona State University

summary: MicroRNAs are “master regulators” of gene expression. To investigate microRNAs involved in the incentive motivation for cocaine elicited by exposure to cocaine-associated cues, we conducted NanoString nCounter analyses of microRNA expression in the nucleus accumbens shell of male rats that had been tested for cue reactivity in a previous study. These rats had been trained to self-administer cocaine while living in isolate housing, then during a subsequent 21-day forced abstinence period they either stayed under isolate housing or switched to environmental enrichment (EE), as this EE intervention is known to decrease cocaine seeking. This allowed us to create groups of “high” and “low” cocaine seekers using a median split of cocaine-seeking behavior. We conducted a differential expression analysis across these two groups that identified 33 miRNAs that were differentially altered in the nucleus accumbens shell. Predicted mRNA targets of these microRNAs are implicated in synaptic plasticity and neuronal signaling. Some of these microRNAs have previously been implicated in substance use disorders, while others are predicted to target large numbers of cocaine-related genes. Of the 33 differentially expressed microRNAs, 8 were specifically downregulated in the low-seeking group and another set of 8 had expression levels that were significantly correlated with cocaine-seeking. These findings suggest that processes involved in cocaine-seeking behavior may alter, or be altered by, multiple microRNAs. Further research examining the mechanisms involved in these microRNA changes and their effects on signaling may reveal novel therapeutic targets for attenuating drug craving.

overall_design: 12 samples (no replicates) of total RNA from the nucleus accumbens shell was collected from male Sprague-Dawley rats. miRNA expression analysis was performed using the Nanostring nCounter platform. Differential expression was performed using "limma" in R

first: Annika

last: Vannan

first: Gregory

last: Powell

first: Michela

last: Dell'Orco

first: Melissa

last: Wilson

first: Nora

middle: I

last: Perrone-Bizzozero


title: Distinct types of stem cell divisions determine organ regeneration and aging in hair follicles

city: Tokyo

first: Hiroyuki

last: Matsumura

state: Bunkyo-ku

address: Room 213, Chemistry East Building, Department of Chemistry, 7-3-1 Hongo

department: Graduate School of Science

country: Japan

institute: The University of Tokyo

summary: Aging organs functionally and structurally decline with the loss of their regenerative capabilities, yet the existence of distinct cell division programs that determine organ fates is unknown. Hair follicles, mammalian mini-organs that grow hair, miniaturize by aging. Here we report that hair follicle regeneration and aging are driven by distinct cell division types of hair follicle stem cells (HFSCs). Cell fate tracing and cell division axis analysis in mice revealed that HFSCs undergo symmetric and asymmetric cell divisions to generate a new bulge, yet preferentially provoke “stress-responsive type” asymmetric cell divisions that generate aberrantly differentiating cells upon age/stress. That dynamic program with repetitive divisions efficiently eradicates those cells through defective association and stabilization of a hemidesmosomal protein COL17A1 and a cell-polarity-protein aPKCλ in HFSCs, thereby causing organ aging. The forced stabilization of COL17A1 rescued organ aging through aPKCλ stabilization. These results demonstrate that distinct cell division programs govern tissue/organ fates.

overall_design: Hair follicle stem cells (HFSCs) and Interfollicular epidermis (IFE) from young/aged Col17a1, aPKCλ cKO and young/aged COL17A1 transgenic mice were FACS isolated and RNA was extracted before being hybridized Agillent microarray. We obtained a gene of list by comparing Young/Aged, Col17a1/aPKCλ cKO and young/aged COL17A1 transgenic mice.

first: Emi

last: Nishimura


title: Adaptive responses to mTOR targeting sustain hematopoietic and leukemia stem cell proliferation II

status: Public on Dec 24 2020

city: Cincinnati

first: Yi

last: Zheng

state: OH

address: 3333 Burnet Ave MLC7013

department: Experimental Hematology and Cancer Biology

institute: CINCINNATI CHILDRENS HOSP MED CTR

summary: mTOR is an important anti-cancer target that integrates diverse signals to control protein synthesis and cell growth. Numerous studies by using mTOR inhibitors and/or gene deletion of mTOR negative regulators have implicated mTOR targeting in suppressing gene expression and cell proliferation. However, we found that gene targeting of mTOR in mouse hematopoietic stem cells (HSCs) results in a loss of quiescence and increased proliferation. Adaptive to mTOR loss, mTOR-/- HSCs increase chromatin access and activate global gene expression, in contrast to short-term inhibition by mTOR inhibitors. Such genomic changes are due to a compensatory activation of a MAPK/Mnk/eIF4E signaling pathway that enhances the translation of RNA pol-II and consequent c-myc expression. This adaptive mechanism can also be adopted by leukemia stem cells undergone long-term mTOR inhibitor treatment to confer resistant to mTOR targeting. Our studies provide new insights and a foregone strategy for overcoming drug resistance in mTOR targeted therapy.

overall_design: Rapamycin and AZD treatments

first: Cuiqing

last: Fan


title: Declining Lamin B1 expression mediates age-dependent decreases of hippocampal stem cell activity

city: Zürich

first: Baptiste

last: Jaeger

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zürich

summary: Neural stem cells (NSCs) generate neurons throughout life in the hippocampal dentate gyrus (DG). With advancing age levels of neurogenesis sharply drop, which has been associated with a decline in hippocampal memory function. However, cell-intrinsic mechanisms mediating age-related changes in NSC activity remain largely unknown. Here we show that the nuclear lamina protein Lamin B1 (LB1) is downregulated with age in mouse hippocampal NSCs. LB1 is cross-regulated with Sun-domain containing protein 1 (SUN1), previously implicated in Hutchinson-Gilford progeria syndrome (HGPS), a disease of premature aging. LB1 and SUN1 govern the strength of a diffusion barrier in the membrane of the endoplasmic reticulum (ER) that is associated with the segregation of aging factors during NSC divisions. Balancing the levels of LB1 and SUN1 in aged NSCs restores the ER-diffusion barrier. Virus-based restoration of LB1 expression in aged NSCs enhances stem cell activity in vitro and increases progenitor cell proliferation and neurogenesis in vivo. Thus, we here identify a novel mechanism associated with the age-related decline of neurogenesis in the mammalian hippocampus.

overall_design: Comparison between young vs old NSCs and between old NSCs retrovirally transduced with IRES-CFP or Lamin B1-over-expressing-IRES-CFP. 100 cells of each condition were flow sorted into one well of a 384-well plate containing lysis buffer. 4 biological replicates were generated per condition (16 samples total). Wells in the 384-well were processed according to the SmartSeq2 protocol using a microliter pipetting robot and sequenced on an Illumunia NovaSeq.

first: Muhammad

last: Imtiaz

first: Sara

last: Bottes

first: Raquel

last: Machado

first: Mojca

last: Vidmar

first: Darcie

last: Moore

first: Sebastian

last: Jessberger


title: RNA-seq analysis of gene expression in cells during Ascl1 mediated astrocyte-to-neuron conversion.

city: Shanghai

first: Ran

last: Wang

address: 320 Yue Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

summary: We analyzed the transcriptomic changes in cells sorted from astrocyte-to-neuron conversion at different stages, identified the differentially expressed genes (DEGs), and functionally validated the critical DEGs.

overall_design: We collected cells and preformed RNA-seq at different time points during direct reprogramming of astrocytes into neurons.

first: Zhiping

last: Rao


title: ChIP-seq analysis of Ascl1 enrichment in astrocytes at day 2 after virus infection.

summary: The genome-wide binding sites of Ascl1 in astrocytes during direct reprogramming.

overall_design: Examination of Ascl1 enrichment distributions in astrocytes at day 2 after virus infection.


title: Multipathogen analysis of IgA and IgG antigen specificity for selected pathogens in milk produced by women from diverse geographical regions: The INSPIRE Study [IgG]

first: Joseph

last: Campo

summary: Breastfeeding provides defense against infectious disease during early life. The mechanisms underlying this protection are complex but likely include the vast array of immune cells and components, such as immunoglobulins, in milk. Simply characterizing the concentrations of these bioactives, however, provides only limited information regarding their potential relationships with disease risk in the recipient infant. Rather, understanding pathogen and antigen specificity profiles of milk-borne immunoglobulins might lead to a more complete understanding of how maternal immunity impacts infant health and wellbeing. Milk produced by women living in 11 geographically dispersed populations was applied to a protein microarray containing antigens from 16 pathogens, including diarrheagenic E. coli,  Shigella spp., Salmonella enterica serovar Typhi, Staphylococcus aureus, Streptococcus pneumoniae, Mycobacterium tuberculosis and other pathogens of global health concern, and specific IgA and IgG binding was measured. Our analysis identified novel disease-specific antigen responses and suggests that some IgA and IgG responses vary substantially within and among populations. Patterns of antibody reactivity analyzed by principal component analysis and differential reactivity analysis were associated with either lower-to-middle-income countries (LMICs) or high-income countries (HICs).  Antibody levels were generally higher in LMICs than HICs, particularly for Shigella and diarrheagenic E. coli antigens, although sets of S. aureus, S. pneumoniae, and some M. tuberculosis antigens were more reactive in HICs. Differential responses were typically specific to canonical immunodominant antigens, but a set of nondifferential but highly reactive antibodies were specific to antigens possibly universally recognized by antibodies in human milk. This approach provides a promising means to understand how breastfeeding and human milk protect (or do not protect) infants from environmentally relevant pathogens. Furthermore, this approach might lead to interventions to boost population-specific immunity in at-risk breastfeeding mothers and their infants.

overall_design: Human breast milk samples were probed on Antigen Discovery Inc. Multipathogen (Gen-1) Protein Microarrays for detection of antigen-specific IgG binding. This investigation was conducted as part of the “INSPIRE” study designed to characterize and compare complex carbohydrate and microbial community structure in milk produced by relatively healthy women around the globe. Briefly, women had to be healthy; breastfeeding or pumping at least 5 times daily; self-reported-healthy and nursing relatively healthy infants; ≥ 18 yr of age; and generally between 1 and 3 mo postpartum. Our 11 cohorts were drawn from 8 countries: rural and urban Ethiopia (ETR and ETU, respectively), rural and urban The Gambia (GBR and GBU, respectively), Ghana (GN), Kenya (KE), Peru (PE), Spain (SP), Sweden (SW) and the United States [Washington (USW) and California (USC)]. Ethics approvals were obtained for all procedures from each participating institution, with overarching approval from the Washington State University Institutional Review Board (#13264). A total of 413 women were enrolled in the study, and milk was collected from 412 of them. Here, we report data obtained from milk collected from 404 women as follows: ETR (n = 38), ETU (n = 40), GBR (n = 40), GBU (n = 40), GN (n = 40), KE (n = 42), PE (n = 43), SP (n = 41), SW (n = 24), USC (n = 15), USW (n = 41).

first: Michelle

last: McGuire

first: Arlo

middle: Z

last: Randall

first: Antti

middle: E

last: Seppo

first: Kirsi

last: Järvinen

first: Courtney

last: Meehan

first: Debela

last: Gindola

first: Janet

last: Williams

first: Daniel

middle: W

last: Sellen

first: Elizabeth

last: Kamau-Mbuthia

first: Egidioh

last: Kamundia

first: Samwel

last: Mbugua

first: Sophie

first: Andrew

last: Prentice

first: James

last: Foster

first: Gloria

last: Otoo

first: Juan

last: Rodríguez

first: Rossina

middle: G

last: Pareja

first: Lars

last: Bode

first: Mark

middle: J


title: Pressure-Driven Mitochondrial Transfer Pipeline Generates Mammalian Cells of Desired Genetic Combinations and Fates

city: Boston

first: Fasih

middle: Mubtasim

last: Ahsan

state: MA

address: 185 Cambridge Street, CPZN 6500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Generating mammalian cells with desired mtDNA sequences is enabling for studies of mitochondria, disease modeling, and potential regenerative therapies. MitoPunch, a high-throughput mitochondrial transfer device, produces cells with specific mtDNA-nDNA combinations by transferring isolated mitochondria from mouse or human cells into primary or immortal mtDNA-deficient (p0) cells. Stable isolated mitochondrial recipient (SIMR) cells isolated in restrictive media permanently retain donor mtDNA and reacquire respiration. However, SIMR fibroblasts maintain a p0-like cell metabolome and transcriptome despite growth in restrictive media. We reprogram non-immortal SIMR fibroblasts into induced pluripotent stem cells (iPSCs) with subsequent differentiation into diverse functional cell types, including mesenchymal stem cells (MSCs), adipocytes, osteoblasts, and chondrocytes. Remarkably, following reprogramming and differentiation, SIMR fibroblasts molecularly and phenotypically resemble un-manipulated control fibroblasts carried through the same protocol. Thus, our MitoPunch ‘pipeline’ enables the production of SIMR cells with unique mtDNA-nDNA combinations for additional studies and applications in multiple cell types.

overall_design: Total ribo-depleted bulk RNA-sequencing of mtDNA depleted (p0) BJ human neonatal foreskin fibroblasts transferred HEK 293 DsRed mitochondria (n = 3) or human peripheral blood mononuclear cell (LP351 PBMC) mitochondria (n = 3), compared to wildtype (BJ, n = 3) and mtDNA depleted (BJ p0, n = 3) fibroblasts. Transferred BJ fibroblasts were reprogrammed into iPSC (n = 2 of three isolated clones each, 6 total) and each clone differentiated into MSC (n = 2 of each matched clone, 6 total) for functional assesment. Reprogramming and differentiations were compared to wildtype BJ fibroblast generation of iPSCs (n = 3) and MSCs (n = 3) (n = 60 total samples).

first: Alexander

last: Patananan

last: Sercel

first: Ting-Hsiang

last: Wu

first: Michael

last: Teitell


title: Multipathogen analysis of IgA and IgG antigen specificity for selected pathogens in milk produced by women from diverse geographical regions: The INSPIRE Study [IgA]

first: Joseph

last: Campo

overall_design: Human breast milk samples were probed on Antigen Discovery Inc. Multipathogen (Gen-1) Protein Microarrays for detection of antigen-specific IgA binding. This investigation was conducted as part of the “INSPIRE” study designed to characterize and compare complex carbohydrate and microbial community structure in milk produced by relatively healthy women around the globe. Briefly, women had to be healthy; breastfeeding or pumping at least 5 times daily; self-reported-healthy and nursing relatively healthy infants; ≥ 18 yr of age; and generally between 1 and 3 mo postpartum. Our 11 cohorts were drawn from 8 countries: rural and urban Ethiopia (ETR and ETU, respectively), rural and urban The Gambia (GBR and GBU, respectively), Ghana (GN), Kenya (KE), Peru (PE), Spain (SP), Sweden (SW) and the United States [Washington (USW) and California (USC)]. Ethics approvals were obtained for all procedures from each participating institution, with overarching approval from the Washington State University Institutional Review Board (#13264). A total of 413 women were enrolled in the study, and milk was collected from 412 of them. Here, we report data obtained from milk collected from 404 women as follows: ETR (n = 38), ETU (n = 40), GBR (n = 40), GBU (n = 40), GN (n = 40), KE (n = 42), PE (n = 43), SP (n = 41), SW (n = 24), USC (n = 15), USW (n = 41).

first: Michelle

last: McGuire

first: Arlo

last: Randall

first: Antti

last: Seppo

first: Kirsi

last: Järvinen

first: Courtney

last: Meehan

first: Debela

last: Gindola

first: Janet

last: Moore


title: MazF toxin causes alterations in Staphylococcus aureus transcriptome, translatome and proteome that underlie bacterial dormancy

city: Manchester

first: Fedor

last: Bezrukov

address: Brunswick Street, Schuster laboratory

department: Department of Physics and Astronomy

country: United Kingdom

institute: The University of Manchester

summary: Bacterial antibiotic resistance is as a serious health problem. Antibiotic resistance appears either because of mutations or as a result of a bacteria dormant state without heritable genetic change. This non-growing state allows bacteria to survive antibiotic treatment. The mechanisms of entrance to the bacterial dormant state are unknown. It has been suggested that toxin-antitoxin systems (TASs) are possible controlling factors for cell dormancy. In Staphylococcus aureus, the role of TASs genome-wide and their link to the dormancy induction mechanisms has not been investigated in detail. In this study, we analyzed the role of MazF toxin on transcriptome, translatome and proteome of S. aureus using RNA-Seq, Ribo-Seq and quantitative proteomics. We characterized the correlation between transcription, translation, and protein levels, and demonstrated that the MazF endonuclease decreases translation directly by cleaving mRNA, and indirectly, by decreasing translation factors and by promoting ribosome hibernation. Thus, MazF represses transcription and translation of many genes rather than a particular set of genes. Nevertheless, several specific pathways affected by MazF were identified: we demonstrated that cell wall thickness is increased and cell division is decreased upon MazF induction. MazF cleaves mRNA in vivo, creating stop-less transcripts and stalled ribosomes. These stalled ribosomes are rescued by SsrA-system, which is activated upon MazF induction. Finally, we described the overall impact of MazF on S. aureus metabolism, and propose one of the mechanisms by which MazF may induce bacterial dormancy.

overall_design: Samples in dupicates RNA-Seq and Ribo-Seq of WT with pRAB11 vector, ΔmazEF with pRAB11, and ΔmazEF with pRAB11 vector expressing inducible MazF. All samples submited to RNA-Seq and Ribo-Seq.

first: Julien

last: Prados

first: Adriana

last: Renzoni

first: Olesya

last: Panasenko


title: Hypermethylation and global remodeling of DNA methylation associated with acquired cisplatin resistance in testicular germ cell tumors

city: Urbana

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

summary: Testicular germ cell tumors (TGCTs) are hypersensitive to cisplatin-based therapy however cisplatin resistance and poor outcomes do occur in a significant number of patients. It has been suggested that a shift toward DNA hypermethylation mediates cisplatin resistance in TGCT cells, although there is little direct evidence to support this claim. Here we utilized a series of isogenic cisplatin resistant cell models and observed a strong association between cisplatin resistance in TGCTs cells and a net increase in global CpG and non-CpG DNA methylation spanning regulatory, intergenic, genic and repeat elements. Hypermethylated loci were significantly enriched for repressive DNA segments, CTCF and RAD21 sites and lamina associated domains, suggesting that global nuclear reorganization of chromatin structure occurred in resistant cells. Hypomethylated CpG loci were significantly enriched for EZH2 and SUZ12 binding and H3K27me3 sites. Integrative transcriptome and methylome analysis showed a strong negative correlation between gene promoter CpG island methylation and gene expression in resistant cells and a weaker positive correlation between gene body methylation and gene expression. A bidirectional shift between gene promoter and gene body DNA methylation occurred within multiple genes that was associate with upregulation of polycomb targets and downregulation of tumor suppressor genes. These data support the hypothesis that global remodeling of DNA methylation is a key factor in mediating cisplatin hypersensitivity and chemoresistance of TGCTs and furthers the rationale for hypomethylation therapy for refractory TGCT patients.

overall_design: Bisulphite converted DNA from the 21 samples were hybridised to the Infinium MethylationEPIC beadchip array

first: Zeeshan

last: Fazal


title: DNA Methyaltion of Human Cortical Organoids

city: Los Angeles

first: Aaron

last: Gordon

address: 695 Charles E. Young Drive South, Gonda 2306, Los Angeles, CA  90095-1761

department: Neurology

institute: UCLA

summary: Assesing DNA methylation patterns of human cortical organoids during long term (>600 days) maturation.

overall_design: 52 samples collected during long term maturation of human cortical spheroids

first: Se

last: Yoon

first: Sergiu

middle: P

last: Pasca

first: Daniel

last: Geschwind


title: Towards a Humanized mouse model of Pneumocystis Pneumonia

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: Humanized NOG-EXL (huNOG-EXL) mice control P. murina infection significantly better than control NOG-EXL mice, as evidenced by markedly decrased lung fungal burdens at both 3 and 6 weeks post-infection. Human cytokine-generating CD4+ and CD8+ T cells in the lung and serum IgM antibody, which were specifically in responses to pneumocystis antigen, were detected in huNOG-EXL mice only. For humanized NOG-EXL mouse group at 6 weeks post-infection, the whole lung RNAseq analyses were performed and the data indicated that the lower lung fungal burden is associated with higher CD209 gene expression.

overall_design: Groups of humanized NOG-EXL and control NOG-EXL mice were infected with Pneumocystis murina. Three and six weeks post-infection, mouse lung fungal burden, cytokine-generating cells and serum antibody levels were measured. For humanized NOG-EXL group at 6 weeks post-infection, the whole lung RNAseq was analyzed.

first: Guaxiang

last: Dai

first: Alanna

last: Wanek

first: Taylor

last: Eddens

first: Paul

last: Volden

first: Kejing

last: Song


title: Dock3 is essential for normal myogenic fusion and alters dystrophin-deficiency pathologies

city: Birmingham

first: Matthew

middle: S

last: Alexander

state: AL

address: 1900 University Blvd. THT 929 Box# 96

department: Pediatrics

institute: University of Alabama at Birmingham

summary:
DOCK3 is a member of the DOCK family of guanine nucleotide exchange factors that function to regulate cell migration, fusion, and overall viability. Previously, we identified a miR-486/Dock3 signaling cascade that was dysregulated in dystrophin-deficient muscle which resulted in the overexpression of DOCK3, however not much else is known about the role of DOCK3 in muscle. In this work, we characterize the functional role of DOCK3 in normal and dystrophic striated muscle.
By utilizing the Dock3 global knockout (Dock3 KO) mice, we found reducing Dock3 gene via haploinsufficiency in DMD mice improved muscle histology, however full loss of Dock3 worsened overall muscle function on a dystrophin-deficient background. Consistent with this, Dock3 KO mice have impaired muscle architecture, myoblast fusion defects, and cardiac functional deficits. Moreover, transcriptomic analyses of Dock3 knockout muscles reveal a decrease in factors known for myoblast fusion, suggesting a possible mechanism of action.
These studies identify DOCK3 as a novel modulator of muscle fusion and muscle health, and may yield additional therapeutic targets for treating dystrophic muscle symptoms.

overall_design: RNA-seq from adult tibialis anterior (TA) skeletal muscles from wild type and Dock3 KO mice (n=3 muscles per genotype cohort).

first: Yimin

last: Wang

first: Andrea

middle: L

last: Reid

first: Rylie

last: Hightower

first: Lara

last: Ianov

first: David

last: Crossman

first: Louis

last: Dell’Italia

first: Thomas

last: van Groen

first: Ganesh

middle: V

last: Halade


title: Transcription landscape of adipose tissue and tumor in response to adipose stromal cell depletion

status: Public on Dec 23 2020

city: Houston

first: Yulin

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

summary: Mice grafted with Myc-Cap tumor were treated (3 weeks) with a pro-apoptotic peptide D-CAN targeting adipose stromal cells or PBS (control).

overall_design: In the end of treatment, tumor cells and stromal/vascular cells from subcutaneous inguinal adipose tissue (SAT) were analyzed.

first: Mikhail

last: Kolonin

first: Alexes

last: Daquinag


title: GLP-1 receptor signaling increases PCSK1 and beta-cell features in human alpha-cells

city: Ithaca

first: Mridusmita

last: Saikia

state: NY

address: 111 Weill Hall, 237 Tower Road

institute: Cornell University

summary: Glucagon-like peptide-1 (GLP-1) is an incretin hormone that potentiates glucose  stimulated insulin secretion. GLP-1 is classically produced by gut L cells; however, under  certain circumstances alpha-cells can express the prohormone convertase required for  proglucagon processing to GLP-1, prohormone convertase 1/3 (PC1/3), and can produce  GLP-1. However, the mechanisms through which this occurs are poorly defined.  Understanding the mechanisms by which alpha-cell PC1/3 expression can be activated  may reveal new targets for diabetes treatment. Here, we demonstrate that the GLP-1  receptor (GLP-1R) agonist, liraglutide, increases alpha-cell GLP-1 expression in a beta  cell GLP-1R-dependent manner. We demonstrate that this effect of liraglutide is  translationally relevant in human islets through application of a new scRNA-sequencing  technology, DART-seq. We find that the effect of liraglutide to increase alpha-cell PC1/3  mRNA expression occurs in a sub-cluster of alpha-cells and is associated with increased  expression of other beta-cell-like genes, which we confirm by IHC. Finally, we find that  the effect of liraglutide to increase bi-hormonal insulin+ glucagon+ cells is mediated by the  beta-cell GLP-1R in mice. Together, our data validate a new high-sensitivity method for  scRNA-sequencing in human islets and identify a novel GLP-1 mediated pathway  regulating human alpha-cell function.

overall_design: Single cell RNA-sequencing was performed on human islet samples obtained from three healthy male donors. Each sample was treated with either Saline (Ctrl) or Liraglutude (Lira). For data analysis all three data sets in each category i.e. Ctrl and Lira, were combined and then compared to obtain differentially expressed genes in response to liraglutide treatment.

first: Marlena

last: Holter

first: Leanne

middle: R

last: Donahue

first: Isaac

last: Lee

first: Qiaonan

middle: C

last: Zheng

first: Journey

last: Wise

first: Jenna

last: Todero

first: Daryl

last: Phuong

first: Reilly

last: Coch

first: Kyle

last: Sloop

first: Adolfo

last: Garcia-Ocana

first: Charles

last: Danko

first: Bethany

last: Cummings


title: Knock down of C11orf67 by shRNA in SUM52PE

city: Nedlands

first: Pilar

last: Blancafort

address: 6 Verdun Street

department: Cancer and Cell Biology

country: Australia

institute: Harry Perkins Institute of Medical Research

summary: SUM52PE cells were lentivirally transduced with PKLO empty vector control (Sigma SHC001 MISSION PLKO.1-PURO CONTROL VECTOR) or shRNA specific for C11orf67 (Sigma Clone ID: NM_024684.2-280s21c1 SHCLND-NM_024684 TRCN0000263814) in biological triplicates. Differentially regulated targets  by the shRNA relative to empty vector control were determined.

overall_design: triplicates

first: Sgro

last: Agustin


title: SUM52PE treated with PI3K-mTOR inhibitors

summary: PI3K/mTOR inhibition alters gene transcription signatures involved in metabolism and cell cycle control in the human breast cancer cell line, SUM52PE

overall_design: SUM52PE cells were cultured in triplicate for 72h with the P13K/mTOR inhibitors dactolisib, everolimus, AZD-8055 or buparlisib, before RNA was isolated and submitted for RNA-Seq

first: Eleanor

last: Woodward

first: Emily

last: Golden

first: Andrew

last: Woo

first: Joseph

last: Cursons


title: An in-vivo screen of noncoding elements reveals that Daedalus is a gatekeeper of a novel Ikaros-dependent checkpoint during haematopoiesis I

city: New Haven

first: Christian

last: Harman

state: Connecticut

address: 300 Cedar Street, The Anlyan Center

department: Genetics/Immunobiology

institute: Yale University

summary: The development of all lymphoid lineages relies on a tightly-controlled series of gene expression patterns as development proceeds through a series of progenitors1-8. These gene expression patterns are understood to be controlled by lineage-specifying transcription factors, however these factors often are found to have broad expression patterns and activities across lineages. Given their role in regulating cell-type specific gene expression, noncoding loci are thought be important in the lineage-specific regulation of this complex process6,9-16. To identify transcripts that might mark such loci, we performed transcriptomic analysis in terminally differentiated murine CD4 effector T lymphocytes. Our analysis identified a variety of loci containing dynamically expressed noncoding RNAs and we tested their role in the lymphoid lineage using an in-vivo CRISPR knockout-mouse screen. This approach revealed that a non-coding locus proximal to the haematopoietic transcription factor Ikaros17,18, named Daedalus, exerted control over the earliest fate decisions during lymphoid lineage commitment. Deletion of Daedalus led to a cell-autonomous reduction in bone marrow and thymic lymphoid progenitor populations, phenocopying Ikaros deficient strains. Strikingly, loss of Daedalus resulted in a loss of Ikaros protein expression without impacting total Ikaros transcript levels. Finally, we identify a novel Ikaros regulated erythroid-lymphoid checkpoint that is governed by Daedalus in a lymphoid-lineage specific manner. Daedalus appears to act as a gatekeeper of Ikaros’s broad lineage specifying functions, selectively stabilizing Ikaros activity in the lymphoid lineage and permitting diversion to the erythroid fate in its absence. To our knowledge, these findings represent the first illustration of how a transcription factor with broad lineage expression must work in concert with non-coding elements to orchestrate haematopoietic lineage specification and commitment.

overall_design: In order to uncover novel non-coding loci with the potential to regulate lymphoid cell biology, whole transcriptomic analysis of purified T-cell populations was conducted. Populations of CD4 “memory-like” (CD44hi CD62L-) and “naïve” (CD44- CD62Lhi) cells were sorted from mouse lymph nodes. Separately, naïve T-cells from wild-type mice were sorted and polarized under neutral “Th0” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th0” culture conditions, antibodies blocking Il-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and Il2 is added to stimulate T-cell differentiation and proliferation. In addition, purified populations of “naïve” CD4 T-cells were sorted from several reporter mouse lines were isolated, polarized into effector subsets in culture and sorted using reporter expression to generate highly purified effector populations. Naïve CD4 T-cells from IFNγ, Il-4, Il-9, Il-17 and FoxP3 reporter mice were sorted and polarized under Th1, Th2, Th9, Th17 and Treg conditions respectively. Purified populations were obtained by fluorescence-activated cell sorting of cells expressing the respective reporter genes to generate CD4 effector T-cell populations with a very high purity. RNA was extracted from these populations, along with from Th0-polarized effector CD4 cells and the naïve and memory populations described previously. This RNA was then used for a transcriptomic analysis by RNA-sequencing in order to identify differentially expressed RNAs between different effector T-cell populations that might mark important noncoding loci.

first: Will

last: Bailis

first: Jun

last: Zhao

first: Rihao

last: Qu

first: Ruaidhrí

last: Jackson

first: Justin

last: Shyer

first: Holly

last: Steach

first: Yuval

last: Kluger

first: Loyal

last: Goff

first: John

last: Rinn

first: Adam

last: Williams

first: Jorge

last: Henao-Mejia

first: Richard

last: Flavell


title: An in-vivo screen of noncoding elements reveals that Daedalus is a gatekeeper of a novel Ikaros-dependent checkpoint during haematopoiesis

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: H-NS-like proteins in Pseudomonas aeruginosa coordinately silence intragenic transcription [ChIP-seq]

middle: M

last: Lippa

address: 300 Longwood Ave

department: Pediatrics, Division of Infectious Diseases

institute: Boston Children's Hospital

summary: The H-NS-like proteins MvaT and MvaU act coordinately as global repressors in Pseudomonas aeruginosa by binding to AT-rich regions of the chromosome. Although cells can tolerate the loss of either protein, identifying their combined regulatory effects has been challenging because the loss of both proteins is lethal due to induction of prophage Pf4 and subsequent superinfection of the cell. In other bacteria, H-NS promotes cellular fitness by inhibiting intragenic transcription from AT-rich target regions, preventing them from sequestering RNA polymerase; however, it is not known if whether MvaT and MvaU function similarly. Here we utilize a parental strain that cannot be infected by Pf4 phage to define the collective MvaT and MvaU regulon and demonstrate that the combined loss of both MvaT and MvaU leads to increased intragenic transcription from loci directly controlled by these proteins. We further show that the loss of MvaT and MvaU leads to a striking redistribution of RNA polymerase containing σ70 to genomic regions vacated by these proteins. Our findings suggest that the ability of H-NS-like proteins to repress intragenic transcription is a universal function of these proteins and point to a second mechanism by which MvaT and MvaU may contribute to the growth of P. aeruginosa.

overall_design: Genome-wide locations of RpoD in a parental strain lacking pilY1 and a strain with additional deletions of mvaU and mvaT. Also, genome-wide locations of MvaT and MvaU in wild-type cells.

first: Michael

last: Gebhardt

first: Simon

last: Dove


title: Multi-scale architecture of archaeal chromosomes

city: Kyoto

first: Naomichi

last: Takemata

address: Kyoto University, Katsura, Nishikyo-ku

department: Synthetic Chemistry and Biological Chemistry

institute: Kyoto University

summary: Chromosome conformation capture (3C) technologies have identified topologically associating domains (TADs) and larger A/B compartments as two salient structural features of eukaryotic chromosomes. These structures are sculpted by the combined actions of transcription and structural maintenance of chromosomes (SMC) superfamily proteins. Bacterial chromosomes fold into TAD-like chromosomal interaction domains (CIDs) but do not display A/B compartment-type organization. Here, we reveal that chromosomes of Sulfolobus archaea are organized into CID-like topological domains in addition to the larger A/B compartment-type structures that we described recently. We uncover local rules governing the identity of the topological domains. We also identify long-range loop structures which provide evidence of a hub-like structure that colocalizes genes involved in ribosome biogenesis. In addition to providing high resolution description of archaeal chromosome architectures, our data provide evidence for multiple modes of organization in prokaryotic chromosomes and yield novel insight into the evolution of eukaryotic chromosome conformation.

sample_organism:
Sulfolobus acidocaldarius
Saccharolobus islandicus

overall_design: 3C-seq and RNA-seq experiments were performed on Sulfolobus acidocaldarius and Sulfolobus islandicus.

first: Stephen

middle: D

last: Bell


title: Genome-scale deconvolution of RNA structure ensembles

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary:
RNA structure heterogeneity is a major challenge when querying RNA structures with chemical probing. We introduce DRACO, an algorithm for the deconvolution of coexisting RNA conformations from mutational profiling experiments.
Analysis of the SARS-CoV-2 genome using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and DRACO, identifies multiple regions that fold into two mutually exclusive conformations, including a conserved structural switch in the 3′ untranslated region. This work may open the way to dissecting the heterogeneity of the RNA structurome.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: DMS-MaPseq

first: Edoardo

last: Morandi

first: Ilaria

last: Manfredonia

first: Lisa

last: Simon

first: Francesca

last: Anselmi

first: Martijn

last: van Hemert

first: Salvatore

last: Oliviero


title: CYGB+ expressing vs non cytoglobin expressing cells (NCE) (MOCK)

first: Garret

last: Rochford

state: West Midlands

address: School of Biosciences

department: School of Biosciences

institute: University of Birmingham

summary: High cytoglobin expressing cells from the PECA/PJ41 parent cells lines were compared against the trancription expression profile of non-cytoglobin expressing cells also from the PECA/PJ41 cell line

overall_design: Two condition experiment: CYGB+ vs NCE (MOCK), Both conditions run in on multiple separate ocassions

first: Lorna

last: Thorne

first: Timothy

first: Andrew

last: Southam

first: Giovanny

last: Rodriguez-Blanco

first: Warwick

last: Dunn

first: Nikolas

last: Hodges


title: ActivinA-derived human embryonic stem cells show increased competence to differentiate into primordial germ cell-like cells

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

summary: Robust differentiation of hPGCLCs starting from hESCs is currently hampered by the inherent heterogenous nature of different hESC lines. Here, we show that hESC lines, that were both derived and cultured in the presence of ActA, show high competence to differentiate to PGCLCs, in particular if transiently converted to the 4i-state prior to differentiation. We performed a robust and systematic comparison of isogenic lines and provide an optimized protocol to obtain PGCLCs from hESCs.

overall_design: mRNA profiles of traditional and Activin A derived hESC in primed and 4i pluripotent states, Primordial germ cell-like cells (PGCLCs) derived from Activin derived hESC, somatic fraction from differentiation of hESCs to PGCLCs

first: Swati

last: Mishra

first: Susana

last: Lopes

first: Jasin

last: Taelman

first: Mina

last: Popovic

first: Evi

last: Duthoo

first: Margot

last: Van der Jeught

first: Dieter

last: Deforce

first: Björn

last: Menten

first: Filip

last: Nieuwerburgh

first: Petra

last: De Sutter

last: Heindryckx


title: Chromatin Protein PC4 Orchestrates B Cell Differentiation by Collaborating with IKAROS and IRF4 (RRBS)

status: Public on Dec 22 2020

city: Sendai

first: Kyoko

last: Ochiai

address: 2-1, Seiryo-machi, Aobaku

department: Biochemistry

institute: Tohoku University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: Chromatin protein positive coactivator 4 (PC4) has multiple functions, including chromatin compaction. However, its role in immune cells is largely unknown. We show that PC4 orchestrates chromatin structure and gene expression in mature B cells. B-cell specific PC4-deficient mice showed impaired production of antibody upon antigen stimulation. The PC4 complex purified from B cells contained transcription factors IKAROS and IRF4. IKAROS protein was reduced in PC4-deficient mature B cells, resulting in de-repression of their target genes in part by diminished interactions with gene silencing components. Upon activation, IRF4 protein amount was not increased in PC4-deficient B cells, resulting in reduction of plasma cells. Importantly, IRF4 reciprocally induced PC4 expression via a super-enhancer. PC4 knockdown in human B-cell lymphoma cells reduced IKAROS protein as an anticancer drug lenalidomide. Our findings establish PC4 as a chromatin regulator of B cells and a possible therapeutic target adjoining IKAROS in B-cell malignancies.

overall_design: Function and regulation of PC4 in B cells.

first: Hitoshi

last: Hiura

first: Takahiro

last: Arima

first: Ryo

last: Funayama

first: Keiko

last: Nakayama

first: Kazuhiko

last: Igarashi


title: Ubiquitin-dependent remodeling of the actin cytoskeleton drives cell fusion

city: Berkeley

first: Michael

last: Rape

address: 1951 Oxford St Li Ka Shing Center, 330A

institute: University of California, Berkeley

summary: Cell-cell fusion is a frequent and essential event during development, and its  dysregulation causes diseases ranging from infertility to muscle weakness. Fusing  cells repeatedly need to remodel their plasma membrane by orchestrated formation  and disassembly of cortical actin filaments, but how the dynamic reorganization of the    actin cytoskeleton control is still poorly understood. Here, we identified a ubiquitin-  dependent toggle switch that establishes reversible actin bundling during mammalian    cell fusion. We found that EPS8-IRSp53 complexes stabilize cortical actin bundles at  sites of cell contact, which in part pushes cells towards each other. Conversely, EPS8  monoubiquitylation by CUL3KCTD10 displaces EPS8-IRSp53 from membranes and  counteracts actin bundling, a dual activity that allows apposed cells to progress with  fusion. We conclude that cytoskeletal rearrangements during development are  precisely controlled by ubiquitylation, raising the possibility to modulate the efficiency of  cell-cell fusion for therapeutic benefit.

overall_design: RNA-seq analysis was performed on undiffernitataed myoblasts cells seeded at subcondluent densities, and treated with ON-TARGETplus Non-targeting Control (Horizon Discovery; D-001810-03 UGGUUUACAUGUUUUCUGA), or ON-TARGET plus siRNA siKctd10 #1 mouse (Horizon Discovery; J-057526-05 CCAGCAAUUCUGACGAUAA)

first: Fernando

last: Rodriguez Perez


title: COCO/DAND5 inhibits developmental and pathological ocular angiogenesis

city: Montreal

first: Bruno

last: Larrivée

state: Quebec

address: 5415 Boul. L'Assomption

country: Canada

institute: Hôpital Maisonneuve-Rosemont

summary: Neovascularization contributes to multiple visual disorders including age-related macular degeneration (AMD). Current therapies for treating ocular angiogenesis are centered on the inhibition of vascular endothelial growth factor (VEGF). While clinically effective, some AMD patients are refractory or develop resistance to anti-VEGF and concerns of increased risks of developing geographic atrophy following long-term treatment have been raised. Identification of alternative pathways to inhibit pathological angiogenesis is thus important. We have identified a novel inhibitor of angiogenesis, COCO/DAND5, a member of the Cerberus-related DAN family. We demonstrate that COCO inhibits sprouting, migration and cellular proliferation of cultured endothelial cells. Intravitreal injections of COCO inhibited retinal vascularization during development and in models of retinopathy of prematurity and AMD. COCO equally abrogated angiogenesis in choroid explants and in a model of choroidal neovascularization. Mechanistically, COCO inhibited the expression of TGFβ and BMP pathwaysand altered ATP production, glucose uptake and redox balance of endothelial cells. Together, these data show that COCO is an inhibitor of retinal and choroidal angiogenesis, possibly representing a therapeutic option for the treatment of neovascular ocular diseases.

overall_design: HUVEC cells treated with or without COCO for 16 hours, in quadruplicate. Transcriptomic analysis using Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific) according to manufacturer's instructions.

first: Natalija

first: Erika

last: Hooker

first: Andrea

last: Barabino

first: Anthony

last: Flamier

first: Frédéric

last: Provost

first: Gilbert

last: Bernier

first: Manuel

last: Buscarlet


title: High-Throughput Analysis of Lung Immune Cells in a Combined Murine Model of Agriculture Dust-Triggered Airway Inflammation with Rheumatoid Arthritis

city: Omaha

first: Rohit

last: Gaurav

state: NE

address: 985910 Nebraska Medical Center

department: Internal Medicine-Allergy

institute: University of Nebraska Medical Center

summary: We report identification of 14 unique immune cell populations among different treatment groups with single-cell RNA sequencing high throughput technology. We identified (a) 3 unique neutrophil populations including inflammatory, transient and immunosuppressive/autoreactive granulocytes among experimental groups, (b) heterogeneity among 5 macrophage populations including metabolically active, proliferative, differentiating, recruited, and residential with classical (M1) and alternatively (M2)-activated genes, (c) identification of 2 stages of T-lymphocytes (differentiating and effector), a B-cell population and a NK cell cluster, (d) variability in the distribution of cellular clusters among the treatment groups representing RA and RA-associated lung disease (CIA and CIA+ODE groups, respectively), (e) identification of gMDSC and mMDSC populations based on cell surface markers, and (f) identification of unique genes (interferon-related/autoimmune and complement cascade) that are found in a mouse model of RA-associated inflammatory lung disease. This study identified unique populations of lung immune cell clusters differentially ascribed to individual treatment conditions. We identified neutrophil subpopulations and heterogeneous macrophage-monocyte populations in addition to unique genes (interferon-related and complement cascade) that could be contributing to the pathogenesis of RA-associated lung disease. Additionally, this information might inform potential candidates that could be exploited in future investigations examining targeted interventions and the identification of informative disease biomarkers.

overall_design: Examination of lung immune cells among treatment groups

first: Jill

middle: A

last: Poole


title: Inflammatory monocyte-derived S1P in the lymph node regulates immune response

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Sphingosine 1-phosphate (S1P), a lipid chemoattractant, guides immune cells from the low-S1P environment of tissues into the high-S1P environment of circulatory fluids.  Most notably, S1P directs T cell exit from lymph nodes (LN), where T cells are initially activated to fight pathogens, into lymph, from which T cells flow into blood and ultimately reach inflamed tissues.  T cells follow these gradients primarily using S1P receptor 1 (S1PR1).  The drugs Gilenya and Siponimod, both FDA-approved for the autoimmune disease multiple sclerosis, target S1PR1.  They blind self-reactive T cells to S1P gradients, block them from exiting LN, and thus prevent them from infiltrating the central nervous system.  While recent work has revealed key aspects of how S1P gradients are established at steady-state, very little is known about S1P distribution in disease, and in turn how changing S1P gradients may affect the immune response.  Here, we find that LN S1P increases during an immune response, which prolongs the time T cells spend in the LN before exiting into lymph.   Inflammatory monocytes, which had not previously been implicated in shaping S1P gradients, are an important source of this S1P.  Inflammatory monocytes must express the early activation marker CD69 to supply S1P to T cells; CD69 represses transcription of S1P receptor 5 (S1pr5), enabling monocytes to infiltrate the LN T zone and efficiently release S1P. Here we compared RNA sequencing of inflammatory monocytes WT or CD69-KO infiltrating the draining lymph node.$

overall_design: 12 hours after Poly (I:C) immunization, WT and CD69 KO inflammatory monocytes (CD11b, Ly6C high), sorted from lymph node of mixed BM chimeras (1:1 WT:CD69-KO BM)  were analyzed by RNA-seq

first: Audrey

last: Baeyens

first: Susan

last: Schwab


title: H-NS-like proteins in Pseudomonas aeruginosa coordinately silence intragenic transcription [RNA-seq]

city: Boston

first: Andrew

last: Lippa

overall_design: RNA-sequencing of P. aeruginosa strain PAO1 ∆pilY1 (parental) and the parental strain lacking either mvaU alone or both mvaU and mvaT.

last: Gebhardt

first: Simon

last: Dove


title: An in-vivo screen of noncoding elements reveals that Daedalus is a gatekeeper of a novel Ikaros-dependent checkpoint during haematopoiesis [scRNA-seq]

first: Christian

last: Harman

overall_design: In order to accurately assess in an unbiased fashion the effect of Daedalus deletion on haematopoiesis a single cell transcriptomic analysis was performed to dissect the specific changes in progenitor populations that occur in the absence of this locus. Single cell sequencing was performed on progenitor populations from wild-type and Daedalus-/- littermate bone marrow, with expression of the tyrosine kinase receptor cKit and exclusion of cells expressing lineage markers (Lineage cocktail consisted of antibodies against CD4, CD8, CD11b, CD11c, CD19, Gr1, NK1.1, TCRgd, and Ter119) used to enrich for haematopoietic progenitors in the bone marrow.

first: Will

last: Bailis

first: Jun

last: Zhao

first: Rihao

last: Qu

first: Ruaidhrí

last: Jackson

first: Justin

last: Shyer

first: Holly

last: Steach

first: Yuval

last: Kluger

first: Loyal

last: Goff

first: John

last: Rinn

first: Adam

last: Williams

first: Jorge

last: Henao-Mejia

first: Richard

last: Flavell


title: An in-vivo screen of noncoding elements reveals that Daedalus is a gatekeeper of a novel Ikaros-dependent checkpoint during haematopoiesis III

overall_design: In order to assess the effect of Daedalus knockout on genome-wide chromatin accessibility, ATAC-seq was performed on sorted progenitors from Daedalus-/- mice and wild-type littermates. This assay permits assessment of changes in chromatin accessibility on a genome-wide scale, enabling determination of whether the loss of Daedalus disrupts histone remodeling at known Ikaros-regulated loci. Ikaros is known to act primarily as a part of the chromatin-modifying NuRD complex, exerting its function on gene expression through epigenetic modifications that affect locus accessibility. Since deletion of the Daedalus locus leads to apparent disruption of Ikaros function, it was hypothesized that changes in chromatin accessibility would be observed in the Daedalus knockout cells.


title: Treatment of granuloma annulare and suppression of pro-inflammatory cytokine activity with tofacitinib [scRNA-Seq]

first: William

last: Damsky

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

summary: Granuloma annulare (GA) is a common inflammatory cutaneous disorder characterized by macrophage accumulation and activation in the skin. Its pathogenesis is poorly understood and there are no reliably effective treatments. Its potential health implications, if any, are unknown. Using single cell RNA sequencing (scRNAseq) we show that in GA, CD4+ T cells over-produce interferon (IFN)-g resulting in inflammatory polarization of macrophages and in altered extracellular matrix (ECM) production induced by the activity of oncostatin M, an interleukin (IL)-6 family cytokine, on fibroblasts. This mechanism identifies Janus kinase (JAK) inhibition as a potential therapeutic strategy, as both IFN-g and OSM signal via the JAK-STAT pathway. Indeed, treatment of five patients with severe, longstanding GA with tofacitinib (a JAK1/3 inhibitor) resulted in clinical and histologic disease remission in three patients and marked improvement in the other two. Treatment was associated with suppression of pathogenic cytokine activity in the skin and dissolution of macrophages. We also found that severe GA was associated with hypercytokinemia in plasma of patients, and JAK inhibition normalized this hypercytokiemia. Together, our results highlight the constitutive activity of the JAK-STAT pathway in GA as a result of IFN-g and OSM and identify JAK inhibitors as a potential molecularly targeted treatment for this disorder.

overall_design: 4 mm punch biopsies of skin were obtained on separate days from 3 patients with GA and 3 healthy volunteers. Biopsies were immediately dissociated using dispase (10 mg/mL) followed by liberase. Live single cells were purified by FACS and single cell libraries were prepared using a 10X chromium controller according to the manufacturer’s instructions and sequenced using an Illumina Hiseq 4000.

first: Alice

last: Wang

first: Nur-Taz

last: Rahman

first: Meaghan

middle: K

last: McGeary

first: Michael

last: Murphy

first: Austin

last: McHenry

first: Danielle

last: Peterson

first: Marcus

last: Bosenberg

first: Brett

last: King


title: Implication of TIGIT+ human memory B cells in immune regulation

city: Scottsdale

first: Sangkon

last: Oh

address: 13400 east Shea street

department: immunology

institute: Mayo Clinic

summary: Regulatory B cells (Bregs) contribute to immune regulation. However, the mechanisms of action of Bregs remain elusive. Here, we report that T cell immunoreceptor with Ig and ITIM domains (TIGIT) expressed on human memory B cells especially CD19+CD24hiCD27+CD39hiIgD−IgM+CD1c+ B cells is essential for effective immune regulation. Mechanistically, TIGIT on memory B cells controls immune response by directly acting on T cells and by arresting proinflammatory function of dendritic cells, resulting in the suppression of Th1, Th2, Th17, and CXCR5+ICOS+ T cell response while promoting immune regulatory function of T cells. TIGIT+ memory B cells are also superior to other B cells at expressing additional inhibitory molecules, including IL-10, TGFβ1, granzyme B, PD-L1, CD39/CD73, and TIM-1. Lack or decrease of TIGIT+ memory B cells is associated with increased donor-specific antibody and TFH response, and decreased Treg response in renal and liver allograft patients. Therefore, TIGIT+ human memory B cells play critical roles in immune regulation.

overall_design: We  divided peripheral blood B cells of healthy individuals into six different populations based on the expression levels of surface molecules, including IgD, CD24, CD27, CD38 and CD39 . 100-200K cells from each subsets were used for RNA extaction just right after cell sorting  and equal number of cells were stimulated with CpG-B for 16 hours, washed and extracted RNA. Cells collected from 6 different donors were used for RNA-seq.

first: M

last: Hasan

first: HyeMee

last: Joo

first: SangKon


title: Transcription factor competition at the γ-globin promoters controls hemoglobin switching [PRO-seq]

last: Liu

address: 300 Longwood Avenue

department: Hematology/Oncology

summary: BCL11A, the major regulator of HbF(α2γ2) level, represses γ-globin expression through direct promoter binding in adult erythroid cells in a switch to adult adult-type HbA (α2β2) production. Yet, the mechanism remains unclear. To uncover how BCL11A initiates repression, we used CRISPR/Cas9 and dCas9 screens to dissect the γ-globin promoters and identified an apparent activator element near the BCL11A binding region. Using CUT&RUN and base editing approaches, we demonstrate that this element, the proximal CCAAT box, is the binding site of transcription activator NF-Y. BCL11A competes with NF-Y binding through steric hindrance to initiate γ-globin repression, and the distance between the two motifs is critical for direct competition. Occupancy of NF-Y is rapidly established upon BCL11A depletion, and precedes γ-globin derepression and LCR-globin loop formation. Our findings reveal that the critical fetal-to-adult hemoglobin switch is initiated by the competition between transcription factors within a discrete region in the γ-globin promoters.

overall_design: CD34 cells under erythroid differentiation were edited with BCL11A sgRNA or AAVS1 control. Cells were collected at 32 or 72 hours after KO and subject to PRO-seq. Two replicates of each time point, each editing were performed.

first: Qiuming

last: Yao

first: Stuart

last: Orkin


title: Transcription factor competition at the γ-globin promoters controls hemoglobin switching

overall_design: Refer to individual Series


title: CDK8 fine-tunes IL-6 transcriptional activities by limiting STAT3 resident time at the gene loci

city: WEST LAFAYETTE

first: Majid

last: Kazemian

state: IN

address: 201 S. University Street

department: Biochemistry and Computer Science

institute: Purdue University

summary: Cytokines are highly pleiotropic ligands that critically contribute to a balanced immune response. We have an incomplete understanding of how cytokines elicit their functional pleiotropy, which has limited their therapeutic use. Here, using Interleukin-6 (IL-6) as a model system, we have performed detailed phosphoproteomic and transcriptomic studies in human Th-1 cells to address the molecular bases defining cytokine functional pleiotropy. We have identified CDK8 as a new negative regulator of STAT3 transcriptional activities that contributes to the diversification of IL-6 responses.  We found that CDK8 is a major regulator of the IL-6 phosphoproteome, and interacts with STAT3 in the nucleus upon IL-6 stimulation. Inhibition of CDK8 activity, using specific small molecules inhibitors, reduced the IL-6-induced phosphoproteome by 23% in Th-1 cells, including STAT3 Ser727 phosphorylation. This, in turn, resulted in retention of tyrosine phosphorylated STAT3 in the nucleus, which increased the binding of STAT3 to target DNA sites in the genome with a concomitant increase in STAT3 mediated transcriptional activity. Importantly, inhibition of CDK8 activity under Th-17 polarizing conditions resulted in an enhancement of Th-17 differentiation. Our results support a model where CDK8 regulates STAT3 transcriptional processivity via modulation of its gene loci resident time, critically contributing to tuning STAT3 mediated responses.

overall_design: Role of CDK8 in IL-6-induced STAT3 mediated transcriptional activity in human T cells.

first: Luopin


title: Transcription factor competition at the γ-globin promoters controls hemoglobin switching [ATACseq]

overall_design: Chromatin accessibility was analyzed in CD34 cells after 32 hrs or 72 hrs of  acute depletion of BCL11A or AAVS1 (control).


title: Transcriptome analysis of ovarian and uterine clear cell malignancies

city: Irvine

first: Farah

middle: B

last: Rahmatpanah

state: CA

address: D440 Medical Sciences I

department: Pathology and Laboratory Medicine

institute: University of California

summary: We performed RNA Sequencing on eleven ovarian clear cell carcinoma and five uterine clear cell carcinoma patients to identify the unique transcriptional expression profiles of clear cell uterine and ovarian cancer, and investigates correlations with demographic factors and tumor characteristics, such as stage and PD-L1 immunohistochemical expression.

overall_design: The Clear cells tumors were identified in the UCI , Tissue Biorepository, that had been collected between 1992 and 2017 for women aged 18 years and over, and were reviewed again to ensure they had pure clear cell histology and adequate available paraffin-embedded formalin-fixed tissue for PD1 and PD-L1 staining.


title: Chromatin Protein PC4 Orchestrates B Cell Differentiation by Collaborating with IKAROS and IRF4 (ChIP-seq)

first: Kyoko

last: Ochiai

summary: B cell development is orchestrated by various transcription factors collaborating with chromatin remodelers that determine the genomic architecture. However, chromatin regulation in mature B cells is still poorly understood. Here, we show the critical function of positive coactivator 4 (PC4), a bona fide non-histone chromatin protein encoded by Sub1. B-cell specific Sub1-deficient mice showed the decreased number and response against antigen stimulation of mature B cells. By combining PC4 chromatin immunoprecipitation-sequencing and complex purification, we identified transcription factor IKAROS as a partner of PC4 in gene regulation. PC4 and IKAROS cooperated to promote heterochromatin formation of their target gene loci and thereby established B cell identity. Importantly, PC4 stabilized IKAROS protein in mature B cells and inhibited IKAROS degradation by the anti-cancer drug lenalidomide in human B-cell lymphoma cells. These findings establish PC4 as not only a chromatin regulator of B cells but also a new therapeutic target in B-cell malignancies.

overall_design: Function and regulation of PC4 in B cells

first: Ryo

last: Funayama

first: Keiko

last: Nakayama

first: Kazuhiko

last: Igarashi


title: An in-vivo screen of noncoding elements reveals that Daedalus is a gatekeeper of a novel Ikaros-dependent checkpoint during haematopoiesis II

first: Christian

last: Harman

summary: The development of all lymphoid lineages relies on a tightly-controlled series of gene expression patterns as development proceeds through a series of progenitors1-8. These gene expression patterns are understood to be controlled by lineage-specifying transcription factors, however these factors often are found to have broad expression patterns and activities across lineages. Given their role in regulating cell-type specific gene expression, noncoding loci are thought be important in the lineage-specific regulation of this complex process6,9-16. To identify transcripts that might mark such loci, we performed transcriptomic analysis in terminally differentiated murine CD4 effector T lymphocytes. Our analysis identified a variety of loci containing dynamically expressed noncoding RNAs and we tested their role in the lymphoid lineage using an in-vivo CRISPR knockout-mouse screen. This approach revealed that a non-coding locus proximal to the haematopoietic transcription factor Ikaros17,18, named Daedalus, exerted control over the earliest fate decisions during lymphoid lineage commitment. Deletion of Daedalus led to a cell-autonomous reduction in bone marrow and thymic lymphoid progenitor populations, phenocopying Ikaros deficient strains. Strikingly, loss of Daedalus resulted in a loss of Ikaros protein expression without impacting total Ikaros transcript levels. Finally, we identify a novel Ikaros regulated erythroid-lymphoid checkpoint that is governed by Daedalus in a lymphoid-lineage specific manner. Daedalus appears to act as a gatekeeper of Ikaros’s broad lineage specifying functions, selectively stabilizing Ikaros activity in the lymphoid lineage and permitting diversion to the erythroid fate in its absence. To our knowledge, these findings represent the first illustration of how a transcription factor with broad lineage expression must work in concert with non-coding elements to orchestrate haematopoietic lineage specification and commitment.

overall_design: In order to better assess the changes resulting from ablation of the Daedalus locus we performed an RNA-seq analysis on progenitors from Daedalus KO and WT mice. Daedalus KO heterozygous mice were bred together to generate Daedalus KO and WT littermates. Bone marrow was extracted from these littermates and progenitor populations from these mice were sorted, replicates pooled, RNA extracted and submitted for RNA sequencing. Two biological replicates for each population were extracted and samples with viable RNA sequenced for a total of 10 samples - Wild Type 1 and 2 (6 populations - 2 each of HSC, MPP and LMPP) and Daedalus knockout (4 populations - 2 MPP populations, 1 each of HSC and LMPP (viable RNA not obtained for KO1_HSC or KO2_LMPP).

first: Will

last: Bailis

first: Jun

last: Zhao

first: Rihao

last: Qu

first: Ruaidhrí

last: Jackson

first: Justin

last: Shyer

first: Holly

last: Steach

first: Yuval

last: Kluger

first: Loyal

last: Goff

first: John

last: Rinn

first: Adam

last: Williams

first: Jorge

last: Henao-Mejia

first: Richard

last: Flavell


title: Transcription factor competition at the γ-globin promoters controls hemoglobin switching [CRISPR Screen]

last: Liu

overall_design: We performed CRISPR/Cas9 dense perturbation throughout the g-globin gene cluster to identify previously unrecognized regulatory elements. We employed adult-type (low HbF) HUDEP-2 cells that stably express 1) Cas9 to mutate target sequences, 2) inactive Cas9 (dCas9) to bind target sequences but not introduce DNA breaks, or 3) dCas9-VP64 or dCas9-KRAB to deliver transcription (co)activators or (co)repressors. Following introduction of pooled, densely spaced gRNAs (9293 gRNAs targeting 106 kb around the b-globin gene cluster, 1 gRNA per ~11 bp), a high HbF cell population was isolated to assess enrichment or depletion of individual gRNAs. In principle, enriched gRNAs may target elements repressive for g-globin expression, whereas depleted gRNAs may pinpoint activating sequences.

first: Shuqian

last: Xu

first: Qiuming

last: Yao

first: Daniel

last: Bauer

first: Stuart

last: Orkin


title: Gene expression after human PANC-1 cells treated with anlotinib by a microarray profiling (Affymetrix)

status: Public on Dec 21 2020

city: Changsha

first: Zewen

last: Song

state: Hunan

address: 138 Tongzipo Road, Yuelu District

department: Oncology

institute: The Third Xiangya Hospital of Central South University

summary: Anlotinib exerted cytotoxity on pancreatic cancer cells. To identify potential anlotinib targets in pancreatic cancer, we performed a microarray profiling (Affymetrix) in human PANC-1 cells treated with anlotinib.

overall_design: Human PANC-1 cells were treated with anlotinib or DSMO, and a microarray profiling (Affymetrix) was conducted to investigate the potential gene expression change.


title: Effect of Dose and Duration of Particulate Matter Exposure on the Transcriptome and DNA Methylome of Bronchial Epithelial Cells

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: This SuperSeries is composed of the SubSeries listed below.


title: Trithorax Cxxc1-directed epigenetic dynamics licensing CD4+ T cell differentiation

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

summary: Different dynamics of gene expression are observed during cell differentiation. In T-cells, genes that are turned on early, or turned off and stay off have been thoroughly studied. However, genes that are initially turned off but then turned on again after stimulation has ceased have not been defined; they are obviously important, especially in the context of acute versus chronic inflammation. Using the Th1/Th2 differentiation paradigm, we found that Cxxc1 subunit of the Trithorax complex directs transcription of genes initially downregulated by TCR stimulation but upregulated again in a later phase. The late upregulation of these genes was impaired either by prolonged TCR stimulation or Cxxc1-deficiency, which led to decreased expression of Trib3 and Klf2 in Th1 and Th2 cells, respectively. Loss of Cxxc1 resulted in enhanced pathogenicity in allergic airway inflammation in vivo. Thus, Cxxc1 plays essential roles in the establishment of a proper CD4+ T-cell immune system via epigenetic control of a specific set of genes.

overall_design: Different dynamics of gene expression during T cell differentiation assessed by ATAC-seq, ChIP-seq and RNA-seq.

first: Atsushi

last: Onodera

first: Kota

last: Kokubo

first: Tomomi

last: Ichikawa

first: Yuki

last: Morimoto

first: Eiryo

last: Kawakami

first: Naoya

last: Takayama

first: Koji

last: Eto

first: Haruhiko

last: Koseki

first: Kiyoshi

last: Hirahara

first: Toshinori

last: Nakayama


title: Multiple Niche Compartments Orchestrate Stepwise Stem Cell Lineage Differentiation

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: The niche controls stem cell self-renewal and progenitor differentiation for maintaining adult tissue homeostasis in various organisms. However, it remains unclear if the niche is compartmentalized to control stem cell self-renewal and stepwise progeny differentiation. In the Drosophila ovary, inner germarial sheath (IGS) cells form a niche for controlling germline stem cell (GSC) progeny differentiation. In this study, we have identified four IGS subpopulations, which form linearly arranged niche compartments for controlling GSC maintenance and multi-step progeny differentiation. Single-cell analysis of the adult ovary has identified four IGS subpopulations (IGS1-4), which identities and cellular locations have been further confirmed by fluorescent in situ hybridization. IGS1 and IGS2 physically interact with GSCs and mitotic cysts to control GSC maintenance and cyst formation, respectively, whereas IGS3 and IGS4 physically interact with 16-cell cysts to regulate meiosis and oocyte development. Finally, one follicle cell progenitor population has also been transcriptionally defined for facilitating future studies on follicle stem cell regulation.  Therefore, this study has structurally revealed that the niche is organized into multiple compartments for orchestrating stepwise adult stem cell development, and has also provided useful resources and tools for further functional characterization of the niche in the future.

overall_design: Sort live single GFP positive cells from GMR71E07-GAL4>UAS-GFP, GMR25A11-GAL4>UAS-GFP or GMR31C09-GAL4>UAS-GFP ovaries via Fluorescence-activated cell sorting (FACS). Then these cells were subjected for scRNA-seq according to Single Cell 3' Reagent kits. v2 User Guide Rev D (10X Genomics).

first: Renjun

last: Tu

first: Bo

last: Duan

first: Xiaoqing

first: Allison

last: Scott

first: Kate

last: Hall

first: Jillian

last: Blanck

first: Dustin

last: DeGraffenreid

first: Hua

last: Li

first: Anoja

last: Perera

first: Jeff

last: Haug

first: Ting

last: Xie


title: Treatment of granuloma annulare and suppression of pro-inflammatory cytokine activity with tofacitinib

city: New Haven

first: William

last: Damsky


title: Treatment of granuloma annulare and suppression of pro-inflammatory cytokine activity with tofacitinib [RNA-Seq]

overall_design: Total RNA was extracted with Qiagen RNeasy Fibrous Tissue Mini kits (Qiagen cat# 74704) according to the manufacturer’s instructions. Homogenization of the tissue was achieved using a rotor-homogenizer (PowerGen 125, ThermoFisher). RNA was submitted to the Yale Stem Cell Center and complementary DNA libraries were prepared and 100-base pair paired-end stranded sequencing was performed on an Illumina HiSeq 4000, also at Yale Stem Cell Center.

first: Alice

last: Wang

first: Nur-Taz

last: Rahman

first: Meaghan

last: McGeary

first: Michael

last: Murphy

first: Austin

last: McHenry

first: Danielle

last: Peterson

first: Marcus

last: Bosenberg

first: Richard

last: Flavell

first: Brett

last: King


title: Selective Vulnerability to Pyrimidine Starvation in Hematologic Malignancies Revealed by AG-636, a Novel Clinical-Stage Inhibitor of Dihydroorotate Dehydrogenase

city: Cambridge

first: Zi Peng

last: Fan

state: MA

address: 88 Sidney Street

institute: Agios Pharmaceuticals

summary: Agents targeting metabolic pathways form the backbone of standard oncology treatments, though a better understanding of differential metabolic dependencies could instruct more rationale-based therapeutic approaches. We performed a chemical biology screen that revealed a strong enrichment in sensitivity to a novel dihydroorotate dehydrogenase (DHODH) inhibitor, AG-636, in cancer cell lines of hematologic versus solid tumor origin. Differential AG-636 activity translated to the in vivo setting. Dissection of the relationship between uridine availability and response to AG-636 revealed a divergent ability of lymphoma and solid tumor cell lines to survive and grow in the setting of depleted extracellular uridine and DHODH inhibition. Metabolic characterization paired with unbiased functional genomic and proteomic screens pointed to adaptive mechanisms to cope with nucleotide stress as contributing to response to AG-636. These findings support targeting of DHODH in lymphoma and other hematologic malignancies and suggest combination strategies aimed at interfering with DNA damage response pathways.

overall_design: A genome-wide CRISPR depletion screen was performed in A549 cells with or without AG-636 to identify specific genes and pathways limiting response to AG-636. Uridine was provided in the medium at a concentration of 5 µM, resulting in alternate periods of uridine availability and depletion over the course of the culture period.

first: Gabrielle

last: McDonald

last: Ulanet

first: Zi


title: Chromatin Protein PC4 Orchestrates B Cell Differentiation by Collaborating with IKAROS and IRF4

first: Kyoko

last: Ochiai


title: Loss of ESRP1 blocks mouse oocyte development and leads to female infertility

status: Public on Dec 20 2020

city: Nanjing

first: Luping

last: Yu

address: Nanjing Medical University, 101 Longmian Rd, Jiangning, Nanjing

institute: State Key Laboratory of Reproductive Medicine (SKLRM)

summary: Alternative splicing(AS) contributes to gene diversification through RNA-binding proteins, but AS regulation during germline development remains largely undefined. Here, we report a comprehensive set of mRNA splicing events mediated by epithelial splicing regulatory proteins 1(Esrp1) to regulate mouse oocyte development. Collectively, our data highlights that ESRP1-mediated AS program are required for oocyte development and female fertility maintainance.

overall_design: MII oocytes from 6-week-old WT and Esrp1-KO females. RNA profiling data form both groups was collected from four biological replicates.

first: Xin

last: Wu


title: Transcription factor competition at the γ-globin promoters controls hemoglobin switching [ChIP-seq]

last: Liu

institute: Boston Children's Hospital

overall_design: Occupancy of NFYA was analyzed in HUDEP-2, HUDEP-1 cells with NFYA KD or control KD using ChIP-seq.

first: Stuart

last: Orkin


title: Transcription factor competition at the γ-globin promoters controls hemoglobin switching [CUT&RUN]

overall_design: Occupany of NFYA or TBP was assessed using CUT&RUN sequencing in erythroid progenitors with BCL11A KO or base editing of TF motifs.


title: RNA-seq analysis of the transcriptome changes on Cenpj depletion cortices at E15.5

city: beijing

first: wenyu

last: ding

address: 15 Datun Road Chaoyang District

institute: University of Chinese Academy of Sciences

summary: Here, we performed RNA-seq to analyze the transcriptome changes on Cenpj depletion cortices at E15.5.RNA-Seq correlation test shows the similarity of the expression patterns between Cenpj+/+ and CenpjCKO was high.By comparing gene expression levels in Cenpj+/+ and CenpjCKO samples, GO term analysis of down-regulated genes in E15.5 CenpjCKO samples showed a significant enrichment of terms related to cell cycle, cell migration, neurogenesis, neuron differentiation and axongenesis, while the up-regulated genes were enriched in cell death, cilium assembly.KEGG signaling pathway analysis revealed that the differentially expressed genes are predicted to be involved in Wnt, MAPK, Hippo, AMPK, Notch, etc. signaling pathways. With Cenpj depletion, we identify a number of genes involved in cilium disassembly were downregulated in developing mouse cortex at E15.5 by RT-PCR, including Kif2a, Kif24, Plk1, Nek2, Ccp110 and Pla2g3, while some cilium assembly genes were upregulated, such as, Rab8a, Mks1, etc., which is in consistent with RNA-seq data, suggesting that RNA-seq data are reliable.

overall_design: The transcriptom changes on Cenpj depletion cortices

first: W

last: Ding

first: X

last: Wang


title: Chromatin Protein PC4 Orchestrates B Cell Differentiation by Collaborating with IKAROS and IRF4 (Agilent microarrays)

city: Sendai

institute: Tohoku University School of Medicine

first: Mari

last: Yamaoka

first: Kazuhiko

last: Igarashi


title: MDM2 inhibitors reverse the transcriptional effects of DMKG plus B87.

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: We reported for the first time that DMKG plus B87 kills cancer cells through a MDM2-dependent cell death mechanism (unpublished results). Moreover, we demonstrated that this effect is reverted by MDM2 inhibitors. We investigated if this effect is transcriptional.

overall_design: We compared different treatments in order to evaluate the transcriptional impact on cell death.

first: Valentina

last: Sica


title: The human aortic endothelium undergoes dose-dependent DNA methylation in response to transient hyperglycemia

status: Public on Dec 19 2020

city: Stanford

first: Mark

middle: Emile

last: Pepin

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

summary: Glycemic control is a strong predictor of long-term cardiovascular risk in patients with diabetes mellitus, and poor glycemic control influences long-term risk of cardiovascular disease even decades after optimal medical management. This phenomenon, termed glycemic memory, has been proposed to occur due to stable programs of cardiac and endothelial cell gene expression. This transcriptional remodeling has been shown to occur in the vascular endothelium through a yet undefined mechanism of cellular reprogramming. Epigenetics offers a novel mechanism whereby a transient glycemic stress is capable of modifying endothelial susceptibility to the pathological remodeling of cardiovascular disease. In the current study, we show that transient glucose exposure triggers widespread alterations in endothelial DNA methylation which may control several recognized pathological mechanisms of cardiovascular disease, such as the nitric oxide signaling cascade. Future mechanistic studies should therefore investigate the extent to which differential methylation potentiates endothelial dysfunction in response to transient glycemic stress.

overall_design: Whole-genome DNA methylation of human endothelial aortic cells (HAECs) was quantified using reduced-representation bisulfite sequencing (RRBS) following exposure to either diabetic (250 mg/dL) and pre-diabetic (125 mg/dL) concentrations of glucose for 24 hrs (n = 2) relative to vehicle controls. We uncovered a broad genomic distribution of changes in dose-dependent DNA methylation that disproportionately affects the coding region of genes. Among the pathways most affected by differential DNA methylation, “Endothelin Signaling” was found as the most enriched pathway, within which the promoter of Nitric Oxide Synthase 3 (NOS3) was found to be hypo-methylated only upon exposure to diabetic-range glucose concentrations (-20.3%, FDR = 0.0015).

middle: E

first: Claudio

last: Napoli

first: Adam

last: Wende

first: Marco

last: Miceli


title: Effect of Dose and Duration of Particulate Matter Exposure on the Transcriptome and DNA Methylome of Bronchial Epithelial Cells [RNA-seq]

first: Bioinformatics

last: Core

summary: Bronchial epithelial cells, which line the airway of the respiratory tract, undergo genome-wide level changes in gene expression and DNA methylation particularly when exposed to fine (< 2.5 µm) PM (PM2.5). Although some of these changes have been reported in other studies, a comparison of how different doses and duration of exposure affect both the gene transcriptome and DNA methylome has not been done. We exposed BEAS-2B, a bronchial epithelial cell line, to a single exposure of high (30 µg/cm2) or low (1 µg/cm2) dose of PM2.5 (obtained from Beijing, China in 2015) for 24 hours. We also exposed BEAS-2B cells to repeated exposures of low dose (1 µg/cm2) PM2.5 every day for seven days. We then examined the transcriptomic changes (by RNA-Seq) and DNA methylomic changes (by enhanced reduced representation bisulfite sequencing). Widespread changes in gene expression occurred after cells were exposed to a single, high dose (30 µg/cm2) exposure of PM2.5 for 24 h. These genes were enriched in pathways regulating MAPK signaling, PI3K-Akt signaling, cytokine interactions, IL6, and P53. DNA methylomic analysis showed that nearly half of the differentially expressed genes were found to also have DNA methylation changes. Cells exposed to a lower dose (1 µg/cm2) of PM2.5 demonstrated a similar, but more attenuated change in gene expression. Cells exposed to repeated doses of PM2.5 for seven days, however, demonstrated a different set of genes that were differentially expressed compared to a single exposure. The DNA methylation changes that occurred with repeated, low dose exposure were also different from single high dose exposures and skewed towards overall hypomethylation. This hypomethylation corresponded with an increase in expression of ten-eleven translocation enzymes. Overall, these data demonstrate how variations in dose and duration of PM2.5 exposure induce distinct differences in the transcriptomic and DNA methylomic profile of bronchial epithelial cells.

overall_design: BEAS-2B cells were treated with either vehicle control or PM2.5 at a dose of 1 or 30 µg/cm2 for 24 hours before being collected for RNA. In experiments examining the effect of repeated exposures, cells were treated with either vehicle control or 1 µg/cm2 of PM2.5 each day for seven days before being isolated for RNA analysis. For experiments involving repeated exposures, cells were washed each day between exposures. Each experiment was performed three indendent times, and each experimental batch is indicated by the last number of the sample ID.

first: Steven

last: Huang

first: Priya

last: Tripathi

first: Lada

last: Koneva

first: Raymond

last: Cavalcatti

first: Dana

last: King

first: Nathan

last: Craig

first: Anne

last: Scruggs

first: Furong

last: Deng

first: Yahong

last: Chen


title: Alzheimer’s, Parkinson’s disease and Amyotrophic Lateral Sclerosis gene expression patterns divergence reveals different grade of RNA metabolism involvement

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

summary: Alzheimer’s disease (AD), Parkinson’s disease (PD) and Amyotrophic Lateral Sclerosis (ALS) are neurodegenerative disorders characterized by progressive degeneration of central or peripheral nervous system.  A central role of RNA metabolism has emerged in these diseases, concerning mRNAs processing and non-coding RNAs biogenesis. We aimed to identify possible crossroads or deviations in the dysregulated pathways of AD, PD and ALS. We performed RNA-seq analysis to investigate the regulation of both coding and long non-coding RNAs (lncRNAs) in ALS, AD and PD patients and controls (CTRL) in Peripheral Blood Mononuclear Cells (PBMCs). A total of 293 differentially expressed (DE) lncRNAs and 87 mRNAs was found in ALS patients. In AD patients a total of 23 DE genes have emerged, 19 protein coding genes and 4 lncRNAs. By performing KEGG and GO analysis we found common affected pathways and biological processes in ALS and AD. In PD patients only 5 genes were found DE. Our data brought the light on the different importance of lncRNAs and mRNAs regulation in the principal neurodegenerative disorders, offering starting points for new investigations about pathogenic mechanism involved in them.

overall_design: Peripheral Blood Mononuclear Cells derived from 6 SALS, 6 AD and 6 PD patients and 14 age- and sex-matched healthy controls (CTR) were were deep-sequenced and included in Real Time PCR experiments.

first: Cecilia

last: Pandini

first: Matteo

last: Bordoni

first: Orietta

last: Pansarasa

first: Federica

last: Rey

first: Stephana

last: Carelli

first: Cristina

last: Cereda

first: Stella

last: Gagliardi


title: Gene expression profiling of SGI-110-treated MDA-MB-231 cells

city: Odense C

first: morten

last: gjerstorff

state: FYN

address: J.B. Winslows Vej 25, 3.

country: Denmark

institute: University of Southern Denmark

summary: In this study we analyse the effect og DNMT inhibitor SGI-110 on the gene expression of MDA-MB-231 cells

overall_design: RNA sequencing of SGI-110- and vehicle-treated MDA-MB-231 cells

first: Morten

middle: F

last: Gjerstorff


title: Effect of Dose and Duration of Particulate Matter Exposure on the Transcriptome and DNA Methylome of Bronchial Epithelial Cells [RRBS]

first: Bioinformatics

last: Core

overall_design: BEAS-2B cells were treated with either vehicle control or PM2.5 at a dose of 1 or 30 µg/cm2 for 24 hours before being collected for DNA. In experiments examining the effect of repeated exposures, cells were treated with either vehicle control or 1 µg/cm2 of PM2.5 each day for seven days before being isolated for DNA methylomic analysis. For experiments involving repeated exposures, cells were washed each day between exposures. Each experiment was performed three independent times, and each experimental batch is indicated by the last number of the sample ID.

first: Steven

last: Huang

first: Priya

last: Tripathi

first: Lada

last: Koneva

last: Cavalcante


title: Hovlinc is a recently evolved class of ribozyme found in human lncRNA

city: Xiamen

first: Fei

last: Qi

address: 4221 South Xiang'an Road

department: School of Life Sciences

institute: Xiamen University

summary: Naturally-occurring catalytic RNA molecules — ribozymes — have attracted a great deal of research interest, yet very few of them have been identified in humans. Here, we developed a genome-wide approach to discover self-cleaving ribozymes and identified one naturally-occurring ribozyme in humans. The secondary structure and biochemical properties of this ribozyme indicate that it belongs to yet un-identified class of small self-cleaving ribozymes. The sequence of the ribozyme exhibits a clear evolutionary path from appearance between ~130 and ~65 million years ago (mya) to gain of self-cleavage activity very recently, ~13–10 mya, in the common ancestor of humans, chimpanzees and gorillas. The ribozyme appears to be functional in vivo and is embedded within an lncRNA belonging to the class of very long intergenic non-coding (vlinc) RNAs. The presence of a catalytic RNA enzyme in lncRNA opens a possibility that these transcripts could function by carrying catalytic RNA domains.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: In identification of self-cleaving ribozyme, 9 samples were analyzed with 3 replicates each containing 2 control samples and 1 RppH&XRN-1 treated sample. To verify the cleavage site of hovlinc ribozyme, 1 sample containing self-cleavage products ligated to an RNA oligo was analyzed.

first: Philipp

last: Kapranov