title: Iron and kidney macrophages in CKD

first: Genomics-core-facility

last: WCM

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Systemic iron metabolism is disrupted in chronic kidney disease (CKD). However, little is known  about local kidney iron homeostasis and its role in kidney fibrosis. Kidney-specific effects of iron  therapy in CKD also remain elusive. Here, we elucidate the role of macrophage iron status in kidney  fibrosis and demonstrate that it is a potential therapeutic target. In CKD, kidney macrophages  exhibited depletion of labile iron pool (LIP) and induction of transferrin receptor 1, indicating  intracellular iron deficiency. Low LIP in kidney macrophages was associated with their defective  antioxidant response and proinflammatory polarization. Repletion of LIP in kidney macrophages  through knockout of ferritin heavy chain (Fth1) reduced oxidative stress and mitigated fibrosis.  Similar to Fth1 knockout, iron dextran therapy, through replenishing macrophage LIP, reduced  oxidative stress, decreased the production of proinflammatory cytokines, and alleviated kidney  fibrosis. Interestingly, iron markedly decreased TGF-β expression and suppressed TGF-β–driven  fibrotic response of macrophages. Iron dextran therapy and FtH suppression had an additive  protective effect against fibrosis. Adoptive transfer of iron-loaded macrophages alleviated kidney  fibrosis, validating the protective effect of iron-replete macrophages in CKD. Thus, targeting  intracellular iron deficiency of kidney macrophages in CKD can serve as a therapeutic opportunity to  mitigate disease progression.

overall_design: RNA was isolated from whole kidney tissues in 3 groups of mice: control, CKD, CKD+iron dextran (parenteral injections)

first: Oleh

last: Akchurin

first: Mary

middle: E

last: Choi

first: Edwin

last: Patino

first: Divya

last: Bhatia


title: Synergy between IDH2 and TET2 mutations modulates Tfh cell functional interaction with the angioimmunoblastic T-cell lymphoma microenvironment [Bisulfite-seq]

status: Public on Feb 01 2023

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

country: USA

institute: Weill Cornell Medical College

type: Methylation profiling by high throughput sequencing

summary: Angioimmunoblastic T-cell lymphoma (AITL) is a peripheral T-cell lymphoma that originates from T follicular helper (Tfh) cells and is characterized by a prominent tumor microenvironment (TME). IDH2 and TET2 mutations co-occur frequently in AITL but their contribution to tumorigenesis is poorly understood. We have developed an AITL mouse model that is driven by Idh2 and Tet2 mutations and in which Tfh cells exhibit aberrant transcriptomic and epigenetic programming. Neoplastic Tfh cells bearing combined Idh2 and Tet2 mutations show altered crosstalk with normal germinal center B cells that promotes B clonal expansion while decreasing Fas-FasL interaction and reducing B cell apoptosis. This altered Tfh-B cell communication could explain the unique relationship between Idh2 mutation and the prototypical AITL TME. Our mouse model also recapitulates important features of human IDH2-mutated AITL, providing a rationale for exploring the therapeutic targeting of Tfh-TME crosstalk for AITL treatment.

overall_design: CD4+ CXCR5+ PD-1+ (Tfh) cells from 2 month old +/-; CD4-Cre (control), Idh2LSL-R172K/+;CD4-Cre, Tet2-/-;CD4-Cre, Idh2LSL-R172K/+; Tet2-/-;CD4-Cre mice were analyzed. For each genotype,  4 mice each (each forming a biological replicate), were analyzed.

first: Julie

last: Leca

first: Francois

last: Lemonnier

first: Jonathan

last: Foox

first: Ari

last: Melnick

first: Christopher

last: Mason

first: Philippe

last: Gaulard

first: Tak

middle: W

last: Mak


title: Gene expression profile as single cell level of chronic diabetic foot ulcers and chronic non-diabetic foot ulcer

city: Pullman

first: Ryan

middle: Roy

last: Driskell

state: Washington

address: 100 Dairy Rd. BLS 202A

department: Molecular Biosciences

institute: Washington State University

type: Expression profiling by high throughput sequencing

summary: We investigate the changes between diabetic and non-diabetic wound healing process in chronic foot ulcer.

overall_design: Discarded tissues from chronic wounds were FACS sorted for viable cells and proceed to scRNA-seq libraries preparation

first: Teresa

last: Sandoval-Schaefer

first: Quan

middle: M

last: Phan


title: Small RNA sequencing of postmortem human Brodmann Area 9 and postmortem human blood from Opioid Use Disorder Subjects and Controls in the University of Texas Health Science Center at Houston Brain Collection

city: Houston

first: Consuelo

last: Walss-Bass

state: Texas

address: 1941 East Road Rm. 3110

department: Louis A. Faillace Department of Psychiatry and Behavioral Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: This dataset includes samples in the UTHealth Brain Collection (UTHBC) from Grimm et al 2022 "MicroRNA-mRNA networks are dysregulated in opioid use disorder postmortem brain: further evidence for opioid-induced neurovascular alterations ", doi: 10.3389/fpsyt.2022.1025346. To understand mechanisms and identify potential targets for intervention in the current crisis of opioid use disorder (OUD), postmortem brains represent an under-utilized resource. To refine previously reported gene signatures of neurobiological alterations in OUD from the dorsolateral prefrontal cortex (Brodmann Area 9, BA9), we explored the role of microRNAs (miRNA) as powerful epigenetic regulators of gene function. Building on the growing appreciation that miRNAs can cross the blood-brain barrier, we carried out miRNA profiling in same-subject postmortem samples from BA9 and blood tissues. miRNA-mRNA network analysis showed that even though miRNAs identified in BA9 and blood were fairly distinct, their target genes and corresponding enriched pathways overlapped strongly. Among the dominant enriched biological processes were tissue development and morphogenesis, and MAPK signaling pathways. These findings point to robust, redundant, and systemic opioid-induced miRNA dysregulation with potential functional impact on transcriptomic changes. Further, using correlation network analysis we identified cell-type specific miRNA targets, specifically in astrocytes, neurons, and endothelial cells, associated with OUD transcriptomic dysregulation. Finally, leveraging a collection of control brain transcriptomes from the Genotype-Tissue Expression (GTEx) project, we identified correlation of OUD miRNA targets with TGF beta, hypoxia, angiogenesis, coagulation, immune system and inflammatory pathways. These findings support previous reports of neurovascular and immune system alterations as a consequence of opioid abuse and shed new light on miRNA network regulators of cellular response to opioid drugs.

overall_design: Raw fastq for 39 brain Brodmann Area 9 samples (24 OUD and 15 controls) and 26 Blood Plasma Samples (18 opioid use disorder and 8 controls) from a subset of the same individuals in the UTHealth Brain Collection (UTHBC, RRID:SCR_022970). These individuals are a subset of those for which total RNA seq was performed in the GEO dataset GSE182321, found at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182321.

first: Grimm

last: Sandra

first: Mendez

last: Emily

first: Stertz

last: Laura

first: Gunaratne

last: Preethi

first: Coarfa

last: Cristian

first: Walss-Bass

last: Consuelo


title: Comparative transcript profiling of a loss-of-function Arabidopsis thaliana mutant (lecrk-I.9-1) vs wild type

city: Auzeville-Tolosane

first: Hervé

last: CANUT

address: Chemin de Borde Rouge

country: France

institute: CNRS-Université Paul Sabatier

summary: We compared the transcriptome of WT roots to that of lecrk-I.9-1 roots to get some insight about the putative functions of LecRK-I.9 (At5g60300).

overall_design: Col-0 and lecrk-I.9-1 (salk_042209) seedlings were grown from seeds in liquid medium for 7 days. Three biological replicates were conducted with one flask yielding a single biological replicate.

first: Kevin

last: BELLANDE


title: Synergy between IDH2 and TET2 mutations modulates Tfh cell functional interaction with the angioimmunoblastic T-cell lymphoma microenvironment

first: Cem

last: Meydan

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: Couch Biomedical Research Bldg 06316

department: Genetics

institute: Washington University of St. Louis

summary: Calling Cards is a platform technology to record a cumulative history of transient protein-DNA interactions in the genome of genetically targeted cell types. The record of these interactions are recovered by next generation sequencing. Compared to other genomic assays, whose readout provides a snapshot at the time of harvest, Calling Cards enables correlation of historical molecular states to eventual outcomes or phenotypes. To achieve this, Calling Cards uses the piggyBac transposase to insert self-reporting transposon (SRT) “Calling Cards” into the genome, leaving permanent marks at interaction sites. Calling Cards can be deployed in a variety of in vitro and in vivo biological systems to study gene regulatory networks involved in development, aging, and disease. Out of the box, it assesses enhancer usage but can be adapted to profile specific transcription factor binding with custom transcription factor (TF)-piggyBac fusion proteins. The Calling Cards workflow has five main stages: delivery of Calling Card reagents, sample preparation, library preparation, sequencing, and data analysis. Here, we first present a comprehensive guide for experimental design, reagent selection, and optional customization of the platform to study additional TFs. Then, we provide an updated protocol for the five steps, using reagents that improve throughput and decrease costs, including an overview of a newly deployed computational pipeline. This protocol is designed for users with basic molecular biology experience to process samples into sequencing libraries in 1-2 days. Familiarity with bioinformatic analysis and command line tools is required to set up the pipeline in a high performance computing environment and to conduct downstream analyses.

overall_design: Calling Cards were transcranially injected with AAV-Calling Cards at P1. Tissue was harvested at P21 and the cortex, midbrain, and hindbrain regions were dissected. Calling Card libraries were prepared to analyze BRD4-binding across the different brain regions.

first: Allen

last: Yen

middle: D

first: Robi

last: Mitra


title: Early PD-1 expression on CD8+ T-cells and the development of a stem-like phenotype are associated with HIV slow-progression in children

city: Oxford

first: Nicholas

last: Lim

state: Oxfordshire

address: 26 Bullingdon Road

department: Paediatrics

country: United Kingdom

institute: University of Oxford

summary: Population RNAseq was performed in PD-1high CD8+ T-cell of RP (rapid progressors) and SP (slow progressors) in the timepoint immediately after analytical treatment interruption. Although large proportion of differentially expressed genes appeared to be driven by individual heterogeneity, the RPs showed higher levels of Tim-3 (HAVCR2), a marker when co-expressed with PD-1+ that also characterizes terminally exhausted CD8+ T-cells

overall_design: PD-1high CD8+ T-cells were sorted of -three SPs and three RPs with at the timepoint before analytical treatment interruption and RNAseq performed using  whole-transcriptome-amplification using Smart-seq2.

first: Vinicius

last: Vieira

first: Alveera

last: Singh

first: Alasdair

last: Leslie

first: Henrik

middle: N

last: Kløverpris

first: Veron

last: Ramsuran

first: Philip

last: Goulder


title: Dynamic changes in gene transcription in response to GRHL2 knockout in MCF7 cells

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

summary: Genome-wide dynamic changes in DNA transcription triggered by GRHL2 loss were investigated by Bru-seq measuring nacent RNA at different time points after GRHL2 deletion in a conditional Cas9 MCF7 knockout model expressing a control or 2 different GRHL2 sgRNAs (sgCTR, sgGRHL2(1) and sgGRHL2(2), respectively).

overall_design: Human breast cancer MCF7 cells were used.

first: Zi

last: Wang

first: Erik

middle: H

last: Danen

first: Michelle

middle: T

last: Paulsen

first: Mats

last: Ljungman


title: Solute carrier family 12 member 5 promotes tumor development of intrahepatic cholangiocarcinoma

city: changsha

first: wei

last: qin

state: State...

address: xiangya

country: China

institute: xiangya

summary: Intrahepatic cholangiocarcinoma (ICC) is the second most common primary malignant tumor of the liver, characterized by high malignancy, poor prognosis, and lack of effective treatment.Solute carrier family 12 member 5 (SLC12A5) is frequently overexpressed in many tumors and is involved in the development and progression of several human cancers. Here, we aimed to investigate the expression and biological function of SLC12A5 in ICC.

overall_design: We established stable SLC12A5-knockdown (sgSLC12A5), SLC12A5-overexpression (LvSLC12A5) and SLC12A5-control  ICC cell lines by CRISPR/Cas9 system in RBE cell lines.we performed RNA-sequencing using control RBE cells, SLC12A5-knockdown, and SLC12A5-overexpression RBE cells.

first: Xundi

last: Xu

first: Wei

last: Qin


title: Deficiency of CFB attenuates renal tubulointerstitial damage via inhibiting ceramide synthesis in diabetic kidney disease

city: Beijing

first: Zijun

last: Sun

address: No 8, Xishiku Street

institute: Peking University First Hospital

summary: Accumulating evidence suggests the pathogenic role of immunity and metabolism in diabetic kidney disease (DKD). Herein, we aimed to investigate the effect of complement factor B (CFB) on lipid metabolism in the development of DKD. We found that in patients with diabetic nephropathy (DN), the staining of Bb, CFB, C3a, C5a, and C5b-9 were significantly elevated in renal tubulointerstitium. Cfb knockout diabetic mice had significantly milder tubulointerstitial injury and less ceramide biosynthesis. The in vitro study demonstrated that cytokine secretion, endoplasmic reticulum stress, oxidative stress, and cell apoptosis were ameliorated in siCFB HK-2 cells under high glucose conditions. Exogenous ceramide supplementation attenuated the protective effect of CFB knockdown in HK-2 cells, while inhibiting ceramide synthases (CERS) with fumonisin B1 in CFB-overexpressing cells rescued the cell injury. CFB knockdown could downregulate the expression of NF-κB p65, which initiates the transcription of CERS3. Furthermore, C3 knockdown abolished CFB-mediated cytokine secretion, NF-κB signaling activation, and subsequently ceramide biosynthesis. Thus, CFB deficiency inhibited activation of the complement alternative pathway and attenuated kidney damage in DKD, especially tubulointerstitial injury, via inhibiting the NF-κB signaling pathway, further blocking the transcription of CERS, which regulates the biosynthesis of ceramide. CFB may be a promising therapeutic target of DKD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cfb knockout mice (STZ/HFD induced diabetic Cfb knockout mice and non-diabetic Cfb knockout mice) and its wide type control (diabetic mice and non-diabetic mice).

first: Zi-jun

first: Dong-yuan

last: Chang

first: Min

last: Chen

first: Ming-hui

last: Zhao


title: A flexible liposomal polymer complex as a platform for specific and regulable immune regulation for individual cancer immunotherapy

city: Hsinchu

first: Ling-ya

last: Huang

state: Taiwan

address: 1001 University Road

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: The aim of this experiment is exploring the efficacy of LPPC treatment by skin administration with anti-immune cell antibody by immune affectived ability.

overall_design: Tumor cells were inoculated in C57BL/6J female mouse,then the tumor mass was treated by different drugs.

first: Chia-Hung

first: Tzu-Han

last: Weng

first: Ling-Ya

first: Hsiao-Hsuan

first: Kai-Yao

first: Pin-Rong

first: Kuang-Yu

last: Yeh

first: Yu-Tzu

last: Chien

first: Cji-Ting

first: Po-Ya

last: Chuang

first: Yu-Ling

last: Lin

first: Nu-Man

last: Tsai

first: Shih-Jen

last: Liu

first: Shun-Long

first: Kuang-Wen

last: Liao


title: Clinical application of autologous tumor infiltrating lymphocytes combined with anti-PD-1 antibody in the treatment of advanced hepatocellular carcinoma

city: Wuhan

first: AnYi

last: Liang

address: 1037 Luoyu Road, Wuchang, Wuhan

institute: Huazhong University of Science and Technology

summary: To study the safety and efficacy of clinical application of autologous tumor infiltrating lymphocytes (TIL) after in vitro amplification，in combination with anti-PD-1 monoclonal antibody for the treatment of advanced hepatocellular carcinoma (HCC)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human HCC issue

first: Lijun

first: Tian

last: Xia


title: Impaired regulatory T cell-dendritic cell interactions contribute to autoimmunity in leukocyte adhesion deficiency type-1

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

summary:
RFP reporter protein expressing splenic regulatory T cells (Treg) were isolated by flow cytometry from mice with a Foxp3-specific knockdown of CD18 (n=3) and the according control mice (n=3).
Aliquots of Treg were stimulated overnight. On the next day all samples were lysed and extracted RNA was subjected to sequencing.

overall_design: Comparative gene expression profiling analysis of CD18-deficient Treg versus control Treg at unstimulated and stimulated state.

first: Tanja

last: Klaus

first: Alicia

last: Wilson

last: Bros


title: Bulk RNA-seq of zebrafish 5dpf embryos comparing Klf9 knockout with matched controls at 3 timepoints flanking zeitgeber (lights on)

city: Bar Harbor

first: Joel

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

institute: MDI Biological Laboratory

summary: Krüppel-like factor 9 (Klf9) is a ubiquitously expressed transcription factor that is a feedforward regulator of multiple stress-responsive and endocrine signaling pathways. We previously described how loss of Klf9 function affects the transcriptome of zebrafish larvae sampled at a single time point 5 days post-fertilization (dpf). However, klf9 expression oscillates diurnally, and the time point that was sampled corresponded to its expression nadir. To determine if klf9-/- function varies with time of day, we performed bulk RNA-seq on 5 dpf zebrafish embryos sampled at three timepoints encompassing the predawn peak and midmorning nadir of klf9 expression. We found that while the major effects of the klf9-/- mutation that we reported previously are robust to time of day, the mutation has additional effects that manifest only at the predawn time point. We used a published single-cell atlas of zebrafish development to map the effects of the klf9-/- mutation onto different cell types and found that the mutation increased representation of genes associated with digestive organs (liver, pancreas, and intestine) and decreased representation of genes associated with differentiating neurons, blood, and somites. Measurements from confocally-imaged larvae suggest that overrepresentation of liver genes in klf9-/- mutants is due to development of enlarged livers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for zebrafish klf9-/- mutant larvae vs wild-type at three times of day.  Klf9 -/- knockouts were generated through CRISPR, creating a 2 bp deletion in the first exon that causes a frameshift and premature stop codon, as previously described in Gans et al, Scientific Reports 10, 11415 (2020). https://doi.org/10.1038/s41598-020-68040-z

first: Laura

last: Drepanos

first: Ian

last: Gans

first: Janelle

last: Grendler

first: Sophia

last: Guitar

first: J

last: Fuqua

first: Nathaniel

middle: J

last: Maki

first: Andrea

middle: R

last: Tilden

first: James

middle: A

last: Coffman


title: CRISPR-mediated rapid arming of poxvirus vectors enables facile generation of the novel immunotherapeutic STINGPOX

city: Ottawa

first: Adrian

last: Pelin

state: Ontario

address: 501 Smyth Rd.

country: Canada

institute: Ottawa Hospital Research Institute

summary:
By utilizing a simple, modular CRISPR/Cas9 assisted-recombinant vaccinia virus engineering (CARVE) system, we demonstrate generation of a recombinant vaccinia virus expressing three distinct transgenes at three different loci in less than 1 week.
This novel vector, STINGPOX, produces cyclic di-AMP, a STING agonist, which drives IFN signaling critical to the anti-tumor immune response.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary human macrophage cells differentiated to an M1 state treated with OncoVACV or STINGPOX.

first: Jack

last: Whelan

first: Ragunath

last: Singaravelu

first: John

middle: C

last: Bell


title: Deep learning-guided discovery of a narrow-spectrum antibiotic against Acinetobacter baumannii

city: Hamilton

first: Gary

last: Liu

state: ON

address: 1280 Main Street West

department: Institute for Infectious Disease Research

institute: McMaster University

summary: Acinetobacter baumannii is a nosocomial Gram-negative pathogen that often displays multidrug-resistance due to its robust outer membrane and its ability to acquire and retain extracellular DNA. Moreover, it can survive for prolonged durations on surfaces and is resistant to desiccation. Discovering new antibiotics against A. baumannii has proven challenging through conventional screening approaches. Fortunately, machine learning methods allow for the rapid exploration of chemical space, increasing the probability of discovering new chemical matter with antibacterial activity against this burdensome pathogen. Here, we screened ~7,500 molecules for those that inhibited the growth of A. baumannii in vitro. We trained a deep neural network with this growth inhibition dataset and performed predictions on the Drug Repurposing Hub for structurally novel molecules with activity against A. baumannii. Through this approach, we discovered abaucin, an antibacterial compound with narrow-spectrum activity against A. baumannii, which could overcome intrinsic and acquired resistance mechanisms in clinical isolates. Further investigations revealed that abaucin perturbs lipoprotein trafficking through a mechanism involving LolE, a functionally conserved protein that contributes to shuttling lipoproteins from the inner membrane to the outer membrane. Moreover, abaucin was able to control an A. baumannii infection in a murine wound model. Together, this work highlights the utility of machine learning in discovering new antibiotics and describes a promising lead with narrow-spectrum activity against a challenging Gram-negative pathogen.

overall_design: Transcriptomic analysis of A. baumannii ATCC 17978 when treated with novel antibiotic compound

first: Denise

middle: B

last: Catacutan

first: Khushi

last: Rathod

first: Kyle

last: Swanson

first: Wengong

last: Jin

first: Jody

last: Mohamed

first: Anush

last: Chiappino-Pepe

first: Saad

last: Syed

first: Meghan

last: Fragis

first: Kenneth

last: Rachwalski

first: Jakob

last: Magolan

first: Michael

middle: G

last: Surette

first: Brian

middle: K

last: Coombes

first: Tommi

last: Jaakkola

first: Regina

last: Barzilay

last: Collins

first: Jonathan

last: Stokes


title: single cell RNA sequencing of SMC specific Yap1 knockout mouse aorta

first: Yanming

last: Li

state: TX

address: One Baylor Plaza

department: Michael E. DeBakey Department of Surgery

institute: Baylor College of Medicine

summary: When aortic cells are under stress, such as increased hemodynamic pressure, they adapt to the environment by modifying their functions, allowing the aorta to maintain its strength. To understand the regulation of this adaptive response, we examined the transcriptomic and epigenomic programs in aortic smooth muscle cells (SMCs) during the adaptive response to angiotensin II (AngII) infusion and determined its importance in protecting against aortic aneurysm and dissection.

overall_design: To understand to adaptive role of Yap1 in smooth muscle cells (SMCs) of aorta, we performed single cell RNAseq of aortic tissues from wild type mice, AngII infused wild type mice, SMC-specific Yap1 KO mice, AngII infused SMC-specific Yap1 KO mice.

first: Chen

last: Zhang

first: Scott

last: LeMaire

first: Ying

last: Shen


title: Machine-learning Classification Identifies Early Systemic Sclerosis Patients that Improve with Abatacept treatment by Modulating CD28-Pathways

city: Lebanon

first: Timothy

last: Sullivan

state: Grafton

address: 1 Medical Center Dr.

department: Biomedical Data Science

institute: Dartmouth College

summary: The efficacy of abatacept in patients with early diffuse systemic sclerosis (dcSSc) was analyzed to test the hypothesis that patients in the inflammatory intrinsic gene expression subset would show the most significant clinical improvement. 84 participants with dcSSc were randomized to receive abatacept or placebo for 12 months. RNA-seq was performed on 233 skin paired biopsies at baseline, 3- and 6-months. Improvement was defined as a 5 point or >20% change in modified Rodnan skin score (mRSS) between baseline and 12 months. Samples were assigned to intrinsic gene expression subset (inflammatory, fibroproliferative, or normal-like). In the abatacept arm, change in mRSS was most pronounced for the inflammatory (p<0.001) and normal-like (p=0.03) subsets relative to placebo. Participants on placebo remained in their molecular subset while inflammatory participants treated with abatacept moved toward normal-like. The CD28 costimulation pathway decreased in patients that improved on abatacept (FDR=5.88x10-4) and was specific to the inflammatory subset (FDR=0%). Patients in the inflammatory subset had elevation of the CD28 costimulation pathway at baseline relative to fibroproliferative (p = 0.0026) and normal-like (p=0.0001) participants. There was a correlation between improved ΔmRSS and baseline expression of the CD28 costimulation pathway (R=-0.62, p=0.02). This study provides an example of precision medicine in SSc clinical trials.

overall_design:
RNA-Seq samples from 84 Systemic Sclerosis clinical trial patients across up to 3 timepoints, treated with Abatacept or placebo
Submitter states that the raw fastq files will be uploaded to dbGaP.

first: Mehta

last: Bhaven K.

first: Espinoza

last: Monica E.

first: Khanna

last: Dinesh

first: Whitfield

last: Michael L.


title: Weimberg pathway an alternative for utilization of D-xylose for Myceliophthora thermophila

city: tianjin

first: Defei

last: Liu

state: 天津

address: xiqidao 32

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: An alternative for utilization of D-xylose, the non-phosphorylative Weimberg pathway was established in M. thermophila. Changes in transcript levels were surveyed in mutants. Transcriptome analysis revealed that the D-xylose dehydrogenase gene was significantly upregulated after deletion of D-xylose reductase when cultured in D-xylose media. Besides, genes belong to ribosome, biosynthesis of amino acids, biosynthesis of cofactors and carbon metabolism involved in growth were enriched in strains containing Weimberg pathway.

sample_organism: Thermothelomyces thermophilus ATCC 42464

overall_design: Strain JG207 was starting strain. Gene typle of DF1102 was JG207, ΔMtxyl1. Gene typle of DF1406 was JG207, ΔMtxyl1, overexpressing Mtxyd1/xylD/xylX/xylA.  Gene typle of DF1501 was JG207, ΔMtxyl1, overexpressing Mtxyd1/xylD/BxxylX/KsaD. All mutants was used to perform transcriptome analysis under induce of xylose.

first: Chaoguang

last: Tian


title: A dual-activity topoisomerase complex promotes both transcriptional activation and repression in response to starvation

city: Baltimore

first: Weidong

last: Wang

state: MD

address: 251 Bayview Blvd

department: National Institute on Aging

institute: Shuaikun Su

summary: Topoisomerases are required to release topological stress generated by RNA polymerase II (RNAPII) during transcription. Here we show that in response to starvation, the complex of topoisomerase 3b (TOP3B) and TDRD3 can promote transcriptional activation or repression. Human HCT116 cells individually inactivated for TOP3B, TDRD3, or TOP3B topoisomerase activity, exhibit similarly disrupted transcription for both starvation-activated genes (SAGs) and starvation-repressed genes (SRGs). Responding to starvation, both TOP3B-TDRD3 and the elongating form of RNAPII exhibit concomitantly increased binding to TOP3B-dependent SAGs, at binding sites that overlap. Strikingly, TOP3B inactivation decreases the binding of elongating RNAPII to TOP3B-dependent SAGs while increased it to SRGs. Furthermore, TOP3B-ablated cells display reduced transcription of several autophagy-associated genes and autophagy per se. Our data suggest that TOP3B-TDRD3 can promote both transcriptional activation and repression by regulating RNAPII distribution. In addition, the findings that it can facilitate autophagy may account for the shortened lifespan of Top3b-KO mice.

overall_design: To identify the regulation of the TOP3B-TDRD3 complex on starvation-induced transcription in HCT116 cells, we performed RNA-seq and ChIP-seq (TDRD3, RNAPII and RNAPII-ser2p) using WT and TOP3B-KO/TDRD3-KO/TOP3B-Y336F-KI HCT116 cells under no treatment and starvation condition.  We used EBSS medium to starve the cells for 6 hours. Then the RNAs were extracted for RNA-seq. The sonicated chromatins were pulled down by TDRD3, RNAPII or RNAPII-ser2p antibody. Then the DNAs were extracted and generated to Illumina libraries for sequencing. The NGS original reads were mapped to human genome (hg38). Most of the experiments contain two or three replications.

first: Shuaikun

last: Su

first: Yutong

last: Xue

first: Seung

last: Lee

first: Yongqing

first: Jinshui

last: Fan

first: Supriyo

last: De

first: Alexei

last: Sharov


title: Lead optimization of aryl hydrocarbon receptor ligands for treatment of inflammatory skin disorders

city: Nijmegen

first: Noa

middle: Johanna Maria

last: van den Brink

address: René Descartesdreef 1

department: Experimental Dermatology

country: Netherlands

institute: Radboudumc

summary: Therapeutic aryl hydrocarbon receptor (AHR) modulating agents (TAMAs) gained attention in dermatology as non-steroidal anti-inflammatory drugs that improve skin barrier properties. By exploiting AHR’s known ligand promiscuity, we generated novel TAMAs by lead optimization of a selective AHR modulator (SAhRM; SGA360). Twenty-two newly synthesized compounds were screened yielding two novel derivatives, SGA360f and SGA388, in which agonist activity led to enhanced keratinocyte terminal differentiation. We questioned whether SGA derivatives can restore the disturbed epidermal differentiation processes that are known for the key AD-associated T helper-2 cytokine, interleukin-4 (IL-4). We performed genome-wide transcriptomic analysis by bulk RNA-sequencing after co-stimulation of human epidermal equivalents with interleukin-4 (IL-4; AD-HEE) and SGA360 (SAhRM activity), SGA360f or SGA388 (coupling of SAhRM to agonist activity), or TCDD (full AHR agonist).

overall_design: Comparative gene expression profiling using bulk RNA-seq for 3 biological replicate kertinocyte donors (PCK15, 16 and 33) either left untreated (control), treated with IL-4 or IL-4 in combination with SGA360, SGA360f, SGA388 or TCDD

first: Gijs

last: Rikken

first: Kayla

last: Smith

first: Jos

middle: P

last: Smits

first: Krishne

last: Gowda

first: Angela

last: Alnemri

first: Gulsum

last: Kuzu

first: Iain

last: Murray

first: Jyh-Ming

last: Lin

first: Ivonne

last: van Vlijmen-Willems

first: Shantu

last: Amin

first: Gary

last: Perdew

first: Ellen

last: van den Bogaard


title: Scleraxis-lineage cells are required for tendon homeostasis and their depletion induces an accelerated extracellular matrix aging phenotype

city: Rochester

first: Antonion

last: Korcari

state: NY

address: 142 Westminster Rd, Appartment number 914 9th floor

institute: University of Rochester Medical Center

summary: Aged tendons have disrupted homeostasis, increased injury risk, and impaired healing capacity. Understanding mechanisms of homeostatic disruption is crucial for developing therapeutics to retain tendon health through the lifespan. Here, we developed a novel model of accelerated tendon extracellular matrix (ECM) aging via depletion of Scleraxislineage (ScxLin) cells in young mice (DTR). DTR recapitulates many aspects of tendon aging including comparable declines in cellularity, alterations in ECM structure, organization, and composition. Single cell RNA-sequencing demonstrated a conserved decline in tenocytes associated with ECM biosynthesis in aged and DTR tendons, identifying the requirement for ScxLin cells during homeostasis. However, the remaining cells in aged and DTR tendons demonstrate functional divergence. Aged tenocytes become pro-inflammatory and lose proteostasis. In contrast, DTR tenocytes demonstrate enhanced remodeling capacity. Collectively, this study defines DTR a novel model of accelerated tendon ECM aging and identifies novel biological intervention points to maintain tendon function through the lifespan

overall_design: Comparative gene expression profiling analysis of single cell RNA-seq data for young WT, young DTR, and aged WT (BL/6) FDL tendons

first: Anne

last: Nichols

first: Mark

last: Buckley

first: Alayna

last: Loiselle


title: Predictive Biomarkers for the Responsiveness of Recurrent Glioblastomas to Activated Killer Cell Immunotherapy

city: Sengnam

first: Sohyun

last: Hwang

address: 59, Yatap-ro, Bundang-gu

department: Pathology

country: South Korea

institute: Cha University

summary: Glioblastoma multiforme (GBM) is the most common and aggressive primary malignant brain tumor, but the current therapeutic approaches have very limited impact on increase of the patients’s survival with GBM. Our recent clinical trial with autologous activated nature killer (NK) cells (AKCs) including 14 patients with recurrent GBM found that the progression-free and overall survival times were significantly increased in some patients in the treatment group. In the present study, we identified TNFRSF18, TNFSF4, and IL12RB2 as biomarkers that predict response to NK cell therapeutics by studying the tumor-immune microenvironment using NanoString and qRT-PCR analyses. In addition, our results show that responders to NK therapy have an immune-activated tumor microenvironment, whereas non-responders do not.   Considering that immune and inflammatory response-enrichment is related to the high-risk group in this tumor type, our findings highlight a new treatment strategy of NK cell therapeutics for patients with highly aggressive recurrent GBM.

overall_design: The mRNA expression of recurred GBM patinets before autologous activated natural killer cell immunotherapy were measured by NanoString nCounter PanCancer Immune Profiling panel.

first: Hee

last: An


title: Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

summary: Eukaryotic genomes are pervasively transcribed by RNA polymerase II. Yet, the molecular and biological implications of such a phenomenon are still largely puzzling. Here, we describe noncoding RNA transcription upstream of the Arabidopsis thaliana DOG1 gene, which governs salt stress responses and is a key regulator of seed dormancy. We find that expression of the DOG1 gene is induced by salt stress, thereby causing a delay in seed germination. We uncover extensive transcriptional activity on the promoter of the DOG1 gene, which produces a variety of lncRNAs. These lncRNAs, named PUPPIES, are co-directionally transcribed and extend into the DOG1 coding region. We show that PUPPIES RNAs respond to salt stress and boost DOG1 expression, resulting in delayed germination. This positive role of pervasive PUPPIES transcription on DOG1 gene expression is associated with augmented pausing of RNA polymerase II, slower transcription and higher transcriptional burst size. These findings highlight the positive role of upstream co-directional transcription in controlling transcriptional dynamics of downstream genes.

overall_design: Comparison of transcriptomes of Col-0 and dog1-3 (SALK_000867) mutant upon seed imbibition - control and salt stress conditions (four biological replicas).

first: Miguel

last: Montez

first: Szymon

last: Swiezewski


title: Differential expression of cardiac mRNAs induced by Dexmedetomidine pretreatment in myocardial ischemia/reperfusion injury of mice

city: Guangzhou

first: Zhaorong

last: Chen

address: Zhongshan Er Road

institute: Sun yat-sen University

summary:
To investigate the cardioprotection of Dexmedetomidine, we established myocardial ischemia/reperfusion models in mice with vehicle or Dexmedetomidine pretreatment.
We then performed mRNA sequencing of cardiac tissues and conducted gene expression profiling analysis.

overall_design: Gene expression profiling analysis of mRNA sequencing data for cardiac tissues of mice.

first: Yu

last: Hong


title: Gene expression profiling of Mycobacterium tuberculosis-infected THP-1 cells with/without treatment with Vitamin C

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Transcriptional response of THP-1 cells infected with Mycobacterium tuberculosis utilizing ‘Active’ Mtb and ‘Dormant’ Mtb infection models at different time points. Analysis of the transcriptomic data deciphered the perturbation of gamut of host cellular pathways that are common and differentially manifested in the ‘Active’ Mtb and ‘Dormant’ Mtb infection models.

overall_design: Agilent one-color experiment,Organism: Homo sapiens  Agilent Microarray Gene Expression 8x60K Arrays AMADID: 27114

first: Sakshi

last: Dhingra Batra

first: Kiran

last: Kumari

first: Jaya

middle: S

last: Tyagi


title: Multimodal human thymic profiling reveals trajectories and cellular milieu for T agonist selection [Spatial transcriptomics]

city: Oslo

first: Benedicte

middle: Alexandra

last: Lie

address: Kirkeveien 166

department: Department of Medical Genetics

country: Norway

institute: University Of Oslo

summary: To prevent autoimmunity, thymocytes expressing self-reactive T cell receptors (TCRs) are negatively selected, however, divergence into tolerogenic, agonist-selected lineages represent an alternative fate. As thymocyte development, selection, and lineage choices are dependent on spatial context and cell-to-cell interactions, we have performed Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) and spatial transcriptomics on paediatric human thymus. Thymocytes expressing markers of strong TCR signalling diverged from the conventional developmental trajectory prior to CD4+ lineage commitment, while markers of different agonist cell populations (CD8αα(I), CD8αα(II), T(agonist), Treg(diff) and Treg) exhibited variable timing of induction. Expression profiles of chemokines and co-stimulatory molecules, together with spatial localization, supported that dendritic cells, B cells, and stromal cells contribute to agonist selection, with different subsets influencing thymocytes at specific developmental stages within distinct spatial niches. Understanding factors influencing agonist T cells is needed to benefit from their immunoregulatory effects in clinical use.

overall_design:
Human thymic tissue samples (N = 8) were collected from paediatric donors (<2 years) undergoing corrective cardiac surgery. Spatial transcriptomics was performed by the 10x visium solution.
***Raw data for human samples not available due to patient privacy concerns***

first: Marte

last: Heimli

first: Siri

last: Flåm

first: Hanne

last: Hjorthaug


title: Characterization of the effects of lysosomal acid lipase deficiency on clustering of gene differentiation in CD11c+ cells

city: INDIANAPOLIS

first: Cong

last: Yan

state: INDIANA

address: 975 W WALNUT ST IB420

institute: Indiana University School of Medicine

summary: Single cell RNA sequencing (scRNA-seq) analysis identified two distinct clusters with differential gene expression patterns, and revealed a major metabolic shift towards glucose utilization and reactive oxygen species (ROS) over-production in lal-/- CD11c+ cells.

overall_design: 2 samples were analyzed, lal-/- CD11c+ cells vs. lal+/+ CD11c+

first: Hong

last: Du

first: Ting

last: Zhao


title: Multimodal human thymic profiling reveals trajectories and cellular milieu for T agonist selection [CITE-seq]

overall_design:
Human thymic tissue samples (N = 5) and blood samples (N = 5) were collected from paediatric donors (<2 years) undergoing corrective cardiac surgery.  CITE-seq was performed by the 10x Genomics 5' immune profiling solution on peripheral blood mononuclear cells (PBMCs)  and on dissociated thymic cells at three stages during a gradual enrichement protocol: 1) on unenriched cells  2) after enrichement for antigen-presenting cells and 3) after CD45 depletion.
***Raw data for human samples not available due to patient privacy concerns***


title: Multimodal human thymic profiling reveals trajectories and cellular milieu for T agonist selection

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

overall_design: Refer to individual Series


title: Gene expression differences in pancreatic cancer cells treated with JTC801

first: jiao

last: liu

state: Guangdong

address: No. 63, Duobao Road, Liwan District

institute: Third Affiliated Hospital of Guangzhou Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Analysis of gene expression changes in three pancreatic cancer cell lines treated with JTC801

overall_design: JTC801 treats three pancreatic cancer cells separately, each in three replicates

first: Daolin

last: Tang

first: Jiao

last: Liu


title: Mapping the Spatial Dynamics of the Human Oral Mucosa in Chronic Inflammatory Disease

city: London

first: Paul

last: Sharpe

address: Guy's Hospital

department: Centre for Craniofacial and Regenerative Biology

institute: King's College London

summary: The interplay among different cells in a tissue is essential for maintaining homeostasis. Although, disease states have been traditionally attributed to individual cell types, increasing evidence and new therapeutic options have demonstrated the primary role of multicellular functions to understand health and disease, opening new avenues to understand pathogenesis and develop new treatment strategies.  We recently described the cellular composition and dynamics of the human oral mucosa; however, the spatial arrangement of cells is needed to better understand a morphologically complex tissue. Here, we link single-cell RNA sequencing, spatial transcriptomics, and high-resolution multiplex fluorescence in situ hybridisation to characterise human oral mucosa in health and oral chronic inflammatory disease. We define highly specialised epithelial and stromal compartments and describe location-specific immune programs. Furthermore, we discovered fine regional fibroblast states, and spatially mapped a rare pathogenic population localised in a highly immunogenic region, responsible for lymphocyte recruitment through CXCL8 and CXCL10 and with a possible role in pathological angiogenesis through ALOX5AP. Collectively, our study provides a comprehensive reference for the study of oral chronic disease pathogenesis.

overall_design: Adult oral mucosa tissue sections from healthy and periodontitis affected individuals were subjected to spatial transcriptomics analyses.

first: A

last: Caetano

first: Y

last: Redhead

first: F

last: Karim

first: P

last: Dhami

first: S

last: Kannambath

first: R

last: Nuamah

last: Volponi

first: L

last: Nibali

first: V

last: Booth

first: E

last: D'Agostino


title: Catechol-O-methyl transferase suppresses cell invasion and interplays with MET signaling in estrogen dependent breast cancer

city: Brno

first: Pavel

last: Bouchal

address: Kamenice 5

department: Biochemistry

country: Czech Republic

institute: Masaryk University, Faculty of Science

summary:
Catechol-O-methyl transferase (COMT) is involved in detoxification of catechol estrogens, playing cancer-protective role in cells producing or utilizing estrogen. Moreover, COMT suppressed migration potential of breast cancer (BC) cells.
To delineate COMT role in metastasis of estrogen receptor (ER) dependent BC, we investigated the effect of COMT overexpression on invasion, transcriptome, proteome and interactome of MCF7 cells, a luminal A BC model, stably transduced with lentiviral vector carrying COMT gene (MCF7-COMT).
We performed comparative gene expression analysis using data obtained from RNA-seq of COMT-overexpressing and control cells in biological duplicates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF7-COMT cells and control cell line (MCF7-GFP).

first: Lucia

last: Janacova

first: Michaela

last: Stenckova

first: Petr

last: Lapcik

first: Pavla

last: Bouchalova

first: Jakub

last: Faktor

first: Eva

last: Budinska

last: Muller


title: DUX4 orchestrates translational reprograming by broadly suppressing translation efficiency [RNA-seq]

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: DUX4, an embryonic transcription factor normally silenced in somatic tissues, was recently shown to reduce major histocompatibility complex I (MHC-I) and promote immune evasion in numerous cancer types. We report that transient expression of DUX4 results in the long-term suppression of interferon-gamma induction of MHC-I and the immunoproteasome. Brief expression of transcriptionally active DUX4 leads to a prolonged decrease in protein synthesis, altering the activity of translation initiation regulators eIF2a, eIF4E, 4EBP1, and translation elongation factor eEF2. Translational profiling identified mRNAs susceptible to DUX4-induced inhibition of translation initiation and elongation, including mRNAs encoding antigen presentation factors. We show that DUX4 orchestrates translational reprogramming by broadly attenuating protein synthesis while inducing the expression of RNAs encoding early embryonic proteins that are translationally up regulated and predicted to be less vulnerable to translational inhibition. Endogenous expression of DUX4 and its target genes in FSHD muscle cells and SuSa germinoma cells also correlates with suppression of protein synthesis and reduced MHC-I presentation. Our findings reveal a novel role of DUX4 in modulating translational control to reshape the cellular translatome with important implications for development and disease.

overall_design: Comparative gene expression analysis of RNA-seq data for MB135iDUX4 myoblasts paired with ribosome footprinting.

first: Danielle

last: Hamm

first: Ellen

last: Paatela

first: Sean

last: Bennett

first: Chao-Jen

last: Wong


title: Expression data from Th17 cells treated with Tinospora Cordifolia

city: Delhi

first: Bhavana

last: Prasher

state: Delhi

address: Sukhdev Vihar

institute: IGIB

summary: Tinospora Cordifolia, an ayurvedic herbal compound, is studied to be an effective drug in Autoimmine disease. Several in vivo mouse model systems are reported to show its efficiency as a drug of therapeutic potential to treat autoimmune diseases.  Th17 cells are the major T cells involved in the inflammatory responses in autoimmune diseases. The mechanistic insight into the therapeutic efficiency of Tinospora cordifolia is yet not studied. In this study we have tried to unravel the mechanism of action for the effect of water extract of Tinospora cordifolia on Th17 cells using genome wide expression approach.

overall_design: Naïve CD4+CD25- T cells were polarized to Th17 cells and were treated with 1500, 1000 and 500 µg/ml of Tinospora Cordifolia water extract (AETC). Untreated samples were used as a control. On day 4, cells were harvested and total RNA was isolated followed by hybridization on Affymetrix Gene Chip MTA 1.0 array according to manufacturer’s instruction. Gene expression analysis was performed using Transcriptome Analysis Console (TAC) and functional analysis done by using the Enrichr tool.

first: Nandan

last: Amrita


title: DUX4 orchestrates translational reprograming by broadly suppressing translation efficiency [Ribo-seq]

overall_design: Comparative ribosome foortprinting RNA-seq analysis for MB135iDUX4 myoblasts: untreated, treated with IFNg, with a DUX4 pulse, or with a DUX4 pulse+IFNg and harvested at 68h.


title: Single-cell gene expression profiles of hESC-derived retinal organoid progenitor cells and photoreceptor precursors from deep full-length scRNA-seq.

city: Los Angeles

first: David

last: Cobrinik

state: CA

address: 4546 Sunset Blvd

institute: Children's Hospital Los Angeles

summary: Human retinal organoids have been invaluable in vitro models of retinal development and disease. To investigate whether cell states and gene expression changes observed in human fetal cone development are accurately replicated in organoids, we produced H9 hESC-derived retinal organoids using two published methods (Kuwahara et al. 2015, Nat Comm 6, 6286, https://doi.org/10.1038/ncomms7286; Zhong et al. 2014, Nat Comm 5, 4047, https://doi.org/10.1038/ncomms5047). We then FACS-enriched cone and rod precursors and retinal progenitor cells every two weeks from 55-140 DIC, as well as at 225 DIC, and performed deep, full-length scRNA-seq chemistry. These data were used to identify maturation differences related to the organoid production method, identify aberrant cell populations or gene expression timing relative to human fetal retina, and define cone and rod photoreceptor trajectories in the retinal organoid setting.

overall_design: Retinal progenitor cells and photoreceptor precursors were FACS-enriched and single cells isolated from dissociated retinal organoids (produced based on two published methodologies) every two weeks from 55-140 DIC and at 225 DIC.

first: Dominic

middle: W

last: Shayler

first: Kevin

last: Stachelek

first: Sunhye

last: Lee

first: Jennifer

last: Aparicio

first: Mitali

last: Singh


title: Airway and parenchyma RNA sequencing in a mouse model of asthma chronic obstructive pulmonary disease overlap

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

summary:
To profile airway and parenchyma transcriptomes in our mouse model of asthma chronic obstructive pulmonary disease overlap, we employed RNA-Seq (TruSeq Stranded mRNA sample preparation, NovaSeq 6000, 20 million 100 bp single reads) as a discovery tool to identify mRNAs of interest in the development of experimental asthma chronic obstructive pulmonary disease overlap. Experimental asthma: Some mice were sensitized and challenged intranasally with house dust mite (HDM) extract 5 days per week for 3 weeks. In other mice, this was HDM treatment 3 times/week from weeks 4-11. Controls received phosphate buffered saline (PBS).
Experimental chronic obstructive pulmonary disease (COPD): Mice were exposed to cigarette smoke (CS) twice per day, 5 days per week for 8 weeks. Control mice were exposed to normal air (AIR).
Experimental asthma-COPD overlap (ACO): Mice were sensitized and challenged intranasally with HDM or PBS. From weeks 4-11, mice were also exposed to CS or AIR.
Treatment with dexamethasone (DEX): Separate groups of mice were treated with DEX during week 11. Lungs were excised, airway and parenchyma tissue were isolated through blunt dissection, and total RNA isolated.

overall_design:
Experimental asthma: Some mice were sensitized and challenged intranasally with house dust mite (HDM) extract 5 days per week for 3 weeks. In other mice, this was HDM treatment 3 times/week from weeks 4-11. Controls received phosphate buffered saline (PBS).
Experimental chronic obstructive pulmonary disease (COPD): Mice were exposed to cigarette smoke (CS) twice per day, 5 days per week for 8 weeks. Control mice were exposed to normal air (AIR).
Experimental asthma-COPD overlap (ACO): Mice were sensitized and challenged intranasally with HDM or PBS. From weeks 4-11, mice were also exposed to CS or AIR.
Treatment with dexamethasone (DEX): Separate groups of mice were treated with DEX during week 11.

In total with all of the combinations above there are 10 treatment groups, with each group having 2 samples (airway and parenchyma). Below is the breakdown of all groups sequenced:
1. 3 week PBS airway
2. 3 week PBS parenchyma
3. 3 week HDM airway
4. 3 week HDM parenchyma
5. 11 week PBS AIR airway
6. 11 week PBS AIR parenchyma
7. 11 week PBS AIR DEX airway
8. 11 week PBS AIR DEX parenchyma
9. 11 week HDM AIR airway
10. 11 week HDM AIR parenchyma
11. 11 week HDM AIR DEX airway
12. 11 week HDM AIR DEX parenchyma
13. 11 week PBS CS airway
14. 11 week PBS CS parenchyma
15. 11 week PBS CS DEX airway
16. 11 week PBS CS DEX parenchyma
17. 11 week HDM CS airway
18. 11 week HDM CS parenchyma
19. 11 week HDM CS DEX airway
20. 11 week HDM CS DEX parenchyma

first: Chantal

last: Donovan

first: Philip

middle: M

last: Hansbro

first: Richard

middle: Y

last: Kim

first: Xiaofan

last: Tu

first: Anthony

last: Bosco


title: Effect of depletion of RBM47 on gene expression on U87 glioma cells

city: shenyang

first: jialing

middle: jia

last: bai

state: liaoning

address: Culture Road No. 103

institute: shenyang pharmaceutical university

summary: To investigate the function of RBM47, we established U87 cell lines in which target gene has been knocked down by siRNA.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of two groups(control and siRBM47).

first: Yanting

last: Gu

first: Jialing

last: Bai


title: Transcriptional profile of brain reward circuits following methamphetamine self-administration

first: Michael

last: McCoy

state: Maryland

address: Molecular Neuropsychiatry Branch, 251 Bayview Blvd. Suite 200, 251 Bayview Blvd. Suite 200, 251 Bayview Blvd. Suite 200

institute: NIDA

summary: Methamphetamine (METH) is a powerful stimulant that has caused addiction (compulsive drug seeking and taking behavior) in millions of people world-wide. METH abuse is also associated with negative impact on the brain. One feature of addiction is uncontrollable drug seeking despite adverse consequences and becomes habitual. To mimic this in a rat model, rats with a history of METH use are given the opportunity to earn METH accompanied by aversive shocks on their feet. Rats that continue to take METH are shock-resistant (SR) and rats that reduce their METH intake are shock-sensitive (SS ).Rats that self-administered saline are controls (CT). In addition, we used controls for shock paradigm. For this purpose, when METH SA rat received a shock, the saline SA rat was also shocked. The separate groups of rats that were yoked (Y) to the corresponding METH shock-resistant (SR) and shock-sensitive (SS) rats are termed YSR and YSS, respectively.

overall_design: Rats self-administered (SA) METH for 21 days followed by footshocks for 8 days. The drug-naïve control rats (CT) will be the same as the METH-trained rats except sterile saline is infused after the active lever press. The control animals for footshock also received saline but were yoked to the METH-trained rats that receive contingent shocks. There were separate groups of rats that were yoked (Y) to the corresponding METH shock-resistant (SR) and shock-sensitive (SS) rats. They are termed YSR and YSS, respectively.

first: Subramaniam

last: Jayanthi

first: Jean

middle: L

last: Cadet


title: Genome-wide binding targets of GBF2 in ER stress

city: East Lansing

first: Dae Kwan

last: Ko

state: MI

address: 612 Wilson Rd.  Plant Biology RM 122

department: Plant Research Laboratories

institute: Michigan State University

summary: To profile in vivo DNA-binding activities of GBF2 in the UPR, we next perform chromatin immunoprecipitation sequencing (ChIP-seq) analyses of GBF2 at 0 h of ER stress recovery (i.e., 6 h of Tunicamycin, an ER stress inducer, treatment or DMSO) using a GBF2 native promoter-driven yellow fluorescent protein for energy transfer (YPet)-tagged GBF2 line (pGBF2:GBF2-YPet). Our analysis pipeline generated 523 Tm sample-specific binding peaks (i.e., not overlapped with peaks found in the corresponding DMSO-treated samples or overlapped with three times higher intensity) of GBF2. Hereafter we refer to these peaks as the UPR-specific binding peaks.

overall_design: A total of 8 samples, which consists of 1 protein with 2 treatments at 1 time-point in 2 biological replicates, were processed.

first: Dae

first: Federeica

last: Brandizzi


title: An early islet transcriptional signature drives local inflammation in autoimmune diabetes

city: Worcester

first: Alan

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: Pancreatic islet cell populations in KRV-infected LEW.1WR1 rats compared to those of controls identifies a population of "hot" endocrine cells that appear to lead to autoimmume diabetes in the infected rats.

overall_design:
Pancreatic islet cells were extracted from LEW.1WR1 rats on Day 11 post-treatment under three conditions - PBS (no-treatment control), injections of polyinosine-polycytidylic acid (poly I:C) on days -3, -2, and -1 (no-KRV control), and poly I:C treatment followed by injection of KRV (Kilham rat virus) on day 0. For the poly IC+KRV treatment pancreatic islet cells were also extracted on days 7 and 9 post-treatment to observe the onset of insulitis over time.
10X single-cell RNA-Seq was performed on each sample and bioinformatic and imaging analysis was applied to identify the cell type subsets and identify the genes and spatial distribution of cells involved in the onset of autoimmune diabetes.

first: Adediwura

last: Arowosegbe

first: Basanthi

last: Satish

first: Sambra

last: Redick

first: Natasha

last: Qaisar

first: Zhiru

last: Guo

last: Vanderleeden

first: Christina

last: Baer

first: David

last: Harlan

first: Dale

last: Greiner

first: Manuel

last: Garber

first: Jennifer

last: Wang


title: TOR early response genes in plant shoots

city: Heidelberg

first: Denis

last: Janocha

address: INF 230

department: Stem cell research

institute: Center for Organismal Studies, Heidelberg University

summary: We identified TOR target genes using three different TOR active site inhbitors AZD8055, TORIN1 and KU63749 in Arabidopsis thaliana shoots

overall_design: We compare the transcriptome of three different TOR active site inhibitors with mock treated plants 8 h after transfer.

first: Anne

last: Pfeiffer

first: Jan

last: Lohmann


title: Lufenuron exposure temporarily repress gene expression and the SUMO pathway in liver of Atlantic salmon

city: Bodø

first: Pål

middle: A.

last: Olsvik

address: Universitetsalléen 11

department: Faculty of Biosciences and Aquaculture

institute: Nord University

summary: Lufenuron is among the insecticides in use to combat salmon lice infestation in marine aquaculture. This benzoylurea drug acts as a chitin synthesis inhibitor, and prevent molting in the developing salmon lice larvae. In this work we aimed to study the molecular response to lufenuron exposure in Atlantic salmon given a standard oral dose. Juvenile salmon weighing about 40 g were treated with the drug for one week, and transcriptional responses were studied in liver tissue one (day 8) and seven days (day 14) after the treatment period. Exposure gave a transient inhibition of transcription in the liver at day 8 (2437 significant DEGs), followed by a weaker compensatory response at day 14 (169 significant DEGs). Many pathways associated with RNA metabolism were impacted at day 8. The sumoylation pathway was most strongly affected at day 8. Potential hepatic biomarkers for lufenuron exposure in fish could be phactr3, mst1r and slc47a1. In conclusion, this study shows that a 7-day standard dose of lufenuron downregulates transcription in liver tissue. The inhibitory effect on transcription was transitory, with a much weaker response one week after the medication period.

overall_design: The four treatment groups were control and exposed fish collected at day 8 (one day after the end of the lufenuron treatment period), and control and exposed fish collected at day 14 (seven days after the end of the lufenuron treatment).

first: Kristine

middle: E

last: Brokke

first: Ole

last: Samuelsen

first: Rita

last: Hannisdal


title: ATAC-seq deconvolution with CiberATAC identifies a prognostic regulon of HMG20B in metastatic colorectal adenocarcinoma

city: San Francisco

first: Hani

last: Goodarzi

address: 600 16th St, Office S312D

institute: University of California, San Francisco

summary: We used a sequential metastasis model of colorectal cancer cell lines and tumours to understand epigenomic regulators of metastasis. We performed scRNA-seq,  scATAC-seq, and bulk ATAC-seq on these samples and discovered the deregulation of HMG20B and its regulon.

overall_design: We used colorectal cancer SW480 and LS174T cell lines. We injected the cell lines to NOD/SCID Gamma male mice. We re-injected the xenografted tumours to new mice to obtain sequential lineages of colorectal cancer liver metastasis. Therefore all samples have a parental, LvM1, and LvM2 forms. We performed scRNA-seq on the pool of parental and LvM lineages from each sample (total of 2 samples, each containing parental and LvM lineages within the library). We performed scATAC-seq on SW480 parental and LvM2 as different libraries. We also performed bulk ATAC-seq for parental, LvM1, and LvM2 samples of SW480 as well as LS174T.

first: Mehran

last: Karimzadeh

first: Johnny

last: Yu

first: Benedict

last: Choi

first: Kristle

last: Garcia

first: Tanvi

last: Joshi

first: Norihiro

last: Yamaguchi

first: Ethan

last: Weinberg

first: Bo


title: Early Postnatal Alterations in Follicular Stress Response and Survival in a Mouse Model of Classic Galactosemia

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

summary: Primary ovarian insufficiency (POI) is characterized by accelerated loss of primordial follicles, which results in ovarian failure and concomitant menopause before age 40.  1-3% of females in the general population are diagnosed with POI and 80% of females with the inherited disease Classic Galactosemia (CG) will develop POI. CG is caused by mutations in the GALT gene encoding the enzyme galactose-1-phosphate uridylyltransferase.  While dietary restriction of galactose is lifesaving in the neonatal period, the development of severe complications including POI is not mitigated.  Additionally, the pattern of follicle loss have not been completely characterized.  The chronic accumulation of aberrant metabolites such as galactose-1 phosphate and galactitol are the suspected culprits in the development of the sequelae, yet the mechanisms remain elusive.   Our group uses a GalT gene-trapped mouse model to study the pathophysiology of CG.  Recently, we showed that alterations in the Integrated Stress Response pathway occur in the ovaries of these mice, likely contributing to the POI phenotype.  Using immunofluorescent staining in whole-ovary histology at progressive ages, we saw evidence of altered Integrated Stress Response activity in granulosa cells and primordial oocytes leading to accelerated primordial follicle growth, aberrant DNA damage repair, and increased cellular stress/death.  RNA-sequencing of whole ovary revealed significant alterations in cholesterol/lipid metabolism and transcriptional regulation.   Overall, our findings indicate abnormal stress response results in accelerated primordial follicle activation or “burnout,” which may explain the POI phenotype of fewer primordial follicles at later ages.

overall_design: We extracted RNA from 3 wildtype and 3 mutant mouse ovaries at P49; Both genotypes were treated with a diet containing 2.5% galactose for 4 weeks after weaning.

first: Synneva

last: Hagen-Lillevik

first: Joshua

last: Johnson

first: Kent

last: Lai


title: High-resolution mapping of transcribing Pol III by CRAC in the WT and C128 mutants

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

institute: IGMM - CNRS

summary: Here we report high-resolution analyses of transcribing RNA polymerase III (Pol III) in a wild-type (WT) strain and three C128 mutants. C128 is the second largest subunit of Pol III, which is the key subunit to recognize termination signal. Mutating key residues in C128 interferes with transcription termination in vitro and affect yeast viability as well, raising the question that whether these mutations provoke Pol III termination defects in vivo. Here we show that C128 mutants display termination defects at most PolIII-dependent genes, indicating that the most disruptive C128 mutations indeed impair Pol III transcription termination in vivo

overall_design: Analysis of the effect of the mutations of C128 on Pol III-dependent transcription genome-wide using CRAC

first: Juanjuan

last: Xie

first: Odil

last: Porrua


title: RNA sequencing data from PC-3 cells overexpressing hPARG

city: Grand Forks

first: Yaroslava

last: Karpova

state: ND

address: 501 Columbia Road

department: Biomedical Sciences

institute: University of North Dakota

summary: PC-3 prostate cancer cell line with stable overexpression of PARG under Doxycycline induction was generated. Transcriptome analysis linked malignance reduction phenotype with changes in chemokine family and tumorogenic pathways downregulation

overall_design: Two stably transduced PC-3 clones PC-3-TetOn-PARG-I4 and PC-3-TetOn-PARG-H6 overexpressing PARG under Doxycycline inducible promoter. Cells were plated to single well of 6 well plate, grown at 37°C in 5% CO2 for 72 hours without or with 500ng/ml doxycycline. Two independent experiments were performed for each clones: "N" (passage#5 and sequencing by Novogen) and "B" (passage #7 and sequencing by QB3).

first: Danping

last: Guo

first: Sarah

first: Alexei

last: Tulin


title: Marker Frequency Analysis of Neisseria elongata subsp. glycolytica ATCC 29315

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

summary: Investigation of replication dynamics (detection of origin of replication, bidirectionality, …)

overall_design: 3 conditions (early exponential (OD600 = 0.3), late exponential (OD600 = 0.6), stationary growth (OD600 = 1))

first: Tobias

last: Viehboeck


title: Wheat transcriptomic responses to long-term feeding by wheat curl mites

city: Lincoln

first: Lise

last: Pingault

state: NE

address: 1700 East Campus Mall, 312F Entomology Hall

institute: University of Nebraska-Lincoln

summary: The economic importance of wheat and its contribution to human and livestock diets has been already demonstrated. However, wheat production is impacted by pests that induce yield reductions. Among these pests, wheat curl mite (WCM, Aceria tosichella Keifer) impacts wheat all around the world. WCM are tiny pests that feed within the whorl of developing leaves and prevent the leaves from unfurling by causing leaves curling. The curling of the leaves provides a protective niche for the WCM. Additionally, WCM are also the vector of serious viruses in wheat. Little is known regarding the impact of the WCM on wheat transcriptome, and to date, only one article has been published describing the wheat transcriptomic changes after 1 day of WCM feeding. To better understand the wheat transcriptome variation after long-term feeding by WCM (10 days post infestation (dpi)), we used an RNA-seq approach. We collected leaves uninfested and infested with WCR from two wheat cultivars: Byrd (WCM resistant) and Settler CL (WCM susceptible) at 10 dpi. Our transcriptomic analysis revealed the common and specific transcriptomic variations in WCM resistant and susceptible wheat cultivars, chromosome specific location of the differentially expressed genes, and also identified the gene functions and pathways involved in WCM resistance. Collectively, our study provides important insights on wheat defense mechanisms against WCM after long-term feeding.

overall_design: Whorl mRNA profiles of 10 days after infestation of resistant (Byrd) and susceptible (Settler CL) wheat cultivar

first: Tran-Kim-Ngan

last: Luong

first: Joe

last: Louis

first: Gary

last: Hein


title: Single-cell RNA sequencing reveals tissue-associated fibroblastic reticular cell heterogeneity in human secondary lymphoid organs

city: Paris

first: Floriane

last: Noël

address: 1 avenue Claude Vellefaux

institute: INSERM

summary: Fibroblastic reticular cells (FRCs) actively support secondary lymphoid organ (SLO) architecture. They regulate innate and adaptive immunity by compartmentalizing immune cells in specialized niches, and tightly interacting with them. The phenotypic and functional diversity of FRCs in human SLOs remains largely uncharacterized. We performed a comprehensive profiling of FRCs by single-cell RNA sequencing on human tonsils and lymph nodes. We provide the first complete description of the tonsillar CD45-negative compartment. We identified and validated in tonsil, a population of follicular dendritic cells restricted to the mantle zone and discovered two CCL21-negative FRC subsets intermingling with T-cell zone reticular cells in the extrafollicular space. We also identified podoplanin-positive epithelial cells as a potential plasma cell (PC) niche. We found two levels of FRC-associated diversity: i) tissue-specific subsets; ii) shared subsets with tissue-specific gene signatures. These findings shed new light on the role of FRCs in supporting SLO-specific immune responses.

overall_design: Palatine tonsils were obtained following routine tonsillectomy for recurrent sleep apnea or airway obstruction at Robert Debré and Bichat Hospitals, in Paris. None of the patients had tonsillitis at the time of surgery. Patients with immunodeficiency or serious infections were excluded. LNs were obtained from cadaveric donors and patients at Bichat Hospital, Paris. Tumor draining LNs were obtained from consenting patients undergoing resection surgery. Resting lymph nodes were obtained from cadaveric donors. After tissue dissociation and CD45-negative single-cell suspension generation, CD45-CD31- cell were stained and sorted by FACS. Sorted CD45-CD31- cells were analyzed with the 10X chromium system (10X Genomics). Single-cell libraries were generated according to the manufacturer’s instructions (chromium 10X Next GEM Single-cell 3’ Kit (V.3.3)). Next-generation sequencing was performed on an Illumina NovaSeq 6000. ScRNAseq data processing and FASTQ file analysis were performed at the NGS platform of the Curie Institute, Paris (Tonsil 1) and the sequencing platform of the Paris Brain Institute (Tonsil 2-4, LNs) with the Cell Ranger pipeline (10X Genomics, version 3). Reads were aligned with the human reference genome hg38.

first: Justine

last: Poirot


title: Quantitative Transcriptomic Analysis of Control and FAM210A Knockout Hearts by Next Generation Sequencing

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

summary:
Purpose: Next-generation sequencing (NGS) provides the change of cellular pathways at the transcriptomic level. The overall goal for this research are to compare the transcriptome profiling by NGS in cardiomyocyte-specific FAM210A conditional knockout (cKO) hearts and control (Ctrl) hearts at two different time points and to evaluate the signaling pathways affected by FAM210A deficiency in the heart at the molecular level.
Methods: Cardiac mRNA profiles of FAM210A cKO and Ctrl hearts were generated by deep sequencing in triplicate at the late stage (~10 weeks post Fam210a cKO by tamoxifen induction) and in quadruplicates at the early stage (~5 weeks post Fam210a cKO by tamoxifen induction).
Results: Using an optimized data analysis workflow from the Genomic Research Center at the University of Rochester, we mapped ~30 millian sequence reads per sample to the mouse genome in the hearts of Ctrl and Fam210a cKO mice at both early and late stages. RNA-seq data comfirmed the knockout of FAM210A in the Fam210a cKO hearts. We identified differentially expressed genes at both early and late stages of FAM210A cKO heart compared with Ctrl hearts (adjust P valuse <0.05). Among upregulated genes, we observed enhanced integrated stress response (ISR) gene signature at both early and late stages in Fam210a cKO hearts compared with Ctrl hearts, including aminoacyl-tRNA synthetases, amino acid synthases, and one-carbon metabolic enzymes. The downregulated genes were not common between the two stages. At the early stage, the top enriched pathways include negative regulation of blood coagulation and wound healing and fatty acid metabolic process. In contrast, at the late stage, the major pathways include sulfide oxidation, glucose import, and mitochondrial ETC complex assembly.
Conclusions: Our study provides the first detailed transcriptomic anslysis of cardiomyocyte specific knockout of Fam210a in the heart at two different time-points by NGS. The RNA-seq data reported here provide a framework for comparative investigation of expression profiles in the hearts of FAM210A cKO compared with Ctrl hearts. Based on our analysis, we conclude that ISR is persistently activated in Fam210a cKO hearts, which may be a pro-survival compensatory response caused by the dysfunction of mitochondria in Fam210a cKO hearts. ISR activation can reprogram global cap-dependent translation and cellular metabolism simultaneously.

overall_design: Transcriptomic profiling was performed using RNA-seq analysis of total RNA extracted from hearts of ~5 weeks and ~10 weeks post tamoxifen-induced αMHC-Cre driven cardiomyocyte-specific knockout of FAM210A and Control αMHC-Cre mice. The selection of the two time points is based on echocardiography measurement of cardiac function in the Fam210a cKO mouse model. Cardiac function is normal at ~5 weeks but dramatically defective at ~10 weeks post tamoxifen-induced Myh6-Cre driven cardiomyocyte-specific knockout of FAM210A.

first: Jiangbin

last: Wu

first: Kadiam

last: Subbaiah

first: Omar

last: Hedaya

first: Si

last: Chen

first: Emma

last: Gira

first: Hani

last: Awad

first: Chen

last: Yan

first: Peng

last: Yao


title: Cancer-associated fibroblasts recapitulate phenotypes and functions across tumor types and species

city: Stanford

first: Michael

last: Januszyk

address: 257 Campus Dr

department: Surgery

institute: Stanford University

summary: Cancer-associated fibroblasts (CAFs) are among the most abundant cell types in desmoplastic tumors. However, CAFs are not yet a treatment target in mainstream cancer therapy likely because CAF heterogeneity and their roles in solid tumors remain incompletely understood. Here, we explored CAF heterogeneity via single-cell gene expression and chromatin accessibility in conjunction with spatial transcriptomics. We found that CAF heterogeneity is recapitulated across solid tumor types and species, and CAF subpopulations fall into two functional categories: mechano-responsive and immuno-modulatory. These categories are spatially-distinct and governed by specific changes in chromatin accessibility. Selective disruption of underlying mechanical force or immune signaling results in predictable shifts in subpopulation distributions and impacts tumor growth. Collectively, this research elucidates the spatial dynamics of CAF biology, delineates CAF subpopulation functions, identifies CAF-specific treatment factors, and provides a multimodal -omics framework for understanding the tumor stromal niche.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mouse tumor tissue samples were profiled using single-cell RNA sequencing and single-cell ATAC sequencing. Tissue was obtained from mouse endogenous breast tumors. Human tumor tissue samples were obtained from core needle biopsies for breast cancer and from Whipple procedures for pancreatic cancer. Human tissue samples were profiled using single-cell RNA sequencing.

first: Deshka

last: Foster


title: Global N6-methyladenosine RNA profiling reveals CSF1R as a target of METTL14 in non-small cell lung cancer.

city: Changsha

first: Yan

last: Hu

address: No.139 Middle Renmin Road

institute: Second Xiangya Hospital of Central South University

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

overall_design: Refer to individual Series


title: Profiling of peripheral blood B-cell transcriptome in children who developed coeliac disease in a prospective study

city: Tartu

first: Raivo

last: Uibo

address: Ravila 18

country: Estonia

institute: University of Tartu

summary: Background: In coeliac disease (CoD), the role of B cells has mainly been considered to be production of antibodies. The functional role of B cells has not been analysed extensively in CoD.  Methods: We conducted a study to characterize gene expression in B cells from children developing CoD early in life using samples collected before and at the diagnosis of the disease. Blood samples were collected from children at risk at 12, 18, 24 and 36 months of age. RNA from peripheral blood CD19+ cells was sequenced and differential gene expression was analysed using R package Limma. Findings: Overall, we found one gene, HNRNPL, modestly downregulated in all patients (logFC -0·7; q=0·09), and several others downregulated in those diagnosed with CoD already by the age of 2 years. Interpretation: The data highlight the role of B-cells in CoD development. The role of HNRPL in suppressing enteroviral replication suggests that the predisposing factor for both CoD and enteroviral infections is the low level of HNRNPL expression.

overall_design: In the present case-control study we set out to investigate changes in B-cell gene expression in genetically predisposed children, prospectively followed from birth until the age of 3 years, who developed celiac disease (CoD) during follow-up. The study material includes PBMC samples from 12 children with HLA-conferred susceptibility to CoD from the international DIABIMMUNE Study. The subjects were matched with controls for sex, HLA DR/DQ genotype, country of birth, and date of birth. Six of them developed CoD during the study period (CoD progressors) and six of them were controls and they did not develop any autoantibodies or CoD during first three years of life. CD19+ B cells were purified from PBMC samples collected at a maximum of four time points (12, 18, 24 and 36 months of age) and analysed with RNAseq.

first: Astrid

last: Oras

first: Henna

last: Kallionpää

first: Tomi

last: Suomi

first: Satu

last: Koskinen

first: Asta

last: Laiho

first: Laura

last: Elo

first: Mikael

last: Knip

first: Riitta

last: Lahesmaa

first: Alar

last: Aints


title: Global N6-methyladenosine RNA profiling reveals CSF1R as a target of METTL14 in non-small cell lung cancer [RIP-seq]

summary: Non-small cell lung cancer (NSCLC) is a common type of lung cancer, characterized by a poor prognosis. N6-methyladenosine (m6A) emerges as one of the most important modification of RNA, and m6A modifier METTL14 were reported to play pivotal role in multiple cancer types. However, there are limited number of studies of METTL14 in lung cancer and there still lacks systematic investigation of the function, clinical significance and targets of METTL14 in NSCLC. Here, we first conducted comprehensive N6-methyladenosine profiling of non-small cell lung cancer patients, and acquired m6A RNA modification atlas and differentially methylated RNAs in non-small cell lung cancer patients. Then we focused on RNA methyl-transferase METTL14, and investigated its clinical significance and function in NSCLC. As a result, METTL14 was correlated with clinical pathological parameters of differentiation and M stage. Addionally, METTL14 promotes NSCLC growth, induces cell death, and enhances cell migration and invasion, in vitro. Finally, to identify potential targets of METTL14, RNA sequencing, METTL14 RIP-Sequencing, and METTL14 MeRIP-Sequencing were conducted. Five genes were commonly identified, including four protein coding genes (PPIEL, AKR1C1, SARS2 and CSF1R) and one lncRNA ASAP1-IT2. After validation with TCGA dataset, Colony Stimulating Factor 1 Receptor (CSF1R) showed significant positive coefficient with METTL14, and was presumed to be the target of METTl14 in lung cancer. In conclusion, this study, uncovered an m6A RNA modification atlas, and revealed the clinical significance, in vitro function and molecular targets CSF1R of METTL14 in NSCLC.

overall_design: Antibody of METTL14 was utilized to immunoprecipitate METTL14 binding RNAs, followed by high-throughput sequencing.

first: Siying

last: Ren


title: Modification of histones and their transcriptional response

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

summary: We show that synthesising histones with different chemical modifications can induce a transcriptional response that alters the phenotype of those cells.

overall_design: Examination of the effect of different histone modifications on the transcriptome of the Hela Cells


title: Global N6-methyladenosine RNA profiling reveals CSF1R as a target of METTL14 in non-small cell lung cancer [meRIP-seq]

overall_design: The meRIP assay was carried out on all the 14 samples, including 7 lung cancer and the paired normal samples, followed by high-throughput sequencing. Additionaly, H1299 cells were applied for meRIP sequencing.


title: Stable overexpression of IRF8 in hepatocellular carcinoma cells

city: Nanjing

first: Hongxi

last: Wu

state: Jiangsu

address: No. 639, LongMian Road, Jiangning District, Nanjing

institute: China Pharmaceutical University

summary: Interferon regulatory factor 8 (IRF8), also known as interferon consensus sequence-binding protein, is an essential lineage-specific transcriptional regulator in the IRF family, controls diverse cellular processes and is has been implicated in innate immunity, immune cell differentiation. IRF8 has been shown to have both oncogenic and tumor suppressor activities, in myeloid cells and nonhematopoietic cells. As a transcription factor, other functions which may contribute to its oncogenic and anti tumor potential are not clear. So it is meaningful to study the role of IRF8 in different diseases. The roles and the underlying mechanisms of intrahepatic IRF8 in Hepatocellular carcinoma have not been reported up to date.

overall_design: mRNA profile of Hepatocarcinoma cell line Hepa1-6 with IRF8-overexpression and vector control were generated by deep sequencing

first: Yang

last: Yong

first: Wu

last: Hongxi


title: Stable overexpression of IRF8 in hepatocellular carcinoma cells hepa1-6 xenograft derived tumors in C57bl/6 mice

overall_design: mRNA profile of Hepatocarcinoma cell line Hepa1-6 with IRF8-overexpression and vector control xenografted into C57bl/6 mice were generated by deep sequencing


title: Single Nucleus ATAC Sequencing Reveals Epigenomic Regulation After Myocardial Infarction

city: Aachen

first: Mingbo

last: Cheng

state: North Rhine-Westphal

address: Pauwelsstr. 19

institute: Uniklinik RWTH Aachen

summary: We generated a single cell accessibility atlas from different time points after murine myocardial infarction as an important source for the field.

overall_design: We used snATAC product from 10x Genomics to profile myocardial infarction (MI) at Day 0, 3 and 10.

first: David

last: Schumacher

first: Christoph

last: Kuppe

first: Zhijian

last: Li

first: Ivan

last: Costa

first: Rafael

last: Kramann


title: Mouse liver [beta]-catenin chip-seq

city: Beijing

first: Fangming

last: Liu

address: No.5 Dongdan 3 Tiao

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Given that [beta]-catenin is a well-known transcriptional coactivator, and its transcriptional downstream genes may mediate [beta]-catenin’s action on hepatocarcinogenesis. Here, we performed ChIP-seq to study genome-wide distribution of [beta]-catenin in [beta]-catenin[delta](ex3)/+ livers in quest of the putative genes.

overall_design: Three [beta]-catenin[delta](ex3)/+ mouse livers were used for [beta]-catenin ChIP-seq. Livers were sonicated using a M220 Focused-ultrasonicator (Covaris, Woburn, MA, USA). Chromatin was immunoprecipitated with 4μg antibodies against [beta]-catenin (Carboxy-terminal Antigen, #9587S) overnight at 4°C. ChIP-Seq libraries were prepared using Kapa LTP Library Preparation Kit (Kapa Biosystems, Sigma-Aldrich). ChIP-Seq was performed on Illumina HiSeq3000. For the bioinformatic analysis of ChIP-Seq data, Bowtie2 was used for alignment. Enriched peaks were identified using MACS2 with FDR < 0.01. ChIPseeker was used for peaks annotation. Peaks enrichment distribution was analyzed by Deeptools


title: ATAC seq data

status: Public on Jan 31 2023

city: Boston

first: TENGTENG

last: YU

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Multiple myeloma is associated with an immunosuppressive bone marrow microenvironment instigated and maintained by crosstalk between multiple myeloma cells and the surrounding cells. This crosstalk is facilitated or hindered by epigenetic modifiers altering the gene expression of receptors. The Polycomb-like protein PHF19/PCL3, which mediates polycomb repressive complex 2 (PRC2) recruitment to chromatin, is a high-risk gene whose expression level correlates with poor prognosis in MM patients. Here, we used ATAC seq to define the chromatin accessibility and transcriptional landscape controlling this process by PHF19.

overall_design: ATAC-seq profiles of multiple myeloma cells with PHF19 overexpression and empty vectors types.

first: Tengteng

last: Yu


title: Gene expression in Tao3−/− RAW264.7 cells infected with VSV and HSV-1

city: Shanghai

first: Taoyong

last: Chen

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: The purpose of this study was to determine what are the effects of TAO3 deficiency on innate antiviral response upon virus infection in RAW264.7 cells. Wild type and Tao3−/− RAW264.7 cells were infected with Vesicular Stomatitis Virus (VSV) or herpes simplex virus 1 (HSV-1) for 6h. Then the differentially regulated genes were analyzed.

overall_design: Wild type and Tao3−/− RAW264.7 cells were infected with Vesicular Stomatitis Virus (VSV, MOI=1) or herpes simplex virus 1 (HSV-1, MOI=5) for 6h. Equal amounts of RNA were assayed for gene expression using Affymetrix mouse 430 2.0 arrays.

first: Zhou

first: Xuelian

first: Xuetao

last: Cao


title: Exon Architecture Controls mRNA m6A Suppression and Gene Expression

city: Chicago

first: Philip

middle: Cody

last: He

state: IL

address: 929 E 57th Street

institute: University of Chicago

summary: N6–methyladenosine (m6A) is the most abundant mRNA modification and plays crucial roles in diverse physiological processes. Utilizing a Massively Parallel Assay for m6A (MPm6A), we discover that m6A specificity is globally regulated by “suppressors” that prevent m6A deposition in unmethylated transcriptome regions. We identify Exon Junction Complexes (EJCs) as m6A suppressors that protect exon junction-proximal RNA within coding sequences from methylation and regulate mRNA stability through m6A suppression. EJC suppression of m6A underlies multiple global characteristics of mRNA m6A specificity, with the local range of EJC protection sufficient to suppress m6A deposition in average-length internal exons, but not in long internal and terminal exons. EJC-suppressed methylation sites co-localize with EJC-suppressed splice sites, suggesting that exon architecture broadly determines local mRNA accessibility to regulatory complexes.

overall_design: MPm6A, m6A-seq and RNA-seq

first: PCody


title: Next Generation Sequencing Facilitates Quantitative Analysis of Vehicle Control and Vismodegib Treated Tumor Transcriptomes

city: Birmingham

first: Dongquan

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

summary: Purpose:  The goal of this study is to compare transcriptome profiling (RNA-seq) between tumors of mammary tumor bearing mice treated with a vehicle control or FDA approved Hedgehog signaling inhibitor, Vismodegib.

overall_design: Methods: mRNA profiles of vehicle control and Vismodegib treated mice were generated by deep sequencing, using Illumina HiSeq. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS).

first: Dominique

last: Hinshaw

first: Ann

last: Hanna


title: Expression of human lungs at cold ischemic time (CIT) and 1-2 hrs. after reperfusion (H)

city: Toronto

first: Mingyao

state: ON

address: 101 College Street

department: Latner Thoracic Resaerch Laboratories

institute: University Health Network

summary: Study on lung transplantation encompassing a comprehensive and detailed investigation of differences at transcription level between lungs before and after transplant.

overall_design: Lung tissue samples were collected at the end of cold ischemia (CIT) and at reperfusion (H) at University Health Network in Toronto, Canada.

first: Cristina

last: Baciu

first: Jason

last: Shin

first: Ricardo

last: Zamel

first: Michael

last: Hsin

first: Shaf

last: Keshavjee


title: RBM4 regulates senescence

city: Dalian

first: Yang

last: Wang

address: No.9 West section, South Lv Road

institute: Dalian Medical University

summary: RNA-seq was performed on A549 and H1299 cells that stably knocking down RBM4 or control, in order to profile the gene expression change that were regulated by RBM4

overall_design: Examination of differential gene expression in 4 types of cells

first: Qianqian

last: Zheng


title: Lack of Fzd6 in Ciliated Cells Suppresses Ferroptotic Alveolar Cell Death induced by LPS and Corona Virus

city: New Haven

first: Barani Kumar

last: Rajendran

state: CT

address: 10 Amistad Street, New Haven, , Yale University

department: Pharmacology

institute: Yale University


title: Single-cell RNA-seq characterization of glioblastoma

city: New York

first: Junfei Zhao

last: Zhao

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

summary: We investigated the tumor microenvironment of glioblastoma at the celluar level using 10x scRNAseq.

overall_design: We performed 10x scRNAseq on tumor-infiltrating CD45+ immune cell population and PBMCs from 2 GBM patients.

first: Junfei

first: Catalina

last: Lee-Chang


title: Mapping and dissecting essential regulatory elements using multi-resolution CRISPR screens

city: Palo Alto

first: David

last: Yao

state: CA California

address: Michael Bassik/Room 4300, 240 Pasteur Dr.,

institute: Stanford University Bassik Lab

summary: Hundreds of thousands of candidate cis-regulatory elements (cCREs) have been identified across a myriad of cell types, but relatively few have been empirically characterized. Here, we present a scalable, phenotype-driven CRISPR screening method to test thousands of regulatory elements in parallel, by perturbing thousands of DNase hypersensitive sites (DHS) around hundreds of essential genes in K562. Integrating data from Cas9 exon-targeting with our CRISPRi screens, we nominate and validate promoters that regulate other nearby genes. Using higher-resolution CRISPR systems (dCas9 alone or Cas9) to tile across several essential enhancers, we resolve distinct peaks of activity and dissect core transcription factor binding sites (TFBSs) within enhancers, highlighting the advantages of complementary CRISPR systems to investigate CREs. Lastly, we use our tiling results to interrogate how TFBSs interact to drive enhancer function at the CBFA2T3 locus. This study demonstrates a scalable CRISPR screening framework for identifying and dissecting CREs that regulate cellular phenotypes.

sample_organism:
Homo sapiens
Synthetic plasmid

platform_organism:
Homo sapiens
Synthetic plasmid

overall_design:
The following datasets are available:
1) Comparative gene expression profiling analysis of RNA-seq data for K562 cells expressing dCas9-KRAB and its knockdown derivatives (sgNFE2 enhancer and sgSafe negative controls).
2) 21 day K562 proliferation screens using multiple CRISPR effector systems (nuclease-active Cas9, dCas9 alone, and dCas9 fused to the KRAB domain from ZNF705), comprehensively targeting significant essential regulatory elements from a large-scale DHS screen with all possible GuideScan sgRNAs. The sgRNA plasmid library is also sequenced and provided.


title: Signaling through the dystrophin glycoprotein complex affects the stress-dependent transcriptome in Drosophila

city: Hannover

first: Halyna

last: Shcherbata

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Cell Biochemistry

institute: Medical School Hannover

summary: Deficiencies in the human dystrophin glycoprotein complex (DGC), which links the extracellular matrix with the intracellular cytoskeleton, cause muscular dystrophies, a group of incurable disorders associated with heterogeneous muscle, brain and eye abnormalities. Stresses such as nutrient deprivation and aging cause muscle wasting, which can be exacerbated by reduced levels of the DGC in membranes, the integrity of which is vital for muscle health and function. Moreover, the DGC operates in multiple signaling pathways, demonstrating an important function in gene expression regulation. To advance disease diagnostics and treatment strategies, we strive to understand the genetic pathways that are perturbed by DGC mutations. Here, we utilize a Drosophila model to investigate the transcriptomic changes in mutants of four DGC components under temperature and metabolic stress. We identify DGC-dependent genes, stress-dependent genes and genes dependent on the DGC for a proper stress response, confirming a novel function of the DGC in stress-response signaling. This perspective yields new insights into the etiology of muscular dystrophy symptoms, possible treatment directions and a better understanding of DGC signaling and regulation under normal and stress conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control (CantonS/w[1118]) and mutant Drosophila melanogaster adult males. Mutants used were Dg[O55]/Dg[O86], Df(3R)Exel6184/Df(3R)Exel6184, Df(2L)BSC230/ΔNos15, and Df(3L)BSC450/ΔSyn1[5-2]. All genotypes were tested in unstressed conditions, under temperature stress, and under metabolic stress.

first: Travis

middle: D

last: Carney

first: Rucha

last: Hebalkar

first: Evgeniia

last: Edeleva

first: Ibrahim

last: Ömer Çiçek

middle: R


title: Profiles of N6-methyladenosine modifications of circular RNAs in oxygen-induced retinopathy

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

summary: To identify the N6-methyladenosine (m6A) modified circular RNAs (circRNAs) involved in a mouse model of oxygen-induced retinopathy (OIR), microarray analysis was performed with the retinal samples from OIR mice and Room air controls.

overall_design: Arraystar Mouse m6A-circRNA Epitranscriptomic microarray was performed to identify the m6A modification profiles of circRNAs in the retinas of OIR and control mice.

first: Yun

last: Li


title: ShRNA screen identifies novel mediator of PDAC metastasis in vivo

city: London

first: Goran

last: Tomic

address: 1 Midland Road

institute: The Francis Crick Institute

summary: An shRNA screen with the aim to investigate the role of pancreatic cancer-associated genes in the metastatic outgrowth in vivo was carried out. The set of candidate genes (284) was selected based on their association with pancreatic cancer, frequency of mutation in pancreatic cancer or on being Ras-regulated.

overall_design: The abundance of shRNAs was assessed in cells prior to injection (Day 0), in isolated lung tumours (Day 28), and in cells grown in culture (Day 28). Each gene was targeted with 3-4 shRNA producing a library size of 1013 shRNA. Nineteen shRNA pools were generated and each contained 8 control shRNA to assess consistency across pools.

first: Clare

last: Sheridan

first: Stuart

last: Horswell

first: Julian

last: Downward