title: CovS Inactivation Reduces CovR Promoter Binding at Diverse Virulence Factor Encoding Genes in Group A Streptococcus

status: Public on Jan 03 2022

first: Anthony

last: Flores

state: TX

address: 6431 Fannin St., MSB 3.130

institute: UTHSC/McGovern Medical School

summary: We performed CovR ChIP-seq analysis in the emm1 strain MGAS2221 and its CovS kinase deficient derivative strain 2221-CovS-E281A.  We identified that CovR bound in the promoter regions of nearly all virulence factor encoding genes in the CovR regulon.  Additionally, direct CovR binding was observed for numerous genes encoding proteins involved in amino acid metabolism, but we found limited direct CovR binding to genes encoding other transcriptional regulators. The consensus sequence AATRANAAAARVABTAAA was present in the promoters of genes directly regulated by CovR, and mutations of highly conserved positions within this motif relieved CovR repression of the hasA and M2221_0187 promoters.  Analysis of strain 2221-CovS-E281A revealed that binding of CovR at repressed, but not activated, promoters is highly dependent on CovR~P state. CovR repressed  virulence factor encoding genes could be grouped dependent on how variation in CovR~P differentially impacted DNA binding and gene transcript levels.

overall_design:
Comparison of WT (MGAS2221), CovS kinase-deficient mutant (E281A)
Please note that CovR-specific antibody was custom made (polyclonal, raised in rabbits against purified untagged CovR protein) and is not commercially available but has been used/validated in previous publications (PMIDs: 24788524, 25561708,  28289082, and 30379939)

first: Nicola

last: Horstmann

first: Chau

middle: N

last: Tran

first: Keven

last: Myers

first: Samuel

last: Shelburne


title: Cellular plasticity upon proton irradiation determines tumor cell radiosensitivity [methylation]

city: Heidelberg

first: Wahyu

middle: Wijaya

last: Hadiwikarta

address: Im Neuenheimer Feld 280

country: Germany

institute: Deutsches Krebsforschungszentrum

summary: Novel particle therapy was implemented into standard-of-care for cancer patients during the last years. However, experimental studies investigating cellular and molecular mechanisms are lacking although prognostic biomarker are urgently needed. The cancer stem cell (CSC)-related marker aldehyde dehydrogenase (ALDH) is known to impact on prostate cancer radiosensitivity through affecting defense against reactive oxygen species (ROS), reducing DNA damage repair and increasing cell survival. Surprisingly, we could show in a previous study that ionizing radiation itself enriches for ALDH-positive CSCs in a time- and dose-dependent manner through alteration in histone methylation.  Within the present study, we investigated CSC marker dynamics upon proton beam irradiation and hypothesized that this novel particle therapy may have increased CSC targeting potential due to its increased ionization potential compared to conventional photon irradiation. However, we found that proton irradiation is affecting cellular dynamics and escape from cell death.

overall_design: Sham, proton treated and photon treated samples were made available to compare effects of proton irradiation and photon irradiation on multiple human tumour cell lines. Samples were collected after 7 days of irradiation. 2 replicates available for majority of the samples.

first: Iñaki

last: Schniewind

middle: W

first: Ina

last: Kurth

first: Claudia

last: Peitzsch


title: Transcripts identified by microarray analysis that were deregulated in E18.5 Tbx18(cre/+);Rbpj(fl/fl) (Rbpj-cKO) ureters

status: Public on Jan 04 2022

city: Hannover

first: Andreas

last: Kispert

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in E18.5 ureters upon loss of Rbpj in the ureteric mesenchyme.

overall_design: Total RNA from dissected ureters of E18.5 Rbpj-cKO and control embryos was analyzed by microarray analysis.


title: Condensins are essential for Pseudomonas aeruginosa corneal virulence through their control of phenotypic programs

status: Public on Jan 05 2022

city: NORMAN

first: Valentin

last: Rybenkov

state: OK

address: 101 Stephenson Parkway

country: USA

institute: University of Oklahoma

type: Expression profiling by high throughput sequencing

summary: Pseudomonas aeruginosa is a significant opportunistic pathogen responsible for numerous human infections. Its high pathogenicity resides in a diverse array of virulence factors and an ability to adapt to hostile environments. We report that these factors are tied to the activity of condensins, SMC and MksBEF, which primarily function in structural chromosome maintenance. This study revealed that both proteins are required for P. aeruginosa virulence during corneal infection. The reduction in virulence was traced to broad changes in gene expression. Transcriptional signatures of smc and mksB mutants were largely dissimilar and non-additive, with the double mutant displaying a distinct gene expression profile. Affected regulons included those responsible for lifestyle control, primary metabolism, surface adhesion and biofilm growth, iron and sulfur assimilation, and numerous virulence factors, including type 3 and type 6 secretion systems. The in vitro phenotypes of condensin mutants mirrored their transcriptional profiles and included impaired production and secretion of multiple virulence factors, growth deficiencies under nutrient limiting conditions, and altered c-di-GMP signaling. Notably, c-di-GMP mediated some but not all transcriptional responses of the mutants. Thus, condensins are integrated into the control of multiple genetic programs related to epigenetic and virulent behavior of P. aeruginosa.

overall_design: The total of four strains, two biological replica each are compared. rRNA was removed nearly to completion using the ribo-Zero kit. Some predictions verified using qRT-PCR and genetics.

first: Hang

last: Zhao

first: April

middle: L

last: Clevenger

middle: V


title: Investigating the impact of cigarette smoke on pulmonary cellular immune responses to influenza virus at the single cell resolution in mice.

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St West

department: Department of Medicine

country: Canada

institute: McMaster University

summary: Single cell RNA-sequencing (scRNAseq) of lung immune cells from mice exposed to room air or cigarette smoke, infected with influenza A virus. Room air saline controls are also included. This analysis facilitates a comparison of cigarette smoke-associated changes to the pulmonary immune environment at the level of individual leukocytes and stromal cells.

overall_design: BALB/c mice were exposed to room air or cigarette smoke for two weeks, and subsequently infected with 50 PFU of influenza A/FM/1/47-MA (H1N1). Control room air-exposed mice administered saline were also included.  Smoke exposure was re-initiated from 3-7dpi, and whole lung samples were sampled and sequenced at 7dpi. n=4-5 mice were pooled per group. Reads were aligned to mouse genome reference and A/FM/1/47-MA cRNAs (details below).

first: Joshua

last: McGrath

first: Martin

last: Stampfli

first: Anna

last: Dvorkin-Gheva


title: Yes tyrosine kinase signaling promotes liver cancer development [DSP294_SNU387]

city: Montreal

first: Sylvain

last: Meloche

state: Quebec

address: 2950, Chemin de Polytechnique

institute: Institute of Research in Immunology and Cancer

summary: Hepatocellular carcinoma (HCC) is a disease with high unmet medical need. Most patients are diagnosed at late stage with few therapeutic options and a dismal prognosis. While molecular genomic studies have been helpful in improving the understanding and treatment of many types of cancer, their impact on HCC has been negligible so far. This is largely due to a poor understanding of the underlying mechanisms of this cancer and the lack of dominant oncogene that can be targeted pharmacologically. Here we report the identification of a novel Yes oncogenic signaling pathway in HCC that has escaped large-scale molecular genetic studies. Using a combination of genetic and pharmacological interventions in cellular and mouse models of HCC, we show that Yes activity is necessary for HCC cell proliferation. Transgenic expression of activated Yes in mouse hepatocytes is sufficient to induce liver tumorigenesis. Mechanistically, we found that Yes directly phosphorylates YAP and TAZ, promoting their nuclear accumulation and transcriptional activity in HCC cells and liver tumors, and that YAP/TAZ are effectors of Yes oncogenic transformation. Src-family kinase activation correlates with YAP tyrosine phosphorylation and nuclear localization in human HCC, and is associated with increased tumor burden. Specifically, high Yes activity predicts significantly shorter overall survival in HCC patients. Our findings identify Yes as a potential therapeutic target in HCC.

overall_design: We compared the transcriptomes of SNU-387 HCC cells infected with non-target shRNA (n=3) or YES1 targeted shRNA (n=3).


title: RNA-Seq of P23-P25 tdTomato+ astrocyte, GlastCre;Ai14 (WT) vs GlastCre;Ptch1fl/fl;Ai14 (Ptch1cKO)

city: Boston

first: Zach

last: Herbert

state: MA

address: 450 Brookline Ave

department: Molecular Biology Core Facilities

institute: Dana-Farber Cancer Institute

summary: This study aimed to understand the role of the SHH receptor Ptch1 in the development of cortical astrocytes in the mouse. Ptch1 was knocked out in astrocytes by using an Glast-Cre driver line in combination with a line carrying floxed Ptch1 alleles and with a Cre-dependent tdTomato reporter line (Ai14). TdTomato+ astrocytes were sorted out from the somatosensory cortex followed by bulk RNA-seq. The sequencing data compares the gene expression profiles of ptch1cKO vs WT at postnatal developmental age (P23-P25).

overall_design: tdTomato astrocytes of 4 each were compared between control (labeled as "WT", containing GlastCre and Ai14 alletes) and mutant (labeled as "Ptch1cKO", homozygous for the floxed version of the Ptch1 allele) samples.

first: Yajun

last: Xie

first: Zachary

middle: T

first: Manal

last: Adam

first: Corey

last: Harwell


title: Genome-wide maps of chromatin state in  WT and Whsc1 ko or Nlrc5  ko CT26 cells [ATAC-seq]

city: shanghai

first: jiale

middle: jia

last: ren

state: shanghai

address: yueyang road 320

department: shanghai institute of nutrition and health

country: China

institute: CAS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone dimethyl transferase WHSC1 drives the transcription of MHC-I machinery in mouse and human colorectal cancer cells (CRCs); thus, WHSC1 downregulation potentiates CRCs to escape from cytotoxic CD8+ T cell responses. WHSC1 directly interacts with MHC-I transactivator, NLRC5 to selectively stimulate MHC-I gene expression. Thus, silencing Whsc1 diminished MHC-I level, impaired anti-tumor immunity and blunted immunotherapy efficacy.

overall_design: ATAC-seq:Examination of chromatin state in WT and Whsc1 KO or Nlrc5 KO cells.

first: Jiale

last: Ren

first: Ni

last: Li

first: Siyu

last: Pei

first: Yannan

last: Lian

first: Jiacheng

last: Guo


title: Transcripts identified by microarray analysis that were deregulated in E13.5 Pax-2cre;Fgfr1(fl/?);Fgfr2(fl/fl) (Fgfr2cKO) ureters.

first: Andreas

last: Kispert

summary: Evaluation of the transcriptional changes in E13.5 ureters upon loss of Fgfr2 (and reduction of Fgfr1) in the ureteric epithelium.

overall_design:
Total RNA from dissected ureters of E13.5 Fgfr2cKO and control mice was analyzed by microarray analysis.

Please note that the "?" (in the genotype) represents either "+" or "fl" since both Pax2cre/+;Fgfr1/+;Fgfr2fl/fl and Pax2cre/+;Fgfr1fl/fl;Fgfr2fl/fl ureters were collected together into the mutant pool.


title: REPROGRAMMING CBX8-PRC1 FUNCTION WITH A POSITIVE ALLOSTERIC MODULATOR

city: Los Angeles

first: Oliver

last: Bell

state: California

address: 1450 Biggy St, NRT6510

institute: USC

summary: Canonical targeting of Polycomb Repressive Complex 1 (PRC1) to repress developmental genes is mediated by cell type-specific, paralogous chromobox (CBX) proteins (CBX2, 4, 6, 7 and 8). Based on their central role in silencing and their dysregulation associated with human disease including cancer, CBX proteins are attractive targets for small molecule chemical probe development. Here, we have used a quantitative and target-specific cellular assay to discover a potent positive allosteric modulator (PAM) of CBX8. The PAM activity of UNC7040 antagonizes H3K27me3 binding by CBX8 while increasing interactions with nucleic acids. We show that treatment with UNC7040 leads to efficient and selective eviction of CBX8-containing PRC1 from chromatin, loss of silencing and reduced proliferation across different cancer cell lines. Our discovery and characterization of UNC7040 not only reveals the most cellularly potent CBX8-specific chemical probe to date, but also corroborates a mechanism of Polycomb regulation by non-specific CBX nucleotide binding activity.

overall_design: 39 samples in total: 26 ChIP-Seq (13x2 replicates each), 13 RNA-Seq (LOVO: 2x2 replicate, SUDHL4: 3x3 replicates)

first: Daniel

last: Bsteh

first: Yibo

last: Si


title: Single Cell Analysis of adult zebrafish jaw joint

city: New York

first: Joanna

last: Smeeton

state: NY

address: 650 W 168TH ST, ROOM 1103A, William Black Building

department: Rehabilitation and Regenerative Medicine

institute: Columbia University Irving Medical Center

summary: To profile the diversity of cell types present in adult zebrafish synovial joints, we performed single-cell RNA sequencing of the uninjured adult jaw joint and identified multiple skeletal, connective tissue, and fibroblast subtypes, including a joint-specific periosteal population.

overall_design: Single cell RNA sequencing of FACS isolated zebrafish joint cells (trps1:eGFP-enriched; sox10:DsRed-enriched) from 3-month-old microdissected jaw joints

first: J

first: G

last: Crump


title: ICP22 of Herpes Simplex Virus 1 decreases RNA Polymerase Processivity

city: Ithaca

first: Joel

middle: D

last: Baines

address: 235 Hungerfordhill Rd

institute: Cornell University

summary: These data files consist of Illumina next seq 500 sequencing data from precision nuclear run-on and global nuclear run-on experiments conducted with human epithelial Hep2 cells that have been infected with human herpes simplex virus-1 (F) strain mutants.   The results of these studies suggest that ICP22 is necessary for reducing Pol II processivity on the viral genome which results in its maintenance on the viral genome over the course of infection.  While human reads continued to decrease over the time course of infection in the repair virus, this did not occur in the ICP22 deletion virus where over time the number of human reads increased over the time course of infection rather than decreasing.  The effects of ICP22 deletion were separable from inhibiting HSV-1 DNA replication to the extent that ICP22 deletion resulted in a decrease in Pol levels only at 6 hpi and not at 3 hpi as was observed in the mutant

sample_organism:
Drosophila melanogaster
Homo sapiens
Human alphaherpesvirus 1

overall_design: PRO-seq and GRO-seq were conducted on cells that had been infected with two different HSV-1 (F) strain viruses.  Infection occurred for either 3 or 6 hours before collection of nuclei for PRO/GRO-seq processing, and the mutant viruses used were a bacterial artificial choromosome derived virus with the ICP22 open reading frame deleted or bearing a genetically restored virus.  These viruses were generated by Maruzuru et. al., 2013, Roles of p53 in Herpes Simplex Virus 1 Replication, Journal of Virology.  After nuclei extraction, and before the run-on reactions, extracted Drosophila melanogaster nuclei were spiked into infected nuclei solution at a ratio of 1 Drosophila melanogaster nuclei for every 1000 infected Homo sapiens nuclei.  Sequencing libraries were prepared from the biotinylated RNA's in the PRO-seq or the Br-UTP RNAs produced during either 5 min or 30 min of GRO-seq run-on for each replicate of each virus at each time point post infection.

first: Claire

last: Birkenheuer

first: Larua

last: Dunn

first: Rachel

last: Dufour


title: Sugar-induced gene expression changes in a Caco-2/HepG2 coculture

city: Gent

first: Amar

middle: van

last: Laar

address: Coupure Links, 653

country: Belgium

institute: Ghent University

summary: We descirbe the impact of monosaccharides (glucose, fructose, L-arabinose versus mannitol) on gene expression, focussing on metabolic health pathways. This is part of a larger study on changes in cellular physiology in the metabolic health context.

overall_design: Caco-2 cells were differentiated for 2 week on a transwell filter and brought in contact with HepG2 cells in a coculture setup. 24-hour exposures were performed at the Caco-2 level before extracting RNA.

last: van Laar

first: John

last: Van Camp

first: Charlotte

last: Grootaert

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: Deforce


title: TRAF6 is a tumor suppressor in AML by directly targeting MYC oncogenic activity [RNA-Seq]

status: Public on Jan 01 2022

first: Bettina

last: Nadorp

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

summary: Clonal hematopoiesis of indeterminant potential (CHIP) is an aging-associated condition characterized by the clonal outgrowth of self-renewing cells that acquire specific mutations. One of the most frequent mutations in CHIP targets the methylcytosine dioxygenase TET2, also observed in number of myeloid neoplasms 1,2. Although individuals with CHIP are healthy, they are at an increased risk of developing hematopoietic malignancies. These findings indicate that additional alterations are needed for the transition from a pre-leukemic (CHIP) stage to frank leukemia, although the identity of such molecular events remains poorly characterized. To identify signaling states that cooperate with CHIP mutant cells we used an in vivo RNAi screening approach. One of the most prominent genes identified was the ubiquitin ligase TRAF6. We demonstrate that TRAF6 is repressed in a subset of acute myeloid leukemia (AML) and myeloproliferative neoplasm (MPN) patients. Loss of TRAF6 in pre-leukemic HSPC results in overt AML/MPN and is associated with induction of MYC-dependent leukemic stem cell signatures. TRAF6 represses MYC activity at enhancers due to the ubiquitination of MYC on Lysine (K)148. Ubiquitination of MYC on K148, does not affect protein stability but rather antagonizes acetylation of MYC on the same lysine and suppresses MYC oncogenic activity by preventing its DNA binding. Our results identify a novel tumor suppressor function for TRAF6 and demonstrate a novel mode of regulation of MYC oncogenic activity

overall_design: RNA-sequence of wild-type, Tet2 KO, Traf6 KO and  Tet2;Traf6 dKO hematopoietic stem and progenitor cells (Lineage-, Sca-1+, cKit+)

last: Starczynowski

first: Iannis

last: Aifantis

first: Tomoya

last: Muto

first: Maria

last: Guillamot


title: TRAF6 is a tumor suppressor in AML by directly targeting MYC oncogenic activity

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Next-generation sequencing analysis to compare expression pattern of relapse and baseline "GMP pattern" MDS samples

city: Houston

first: Ganiraju

last: Manyam

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

summary: Transcriptional changes occurring in the expanding LMPP population of "GMP pattern" MDS patients with blast expansion post-HMA failure were compared with the transcriptional profile of untreated (baseline) "GMP pattern" MDS patients.

overall_design:
CD34+CD38-CD45RA+CD90- LMPPs were FACS-purified from magnetically CD34-enriched mononuclear cells isolated by density gradient from fresh bone marrow aspirates. Total RNA was purified using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific). Quality checks were performed in a 2100 Expert bioanalyzer (Agilent). cDNA libraries were prepared using the Ovation Single Cell RNA-Seq System (NuGEN Technologies). RNA-seq was performed with the HiSeq 4000 System (Illumina), generating 76-base pair reads.

**The submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns.**

first: Irene

last: Ganan-Gomez

first: Jing

last: Wang

first: Simona

last: Colla


title: Next-generation sequencing analysis to compare expression pattern of relapse and baseline "CMP pattern" MDS samples

summary: Transcriptional changes occurring in the expanding LT-HSC population of "CMP pattern" MDS patients with blast expansion post-HMA failure were compared with the transcriptional profile of untreated (baseline) "CMP pattern" MDS patients.

overall_design:
CD34+CD38-CD45RA-CD90+ LT-HSCs were FACS-purified from magnetically CD34-enriched mononuclear cells isolated by density gradient from fresh bone marrow aspirates. Total RNA was purified using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific). Quality checks were performed in a 2100 Expert bioanalyzer (Agilent). cDNA libraries were prepared using the Ovation Single Cell RNA-Seq System (NuGEN Technologies). RNA-seq was performed with the HiSeq 4000 System (Illumina), generating 76-base pair reads.

**The submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns.**


title: Patterning the embryonic pulmonary mesenchyme

city: Princeton

first: Katharine

last: Goodwin

state: NJ

address: Hoyt Laboratory, 25 William St

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Smooth muscle guides morphogenesis of epithelia during development of several organs, including the mammalian lung. However, it remains unclear how airway smooth-muscle differentiation is spatiotemporally patterned and whether it originates from distinct mesenchymal progenitors. Using single-cell RNA-sequencing of embryonic mouse lungs, we show that the pulmonary mesenchyme contains a continuum of cell identities, but no distinct progenitors. Transcriptional variability correlates with sub-epithelial and sub-mesothelial mesenchymal compartments that are regulated by Wnt signaling. Live-imaging and tension sensors reveal patterned migratory behaviors and cortical forces in each compartment, and show that sub-epithelial mesenchyme gives rise to airway smooth muscle. Differentiation trajectory reconstruction reveals that cytoskeleton, adhesion, and Wnt signaling pathways are activated early in differentiation. Finally, we show that Wnt activation stimulates the earliest stages of differentiation and induces local accumulation of mesenchymal F-actin, which influences epithelial morphology. Our work provides the first single-cell view of pulmonary mesenchymal patterning during branching morphogenesis.

overall_design: Mouse embryos were collected at E11.5. Lungs were dissected and the left lobe of each was dissociated in dispase. Individual cells from two biological replicates were processed in the 10x Genomics Chromium system. The tissues we isolated contain all expected cell types of embryonic lungs, including mesenchymal cells at each stage of differentiation into smooth muscle.

first: Celeste

middle: M

last: Nelson


title: Transcripts identified by microarray analysis that were deregulated in E14.5 Tbx18(cre/+);Rbpj(fl/fl) (Rbpj-cKO) ureters

first: Andreas

last: Kispert

summary: Evaluation of the transcriptional changes in E14.5 ureters upon loss of Rbpj in the ureteric mesenchyme.

overall_design: Total RNA from dissected ureters of E14.5 Rbpj-cKO and control embryos was analyzed by microarray analysis.


title: Analysis of mRNA decay intermediates in Bacillus subtilis 3' exoribonuclease and RNA helicase mutant strains

first: David

middle: Herman

last: Bechhofer

address: 1 Gustave L. Levy Place

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: The Bacillus subtilis genome encodes four 3’ exoribonucleases: polynucleotide phosphorylase (PNPase), RNase R, RNase PH, and YhaM.  Previous work showed that PNPase, encoded by the pnpA gene,   is the major 3’ exonuclease involved in mRNA turnover; in a pnpA deletion strain, numerous mRNA decay intermediates accumulate.  Whether B. subtilis mRNA decay occurs in the context of a degradosome   complex is controversial.  In this study, global mapping of mRNA decay intermediate 3’ ends within coding sequences was performed in strains that were either deleted for, or had an inactivating point mutation in,   the pnpA gene.  The pattern of 3’ end accumulation in these strains was highly similar, suggesting that mRNA decay was not occurring in the context of a degradosome, whose structure would be affected by the absence of PNPase.  A comparison with mapped 3’ ends in a strain lacking CshA, the major RNA helicase, indicated that different mRNAs may require both PNPase and CshA for efficient decay.  RNA-seq analysis of strains lacking RNase R suggested that this enzyme did not play a major role in mRNA turnover in the wild-type strain.  Strains were constructed that contained only one of the four known 3’ exoribonucleases.  When RNase R was the only 3’ exonuclease present, it was able to degrade a model mRNA efficiently, showing processive decay even through a strong stem-loop structure that inhibits PNPase processivity.  Strains containing only RNase PH or only YhaM were also insensitive to this RNA secondary structure, suggesting the existence of another, as-yet unidentified, 3’ exoribonuclease.

overall_design: Term-seq/RNA-seq analysis from Bacillus subtilis strains with pnpA gene deleted or mutated to be catalytically inactive or cshA gene deleted.   Triplicate samples.

first: Shivani

last: Chhabra

first: Zachary

middle: F

last: Mandell


title: Comprehensive evaluation of adenine base editors induced mutations at genomic and transcriptional level [WGS]

city: Beijing

first: shaofang

last: Li

state: Beijing

address: No 50, ZhanghuaLu, HAIDIAN

department: Beijing Vegetable Research Center

institute: Beijing Academy of Agriculture and Forestry Science

type: Genome variation profiling by high throughput sequencing

summary: Adenine base editors (ABEs) with wide CRISPR compatibility and high activity improves the editing efficiency and arouses the off-target challenges as well. Here, we carried out a comprehensive evaluation of ABE8e and ABE9 induced DNA and RNA mutations in model organism rice. The whole-genome sequencing analysis on plants with rBE46b (SpCas9n-TadA8e), rBE49b (SpCas9n-TadA9), rBE50 (SpCas9n-NG-TadA8e), rBE53 (SpCas9n-NG-TadA9) reveals that the ABEs with TadA9 lead to a higher number of off-target A>G SNVs and ABEs with SpCas9n-NG lead to a higher total number of off-target SNVs. The analysis of T-DNAs (ABEs carrier) disclosed that the on-target mutations could happen before T-DNA integration to plant genomes as well as after T-DNA integration to plant genomes, while ABEs integrated into plant genomes lead to more A>G SNVs. We also detected off-target A>G RNA mutations in plants with higher expression of ABEs but not in plants with lower expression of ABEs. The off-target A>G RNA mutations tend to cluster while off-target A>G DNA mutations cluster in a very rare manner. The findings that CRISPRs, TadA variants, T-DNA integration, and ABE expression contribute ABEs’ specificity provide alternative ways to increase the specificity of ABEs.

overall_design: To study adenine base editors induced DNA and RNA off-targets, genome and transcriptome were sequenced on T0 plants through tissue culture, agrobacterium transformation with or without ABEs

first: Shaofang


title: BulkRNA sequencing of small intestinal IEC epithelial cells of Casp3/7ΔIEC mice and Casp3/7FL/FL littermates

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

institute: University Gent

summary: Apoptosis is widely believed to be crucial for epithelial cell death and shedding in the intestine, thereby shaping the overall architecture of the gastrointestinal tract, but also regulating tolerance induction during homeostasis. To experimentally address this concept, we generated intestinal epithelial cell (IEC)-specific knockout mice that lack both executioner caspase-3 and caspase-7 (Casp3/7?IEC), which are the converging point of the extrinsic and intrinsic apoptotic pathway. Surprisingly, the overall architecture, cellular landscape and proliferation rate remained unchanged in these mice. However, non-apoptotic cell extrusion was increased in Casp3/7?IEC mice, compensating apoptosis deficiency, maintaining the same physiological level of IEC shedding. Microbiome richness and composition stayed unaffected, bearing no sign of dysbiosis. Transcriptome and single cell RNA sequences analyses of IECs and immune cells revealed no differences in signaling pathways of differentiation and inflammation. These findings demonstrate that during homeostasis apoptosis per se is dispensable for IEC turnover at the top of intestinal villi intestinal tissue dynamics, microbiome composition and immune regulation.

overall_design:
To examine possible other compensatory signaling pathways in Casp3/7ΔIEC mice that could mediate an adaptive alternative developmental reprogramming in the gut in the absence of IEC apoptosis, we performed a transcriptomic analysis of bulk IEC material isolated and sorted live EPCAM+/CD45- epithelial cells from both WT and Casp3/7ΔIEC mice.
We used for each genotype four biological replicates (4 times WT and 4 times DKO)

first: Farzaneh

last: Ghazavi

first: Jelle

last: Huysentruyt

first: Stephanie

last: Kourula

first: Sofie

last: Martens

first: Behrouz

last: Hassania

first: Tim

last: Wartewig

first: Tatyana

last: Divert

first: Ria

last: Roelandt

first: Bastian

last: Popper

last: Hiergeist

first: Peter

last: Tougaard

first: Tom

last: Vanden Berghe

first: Marie

last: Joossens

first: Geert

last: Berx

first: Nozomi

last: Takahashi

first: Adam

last: Wahida

last: Vandenabeele


title: Nanopore Sequencing for the screening of Myeloid and Lymphoid neoplasms with eosinophilia and rearrangement of PDGFRa, PDGFRb, FGFR1 or PCM1-JAK2.

city: Florence

first: Paola

last: Chiarugi

state: Florence

address: Viale Morgagni 50

department: Department of Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Primary Eosinophilic Disorders (PED) represent a group of diseases with heterogeneous pathophysiology and diversified clinical phenotypes. Among the clonal alterations found in PED, gene fusions involving PDGFR, PDGFR, FGFR1 or JAK2 cluster in the WHO category of myeloid and lymphoid neoplasms with eosinophilia. The heterogeneous nature of genomic aberrations and the promiscuity of fusion partners, may limit the diagnostic accuracy of conventional cytogenetic approaches. To address such technical challenges, we exploited a nanopore-based sequencing platform to screen a cohort of patients referred for the characterization of a PED. We show that nanopore sequencing enables fast (within 60 hours) and precise identification of genomic fusion events, starting from whole blood DNA.

overall_design: We report the application of Oxford Nanopore sequencing technology for the identification of gene fusions involving PDGFRa, PDGFRb, FGFR1 and JAK2

first: Simone

last: Romagnoli

first: Niccolò

last: Bartalucci

last: Guglielmelli

first: Alessandro

last: Vannucchi


title: Metabolic incorporation of electron-rich ribonucleosides enhances APEX-seq for profiling spatially restricted nascent transcriptome

first: Ran

last: Li

address: Yiheyuan Road No.5

institute: Peking University

summary: We present MERR APEX-seq, a method for newly transcribed RNAs subcellular profiling combined metabolic incorporation of electron-rich ribonucleosides, 6-thioguanosine and 4-thiouridine, with the peroxidase-mediated RNA labeling method, APEX-seq. MERR APEX-seq offers both high spatial specificity and high coverage in the mitochondrial matrix and at the endoplasmic reticulum membrane. Application of MERR APEX-seq at nuclear lamina of human cells reveals that the mRNA components tend to encode for transcripts processing related proteins. MERR APEX-seq with high spatial specificity and high coverage could be widely used to expand our knowledge of RNA localization and function at subcellular compartments.

overall_design: MERR APEX-seq libraries were generated for the following constructs with APEX2: (1) MITO (mitochondrial matrix), (2) ERM (endoplasmic reticulum membrane), (3) NES (cytosol) and (4) LMNB1 (nuclear lamina). 16 libraries were prepared for MITO before (INPUT) and after (ENRICH) enrichment (2 biological replicates for labeled targets of s6G-APEX-labeling, s4U-APEX-labeling and APEX labeling each and 2 biological replicates for unlabeled control of no metabolism and no probe), 8 libraries were prepared for ERM before (INPUT) and after (ENRICH) enrichment (4 biological replicates for labeled targets of s6G-APEX-labeling), 4 libraries were prepared for NES before (INPUT) and after (ENRICH) enrichment (2 biological replicates for labeled targets of s6G-APEX-labeling) and 12 libraries were prepared for LMNB1 before (INPUT) and after (ENRICH) enrichment (2 biological replicates for labeled targets of s6G-APEX-labeling and APEX labeling each and 2 biological replicates for unlabeled control).

first: Zhongyu

last: Zou

first: Wentao

last: Wang

first: Peng


title: Interplay of vascular endothelial growth factor receptors in organ-specific endothelial cell survival

city: Helsinki

first: Sinem

last: Karaman

address: Haartmaninkatu 8

department: Individualized Drug Therapy Research Program / Faculty of Medicine

country: Finland

institute: University of Helsinki

summary: The aim was to study immediate changes in gene expression of lung and heart endothelial cells after single or compound deletions of vascular endothelial growth factors.

overall_design: scRNA sequencing analysis of murine pulmonary and cardiac endothelial cells deleted of vascular endothelial growth factor receptors for 48 hours. Deletions include i) single deletions of Vegfr1, Vegfr2, and Vegfr3; ii) double deletions Vegfr1;Vegfr2 and Vegfr2;Vegfr3, and iii) triple deletion of Vegfr1;Vegfr2;Vegfr3. Naming of the files: a) C69, C72 etc indicates running number of experimental cohorts. R1=VEGFR1, R2=VEGFR2 and R3=VEGFR3. Ctrl samples are collected from tamoxifen treated littermate controls, Del samples had Cdh5-BAC-CreERT2. In each Ctrl and Del sample, equal amounts of sorted cells from 2-3 mice are pooled.

first: Madeleine

middle: H

last: Lackman

first: Satu

last: Paavonsalo

first: Karthik

middle: A

last: Hemanthakumar

first: Kari

last: Alitalo


title: Role of the COP1 E3 ligase in ERalpha signaling

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

institute: University of Liège

summary: Our study defines the E3 ligase COP1 as a positive modulator of ERalpha-dependent gene transcription. We carried our RNA-Seq experiments with total RNAs from control or COP1-depleted MCF7 cells treated or not with estrogens and identified a signature of genes known to be regulated by estrogens whose transcription is deregulated upon COP1 deficiency.

overall_design: Total RNAs were extracted from control or COP1-depleted MCF7 cells treated or not with estrogens (10 nM) for 5 hours. Experiments were carried out in triplicates.

first: Kateryna

last: Shostak


title: Gene expression of white and grey matter demyelinated areas and normal appearing matter from Multiple Sclerosis leukocortial lesions  of human post-mortem tissue

status: Public on Jan 02 2022

city: Amsterdam

first: Anne-Marie

last: Dam

state: Noord Holland

address: De Boelelaan 1108

department: Anatomy and Neurosciences

country: Netherlands

institute: Amsterdam UMC, location VUmc

summary:
Using laser capture microscopy, white (WM) and grey matter (GM) demyelinated areas and normal appearing matter was collected from histologically verified leukocortical lesions from snap-frozen human post mortem tissuederived from Multiple Sclerosis patients.
Our data shows large differences in gene expression in WM and GM demyelinated areas (compared to their respective normal appearing matter) even when the demyelinated areas are spatially connected such as in leukocortical lesions.
Thus, we show that WM demyelinated areas and GM demyelinated areas are distinct entities with distinct pathology. Therefore findings observed in WM demyelinated areas cannot be generalized to GM demyelinated areas.

overall_design:
Sequencing libraries of 11 leukocortical lesions (4 areas per lesion) were prepared with the Quant Seq 3' mRNA-Seq Library Prep Kit FWD

Please note that, for clarification and ease of use, the records was updated with clinical information (in the 'Clinical_Info.xlsx' file, on April 25, 2022).

first: Thecla

last: van Wageningen

first: Emma

last: Gerrits

first: Nieske

last: Brouwer

first: Jeroen

last: Geurts

first: Bart

last: Eggen

first: Erik

last: Bodekke

last: van Dam


title: Prostate-specific Oncogene OTUD6A Promotes Prostatic Tumorigenesis via Deubiquitinating and Stabilizing c-Myc

city: boston

first: jing

last: liu

state: Massachusetts

address: 330 brookline ave

institute: BIDMC

summary: In this study, we found that OTUD6A is a physiological deubiquitinase for c-Myc in prostate cancer setting and  promotes prostatic tumorigenesis through stabilizing c-Myc oncoprotein. Moreover, knockout of Otud6a in mice retarded the prostatic tumorigenesis in Hi-Myc prostate cancer mice model

overall_design: RNA-seq study of prostate tissue and tumor samples in the littermate derived from Hi-Myc genetically engineered mouse model (GEMM) crossing with Otud6a-null mice. There are a total of four genetypes, inluding Otud6a+/y, Otud6a-/y, Hi-Myc; Otud6a+/y and Hi-Myc; Otud6a-/y mice. The normal prostate tissue form Otud6a+/y and Otud6a-/y, and prostate tumor samples from Hi-Myc; Otud6a+/y and Hi-Myc; Otud6a-/y mice were subjected for RNA-seq.

first: Yunhua

last: Peng

first: Jing

last: Liu

first: Jiankang

first: Jiangang

last: Long


title: The impact of long-term physical inactivity on adipose tissue immunometabolism

first: William

last: Trim

address: 25 Shuttack Street

department: Systems Biology

institute: Harvard Medical School

summary: RNAsequencing from 20 young healthy male (20-45 years) abdominal subcutaneous adipose tissue before and after 60 days' head-down bed rest.

overall_design: Examination of the effect of long-term bed rest on adipose tissue transcriptomes in healthy, active young males

first: Jean-Philippe

last: Walhin

first: Francoise

last: Koumanov

first: Anne

last: Bouloumie

first: Mark

last: Lindsay

first: Rebecca

last: Travers

first: James

middle: E

last: Turner

first: Dylan

last: Thompson


title: PERK is a critical metabolic hub for immunosuppressive function in macrophages

city: Columbus

first: Chan-Wang

middle: Jerry

last: Lio

state: Ohio

address: 460 W 12th Ave

institute: Ohio State University

summary: Here we report that the Th2 cytokine IL-4 and the tumor microenvironment activated protein kinase RNA-like ER kinase (PERK) stress signaling cascade to promote immunosuppressive M2 activation and proliferation. PERK activation mediated the upregulation of PSAT1 and serine biosynthesis via the downstream transcription factor ATF4. We found that Increased serine biosynthesis could result in enhanced mitochondrial function and α-ketoglutarate (α-KG) production required for JMJD3-dependent epigenetic modification.

overall_design: Examination of H3K27me3 in WT and PERK-KO macrophages in different polarizing conditions. A total of 10 samples were included in the study. One sample from each WT and KO for naïve (M0) macrophages; two biological replicates from each WT and KO for M1 and M2 conditions.

first: Lydia

last: Raines

first: Heng-Yi

last: Chen

first: Jerry

first: Stanley

last: Huang


title: A wave of Foxp3 + regulatory T cell accumulation in the neonatal liver plays unique roles in maintaining self-tolerance

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Rd.

department: Tongji Hospital

institute: Tongji University

summary: The liver in newborn animals undergo a maturation process in order to adapt to a plethora of changes and challenges in the extra-uterine life. The influx of regulatory T cells during 1-2-week period protect the animals from autoimmune hepatitis and govern the transformation of a neonatal liver to a crucial metabolic organ in adults.

overall_design: CD4+GFP+ Treg cells from the liver and spleen of Foxp3GFP knock-in mice (12-day-old) were purified by flow cytometry.

first: Mingyang

last: Li

first: Qing

last: Ge


title: Subcutaneous nanotherapy repurposes the immunosuppressive mechanism of rapamycin to enhance allogeneic islet graft viability

city: Evanston

first: Reese

middle: Anthony Keith

last: Richardson

state: IL

address: 2145 Sheridan Road

department: Chemical and Biological Engineering

institute: Northwestern University

summary: Oral rapamycin administration rapamycin is plagued by poor bioavailability and wide biodistribution. Thus, this pleotropic mTOR inhibitor has a narrow therapeutic window, numerous side effects and provides inadequate transplantation protection. Parental formulation was not possible due to rapamycin’s hydrophobicity (log P 4.3). Here, we demonstrate that subcutaneous rapamycin delivery via poly(ethylene glycol)-b-poly(propylene sulfide)(PEG-b-PPS) polymersome (PS) nanocarriers modulates cellular biodistribution of rapamycin to change its immunosuppressive mechanism for enhanced efficacy while minimizing side effects. While oral rapamycin inhibits naïve T cell proliferation directly, subcutaneously administered rapamycin-loaded polymersomes (rPS) instead modulated Ly-6Clow monocytes and tolerogenic semi-mature dendritic cells, with immunosuppression mediated by CD8+ Tregs and rare CD4+ CD8+ double-positive T cells.  As PEG-b-PPS PS are uniquely non-inflammatory, background immunostimulation from the vehicle was avoided, allowing immunomodulation to be primarily attributed to rapamycin’s cellular biodistribution. Repurposing mTOR inhibition significantly improved maintenance of normoglycemia in a clinically relevant, MHC-mismatched, allogeneic, intraportal (liver) islet transplantation model. These results demonstrate the ability of engineered nanocarriers to repurpose drugs for alternate routes of administration by rationally controlling cellular biodistribution.

overall_design: Single cell RNA seq profiles of splecic T cells from wild type mice treated with rapamycin-loaded poly(ethylene glycol)-b-poly(propylene sulfide) (PEG-b-PPS) polymersomes or controls

first: Jacqueline

last: Burke


title: Mechanical control of innate immune responses against viral infection revealed in a human Lung Alveolus Chip

city: Boston

first: Haiqing

last: Bai

address: 5th floor, Center for Life Science, 3 Blackfan Circle

institute: Wyss Institute

summary: Mechanical forces associated with breathing play fundamental role in lung development and disease but the molecular pathways remain largely unknown. Here, we used a mechanically actuatable Human Lung Alveolus Chip that recapitulates human lung alveolar type I and type II cell differentiation, alveolar-capillary interface formation, and genome-wide gene expression profiles characteristic of the distal lung to investigate the role of physical forces associated with cyclic breathing motions in lung innate immune responses to viral infection. When the mechanically active Alveolus Chips are infected with influenza H3N2 virus, a cascade of host responses is elicited on-chip, including increased production of cytokines and expression of inflammation-associated genes in pulmonary epithelial and endothelial cells, resulting in enhanced recruitment of circulating immune cells as occurs during viral infection in vivo. Surprisingly, studies carried out in parallel with static chips revealed that physiological breathing motions suppress viral replication by activating protective innate immune responses in epithelial and endothelial cells. This is mediated at least in part through upregulation of S100 calcium-binding protein A7 (S100A7), which binds to the Receptor for Advanced Glycation End Products (RAGE), an inflammatory mediator that is most highly expressed in the lung alveolus in vivo. This mechano-immunological control mechanism is further supported by the finding that existing RAGE inhibitor drugs can suppress production of inflammatory cytokines in response to influenza virus infection in this model. S100A7-RAGE interactions and modulation of mechanical ventilation parameters could therefore serve as new targets for therapeutic intervention in patients infected with influenza and other potential pandemic viruses that cause life-threatening lung inflammation.

overall_design: This study analyzed gene expression of alveolar epithelium and endothelium time-course on-chip (day 0, day 8 and day 14)

first: Donald

last: Ingber


title: RNAseq of GFP-FOXR1 and GFP-FOXR1 M280L vs GFP CTL

first: Uwe

last: Beffert

address: 24 Cummington Mall

department: Biology

institute: Boston University

summary: The forkhead box (Fox) family of transcription factors are highly conserved and play essential roles in a wide range of cellular and developmental processes. We report an individual with severe neurological symptoms including postnatal microcephaly, progressive brain atrophy and global developmental delay associated with a de novo missense variant (M280L) in the FOXR1 gene. At the protein level, M280L impaired FOXR1 expression and induced a nuclear aggregate phenotype due to protein misfolding and proteolysis. RNAseq and pathway analysis showed that FOXR1 acts as both a transcriptional activator and repressor with central roles in heat shock response, chaperone cofactor-dependent protein refolding and cellular response to stress pathways. Indeed, FOXR1 expression is increased in response to cellular stress, a process in which it directly controls HSPA6, HSPA1A and DHRS2 transcripts. The M280L mutant compromises FOXR1’s ability to respond to stress, in part due to impaired regulation of downstream target genes that are involved in the stress response pathway. Quantitative PCR of mouse embryo tissues show Foxr1 expression in the embryonic brain. Using CRISPR/Cas9 gene editing, we found that deletion of mouse Foxr1 led to a severe survival deficit while surviving newborn Foxr1 knockout mice had reduced body weight. Further examination of newborn Foxr1 knockout brains revealed a decreased in cortical thickness and enlarged ventricles compared to littermate wild-type mice, suggesting that loss of Foxr1 leads to atypical brain development. Combined, these results suggest FOXR1 plays a role in cellular stress response pathways and is necessary for normal brain development.

overall_design: Examination of FOXR1 expression in HEK-293 cells.

first: Andressa

last: Mota

first: Angela

last: Ho

first: Rui

last: Hong

first: Christine

last: Cheng


title: Stage-specific control of oligodendrocyte survival and morphogenesis by TDP-43

city: Baltimore

first: Dwight

last: Bergles

state: MD

address: 725 North Wolfe St., WBSB 1001

department: Neuroscience

institute: Johns Hopkins University

summary: We performed bulk RNA-seq on FACS-isolated oligodendrocytes from P30 Mobp-TDP43 and Mog-TDP43 mouse lines to determine the effect of TDP-43 loss at different stages of oligodendrocyte development.

overall_design: Splicing analysis to determine the effect of TDP-43 loss in oligodendrocytes (Mobp-TDP43 Control vs. Mobp-TDP43 KO & Mog-TDP43 Control vs. Mog-TDP43 KO)

first: Dongeun

last: Heo

first: Jonathan

middle: P

last: Ling

first: Riki

last: Kawaguchi


title: PD-L1 AND ICOSL DISCRIMINATE HUMAN SECRETORY AND HELPER DENDRITIC CELLS IN CANCER, ALLERGY AND AUTOIMMUNITY

city: Paris

first: Floriane

last: Noël

address: 1 avenue Claude Vellefaux

country: France

institute: INSERM

summary: In this study, we define a novel phenotypic and functional dichotomy of human dendritic cells (DC), with strong relevance to cancer, allergy, and autoimmunity. Using 16 different stimuli in vitro (130 observations), we describe two states of human activated DC. PD-L1highICOSLlow Secretory DC produced large amounts of inflammatory cytokines and chemokines but induced very low levels of T helper (Th) cytokines following DC-T co-culture; conversely PD-L1lowICOSLhigh Helper DC produced low levels of secreted factors but induced high levels and a broad range of Th cytokines. Secretory DC were aligned with mature migratory LAMP3+ DC in three different cancer types, atopic dermatitis, and lupus nephritis by single-cell transcriptomics. They were associated with T cell inflammation, overexpressed stimulatory and inhibitory checkpoints, acquired increased cell-cell communication, and were associated with good prognosis in head and neck squamous cell carcinoma, and with response to checkpoint blockade in Melanoma. This functional dichotomy of DC has broad implications in inflammation and immunotherapy.

overall_design: Fresh samples of HNSCC tumor tissues and blood of untreated patients with head and neck cancers were obtained from the pathology departments of the Institut Curie and the Pitié-Salpêtrière hospital. Single Cell RNA Purification Kit (Norgen Bioteck) was used for RNA extraction, including on-column DNase digestion (Qiagen), as described by the manufacturer's protocol. RNA integrity was controlled with Agilent RNA 6000 Pico Kit (Agilent Technologies) in BioAnalyzer. cDNA was generated with SMARTer Ultra Low input RNA for Illumina Sequencing-HV (Clontech), following manufacturer’s protocol with 14 cycles for amplification. Quality controls were performed with Qubit dsDNA high sensitivity (Thermofisher) and an Agilent RNA 6000 Nano Kit (Agilent Technologies). Multiplexed paired-end libraries 50nt in length were obtained using Nextera XT kit (Clontech). Sequencing was performed in a single batch with Illumina HiSeq 2500 using an average depth of 15 million reads. Library, sequencing, and quality controls were performed by the NGS facility at the Institut Curie. Reads were mapped to the human genome reference (hg19/GRCh37) using Tophat2 version 2.0.14. Gene expression values were quantified as read counts using HTSeq-count version 0.6.1. Genes with less than one read count in at least one sample were filtered out and.

first: Caroline

last: Hoffmann


first: Stanley

last: Huang

state: OH

address: 3113 Pelotonia Research Center, 2255 Kenny Road

department: Microbial Infection and Immunity

institute: The Ohio State University

summary: Here we report that the Th2 cytokine IL-4 and the tumor microenvironment activated protein kinase RNA-like ER kinase (PERK) ER stress signaling cascade to promote immunosuppressive M2 activation and proliferation. Lacking PERK signaling impeded mitochondrial respiration and lipid oxidation critical for M2 macrophages. In addition, PERK activation mediated the upregulation of PSAT1 and serine biosynthesis via the downstream transcription factor ATF4.

overall_design: mRNA of IL-4-stimulated, or naïve bone marrow-derived macrophages from PERK WT or KO mice

first: Lydia

last: Raines

first: Haoxin

last: Zhao

first: Yuzhu

last: Wang

first: Wei

last: Cao


title: Eosinophil-mediated suppression and Anti-IL-5 enhancement of plasmacytoid dendritic cell interferon responses in asthma

city: Seattle

first: Kimberly

last: Dill-McFarland

state: WA

address: 750 Republican St

department: Allergy and Infectious Diseases

institute: University of Washington

summary: Blood plasmacytoid dendritic cells (pDCs) purified from anonymous donors were stimulated ex vivo with rhinovirus-16 (RV) in the presence or absence of eosinophil supernatants. Purified pDCs from 8 individuals with moderate-severe asthma, treated or not treated with anti-IL-5/5Rα therapy, were cultured with or without RV. Transcriptome analysis revealed global repression of pDC IFN response patterns by eosinophils, most notably in basal expression of interferon stimulated genes (ISGs). Increased RV-induced IFNα secretion and transcription as well as increased basal ISG expression was detected in pDCs from participants treated with anti-IL-5/5Rα therapy. Our findings highlight a novel mechanism through which T2 inflammation regulates pDC IFNα responses relevant to RV respiratory infections in the context of eosinophilic airway disease and suggest one potential mechanism through with eosinophil-depleting therapies may reduce the severity of RV illness.

overall_design: pDC virus-stimulated gene expression responses to eosinophils ex vivo or eosinophil-depleting Anti-IL-5 therapy in vivo

first: Justin

last: Schwartz

first: Patricia

middle: C

last: Fulkerson

first: Matthew

last: Altman

first: Michelle

last: Gill


title: PD-L1 AND ICOSL DISCRIMINATE HUMAN SECRETORY AND HELPER DENDRITIC CELLS IN CANCER, ALLERGY AND AUTOIMMUNITY [CITE-seq]

overall_design: Fresh samples of HNSCC and breast tumor tissues of untreated patients were obtained from the pathology departments of the Institut Curie and the Pitié-Salpêtrière hospital. After tissue dissociation and single-cell suspension generation, cell sorting was done by FACS to enrich for immune cell populations. Single-cell sequencing of final samples was performed using Single Cell 3’ kit V1 (Breast cancer sample), v2 (HNSCC Pt1) and v3 (HNSCC Pt2) (10X Genomics), according to the manufacturer protocol (10X Genomics), including the CITE-seq libraries (HNSCC samples). Sample quality was checked with Bioanalyzer Agilent 2100 using a HighSensitivity DNA chip (Agilent Genomics). Samples were sequenced on an Illumina HiSeq (Breast cancer sample) and Novaseq (HNSCC samples) with a depth of sequencing of 50000 reads/cells (Breast cancer) and 100000 reads/cells (HNSCC samples).


title: Interdependencies of Intratumoral Genetic Heterogeneity and the Immune Microenvironment in Chronic Lymphocytic Leukemia (Bulk RNA)

city: Bethesda

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

summary: The tumor microenvironment (TME) and somatic mutations drive progression of chronic lymphocytic leukemia (CLL). Integrated bulk and single-cell RNA sequencing (RNA-seq) of paired peripheral blood (PB) and lymph node (LN) samples from patients with treatment naïve CLL showed upregulation of oncogenic processes in LN attributable to a minor population of activated tumor cells. A 10-gene activated tumor signature was positively correlated with activated CD4+ T cells and M2 macrophages in the TME. Whole exome sequencing of paired PB and LN samples showed subclonal expansion in LN in some patients. In remaining patients with clonal stability between PB and LN, a T-cell inflamed TME was detected by RNA-seq. These data connect the TME with molecular events in the pathogenesis of CLL.

overall_design: Bulk RNA sequencing (RNA-seq) of (1) immunomagnetically purified CD19+ cells from peripheral blood (n = 29), (2) CD19+ cells from lymph node single cell suspensions (n = 29), and (3) lymph node biopsies (n = 38). All samples were matched in 29 patients with CLL. RNA-seq of lymph node biopsies only were done in 5 patients and 4 normal controls.

first: Clare

last: Sun

first: Yun-Ching

last: Chen

first: Adrian

last: Wiestner


title: MiRNA-based on genome-wide maps in MDA-MB-231 cells treated with or without Tanshinone IIA (TSA).

city: Nanjing

first: Lufeng

last: Zheng

state: Jiangsu

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

institute: China Pharmaceutical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Analysis of MDA-MB-231 cells following  TSA treatment or not. TSA regulates various miRNA expression in MDA-MB-231 cells.Results provide insight into the role of miRNAs-involved mechanisms underlying TSA-mediated effects on breast cancer stemness.

overall_design: MiRNA profiles of MDA-MB-231 cells treated with or without TSA were generated by deep sequencing, in two repeats.

first: Xiaoman

last: Li

first: Yin

last: Lu


title: Comprehensive evaluation of adenine base editors induced mutations at genomic and transcriptional level

first: shaofang

address: No 50, ZhanghuaLu, HAIDIAN

institute: Beijing Academy of Agriculture and Forestry Science

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

overall_design: Refer to individual Series


title: Comprehensive evaluation of adenine base editors induced mutations at genomic and transcriptional level [transcriptome]

summary: Adenine base editors (ABEs) with wide CRISPR compatibility and high activity improves the editing efficiency and arouses the off-target challenges as well. Here, we carried out a comprehensive evaluation of ABE8e and ABE9 induced DNA and RNA mutations in model organism rice. The whole-genome sequencing analysis on plants with rBE46b (SpCas9n-TadA8e), rBE49b (SpCas9n-TadA9), rBE50 (SpCas9n-NG-TadA8e), rBE53 (SpCas9n-NG-TadA9) reveals that the ABEs with TadA9 lead to a higher number of off-target A>G SNVs and ABEs with SpCas9n-NG lead to a higher total number of off-target SNVs. The analysis of T-DNAs (ABEs carrier) disclosed that the on-target mutations could happen before T-DNA integration to plant genomes as well as after T-DNA integration to plant genomes, while ABEs integrated into plant genomes lead to more A>G SNVs. We also detected off-target A>G RNA mutations in plants with higher expression of ABEs but not in plants with lower expression of ABEs. The off-target A>G RNA mutations tend to cluster while off-target A>G DNA mutations cluster in a very rare manner. The findings that CRISPRs, TadA variants, T-DNA integration, and ABE expression contribute ABEs’ specificity provide alternative ways to increase the specificity of ABEs.

overall_design: To study adenine base editors induced DNA and RNA off-targets, genome and transcriptome were sequenced on T0 plants through tissue culture, agrobacterium transformation with or without ABEs

first: Shaofang


title: Conophylline effect on CAFs in HCC

city: maebashi

first: takahiro

last: yamanaka

address: Showa

country: Japan

institute: Gunma Univ

summary: Hepatocellular carcinoma (HCC) is a malignancy that is challenging to treat. Cancer-associated fibroblasts (CAFs) are reported to promote the malignant behavior of HCC cells via cytokines. Conophylline (CnP) has been reported to suppress activated hepatic stellate cells in liver fibrosis. We aimed to determine whether CnP is useful in suppressing tumor growth in HCC. We investigated whether CnP could suppress the HCC-promoting effect of CAFs derived from HCC tissues in vitro and in vivo. CAFs promoted the proliferation and invasion of HCC cells. CnP suppressed activated CAFs expressing α-smooth muscle actin (αSMA) and inhibited the HCC-promoting effects of CAFs. CnP significantly reduced the levels of cancer-promoting cytokines such as interleukin (IL)-6 (IL-6), IL-8, C-C Motif Chemokine Ligand 2 (CCL2), angiogenin, and osteopontin, which are secreted by CAFs. An in vivo study demonstrated that combined therapy with CnP and sorafenib against CAFs and HCC cells showed the strongest inhibition of tumor growth compared with the control and single treatment groups. Transcriptome analysis revealed that GPR68 in CAFs was strongly suppressed by CnP. The cancer-promoting effects of cytokines were eliminated by knockdown of GPR68 in CAFs. CnP inhibited the HCC-promoting effect of CAFs by suppression a number of HCC-promoting cytokines, which are secreted from CAFs expressing GPR68. Combination therapy with CnP and existing anti-cancer agents may be a promising therapeutic strategy in overcoming refractory HCC with activated CAFs.

overall_design: Evaluation of conophylline effect on CAFs in HCC cells using transcriptome analysis

first: Takahiro

last: Yamanaka

first: Dolgormaa

last: Gantumur

first: Yokobori

last: Takehiko


title: DNA methylation profile of the Mediterranean fin whale (Balaenoptera physalus) exposed to organochlorine contaminants.

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

institute: University of Ferrara

type: Methylation profiling by high throughput sequencing

summary: We sampled skin and blubber from 6 fin whale (Balenoptera physalus) individuals living in the northern Mediterranean Sea. Blubber was analyzed for Organochlorines levels while genomic DNA extracted from the skin of the animals with the lowest (mean value = 19 µg/g lipid basis, l.b.) (group 1, n=3) and the highest (mean value = 53 µg/g l.b.) (group 2, n=3) levels of contaminants were used for DNAm profiling through reduced representation bisulfite sequencing (RRBS).

overall_design: Examination of the differences in the methylation patterns observed comparing group 1 to group 2 and potential correlation to environmental contaminant exposure and load in the whale tissues

first: Luigi

last: Abelli

first: Matteo

last: Baini

first: Maria

last: Fossi

first: Cristina

last: Panti


title: RNA sequencing of invasive vulvar squamous cell carcinoma (VSCC)

city: Dallas

first: Richard

last: Wang

state: TX

address: 5323 Harry Hines Blvd

department: Dermatology

institute: UT Southwestern

summary: We retrospectively identified cases of invasive vulvar squamous cell carcinoma. Formalin fixed, paraffin embedded tissues samples were retrieved. Sections were confirmed by H&E staining prior to analysis. Sections were processed by ribosomal RNA depletion and RNA-sequencing (KAPA RNA HyperPrep with RiboErase) (HMR). 23 patient samples had RNA of sufficient quality for analysis. HPV status was determined by a consensus of high-risk HPV RNA-ISH and HPV DNA PCR. Only samples that were positive in both assays were considered  'HPV-positive'.

overall_design: Retrospective cohort study

first: Elysha

last: Kolitz

first: Jiwoong

last: Kim


title: Novel, abundant Drosha isoforms are deficient in miRNA processing in cancer cells

city: Frederick

first: Lisheng

last: Dai

address: 1050 Boyles St.

institute: NCI-Frederick

summary: MicroRNAs (miRNAs) are a class of small noncoding RNAs about 22-nucleotide (nt) in length that collectively regulate more than 60% of coding genes. Aberrant miRNA expression is associated with numerous diseases, including cancer. miRNA biogenesis is licensed by the ribonuclease (RNase) III enzyme Drosha, the regulation of which is critical in determining miRNA levels. We and others have previously revealed that alternative splicing regulates the subcellular localization of Drosha. To further investigate the alternative splicing landscape of Drosha transcripts, we performed PacBio sequencing in different human cell lines. We identified two novel isoforms resulting from partial intron-retention in the region encoding the Drosha catalytic domain. One isoform (AS27a) generates a truncated protein that is unstable in cells. The other (AS32a) produces a full-length Drosha with a 14 amino acid insertion in the RIIID domain. By taking advantage of Drosha knockout cells in combination with a previously established reporter assay, we demonstrated that Drosha-AS32a lacks cleavage activity. Furthermore, neither Drosha-27a nor Drosha-32a were able to rescue miRNA expression in the Drosha knockout cells. Interestingly, both isoforms were abundantly detected in a wide range of cancer cell lines (up to 15% of all Drosha isoforms). Analysis of the RNA-seq data from over 1000 breast cancer patient samples revealed that the AS32a is relatively more abundant in tumors than in normal tissue, suggesting that AS32a may play a role in cancer development.

overall_design: For Pacbio sequencing, 4 human cell lines, including HEK293T, HeLa, MCF-7, U2OS were used, and in total 4 samples. For small RNA sequencing, HEK293T and HeLa cells were used, and in total 6 samples in HEK293T cells and 2 samples in HeLa cells. There are 2 replicates for small RNA sequencing. See sample description for the details of cell lines.

first: Shuo

last: Gu


title: Thioguanine suppresses growth in triple-negative breast  cancer by inhibiting PI3K-AKT pathway and inducing apoptosis

city: Changchun

first: Daoyu

last: Zhang

address: Xinzhu street 1977

institute: Jilin University

summary: Triple-negative breast cancer (TNBC) is difficult to treat due to the lack of biological targets and poor sensitivity to conventional therapies. Chemotherapy is the main treatment in the clinic, but there is still no effective screening strategy for chemotherapy drugs. Several studies have attempted to find the pathogenesis through sequencing, but the integration of transcriptome maps of various tumors for drug discovery has been slow. Drug repurposing has attracted increasing attention in recent years. We first found there were common features between leukemia and TNBC. Therefore, we chose a classic leukemia drug thioguanine (6-TG) as a candidate drug. We utilized RNA-seq and DNA methylation arrays to evaluate its role in MDA-MB-231 cells. Our results demonstrated that 6-TG inhibited cell proliferation by suppressing PI3K-AKT pathway via downregulating the DNA methylation level of PTEN. Moreover, apoptosis was induced via the activation of PI3K-AKT downstream molecular TSC1 and the downregulation of methylation levels of DAXX, TNF, FADD and CASP8 etc., these genes involved in apoptosis pathways. 6-TG presents anti-tumor effects in vitro and vivo by regulating the DNA methylation levels of PI3K-AKT pathway and apoptosis pathway. Meanwhile, we proved transcriptome-based drug screening has potential implications for breast cancer therapy and drug selection.

overall_design: effect of 6-TG on MDA-MB-231 cells

first: Xinglan

last: An


title: Forkhead Box B1 regulates the differentiation timing and neurogenic potential of human neural crest cells [RNA-Seq 2]

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Human neural crest cell development progresses via a pre-neural border (pNB) cell state that precedes the induction of the neurectoderm and the neural border. Here, we identify a set of pNB gene candidates, including forkhead box B1 (FOXB1), and their associated enhancers, that are rapidly activated by β-catenin-mediated signaling during human embryonic stem (ES) cell differentiation towards neural crest cells. FOXB1 simultaneously maintains neuroectoderm competency and controls the timing of differentiating ES cells to acquire neural crest fate by directly targeting key neural crest and neural progenitor loci in a context-dependent manner. Notably, the transient expression of FOXB1 in pre-neural crest cells also establishes autonomic neurogenic potential in mature neural crest cells, likely via its regulation of the expression of ASCL1, a master regulator of autonomic neurons. Altogether, our data implicates pNB cell state as the missing link bridging the exit of pluripotency to the acquisition of neural crest fate and its diverse ecto-mesenchymal differentiation potentials.

overall_design: Examining the effect of b-Catenin knockdown on gene expression dynamics during neural crest induction

first: Alan

middle: W

last: Leung

last: López-Giráldez


title: TRAF6 is a tumor suppressor in AML by directly targeting MYC oncogenic activity [scRNA-Seq]

city: New York

first: Bettina

last: Nadorp

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

summary: Single-cell RNA-seq of healthy human bone marrow.

overall_design: Cryopreserved primary human bone marrow mononuclear cells were obtained from STEMCELL Technologies (catalog #70001) or from StemExpress (catalog #BMMNC025C). Frozen human bone marrow samples were thawed and dead cells were depleted using a dead cell removal kit (Miltenyi Biotec, 130-090-101). Cells were tagged with cell hashing (Stoeckius et al., 2018) oligo-tagged antibodies (BioLegend) according to manufacturer's instructions and pooled on a 10x Chromium instrument (10x Genomics) to generate barcoded single-cell beads-in emulsion (GEM) according to the manufacturer's protocol.

first: Audrey

last: Lasry Sandler

last: Guillamot-Ruano

first: Iannis

last: Aifantis


title: Forkhead Box B1 regulates the differentiation timing and neurogenic potential of human neural crest cells


title: Cellular plasticity upon proton irradiation determines tumor cell radiosensitivity

status: Public on Dec 31 2021

city: Heidelberg

first: Wahyu

middle: Wijaya

last: Hadiwikarta

address: Im Neuenheimer Feld 280

institute: Deutsches Krebsforschungszentrum

summary: Novel particle therapy was implemented into standard-of-care for cancer patients during the last years. However, experimental studies investigating cellular and molecular mechanisms are lacking although prognostic biomarker are urgently needed. The cancer stem cell (CSC)-related marker aldehyde dehydrogenase (ALDH) is known to impact on prostate cancer radiosensitivity through affecting defense against reactive oxygen species (ROS), reducing DNA damage repair and increasing cell survival. Surprisingly, we could show in a previous study that ionizing radiation itself enriches for ALDH-positive CSCs in a time- and dose-dependent manner through alteration in histone methylation.  Within the present study, we investigated CSC marker dynamics upon proton beam irradiation and hypothesized that this novel particle therapy may have increased CSC targeting potential due to its increased ionization potential compared to conventional photon irradiation. However, we found that proton irradiation is affecting cellular dynamics and escape from cell death.

overall_design: Sham, proton treated and photon treated samples were made available to compare effects of proton irradiation and photon irradiation on multiple human tumour cell lines. Majority of samples were collected after 7 days of irradiation. Some samples were collected after 4 and 12 hours of irradiation. Up to 3 replicates exist for majority of the samples.

first: Iñaki

last: Schniewind

first: Ina

last: Kurth

first: Claudia

last: Peitzsch


title: Identifying genetic etiology of CHD using SNP Array

city: Pittsburgh

first: Polakit

last: Teekakirikul

address: 530 45th street 8120 Rangos Research Center

institute: university of pittsburgh

type:
Genome variation profiling by array
Genome variation profiling by SNP array

summary: High density genotyping of 7 affected and 3 unaffected family members was performed using the Illumina Omni2.5-8 v1.3 BeadChip SNP.

overall_design: To investigate the genetic etiology of the ASD in this multigenerational family, we conducted genome wide linkage analysis on the proband, and also 7 affected and 3 unaffected family members.This analysis yielded three regions with the maximum peak log-of-odds (LOD) score.

first: Cecilia

last: Lo


title: An adipose lncRAP2 - Igf2bp2 complex enhances adipogenesis and energy expenditure by stabilizing target mRNAs [RIP-seq]

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: lncRAP2 is a conserved cytoplasmic lncRNA enriched in adipose tissue and required for adipogenesis. Using purification and in vivo interactome analyses, we show that lncRAP2 forms complexes with proteins that stabilize mRNAs and modulate translation, among them Igf2bp2. Surveying transcriptome-wide Igf2bp2 client mRNAs in white adipocytes reveals selective binding to mRNAs encoding adipogenic regulators and energy expenditure effectors, including Adiponectin. These same target proteins are downregulated when either Igf2bp2 or lncRAP2 is downregulated, hindering adipocyte lipolysis. Proteomics and ribosome profiling show this occurs predominantly through mRNA accumulation, as lncRAP2-Igf2bp2 complex binding does not impact translation efficiency. Phenome-wide association studies reveal specific associations of genetic variants within both lncRAP2 and Igf2bp2 with body mass and type 2 diabetes, and both lncRAP2 and Igf2bp2 are suppressed in adipose depots of obese and diabetic individuals. Thus, the lncRAP2-Igf2bp2 complex potentiates adipose development and energy expenditure and is associated with susceptibility to obesity-linked diabetes.

overall_design: Analysis of transcriptome-wide Igf2bp2 client RNAs in adipocytes differentiated in culture, sequenced using an Illumina HiSeq instrument.


title: GCN2 kinase Activation by ATP-competitive Kinase Inhibitors

first: Colin

last: Tang

address: 1300 York Ave.

institute: Weill Cornell Medicine

summary: Purpose: Use next generation sequencing to determine which CRISPR knockouts confer resistance to EGFR inhibitors and to determine which cellular pathways get upregulated in response to neratinib.

overall_design: Glioblastoma cell lines were transduced with the TKOv3 CRISPR KO library and treated with vehicle or neratinib for 14 or 21 days. Transcriptomic data was obtained by treating parental or GCN2-KO SF268 cells with neratinib for 0, 6, or 72 hours.

first: Olivier

last: Elemento

first: Ingo

last: Mellinghoff


title: Implementation of epigenetic variation in sorghum selection and implications for crop resilience breeding

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

summary: Crop resilience and yield stability are complex traits essential for food security. Sorghum bicolor is an important grain crop that  shows promise for its natural resilience to drought and potential for marginal land production. We have developed sorghum lines  in the Tx430 genetic background suppressed for MSH1 expression as a means of inducing de novo epigenetic variation and have  used these materials to evaluate changes in plant growth vigor. Plant crossing and selection in two distinct environments revealed  features of phenotypic plasticity derived from MSH1 manipulation. Introduction of epigenetic variation to an isogenic sorghum  population, in the absence of selection, resulted in 10% yield increase under ideal field conditions and 20% increase under extreme low nitrogen conditions. However, incorporation of early-stage selection amplified these outcomes to 36% yield increase under ideal conditions and 64% increase under marginal field conditions. Interestingly, the best outcomes were derived by selecting mid-range performance early-generation lines rather than highest performing. Data also suggested that phenotypic plasticity derived from epigenetic variation was non-uniform in its response to environmental variability but served to reduce genotype x environment interaction. The MSH1-derived growth vigor appeared to be associated with enhanced seedling root growth and  altered expression of auxin response pathways, and plants showed evidence of cold tolerance, features consistent with  observations made previously in Arabidopsis. These data imply that the MSH1 system is conserved across plant species, pointing to  the value of parallel model plant studies to help devise effective plant selection strategies for epigenetic breeding in multiple crops.

overall_design: 3 biological replicated of epiF3 non-enhanced (Epi15) and 2 biological replicates of EpiF3 enhanced (Epi68) lines were sequenced.

first: Xiaodong

last: Yang

first: Sally

last: Mackenzie


title: Transcriptome analysis of peripheral blood mononuclear cells in pulmonary sarcoidosis

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

institute: Chiba University

summary:
Purpose: This study aimed to explore the pathobiological markers of sarcoidosis in PBMCs by comparing the transcriptional signature of PBMCs from patients with pulmonary sarcoidosis and those of healthy controls by RNA sequencing.
Methods:PBMC samples were collected from subjects with pulmonary sarcoidosis with no steroid/immunosuppressant drugs (n = 8) and healthy controls (n = 11) from August 2020 to April 2021, and RNA sequencing was performed with the PBMC samples.
Results: Variety of DEGs were determined between groups leading to the enrichment analysis.
Conclusions:  The present study demonstrated that bulk gene expression patterns in PBMCs were different between patients with pulmonary sarcoidosis and healthy controls. The changes in the gene expression pattern of PBMCs could reflect the existence of sarcoidosis lesions and influence granuloma formation in sarcoidosis.

overall_design: Examination of  11 healthy controls and 8 pulmonary sarcoidosis ptatients PBMC samples by RNA sequencing.

first: Keiichiro

last: Yoshioka

first: Hironori

last: Sato

first: Daisuke

last: Ishii

first: Takuro

last: Imamoto

first: Mitsuhiro

last: Abe

first: Yoshinori

last: Hasegawa

first: Osamu

last: Ohara

first: Koichiro

last: Tatsumi

first: Takuji

last: Suzuki


title: Mice transgenic for human CTLA4-CD28 fusion gene develop adult T cell leukemia/lymphoma-like lymphoma

city: Daejeon

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

country: South Korea

institute: Korea Institute of Science and Technology Information

summary: CTLA4-CD28 gene fusion has been reported to occur in diverse types of T-cell lymphoma. The fusion event is expected to convert inhibitory signals to activating signals promoting proliferation and potentially transformation of T-cells. To test the function of the CTLA4-CD28 fusion gene in vivo, we generated a murine model that expresses the gene in a T-cell specific manner. The transgenic mice show shorter life spans and inflammatory responses including lymphadenopathy and splenomegaly. T-cells show higher levels of activation and infiltrate various organs including skin and lung. T-cells, in particular CD4+ helper T-cells, were also readily transplanted to immunocompromised mice. Transcriptomic profiling revealed that the gene expression pattern in CD4+ cells most closely resembles that of adult T cell leukemia/lymphoma (ATLL). Consistently, we detected supernumerary Foxp3+ cells in transgenic and transplanted mice. This is the first report demonstrating the transforming activity of the CTLA4-CD28 fusion gene in vivo, and this murine model should be useful in dissecting the molecular events subsequent to the mutation in ATLL.

overall_design: Examination of transcriptome on wildtype and CTLA4-CD28 fusion mice by deep sequencing

first: Gyu

last: Lee

first: Yoon

last: Jeon

first: Daekee

first: Sanghyuk

first: Jaesang

last: Kim


title: Cell-specific neuropathology and multiple morphogenic mechanisms in 3D human-derived tissue

first: Friederike

last: Dündar

state: New York

address: 1300 York Ave

department: Physiology & Biophysics

summary: Single-cell sequencing of donor-derived 3D cerebral organoids comparing those from schizphrenic patients to those from healthy donors.

overall_design: 4 controls vs. 3 Scz

first: Michael

last: Notaras

first: Dilek

last: Colak


title: Single-cell RNA sequencing of primary cultures of neonatal digit amputation wound cells 4 days post-amputation

city: College station

first: Ling

last: Yu

address: 588 Raymond Stotzer Pkwy

institute: TAMU

summary: Here we present single-cell RNA sequencing (scRNA-seq) data of untreated digit amputation wound cells that can be induced by BMP9 to undergo chondrogenesis to determine the responsive cell type

overall_design: Cells of one sample was prepared using a 10X Genomics Chromium Controller and deeply sequenced.

first: Yu-Lieh

last: Lin

first: Mingquan

last: Yan

first: Tao

last: Li

first: Emily

middle: Y

last: Wu

first: Katherine

last: Zimmel

first: Osama

last: Qureshi

first: Alyssa

last: Falck

first: Kirby

last: Sherman

first: Shannon

middle: S

last: Higgins

first: Daniel

middle: O

last: Hurtado

first: Larry

last: Suva

first: Dana

last: Gaddy

first: James

middle: J

last: Cai

first: Regina

last: Brunauer

first: Lindsay

last: Dawson

first: Ken

last: Muneoka


title: Validation of dedifferentiated liposarcoma (DDLS) cell lines with the original tumors via copy number alteration analysis

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

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

overall_design: Refer to individual Series


title: Validation of dedifferentiated liposarcoma (DDLS) cell lines with the original tumors via copy number alteration analysis [array]

summary:
We validated patient's tumor-derived cell lines of liposarcoma by analysing copy number alterations using aCGH or WGS and comparing with the original tumor tissues.
examination of copy number alterations for 2 cell lines, one of the original tumor, one PDX-tumor and its original tumor.

overall_design: Tomoyo,Okada

first: Rodrigo

last: Gularte-Merida

first: Yawei

last: Shen

first: Samuel

last: Singer


title: Validation of dedifferentiated liposarcoma (DDLS) cell lines with the original tumors via copy number alteration analysis [sequencing]

summary: We validated patient's tumor-derived cell lines of liposarcoma by analysing copy number alterations using aCGH or WGS and comparing with the original tumor tissues.

overall_design: examination of copy number alterations for 2 cell lines, one of the original tumor, one PDX-tumor and its original tumor.

first: Tomoyo

last: Okada


title: Wnt Signaling Rescues Amyloid Beta-Induced Gut Stem Cell Loss

city: Singapore

first: Nicholas

last: Tolwinski

address: 16 #01-220, College Ave West

country: Singapore

institute: Yale-NUS College

summary: Wnt signaling has well established roles in development and cancer progression. Its roles during normal adult homeostasis are less well studied, but Wnt is a major stem cell regulating factor in adult tissues. Here we use an optogenetic model of amyloid beta aggregation to examine the effect of Wnt signaling on protein aggregation. We observe that Wnt activation rescues the detrimental effects of Amyloid. We analyze the gene expression changes downstream of Wnt that contribute to this rescue and find a protein misfolding response and a metabolic response, but the major factor we focus on is inflammation. Wnt expression reduces inflammation through repression of Toll activating factors, and chronic Toll activation reduces lifespan. We propose that the protective effect observed for lithium treatment functions at least in part through Wnt activation and inhibition of inflammation.

overall_design: Drosophila midgut RNA profiles of wild type (WT), Wg, Aβ-CRY2-mCh + Wg, and Aβ-CRY2-mCh exposed to light.

first: Prameet

last: Kaur

first: Wen

middle: K

last: Lim

first: Nathan

last: Harmston

first: Ellora

last: Chua


title: Exportin 1 modulates lifespan by regulating nucleolar 1 dynamics via the autophagy protein LGG-1/GABARAP [RNA-seq]

city: Providence

first: Louis

last: Lapierre

address: 185 Meeting St.

institute: Brown

summary: RNA-seq perofrmed for studying transcriptomic changes induced by RNAi-mediated silencing of gene encoding nuclear export receptor XPO-1 in C. elegans nematodes.

overall_design: Comparison of transcript expression between Day 1 adult nematodes fed E. coli expressing dsRNA against xpo-1 for 96h vs nematodes fed E. coli expressing the empty vector (L4440).


title: AR signalling in castration resistant prostate cancer (CRPC)

city: Houston

first: Basil

last: Paul

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: Castration-resistant PCa (CRPC) remains androgen receptor (AR) dependent. There are multiple mechanisms for reactivation of AR including expression of the constitutively active AR splice variant, AR-V7 (AR3). Earlier studies suggest that though the variants regulate many of the same genes as AR, they also have unique targets. Another argument is that the variant is a “weak” AR without unique targets. We have used an LN95 cell line that endogenously expresses AR and a low level of AR-V7 to compare the activities of the isoforms and to determine whether there is differential regulation of target genes. The transcriptomes for AR and AR-V7 were identified using RNA-Seq.

overall_design: Androgen receptor splice variant transcriptome from LN95 cells

first: Nancy

last: Weigel

first: Amit

last: Dash

first: Paul

last: Basil


title: Rhesus macaques self-curing from a schistosome infection can display complete immunity to challenge

city: Sao Paulo

first: Ana

middle: Carolina

last: Tahira

state: São Paulo

address: Avenida Vital Brasil, 1500 prédio 55

department: Parasitologia

country: Brazil

institute: Instituto Butantan

summary: The rhesus macaque provides a unique model of acquired immunity against schistosomes, which afflict >200 million people worldwide. By monitoring bloodstream levels of parasite-gut derived antigen, we show that from week 10 onwards an established infection with Schistosoma mansoni was cleared in an exponential manner, eliciting resistance to reinfection. Secondary challenge at week 42 demonstrated that protection was strong in all animals and complete in some. Antibody profiles suggest that antigens mediating protection are the released products of developing schistosomula. In culture they are killed by addition of rhesus plasma, collected from week 8 post-infection onwards, and even more efficiently with post-challenge plasma. Furthermore, cultured schistosomula lose chromatin activating marks at the transcription start site of genes related to worm development as well as showing altered expression of genes related to lysosomes and lytic vacuoles involved with autophagy. Overall, our results indicate that enhanced antibody responses against the challenge migrating larvae mediate the naturally acquired protective immunity and will inform the route to an effective vaccine.

overall_design: Stranded tagged cDNA libraries were prepared by BGI using the Strand-Specific Transcriptome Library Construction Protocol (DNBSEQ, SOP-SS-115) and quantification and quality were performed on a 2100 Bioanalyzer (Agilent). Libraries were pooled and sequenced (300 cycles, paired-end sequencing) on a MGISEQ-2000 instrument.

first: Murilo

last: Amaral

first: Daisy

last: Santos

first: Adriana

last: Pereira

last: CTahira

first: João

middle: V

last: Malvezzi

first: Patrícia

last: Miyasato

first: Rafaela

last: de Paula Freitas

first: Jorge

last: Kalil

first: Elisa

middle: M

last: Fat

first: Claudia

last: deDood

middle: L

last: Corstjens

first: Govert

last: van Dam

first: Eliana

last: Nakano

first: Simone

last: Casto

first: Vânia

middle: G

last: Mattaraia

first: Ronaldo

last: Augusto

first: Christoph

last: Grunau

first: R

last: Wilson

first: Sergio

last: Verjovski-Almeida


title: RAD21-R450C variant is associated with corneal stroma disorganization

city: Worcester

first: Yu

last: Liu

address: AS5-1018, 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School

summary: In this study, a RAD21 variant, R450C, is found associated with a peripheral sclerocornea pedigree. Omics analyses including RNAseq and Hi-C were applied to identify the expression and chromosome conformation of cell adhesion genes were affected by this variant.

overall_design: Lymphoblastoid cells were isolated from peripheral sclerocornea patients. RNAseq and Hi-C were performed on these cells to profiling these cells.

first: Bi

middle: N

last: Zhang

first: Job

last: Dekker

first: Wai

last: Chu


title: Effects of HGF neutralizing antibody on three-dimensional co-culture of periodontitis-associated fibroblasts (PAF)

city: Tokyo

first: Akira

last: Saito

address: 7-31-, Hongo, Bunkyo

institute: Tokyo University

summary: We compared gene expression profiles of three-dimensional co-culture of periodontitis-associated fibroblasts embedded in collagen gels treated with control IgG or HGF neutralizing antibody.

overall_design: RNA was collected from collagen gels treated with control IgG or HGF neutralizing antibody.

first: Yoko

last: Yamaguchi

first: Masafumi

last: Horie

last: Aoki

first: Patrick

last: Micke

first: Mitsuhiro

last: Ohshima

first: Kai

last: Kappert


title: Grouping of UVCB Substances with Dose-Response Transcriptomics Data from Human Cell-Based Assays

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

summary: Six human cell lines were treated in a log dose response to 141 petroleum substance extracts containing unknown or variable composition, complex reaction products and biological materials (UVCBs) to be used for grouping and read across strategies.   The six cell lines consisted of human induced pluripotent stem cell (iPSC)-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, as well as the human MCF7 and A375 cell lines. All transcriptomics were targeted with BioSpyder S1500+ gene list.

overall_design: Transcriptomic Dose Response Characterizations Across Petroleum Based UVCBs

first: Fabian

middle: A

last: Grimm

first: William

middle: D

last: Klaren

first: Abigail

last: Dalzell

first: Srikeerthana

last: Kuchi

first: Shu-Dong

first: Klaus

last: Lenz

first: Peter

last: Boogaard

first: Hans

middle: B

last: Ketelslegers

first: Timothy

last: Gant

first: Ivan

last: Rusyn

first: Fred

last: Wright


title: Exportin 1 modulates lifespan by regulating nucleolar 1 dynamics via the autophagy protein LGG-1/GABARAP [polysome RNA]

first: Louis

last: Lapierre

summary: RNA-seq perofrmed for studying changes in total, monosome, and polysome-associated mRNA induced by RNAi-mediated silencing of gene encoding nuclear export receptor XPO-1 in C. elegans nematodes.

overall_design:
Comparison of transcript expression between Day 1 adult nematodes fed E. coli expressing dsRNA against xpo-1 for 96h vs nematodes fed E. coli expressing the empty vector (L4440).

>>>Submitter states that raw data files are unavailable due to file loss<<<

first: Anita

last: Kumar

first: Aric

last: Rogers


title: The angiopoietin-Tie2 pathway regulates Purkinje cell dendritic morphogenesis in a cell-autonomous manner

city: Mannheim

first: Carmen

last: Ruiz de Almodóvar

address: Ludolf-Krehl-Straße 13-17

institute: ECAS

summary: Neuro-vascular communication is essential to synchronize central nervous system development. Yet, the specific cellular players, defined developmental processes and molecular mechanisms involved in this crosstalk remain poorly characterized. Here we identify the angiopoietin/Tie2 signaling axis as a crucial regulator of dendritic morphogenesis of Purkinje cells (PC) during cerebellum development. We show that in the developing cerebellum Tie2 expression is not restricted to blood vessels but it is also in PCs. Its ligands angiopoietin-1 (Ang1) and angiopoietin-2 (Ang2) are expressed in neural cells and endothelial cells (ECs), respectively. PC-specific deletion of Tie2 results in reduced dendritic arborization, which is recapitulated in neural-specific Ang1-knockout and Ang2 full-knockout mice. Mechanistically, RNA sequencing reveals that Tie2 deficient PCs present alterations in gene expression of multiple genes involved in cytoskeleton organization, dendritic formation, growth and branching. Functionally, those morphological changes are accompanied by alterations in PC network electrophysiology. Altogether, our data propose that the Ang/Tie2 signaling axis serve as mediator of intercellular communication between neural cells, ECs and PCs, required to regulate PC dendritic morphogenesis and function.

overall_design: We used the triple transgenic mouse line Pcp2Cre:Tie2flox/flox:Rpl22HA/HA to isolate and sequence mRNAs being translated specifically in PCs lacking Tie2 at P56. As control, we also isolated and sequenced mRNAs being translated in PCs from P56 Pcp2Cre:Rpl22HA/HA mice.

first: Robert

last: Luck

first: Andromachi

last: Karakatsani

first: Bhavin

last: Shah

first: Geza

last: Schermann

first: Heike

last: Adler

first: Janina

last: Kupke

first: Nathalie

last: Tisch

first: Hyun-Woo

last: Jeong

first: Michaela

last: Müller

first: Florian

last: Hetsch

first: Anna

last: D’Errico

first: Michele

last: De Palma

first: Ellen

last: Wiedtke

first: Dirk

first: Amparo

last: Acker-Palmer

first: Jakob

last: von Engelhardt

first: Ralf

middle: H

last: Adams

first: Hellmut

last: Augustin


title: Germline RUNX1 Variation and Predisposition to Childhood Acute Lymphoblastic-ChIP-Seq

city: Memphis

first: Jun

middle: J.

last: Yang

state: TN

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: Somatic mutations of RUNX1, which encodes the myeloid and lymphoid transcriptional factor RUNX1, are common in both B- and T- acute lymphoid leukemia (ALL) and are associated with poor prognosis of T-ALL. However, there has been no comprehensive investigation of the pattern or prevalence of RUNX1 germline mutation in both B- and T-ALL. Here we report germline RUNX1 variants in 1.23% of B-ALL and 2.11% of T-ALL, identifying 31 unique variants in 62 B-ALL and 18 unique variants in 26 T-ALL children. The majority of frameshift and nonsense variants affected RUNX1 function in transcriptional regulation, hematopoiesis, and cellular proliferation. We identified JAK3 as the most frequent somatic mutation in T-ALL with RUNX1 variants. These results not only identify RUNX1 as a leukemia predisposition gene but also further underline the importance of germline genetic variants to the development of ALL

overall_design: Investigation of RUNX1 binding sites in parental or RUNX1 mutation (R232fs, Y287X and G365R) knock-in single clones of Jurkat T-ALL cells. HA: RUNX1 mutation tag or Wild type (WT) in parental cell, TY1: WT tag.

first: Yizhen

last: Li


title: Germline RUNX1 Variation and Predisposition to Childhood Acute Lymphoblastic-RNA-Seq

overall_design: Investigation of gene expression pattern in parental or RUNX1 mutation (R232fs, Y287X and G365R) knock-in single clones (sc1, 22, 2, 5) of Jurkat T-ALL cells.


title: RNA-Seq of femoral shaft RNA from Catalase knockout (KO) and wild-type (WT) male mice at 12 weeks of age given binge ethanol or control PBS for four consecutive days.

city: New Orleans

first: Kim

last: Pedersen

state: LA

address: 1901 Perdido St., Rm 5206

department: Pharmacology and Exp. Therapeutics

institute: LSU Health Sciences Center, Dept. of Pharmacology

summary: The objective was to determine how binge ethanol and knockout of the catalase gene affect the transcriptome of the femoral shaft in mice.

overall_design: Mice were of two genotypes, Catalase knockout mice (Cat -/-) and wild-type mice (Cat +/+). At 12 weeks of age, mice received either binge ethanol in the form of 3, 3, 4, and 4.5 g ethanol/kg body weight by gavage from a 31.5 % (v/v) ethanol solution on four consecutive days or isovolumetric amounts of PBS. Femoral shaft RNA was isolated. Each sample is a pool of femoral shaft RNA from two male mice.

first: Alexandra

last: Denys

first: Martin

last: Ronis


title: An adipose lncRAP2 - Igf2bp2 complex enhances adipogenesis and energy expenditure by stabilizing target mRNAs [RIA-seq]

first: Juan

middle: R

last: Alvarez-Dominguez

address: 7 Divinity Ave

institute: Harvard University

summary: lncRAP2 is a conserved cytoplasmic lncRNA enriched in adipose tissue and required for adipogenesis. Using purification and in vivo interactome analyses, we show that lncRAP2 forms complexes with proteins that stabilize mRNAs and modulate translation, among them Igf2bp2. Surveying transcriptome-wide Igf2bp2 client mRNAs in white adipocytes reveals selective binding to mRNAs encoding adipogenic regulators and energy expenditure effectors, including Adiponectin. These same target proteins are downregulated when either Igf2bp2 or lncRAP2 is downregulated, hindering adipocyte lipolysis. Proteomics and ribosome profiling show this occurs predominantly through mRNA accumulation, as lncRAP2-Igf2bp2 complex binding does not impact translation efficiency. Phenome-wide association studies reveal specific associations of genetic variants within both lncRAP2 and Igf2bp2 with body mass and type 2 diabetes, and both lncRAP2 and Igf2bp2 are suppressed in adipose depots of obese and diabetic individuals. Thus, the lncRAP2-Igf2bp2 complex potentiates adipose development and energy expenditure and is associated with susceptibility to obesity-linked diabetes.

overall_design: Analysis of lncRAP2-interacting RNAs in adipocytes differentiated in culture using two independent pools of lncRAP2-targeting probes, sequenced using an Illumina HiSeq instrument.


title: Differential gene expression in embryonic lung and small intestine after epithelial deletion of centrioles

city: San Francisco

first: Chang

last: Xie

state: CA

address: 555 Mission bay blvd South, 384G

institute: University of California, San Francisco

summary: Epithelial specific disruption of centrioles but not cilia results in severe phenotype in the lung but not in the intestine. Compare gene expression in lung and small intestine of control (ShhCre Cenpj+/lox), epithelial centriole disrupted (ShhCre Cenpj-/lox), and epithelial cilia disrupted (ShhCre Ift88-/lox).

overall_design: Each group contains 4 samples. Samples were taken at embryonic day E11.5 before there is obvious phenotype.

first: Lauren

last: Byrnes

first: Jeremy

last: Reiter

first: Matthew

last: Aber

first: Josh

last: Rudolph

first: Walter

last: Eckalbar

first: Andrea

last: Barczak

first: David

last: Erle