title: Macrophage migration inhibitory factor is overproduced through EGR1 in TET2low resting monocytes

status: Public on Nov 13 2021

city: Miami

first: Qin

last: Yang

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

summary: Somatic mutation in TET2 gene is one of the most common clonal genetic events detected in age-related clonal hematopoiesis as well as in chronic myelomonocytic leukemia (CMML). In addition to being a pre-malignant state, TET2 mutated clones are associated with an increased risk of death from cardiovascular disease, which could involve cytokine/chemokine overproduction by monocytic cells. Here, we show in mice and in human cells that, in the absence of any inflammatory challenge, TET2 down-regulation promotes the production of MIF (macrophage migration inhibitory factor), a pivotal mediator of atherosclerotic lesion formation. In healthy monocytes, TET2 is recruited to MIF promoter and interacts with the transcription factor EGR1 and histone deacetylases. Disruption of these interactions as a consequence of TET2-decreased expression favors EGR1-driven transcription of MIF gene and its secretion. MIF favors monocytic differentiation of myeloid progenitors. These results designate MIF as a chronically overproduced chemokine and a potential therapeutic target in patients with clonal TET2 down-regulation in myeloid cells.

overall_design: Age-matched control monocytes, CMML TET2 WT monocytes versus TET2 mutated monocytes

first: Maria

middle: E

last: Figueroa


title: Sex and mutation specific p53 gain-of-function activity in gliomagenesis [ChIP-seq]

status: Public on Nov 16 2021

city: St Louis

first: Joshua

middle: B

last: Rubin

state: Missouri

address: 660 South Euclid Ave

department: Pediatrics

country: USA

institute: Washington University In St Louis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq analysis of Primary cortical astrocytes harboring a single floxed Trp53 allele harvested from male and female postnatal day one pups, and transduced with mutant p53;IRES GFP followed by CRE recombinase. p53 protein was immunoprecipated from fixed whole chromatin from cells expressing one of three mutants or p53 KO control.

overall_design:
p53 immunoprecipitation from male and female primary mouse astroyctes expressing p53:R172H, p53:Y202C, p53:Y217C, or p53 KO.
Please note that each processed data was generated from all replicates and is linked to the corresponding rep1 (or rep2 for f1_r172h) sample records.

first: Nathan

last: Rockwell


title: Resolvin E1-ChemR23 Axis Regulates the Hepatic Metabolic and Inflammatory Transcriptional Landscape at the Whole Genome and Exon Level in Obesity

city: Chapel Hill

first: Abrar

last: Al-Shaer

state: NC

address: 135 Dauer Dr

department: Nutrition

institute: University of North Carolina Chapel Hill

type: Expression profiling by high throughput sequencing

summary: Livers of diet induced obese and lean wildtype and ChemR23 knocout mice injected with and without resolvin E1 (RvE1) were run on the NovaSeq 6000 for total mRNA sequencing.

overall_design: Livers were sequenced from 6 different murine groups (1) Lean wildtype (WT) (2) High fat WT (3) Lean ChemR23 knockouts (KO) (4) High fat ChemR23 KO (5) High fat WT+RvE1 (6) High fat ChemR23 KO+RvE1

first: Anandita

last: Pal

first: Saame

middle: R

last: Shaikh


title: Tbet expression by Tregs is needed to protect against Th1-mediated immunopathology during Toxoplasma infection in mice

status: Public on Nov 12 2021

city: Buffalo

first: Jie

last: Yu

state: NY

address: 955 Main Street

department: Department of Obstetrics and Gynecology

institute: SUNY Buffalo

summary: Tregs dynamically respond to the inflammatory environment by acquiring features of the inflammatory cells they regulate. This is called Treg plasticity. We aimed to understand how Treg plasticity impacts the immune response to the protozoan parasite, T. gondii during the acute infection phase in the mouse model. Our study provides unique information of how plasticity of Tregs positivily impacts the overall fitness of the Treg during an infection.

overall_design: The goal of this study is to understand how the transcription factor Tbet orchastreates the Treg response to Th1 mediated inflammation and determine the gloabal gene expressions program in Tregs isolated from mice acutely infected with T. gondii.Total RNA was extracted from WT (Foxp3YFPCre+/+) and KO (Tbx21f/f-Foxp3YFPCre+/+) mice and submitted for RNA-seq.

first: E

middle: A

last: Wohlfert


title: AML patients for in vivo study of venetoclax plus AraC treatment

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Therapy resistance represents a major clinical challenge in acute myeloid leukemia (AML). Here we define a “MitoScore” signature that identifies high mitochondrial oxidative phosphorylation (OxPHOS) in vivo and in AML patients. Primary AML cells with cytarabine (AraC) resistance and high MitoScore relied on mitochondrial Bcl2 and were highly sensitive to venetoclax (VEN) plus AraC (but not to VEN plus azacytidine, AZA). Single-cell transcriptomics of VEN+AraC-residual cell populations revealed adaptive resistance associated with changes in OxPHOS, electron transport chain complex (ETC) and the TP53 pathway.

overall_design: AML patient cells were xenografted into NSG mice (PDX) and in vivo treated with venetoclax plus AraC in order to compare the in vivo treatment response to the gene expression at diagnosis.

first: Claudie

last: Bosc

first: Clément

last: Larrue

last: Kaoma

first: Astrid

last: Melotti

first: Jérome

last: Tamburini

first: Jean-emmanuel

last: Sarry


title: The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

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

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: Refer to individual Series


title: In vivo study of venetoclax plus AraC treatment

summary: 3 different MOLM14 cell line xenografts (CLDXs) on NSG mice, treated with venetoclax plus AraC.

overall_design: MOLM-14 cells were injected into mice for a Cell Line Derived Xenograft (CLDX). Briefly, mice (6-9 weeks old) were sublethally treated with 20 mg/kg of busulfan, 24 hours later AML cells were washed in PBS, and suspended in Hank’s Balanced Salt Solution (HBSS) at a final concentration of 2x106 cells per 200μL of HBSS per mouse for tail vein injection. All experiments include male and female mice and experimental groups were randomly assigned. 10 days later, 1 week of treatment begin, consisting in 5 days of AraC treatment (30 mg/kg) by intra-peritoneal injection, in association with 7 days of venetoclax treatment (100 mg/kg) by oral gavage. After one week of treatment, mice bone marrow and spleen were collected. Then viable bone marrow human AML cells (CD45+CD33+AnnexinV-) were sorted and RNA-seq was processed. The experiment was done 3 times into 3 different MOLM14 CLDX.

first: Nathalie

last: Nicot


title: ChIP-Seq data of H3K79succ modification of mononuclear bodies in PHH cells infected with HBV

status: Public on Nov 14 2021

city: Chongqing, China

first: yi ping

last: Qin

address: Room 617, College of Life Sciences Building, 1 YiXueYuan Road, YuZhong District, Chongqing

country: China

institute: Chongqing Medical University

summary: Cell: HBV-infected PHH cells. Methods: PHH cells were infected with 2000 genome equivalents/cell of HBV particles in the presence of 4% PEG8000. Seven days after HBV infection, ChIP-Seq analysis of cccDNA in HBV-infected PHHs was carried out. HBV-infected PHH cells were digested with micrococcal nuclease and resulting mononucleosomes purified by sucrose gradient centrifugation. Nucleosomes were enriched with anti-H3K79succ antibodies by ChIP assay and the associated DNA contained both human and HBV DNA fragments was analyzed by deep sequencing. The HBV-specific reads in ChIP-Seq pilot experiments was quantified and normalized by the reads mapped to the human genome.

overall_design: Detection of H3K79succ histone modification on cccDNA in HBV-infected PHH cells.

first: Yi

middle: P


title: Dependence on Bcl6 and Blimp1 identifies distinct mechanisms driving memory and follicular helper CD4+ T cell differentiation

city: Bethesda

first: Remy

last: Bosselut

state: Maryland

address: 9000 Rockville Pike, Building 37

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health


title: Single-cell RNA-Seq of NonTg, PS2APP and TauPS2APP mouse hippocampi, 20-22 months old

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

institute: Genentech

summary: Here we studied cellular level changes of hippocampal cells by unbiased single cell RNA-seq using AD mouse models bearing amyloid pathology (PS2APP), or amyloid and tau combined pathology (TauPS2APP) by single cell RNA-seq. We identified 16 different cell types and further characterized responses of microglia, oligodendrocytes, astrocytes and T cells to amyloidosis only and amyloid plus tau combined pathology. Both mouse models exhibited robust microglial responses. We also found distinct responses of oligodendrocytes to different AD pathologies. We observed increased T cell numbers in both mouse models. Current dataset presents diverse transcriptomic responses to AD pathology and provides resources to study molecular mechanisms underlying disease onset and progression.

overall_design: RNA isolated from sorted hippocampi from male non-transgenic (n=4), PS2APP (n=4), and TauPS2APP (n=3) mice. All mice were 20-22 months at the time of perfusion.

first: Seung-Hye

last: Lee

first: Chris

last: Bohlen

first: Brad

last: Friedman

first: Bill

last: Meilandt


title: Measuring Minimal Residual Disease beyond 10-5 through IGHV leader-based NGS increases Prognostic Discrimination in Chronic Lymphocytic Leukemia

city: Rotterdam

first: Paul

last: Hengeveld

address: Dr Molewaterplein 40

department: Immunology

country: Netherlands

institute: Erasmus MC

summary: The sensitivity of conventional techniques for the quantification of minimal/measurable residual disease (MRD) in chronic lymphocytic leukemia (CLL) is limited to MRD 10-4. Measuring MRD <10-4 could help to further distinguish between CLL patients with durable remission and those at risk of early relapse. We here present a novel, academically developed IGHV leader-based next-generation sequencing (NGS) assay for the quantification of MRD in CLL. We demonstrate, based on measurements in contrived MRD samples, that the linear range of detection and quantification of our novel assay reaches beyond MRD 10-5. If provided with sufficient DNA input, MRD can even be detected down to MRD 10-6. There was high inter-assay concordance between measurements of the IGHV leader-based NGS assay and allele-specific oligonucleotide quantitative PCR (r=0.92, [95%CI 0.86-0.96]) and droplet digital PCR (r=0.93, [95%CI 0.88-0.96]) on contrived MRD samples. In a cohort of 37 patients from the CLL11 trial, using MRD 10-5 as a cut-off, MRD undetectability was associated with superior progression-free survival (PFS) and time to next treatment. Importantly, deeper MRD measurement allowed for additional stratification of patients with MRD <10-4 but ≥10‑5. Whereas the PFS of these patients was significantly shorter, compared to patients with MRD <10-5 (HR 4.9, [95%CI 1.3-17.9], P=0.017), their PFS was superior to those with MRD ≥10‑4 (HR 0.18, [95%CI 0.06-0.46], P<0.001). These results clearly demonstrate the clinical utility of the novel IGHV-leader based NGS assay.

overall_design: B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of serial dilutations and post-treatment samples from CLL patients enrolled in the CLL11 trial

first: A

middle: W

last: Langerak

first: P

middle: J


title: Macrophages are metabolically heterogenous within the tumor microenvironment

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Macrophages are often prominently present in the tumor microenvironment, where distinct macrophage populations can differentially affect tumor progression. Although metabolism influences macrophage function, studies on the metabolic characteristics of ex vivo tumor-associated macrophage (TAM) subsets are rather limited. Using transcriptomic and metabolomic analyses, we now reveal that pro-inflammatory MHC-IIhi TAMs display a hampered TCA cycle, while reparative MHC-IIlo TAMs show a higher oxidative and glycolytic metabolism. Although both TAM subsets rapidly exchange lactate in high lactate conditions, only MHC-IIlo TAMs use lactate as an additional carbon source. Accordingly, lactate supports the oxidative metabolism in MHC-IIlo TAMs, while it decreased the metabolic activity of MHC-IIhi TAMs. Lactate subtly affected the transcriptome of MHC-IIlo TAMs, increased L-arginine metabolism and enhanced T-cell suppressive capacity of these TAMs. Overall, our data uncover the metabolic intricacies of distinct TAM subsets and identify lactate as a carbon source, and metabolic and functional regulator of TAMs.

overall_design: Bulk RNA Seq: MHC-IIhi and MHC-IIlo TAMs derived from 3LL-R tumor-bearing C57Bl/6 mice.Freshly sorted TAM subsets and TAM subsets incubated for 24h in presence or absence of 20mM sodium L-lactate.

first: Xenia

last: Geeraerts

first: Juan

last: Fernández-Garcia

first: Felix

last: Hartmann

first: Kyra

last: de Goede

first: Liesbet

last: Martens

first: Yvon

last: Elkrim

first: Ayla

last: Debraekeleer

first: Benoit

last: Stijlemans

first: Anke

last: Vandekeere

first: Gianmarco

last: Rinaldi

first: Riet

last: De Rycke

first: Mélanie

last: Planque

first: Dorien

last: Broekaert

first: Elisa

last: Meinster

first: Emile

last: Clappaert

first: Pauline

last: Bardet

first: Aleksandar

last: Murgaski

first: Conny

last: Gysemans

first: Frank

last: Aboubakar Nana

first: Yvan

last: Saeys

first: Sean

middle: C

last: Bendall

first: Damya

last: Laoui

first: Jan

last: Van den Bossche

first: Sarah-Maria

last: Fendt

first: Jo

last: Van Ginderachter


title: Transcriptome analysis of skeletal muscle tissue from Hras G12V mutant mice

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Costello syndrome (CS) is a congenital disorder caused by heterozygous activating germline HRAS mutations in the canonical Ras/mitogen-activated protein kinase (Ras/MAPK) pathway. CS is one of the RASopathies, a large group of syndromes due to mutations within various components of the Ras/MAPK pathway. An important part of the phenotype that greatly impacts quality of life is hypotonia. To gain a better understanding of the mechanisms underlying hypotonia in CS, a mouse model with an activating HrasG12V allele was utilized. We identified a skeletal myopathy that was due in part to an inhibition of embryonic myogenesis and myofiber formation, resulting in a reduction of myofiber size and number that led to reduced muscle mass and strength. In addition to hyperactivation of the Ras/MAPK and PI3K/AKT pathways, there was a significant reduction of p38 signaling, as well as global transcriptional alterations consistent with the myopathic phenotype. Inhibition of Ras/MAPK pathway signaling using a MEK inhibitor rescued the HrasG12V myopathy phenotype both in vitro and in vivo, demonstrating that increased MAPK signaling is the main cause of the muscle phenotype in CS.

overall_design: The study consisted of 2 groups of mice with triplicate samples per group. The experimental group consisted of mice that were heterozygous (HrasG12V/+) for the HrasG35T (p.G12V) mutation. Control mice were homozygous (Hras+/+) for wild type Hras. Gastrocnemius muscle tissue was harvested from 21-day-old mice and snap-frozen for subsequent RNA extraction and transcriptome profiling with RNA-Sequencing (RNA-Seq) analysis.

first: William

last: Tidyman

first: Katherine

last: Rauen


title: Blocking immunosuppressive neutrophils deters pY696-EZH2-driven brain metastases

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

summary: In brain metastatic cells, enhancer of zeste homologue 2 (EZH2) is highly expressed and phosphorylated at tyrosine-696 (pY696-EZH2) by nuclear-localized Src tyrosine kinase. Phosphorylation of EZH2 at Y696 changes its binding preference from histone H3 to RNA polymerase II, which consequently switches EZH2’s function from a methyltransferase to a transcription factor that increases c-Jun expression. c-Jun upregulates pro-tumorigenic inflammatory cytokines, including granulocyte-colony stimulating factor (G-CSF), which recruits Arg1-positive and PD-L1-positive immunosuppressive neutrophils into the brain to drive metastasis outgrowth.

overall_design: We examined Pol II binding in samples with differential EZH2 activity (wild-type EZH2, EZH2 knockout, and re-expression of mutant EZH2) using ChIPseq.

first: Lin

last: Zhang

first: Jun

last: Yao

first: Yongkun

last: Wei

first: Zhifen

last: Zhou

first: Ping

last: Li

first: Jingkun

last: Qu

first: Akosua

last: Badu-Nkansah

first: Xiangliang

last: Yuan

first: Yu

last: Huang

first: Kazutaka

last: Fukumura

first: Xizeng

last: Mao

first: Wei

last: Chang

first: Jodi

last: Saunus

first: Sunil

last: Lakhani

first: Jason

middle: T

last: Huse

first: Mien

last: Hung

first: Dihua

last: Yu


title: Sequence determinants of human gene regulatory elements, STARR-seq random promoter enhancer experiments

city: Helsinki

first: Teemu

last: Kivioja

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: DNA determines where and when genes are expressed, but the full set of sequence determinants that control gene expression is not known. Here, we measured transcriptional activity of DNA sequences that represent ~100 times larger sequence space than the human genome using massively parallel reporter assays. Machine learning models revealed that transcription factors (TFs) act generally in an additive manner with weak grammar, and that enhancers increase expression from a promoter by a mechanism that does not involve specific TF-TF interactions. The enhancers themselves can be classified into three distinct types: classical, closed chromatin and chromatin-dependent enhancers. We also show that few TFs are strongly active in a cell, with most activities similar between cell types. Individual TFs can have multiple gene regulatory activities, including chromatin opening, enhancing, promoting and TSS determining activity – consistent with the view that the TF binding motif is the only atomic unit of gene expression.

overall_design: STARR-seq random promoter and random enhancer library (binary design) performed in three cell lines GP5d (two replicates) , HepG2 and RPE1 (one replicate each). Input DNA library used as a control and to link sequenced enhancers to corresponding promoters.

first: Biswajyoti

last: Sahu

first: Tuomo

last: Hartonen

first: Päivi

last: Pihlajamaa

first: Bei

first: Kashyap

last: Dave

first: Fangjie

last: Zhu

first: Eevi

last: Kaasinen

first: Katja

last: Lidschreiber

first: Michael

first: Carsten

middle: O

last: Daub

first: Patrick

last: Cramer

first: Jussi

last: Taipale


title: Sequence determinants of human gene regulatory elements, TSS experiments

overall_design: 5' end capture using template switching from  random STARR-seq promoter-enhancer (binary) library RNA sequences for TSS positioning. Two replicate template-switch libraries and the input DNA library for control and determining the promoter sequence 3' of TSS.

last: Wei


title: Double Stranded DNA Breaks and Genome Editing Trigger Ribosome Remodeling and Translational Shutdown

status: Public on Nov 15 2021

city: Berkeley

first: Nicholas

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: DNA damage activates a robust transcriptional stress response, but much less is known about how DNA damage impacts translation. The advent of genome editing with Cas9 has intensified interest in understanding cellular responses to DNA damage. Here, we find that DNA double-strand breaks (DSBs), including those induced by Cas9, trigger the loss of ribosomal protein RPS27A from ribosomes via p53-independent proteasomal degradation. Comparisons of Cas9 and dCas9 ribosome profiling and mRNA-seq experiments reveal a global translational response to DSBs that precedes changes in transcript abundance. Our results demonstrate that even a single DSB can lead to altered translational output and ribosome remodeling, suggesting caution in interpreting cellular phenotypes measured immediately after genome editing.

overall_design: mRNA-Seq and ribosome profiling on HEK293 cells after inducing double-strand breaks by Cas9 RNP nucleofection, 36 hours and 72 hours after

first: Celeste

last: Riepe

first: Elena

last: Zelin

first: Samantha

middle: G

last: Fernandez

first: Phillip

last: Frankino

first: Zuriah

last: Meacham

first: Jacob

last: Corn


title: Sequence determinants of human gene regulatory elements, genomic STARR-seq experiments

first: Teemu

last: Kivioja

overall_design: STARR-seq libraries from genomic fragments in different conditions in GP5d and HepG2 (two replicates) cell lines. Genomic Input library provided as control.

first: Biswajyoti

last: Sahu

first: Tuomo

last: Hartonen

first: Päivi


title: Sequence determinants of human gene regulatory elements, STARR-seq motif library experiments

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: STARR-seq library containing known TF motifs with different orientations and spacings. Experiments done with two different plasmids, each having its own control.

last: Pihlajamaa

first: Bei

first: Kashyap

last: Dave

first: Fangjie

last: Zhu

first: Eevi


title: Sequence determinants of human gene regulatory elements, STARR-seq random enhancer experiments

overall_design: STARR-seq with random enhancer library performed in two cell lines GP5d (two replicates) and HepG2 (one replicate). Input DNA library used as a control.

last: Kaasinen

first: Katja

last: Lidschreiber

first: Michael

first: Carsten

last: Daub

first: Patrick


title: Single-Cell RNA-Seq of PS2APP mouse hippocampi

first: Mitchell

last: Rezzonico

summary: Non-neuronal responses in neurodegenerative disease have received increasing attention as  important contributors to disease pathogenesis and progression. Here we utilize single-cell  RNA-sequencing to broadly characterize responses of twelve cell types in three different mouse  models of Alzheimer’s Disease, capturing the effects of tau-only, amyloid-only, or combined tau-  amyloid pathology. We characterize microglia, oligodendrocyte, astrocyte, and T cell responses  and compare them across these models. Notably, we identify two distinct transcriptional states  for oligodendrocytes induced during disease and determine their spatial distribution.  Furthermore, we explore the impact of Trem2 deletion in the context of combined pathology.  Trem2 knockout mice exhibit severely blunted microglial responses to combined tau and  amyloid pathology, but responses from non-microglial cell types (oligodendrocytes, astrocytes,  and T cells) are relatively unchanged. These results delineate core transcriptional states that  are accessible in the degenerating brain and how they are influenced by a key Alzheimer’s  Disease risk gene, Trem2.

overall_design: RNA isolated from sorted hippocampi from female non-transgenic (n=3) and TauPS2APP (n=3) perfused at 7 months and male non-transgenic (n=3) and TauPS2APP mice (n=3) perfused at 15 months.

first: Seung-Hye

last: Lee

first: Brad

last: Friedman

first: Chris

last: Bohlen


title: Sequence determinants of human gene regulatory elements, CAGE experiment

overall_design: Cap analysis of gene expression (CAGE) for determination of transcription start sites in human colon cancer cells by isolation and sequencing of short tags originating at the 5' end of messenger RNA.

last: Wei

last: Cramer

first: Jussi

last: Taipale


title: Sequence determinants of human gene regulatory elements, ATI experiment

first: Teemu

overall_design: One ATI experiment, cycles 4 and 0 (input control) compared.


title: Sequence determinants of human gene regulatory elements, RNA-seq experiments

overall_design: Gene expression profiling by RNA-sequencing in human colon cancer cells line, GP5d and hepatocellular carcinoma cell line, HepG2 in mock control and transfected with STARR-seq (SS) library or treated with 5-fluorouracil (5-FU).

first: Biswajyoti


title: Sequence determinants of human gene regulatory elements, ATAC-seq experiments

overall_design: Chromatin accessibility was analyzed by ATAC-seq in human colon cancer cells line, GP5d and hepatocellular carcinoma cell line, HepG2 in control untreated and transfected with STARR-seq (SS) library or treated with 5-fluorouracil (5-FU).

first: Tuomo


title: Next-generation sequencing of anterior cingulate cortex neurons in a social problem setting in rats

city: Daegu

first: JA WOOK

last: KOO

address: 61 Cheomdan-ro, Dong-gu

country: South Korea

institute: Korea Brain Research Institute

summary: We studied the brain mechanisms of ‘social problem’ where a worker’s credit is exploited in a group setting. A stable ‘worker-parasite’ relationship developed when three individually operant-conditioned rats were placed together in a Skinner box equipped with response lever and food dispenser on opposite sides. Specifically, one rat, the ‘worker,’ engaged in lever-pressing while the other ‘parasitic’ rats profited by crowding the feeder in anticipation. c-Fos expression in the anterior cingulate cortex (ACC) was significantly higher in worker rats than in parasite rats. ACC inactivation suppressed the worker’s lever-press behavior under the social dilemma settings. Importantly, our RNA sequencing and the differential expression analysis showed that GABA- and potassium channel-related mRNA expressions decreased in the worker’s ACC. In contrast, network disinhibition induced-activity responsive genes such as Cyr61, Arc, and Klf are upregulated. These results suggest that downregulation and upregulation of network inhibitory and excitatory factors, respectively, in the ACC of the worker compared to parasite rats.

overall_design: RNA profiles of anterior cingulate cortex neurons in the worker versus parasite rats in a social problem setting

first: Ja

last: Koo

first: Min

last: Jung

first: Jeansok

last: Kim

first: Soyoun

last: Ahn

first: Yujeong

last: Kang

first: Jong-Won

first: Se

last: Jeong

first: You

first: Soomin


title: HDAC2 maintains receptor tyrosine kinase signaling of undifferentiated pancreatic cancer cells (ChIP-Seq)

city: Planegg-Martinsried

first: Andrea

last: Terrasi

address: Großhaderner Strasse 9

department: Biomedical Center Munich

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: H3K27ac ChIP-se and ATAC-seq were used to determine epigenetic differences between Hdac2 knockout versus Hdac2 wildtype pancreatic cancer cells.

overall_design: DNA was extracted from a total of 2 KrasG12D driven primary pancreatic cancer cell lines with indicated Hdac2 status

first: Gunnar

last: Schotta

first: Filippo

last: Cernilogar


title: MTHFD2 inhibition dramatically alters histone methylation landscape in Th17 cells

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: MTHFD2 is a mitochondrial enzyme within the folate cycle of one carbon metabolism. We found that MTHFD2 deficiency leads to impaired proliferation and induction of FoxP3 expression in Th17 cells and Treg cells differentiated in low TGFß conditions. Mechanistically, this occured through depleted purine pools, accumulation of purine synthesis intermediates, dampened mTORC1 activity, and altered DNA and histone methylation.

overall_design: Treg and Th17 cells were treated with either DMSO (vehicle) or 500nM DS18561882 (MTHFD2i) for 72 hours.

first: Ayaka

last: Sugiura

first: Jeffrey

first: Matthew

middle: Z

last: Madden

first: Xiang

last: Ye


title: Sequence determinants of human gene regulatory elements

first: Teemu

last: Kivioja

overall_design: Refer to individual Series


title: Sequence determinants of human gene regulatory elements, ChIP-seq experiments

overall_design: Transcription factor (TF) binding and enrichment of histone modifications were analyzed by chromatin immunoprecipitation followed by deep sequencing (ChIP-seq)

first: Biswajyoti

last: Sahu

first: Tuomo

last: Hartonen

first: Päivi

last: Pihlajamaa

first: Bei

last: Wei

first: Kashyap

last: Dave

first: Fangjie

last: Zhu

first: Eevi

last: Kaasinen

first: Katja

last: Lidschreiber

first: Michael

first: Carsten

last: Daub

first: Patrick

last: Cramer

first: Jussi


title: HDAC2 maintains receptor tyrosine kinase signaling of undifferentiated pancreatic cancer cells (ATAC-Seq)

first: Andrea

last: Terrasi

first: Gunnar

last: Schotta

first: Christine

last: Klement


title: RNA-seq based transcriptome profiling of Carpesium cernuum extract (CCE) treated MDA-MB-231 cell lines

city: Beijing

first: Honglei

last: Dang

address: 18 Life Science Parkway, Changping District

institute: National Engineering Research Center for Beijing Biochip Technology

summary: To understand the molecular mechanism of CCE, we performed the RNA-seq analysis. Cells were seeded at 5x10^5 cells/well in 6-well plates then treated with 1μg/mL CCE for 24 h. MDA-MB-231 cells were harvested, and RNA was isolated with TRIzol. The libraries were constructed by using the Quick cDNA Library Preparation Kit and sequenced on an XTEN sequencing system. RNA-seq data were mapped to the reference genome (hg19) by using HISAT2. The reads were counted, and StringTie was used to calculate the FPKM value of the genes. The differentially expressed genes (DEGs) were identified by comparing the experimental group with the control group.

overall_design: mRNA profiles of control group and CCE group were generated by RNA sequencing.

first: Lili

last: Deng

first: Lan

last: Xie


title: Forkhead box F1 overexpression initiates Barrett’s like metaplasia by promoting trans-differentiation and wound repair

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: The forkhead box (FOX) family of transcriptional regulators is characterized by a distinct forkhead DNA-binding domain11. FOXF1 gene is highly conserved across species and implicated in embryonic digestive tract morphogenesis. In an in-vitro established model, normal esophageal squamous cells, EPC2, were transfected with FOXF1 to determine pathways regulated by FOXF1 during the squamous to columnar change in cells.

overall_design: Normal esophageal squamous cells, EPC2, were transfected in biological triplicates with FOXF1 plasmid or empty vector by using Lipofectamine 2000. Three groups were compared: untreated (Ctrl), group transfected with empty vector by using Lipofectamine 2000 (Lipo) and the group transfected with FOXF1 plasmid (Fox)

first: Alok

last: De

first: Jianping

last: Zhou

first: Sharad

last: Mathur

first: Lane

last: Christenson

first: Mukut

last: Sharma

first: Ajay

last: Bansal


title: Identification of accessible chromatin regions in response to cold stress in Vitis amurensis

first: Luming

last: Zou

state: PR

address: Haidian strict, Xiang Mountain South Road, Xiang Mountain South Village 20#

department: Institute of Botany

institute: University of Chinese Academy of Sciences

summary: We report the Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) for high-throughput profiling of accessible chromatin regions after cold treatment in Vitis amurensis

overall_design: Examination of accessible chromatin regions in in vitro V. amurensis plants under control and cold stress conditions

first: Chong

last: Ren

first: Zhenchang

last: Liang


title: HDAC2 maintains receptor tyrosine kinase signaling of undifferentiated pancreatic cancer cells

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


title: MicroRNA function transitions from regulating developmental genes to transposable elements during the maturation of pollen

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Small non-coding RNAs play important roles during the development of eukaryotic organisms. Both animal and plant miRNAs are essential for the spatio-temporal regulation of development but together with this role, plant miRNAs, also control transposable elements and stimulate the production of epigenetically-active small interfering RNAs. This last role is evident in the plant male gamete containing structure, the male gametophyte or pollen grain but how the dual role of plant miRNAs is integrated during its development is unknown. Here, we provide a detailed analysis of miRNA dynamics during pollen development and their genic and transposable element targets using small RNA and PARE high-throughput sequencing. Furthermore we uncover the miRNAs loaded in the two main AGOs in the mature pollen grain, AGO1 and AGO5. Our results indicate that the progression from microspore to mature pollen grain is characterized by a reprogramming from miRNAs focused on the control of development to miRNAs focused in transposable element control.

overall_design: Analysis of sRNA accumulation during pollen grain development and PARE sequencing on mature pollen grains


title: Endogenous Smad7 restrains myofibroblast activation and protects from post-infarction heart failure by suppressing TGF-b signaling and by directly inhibiting Erbb2

status: Public on Nov 11 2021

city: New York

first: CLAUDIO

middle: DIEGO

last: HUMERES

state: New York

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

summary: Repair of the infarcted heart requires TGFβ-Smad3 signaling in cardiac myofibroblasts. However, TGF-β-driven myofibroblast activation needs to be tightly regulated in order to prevent excessive fibrosis and adverse remodeling that may precipitate heart failure. We hypothesized that induction of the inhibitory Smad, Smad7 may restrain infarct myofibroblast activation, and we examined the molecular mechanisms of Smad7 actions. In a mouse model of non-reperfused infarction, Smad3 activation triggered Smad7 synthesis in β-SMA+ infarct myofibroblasts, but not in β-SMA-/PDGFRα+ fibroblasts. Myofibroblast-specific Smad7 loss increased heart failure-related mortality, worsened dysfunction, and accentuated fibrosis in the infarct border zone and in the papillary muscles. Smad7 attenuated myofibroblast activation and reduced synthesis of structural and matricellular extracellular matrix proteins. Smad7 actions on TGF-β cascades involved de-activation of Smad2/3 and non-Smad pathways, without any effects on TGF-β receptor activity. Unbiased transcriptomic and proteomic analysis identified receptor tyrosine kinase signaling as a major target of Smad7. Smad7 interacted with Erbb2 in a TGF-independent manner and restrained Erbb1/Erbb2 activation, suppressing fibroblast expression of fibrogenic proteases, integrins and CD44. Smad7 induction in myofibroblasts serves as an endogenous TGF-β-induced negative feedback mechanism that inhibits post-infarction fibrosis by restraining Smad-dependent and Smad-independent TGF-β responses, and by suppressing TGF-independent fibrogenic actions of Erbb2.

overall_design: Comparison of the transcriptomic profile of In vitro cultured control and Smad7KO cardiac fibroblasts (passage 2), in presence/absence of TGF-β stimulation. Smad7 loss was achieved via Adenoviral Cre expression in fibrobrasts isolated from Smad7 floxed animals. 4 conditions (Control, Smad7KO, Control + TGFβ, S7KO + TGFβ); 3 indepent samples per condition. 12 samples total.

first: Claudio

last: Humeres

first: Arti

last: Shinde

first: Anis

last: Hanna

first: Silvia

last: Hernandez

first: Ruoshui

last: Li

first: Bijun

last: Chen

first: Nikolaos

last: Frangogiannis

first: Simon

last: Conway


title: RNA-seq: Transcriptome profile between wild type control and kah mutants in Drosophila embryo

city: Gothenburg

first: Ruth

last: Palmer

address: Medicinaregatan 9A, Shalgrenska Academy

department: Medical Biochemistry & Cell Biology

institute: Gothenburg University

summary: We assessed the differential expression of genes in the Drosophila embryo of kah mutants and control to understand how the transcriptional responce in kah mutants.

overall_design: Two groups of Drosophila embryos (two kah mutants and controls) with three biological replicates per group

first: Badrul

last: Arefin


title: Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1 [ChIP-seq]

city: Solna

first: Vladislav

last: Kuzin

state: Stockholm

address: Solnavägen 9

department: Cell and Molecular Biology

institute: Karolinska Institute

summary: By following chromatin occupancy of RNAPII and TOP1 using ChIP-seq throughout mitosis, we found that TOP1 is required for RNAPII translocation along genes. The stimulation of TOP1 activity through its interaction with RNAPII during elongation, allowed RNAPII clearance from genes in prometaphase and enabled proper chromosomal segregation. Interference with the TOP1-RNAPII interaction or acute depletion of TOP1 at the onset of mitosis impaired RNAPII spiking at promoters, which is necessary for the first pioneering round of transcription during mitotic exit, and triggered defects in the transcriptional program of the post-mitotic cells.

overall_design: ChIP-seq of RNAPII, Top1 and H3K4me3 throughout mitosis at three different timepoints: early, mid and late (PM, 0 and 40/60). To synchronize in mitosis cells were blocked in S phase by addition of 2.5mM thymidine (Sigma, T9250) for 19-24h and, after washing with fresh medium, transferred in fresh medium containing 400ng/ml nocodazole (Sigma, M1404) and allowed to progress to mitosis. Mitotic cells were collected and released to different mitotic stages before harvest and fixation for ChIP. All experiments were performed in HCT116 and derived cell lines.

first: Anika

last: Wiegard

first: Donald

last: Cameron

first: Jan

last: Grosser

first: Michele

last: Ceribelli

first: Rashid

last: Mehmood

first: Roberto

last: Ballarino

first: Francesco

last: Valant

first: Radosław

last: Grochowski

first: Ivana

last: Karabogdan

first: Nicola

last: Crosetto

first: Arne

last: Lindqvist

first: Anna

middle: H

last: Bizard

first: Fedor

last: Kouzine

first: Toyoaki

last: Natsume

first: Laura

last: Baranello


title: Epithelial Colonization by Gut Dendritic Cells promotes their Functional Diversification

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Dendritic cells (DCs) patrol tissues and transport antigens to lymph nodes to initiate adaptive immune responses. Within tissues, DCs constitute a complex cell population composed of distinct subsets that can exhibit different activation states and functions. How tissue-specific cues orchestrate DC diversification remains elusive. Here, we show that the small intestine included two pools of cDC2s originating from common preDC precursors: (1) lamina propria (LP) CD103+CD11b+ cDC2s that were mature-like pro-inflammatory cells and (2) intraepithelial cDC2s that exhibited an immature-like phenotype as well as tolerogenic properties. These phenotypes resulted from the action of food-derived retinoic acid (ATRA), which enhanced actomyosin contractility and promoted LP cDC2 transmigration into the epithelium. There, cDC2s were imprinted by environmental cues including ATRA itself and the mucus component Muc2. Hence, by reaching distinct sub-tissular niches, DCs can exist as immature and mature cells within the same tissue, revealing an additional mechanism of DC functional diversification.

overall_design: Expression profiling by high throughput sequencing

first: Claudia

last: Rivera

first: Christel

last: Goudot

first: Ana-Maria

last: Lennon-Duménil


title: Population and molecular responses to warming in Netzelia tuberspinifera – An endemic and sensitive protist from East Asia

city: Xiamen

first: Jun

last: Yang

address: 1799 Jimei Road, Xiamen, 361021 PR China

institute: Chinese Academy of Sciences

summary: In this study, we measured growth rate of Netzelia tuberspinifera(basionym Difflugia tuberspinifera) under different temperatures and revealed the molecular mechanisms of temperature adaptation based on the transcriptomics along a temperature gradient (15, 25 and 35 °C). This study can provide a reference for in-depth study on testate amoebae in future researches.

overall_design: The nine transcriptomics datas of N. tuberspinifera along a temperature gradient (15, 25 and 35 °C)

first: Wenping

last: Wang

first: Xiaofei

last: Gao

first: Jean

last: Ndayishimiye

first: Kexin

last: Ren

first: Huihuang

last: Chen


title: Hierarchy of TGFβ/SMAD, Hippo/YAP/TAZ and Wnt/β-catenin signaling in melanoma phenotype switching

city: Basel

first: Gerhard

last: Christofori

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: In melanoma, a switch from a proliferative melanocytic to an invasive mesenchymal phenotype is based on dramatic transcriptional reprogramming which involves complex interactions between a variety of signaling pathways and their downstream transcriptional regulators. TGFb/SMAD, Hippo/YAP/TAZ and Wnt/b-catenin signaling pathways are major inducers of transcriptional reprogramming and converge at several levels. Here, we report that TGFb/SMAD, YAP/TAZ and b-catenin are all required for a proliferative-to-invasive phenotype switch. Loss and gain of function experimentation, global gene expression analysis, and computational nested effects models revealed the hierarchy between these signaling pathways and identified shared target genes. SMAD-mediated transcription at the top of the hierarchy leads to the activation of YAP/TAZ and of b-catenin, with YAP/TAZ governing an essential sub-program of TGFb-induced phenotype switching. Wnt/b-catenin signaling is situated further downstream and exerts a dual role: it promotes the proliferative, differentiated melanoma cell phenotype and it is essential but not sufficient for SMAD or YAP/TAZ-induced phenotype switching. The results identify epistatic interactions among the signaling pathways underlying melanoma phenotype switching and highlight the priorities in targets for melanoma therapy.

overall_design: Stimulation of two melanoma cell lines with TGFb1 and Wnt-3a, and siRNA knock-downs of LATS1/2 in all possible combinations including two controls  (total 9 samples per cell line). Technical duplicates were sequenced.

first: Fabiana

last: Lüönd

first: Martin

last: Pirkl

first: Ravi

middle: K

last: Kalathur

first: Niko

last: Beerenwinkel

first: Mizue

last: Hisano

first: Vincenzo

last: Prestigiacomo

first: Christian

last: Beisel


title: The Long Non Coding RNA SAMMSON is a regulator of chemosensitivity and metabolic orientation in doxorubicin resistant breast cancer cells

status: Public on Nov 10 2021

city: Angers

first: Charlotte

last: ORRE

address: Rue des Capucins (Institut de Biologie en Santé, CHU d'Angers)

institute: MitoVasc, Mitolab team

summary: Despite improvements in therapeutic strategies for treating breast cancers, tumor relapse and chemoresistance remain major issues in patient outcomes. Indeed, cancer cells display a metabolic plasticity allowing a quick adaptation to tumoral microenvironment and to cellular stresses induced by chemotherapy. Recently, long non-coding RNA molecules (lncRNAs) have emerged as important regulators of cellular metabolic orientation. In the present study, we addressed the role of the long non-coding RNA molecule (lncRNA) SAMMSON on the metabolic reprogramming and chemoresistance of MCF-7 breast cancer cells resistant to doxorubicin (MCF-7dox). Our results showed an overexpression of SAMMSON in MCF-7dox compared to doxorubicin-sensitive cells (MCF-7). Silencing of SAMMSON expression by siRNA in MCF-7dox cells resulted in a metabolic rewiring with improvement of oxidative metabolism, decreased mitochondrial ROS production, increased mitochondrial replication, transcription and translation and an attenuation of chemoresistance. These results highlight the role of SAMMSON in the metabolic adaptations leading to the development of chemoresistance in breast cancer cells. Thus, targeting SAMMSON expression levels represents a promising therapeutic route to circumvent doxorubicin resistance in breast cancers.

overall_design: Transcriptomic analysis of differentially expressed genes between siRNA-induced inhibition of SAMMSON lncRNA expression in MCF7-dox chemoresistant breast cancer cells (6 samples), compared to MCF-7dox cells transfected with a no-target siRNA (6 samples)

last: Orre

first: Valerie

last: Desquiret-Dumas

first: Delphine

last: Prunier-Mirebeau


title: eIF2B-capturing viral protein NSs suppresses the integrated stress response

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

summary: Various stressors such as viral infection lead to the suppression of cap-dependent translation and the activation of the integrated stress response (ISR), since the stress-induced phosphorylated eukaryotic translation initiation factor 2 [eIF2(αP)] tightly binds to eIF2B to prevent it from exchanging guanine nucleotide molecules on its substrate, unphosphorylated eIF2. Sandfly fever Sicilian virus (SFSV) evades this cap-dependent translation suppression through the interaction between its nonstructural protein NSs and host eIF2B. However, its precise mechanism has remained unclear. Here, our cryo-electron microscopy (cryo-EM) analysis revealed that SFSV NSs binds to the α-subunit of eIF2B in a competitive manner with eIF2(αP). Together with SFSV NSs, eIF2B retains nucleotide exchange activity even in the presence of eIF2(αP), in line with the cryo-EM structures of the eIF2B•SFSV NSs•unphosphorylated eIF2 complex. A genome-wide ribosome profiling analysis clarified that SFSV NSs expressed in cultured human cells attenuates the ISR triggered by thapsigargin, an endoplasmic reticulum stress inducer. Furthermore, SFSV NSs introduced in rat hippocampal neurons and human induced-pluripotent stem (iPS) cell-derived motor neurons exhibited neuroprotective effects against the ISR-inducing stress. Since ISR inhibition is beneficial in various neurological disease models, SFSV NSs is promising as a therapeutic ISR inhibitor.

overall_design: Ribosome profiling and RNA-seq of SFSV NSs-expressing cells upon endoplasmic reticulum stress

first: Kazuhiro

last: Kashiwagi

first: Yuichi

last: Shichino

first: Tatsuya

last: Osaki

first: Ayako

last: Sakamoto

first: Madoka

last: Nishimoto

first: Mari

last: Takahashi

last: Mito

first: Friedemann

last: Weber

first: Yoshiho

last: Ikeuchi

first: Takuhiro

last: Ito


title: RNA-seq of zinc-replete wild type and zinc-limited wild type, altRP operon deletion mutant and its complement strain in Mycolicibacterium (Mycobacterium) smegmatis

city: Honolulu

first: Sladjana

last: Prisic

state: HI

address: 2538 McCarthy Mall

department: School of Life Sciences

institute: University of Hawaii, Manoa

summary: The study was designed to describe the effects of zinc limitation on gene expression in M. smegmatis by comparing the transcriptomes of zinc-replete and zinc-limited wild type. Additionally, the study informs how loss of the altRP operon impacts the transcriptomic changes during zinc limitation by comparing the transcriptomes of zinc-limited ΔaltRP mutant to the zinc-replete and zinc-limited wild type, and to confirm which changes are complemented in the complement strain (ΔaltRP/c).

overall_design: There are 12 samples in total. For each strain (wild type, ΔaltRP and ΔaltRP/c) and condition (ie, zinc-replete and zinc-limited) three biological replicates are analyzed.

first: Allexa

last: Dow


title: Transcriptomic Characterization of Local Invasion in Human Bladder Cancer by Single Cell RNA Sequencing

city: Shanghai

first: Jia

last: Wang

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

summary: Investigating intra-tumor heterogeneity of bladder cancer has been largely based on conventional pathological staging and bulk samples sequencing for analyzed multiple spatially separated regions within one tumor. However, it still lack a comprehensive understanding for this question at single cell resolution.

overall_design: Single cell mRNA profiles of seven primary tumor samples and one paracancerous tissue sample from seven patients with bladder cancer were generated by 10X Genomics plartform, without technical replication, and sequenced by NovaSeq 6000 (Illumina)

first: Wei-Qiang

last: Gao


title: RNAseq data for murine BMDM infected with wild-type Mycobacterium tuberculosis, a PDIM mutant, or an ESX-1 mutant.

city: Cambridge

first: Amy

middle: K.

last: Barczak

state: MA

address: The Ragon Institute, 400 Technology Square

department: Medicine/Infectious Diseases

institute: Massachusetts General Hospital

summary: C57BL6 murine bone marrow-derived marcrophages were infected with Mycobacterium tuberculosis H37Rv, a PDIM mutant (H37RvΔmas) or an ESX-1 mutant (Tn::eccCa1) strains at an MOI of 2:1. RNA was harvested at 4, 8, 12, and 16 hours post-infection for comprehensive transcriptional profiling.

overall_design: Uninfected cells at time 0, wild-type infected, PDIM mutant-infected, and ESX-1 mutant-infected cells at 4, 8, 12, and 16 hours post-infection.


title: High throughput single cell epigenomic profiling by targeted insertion of promoters (TIP-seq)

city: Tallahassee

first: Daniel

last: Bartlett

state: Florida

address: 319 Stadium Drive

department: Biological Sciences

institute: Florida State University

summary: Chromatin profiling in single cells has been extremely challenging and almost exclusively limited to histone proteins. In cases where single cell methods have shown promise, many require highly specialized equipment or cell type specific protocols and are relatively low throughput. Here, we combine the advantages of tagmentation, linear amplification and combinatorial indexing to produce a high throughput single cell DNA binding site mapping method that is simple, inexpensive and capable of multiplexing several independent samples per experiment. Targeted Insertion of Promoters (TIP-seq) uses Tn5 fused to protein A to insert a T7 RNA polymerase promoter adjacent to a chromatin protein of interest. Linear amplification of flanking DNA with T7 polymerase prior to sequencing library preparation provides ~10-fold higher unique reads per single cell compared to other methods. We apply TIP-seq to map histone modifications, RNA Polymerase II (RNAPII) and transcription factor CTCF binding sites in single human and mouse cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Targeted insertion of promoters (TIP-seq) uses a custom-designed proteinA-Tn5 transposase fusion protein (pA-Tn5), that carries with it a transposon containing a T7 promoter, that is recruited to antibody-bound chromatin sites where the Tn5 transposome simultaneously cuts and inserts (tagmentation) the T7 promoter into adjacent genomic DNA to permit linear amplification. In-vitro transcription (IVT) by T7 RNA polymerase creates thousands of RNA copies of the insertion sites, and after reverse transcription, second-strand synthesis, and cDNA fragmentation, TIP-seq amplicons are prepared for sequencing via limited-cycle number PCR indexing.

first: Vishnu

last: Dileep

first: Tetsuya

last: Handa

first: Yasuyuki

last: Ohkawa

first: Hiroshi

last: Kimura

first: Steven

last: Henikoff

first: David

middle: M

last: Gilbert


title: Comparison of transcriptional profiles of peripheral blood mononuclear cells from AIDS patients and healthy control group

city: Chengdu

first: Fangyuan

last: Shen

address: No.29 Wangjiang Road

institute: Sichuan University

summary: With the purpose of identifying the cascaded miRNA-mRNA regulatory relationships related to infection of HIV in gene level, we extracted mRNA from Peripheral blood mononuclear cells from 50 AIDS patients and 7 uninfected health controls. All AIDS patients in sample were received Antiretroviral Therapy. To further analysis the gene expression pattern in different virus load, we classified high virus loads (HVL, n=14) and low virus loads (LVL, n=16). 2635 and 2826 differentially expressed genes (DEGs) were selected, respectively in LVL and HVL. Functional enrichment analysis indicated DEGs which involved in immune response and apoptosis, played a crucial role in HIV infection. Further, we identified 5 most influential TFs to build miRNA-TF-mRNA regulatory network.

overall_design: In this study, we have included 8 healthy controls and 50 AIDS patients.  Peripheral blood mononuclear cells (PBMCs) from morning fasting venous blood samples were collected for RNA extraction and were ran on  Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version).

first: Quansheng

last: Feng

first: Xiao

last: Li


title: Genome-wide analysis of Ischaemia-Reperfusion damage in human bowel

city: Maastricht

first: Marco

last: Manca

state: Limburg

address: P. Debyelaan 25

department: CARIM

institute: University of Maastricht

summary: Comprehensive understanding of the transcriptional foundations of human intestinal ischemia-reperfusion (IR) injury is imperative to find therapeutic targets and improve patient outcome. Here we analysed transcriptomes of the IR-injured human intestine, and showed that over 1,800 genes were significantly differentially expressed, predominantly during reperfusion. Intriguingly, protein processing in endoplasmic reticulum (ER) was one of the most perturbed pathways, which was supported by ontology analysis. The IR-triggered transcriptome is organized into distinct co-expression networks, and implied a role for HIF1-alpha in the response towards unfolded proteins. Unfolded protein response activation as a consequence of ER stress was further validated in a large sample set, revealing strong correlations between expression of ER stress genes IRE1, XBP1 and BiP and autophagy gene LC3B. Moreover, signs of ER stress and autophagy, particularly ER phagy, were apparent in Paneth cells. Collectively, these findings provide new evidence for key involvement of protein folding stress in IR-induced intestinal injury in man. The ensuing ER stress, together with its manifestations in Paneth cells, likely contributes to IR-induced complications including bacterial penetration and inflammation.

overall_design:
Total RNA obtained from jejunal segments subjected to 45-60 minutes of ischaemia or following 30 minutes or 120 minutes of reperfusion, or control segments, during a Whipple surgery procedure.

This work was supported by the Dutch Society for Gastroenterology (Gastrostart grant 2009-23 9 to K. Lenaerts).

first: Kaatje

last: Lenaerts


title: miRNA profiling of peripheral blood mononuclear cells from AIDS patients and healthy control group

summary: With the purpose of identifying the cascaded miRNA-mRNA regulatory relationships related to infection of HIV in gene level, we extracted mRNA from Peripheral blood mononuclear cells from 50 AIDS patients and 7 uninfected health controls. All AIDS patients in sample were received Antiretroviral Therapy. To further analysis the miRNA expression pattern in different virus load, we classified high virus loads (HVL, n=14) and low virus loads (LVL, n=16). 145 and 129 differentially expressed miRNAs (DEMs) were selected, respectively in LVL and HVL. Functional enrichment analysis indicated miRNA-correlated targets which involved in immune response and apoptosis, played a crucial role in HIV infection. Further, we identified 5 most influential TFs to build miRNA-TF-mRNA regulatory network.

overall_design: In this study, we have included 8 healthy controls and 50 AIDS patients. Peripheral blood mononuclear cells (PBMCs) from morning fasting venous blood samples were collected for RNA extraction and were ran on Agilent Human miRNA (8*60K) V19.0.


title: Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide phosphodiesterase (CNPase) in Salmonella Typhimurium 14028s (Salmonella) I.

status: Public on Nov 09 2021

city: University Park

first: Emily

last: Weinert

state: PA

address: 306 Althouse Laboratory

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: The impact of Ribonuclease I (RNase I) on global gene expression in Salmonella was investigated by deletion of the 'rna' gene which encodes RNase I.  RNase I is capable of hydrolyzing RNA into 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) such that deletion of 'rna' drastically reduces 2',3'-cNMPs presence to undetectable levels. This 'rna' deletion mutant was compared to Salmonella 14028s WT strain.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Global transcript levels in a 'rna' deletion strain of Salmonella were compared to levels in 14028s WT control cells in order to identify cellular processes modulated by RNase I.

first: Benjamin

last: Fontaine

first: Jennifer

middle: E

last: Kurasz

first: Yashasvika

last: Duggal

first: Shikha

last: Chauhan

first: Nick

last: Marotta

first: Anna

last: Karls


title: Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide monophosphates in Salmonella enterica serovar Typhimurium (S. Typhimurium)

summary: The impact of 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) on global gene expression in S. Typhimurium was investigated by heterologous expression of a 2',3'-cyclic nucleotide phosphodiesterase (CNPase), which reduces intracellular 2',3'-cNMP levels.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Global transcript levels in S. Typhimurium expressing CNPase were compared to levels in control cells expressing a catalytically inactive variant of the enzyme to identify cellular processes modulated by 2',3'-cNMPs.

first: Gregory

last: Tharp


title: Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide phosphodiesterase (CNPase) in Escherichia coli K12 BW25113 (E. coli)

summary: The impact of 2',3'-cyclic nucleotide phosphodiesterase (CNPase) on global gene expression in E. coli was investigated by heterologous expression of mammalian CNPase in a strain containing a deletion of the 'rna' gene. 'rna' encodes an endoribonuclease capable of hydrolyzing RNA into 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) such that deletion of 'rna' drastically reduces 2',3'-cNMPs levels to undetectable levels. Expression of CNPase in this strain allowed any effects of CNPase unrelated to 2',3'-cNMPs to be observed.

overall_design: Global transcript levels in a 'rna' deletion strain of E. coli expressing CNPase were compared to levels in control cells with the same deletion expressing a catalytically inactive variant of CNPase in order to identify cellular processes modulated by CNPase that are unrelated to  2',3'-cyclic nucleotide monophosphates.


title: High-throughput Microwell-seq 2.0 reveals massively multiplexed chemical perturbation

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

summary: Combining in-cell RT and Microwell-seq 1.0, we established Microwell-seq 2.0 for cost-effective HTS with scRNA-seq-based phenotyping. To assess the fidelity of the Microwell-seq 2.0, we performed a species-mixing experiment with cultured human (293T) and mouse (3T3) cells. Moreover, we assessed the platform on tissue cells with more heterogeneous cell types. By harnessing the power of Microwell-seq 2.0, we analyzed massively multiplexed chemical perturbation of human embryonic stem cells (hESCs) at the single-cell resolution.

first: Haide

last: Chen

first: Yuan

last: Liao

first: Zhongyi

last: Sun


title: Human Reproduction is Regulated by Retrotransposons derived from Ancient Hominindae-Specific Viral Infections [ChIP-seq]

city: Haining

first: Xinyu

last: Xiang

address: East Haizhou Road

department: Zhejiang University-University of Edinburgh Institute

institute: Zhejiang University

summary: Here, we report the genomic binding profile of NANOG and SOX17 in human embryonic stem cells and human primordial germ cell-like cells.

overall_design: There are 16 samples in total. For both NANOG and SOX17 ChIP-seq in hESCs and hPGCLCs, two biological replicates were conducted, together with corresponding input control.

first: Wanlu

last: Liu

first: Amander

last: Clark


title: Processing of NODULE INCEPTION controls transition to nitrogen fixation in root nodules

city: Cologne

first: Tak

last: Lee

address: Carl-von-Linne weg 10

institute: Max Planck Institute for Plant Breeding Research

summary: To understand the role of Medicago truncatula NODULE INCEPTION (MtNIN) in nodule development, we analyzed the transcriptome of roots ectopically overexpressing NIN, nodules of weak mutant allele nin-16, and nodules of dnf1-2 mutant.

overall_design: To generate NIN and GFP over-expression plants, both NIN and GFP were cloned into level 2 binary vectors under the control of the L. japonicus UBIQUITIN promoter and transformed using A. rhizogenes. The transcriptional response to NIN overexpression (NINox) in 3-week old hairy roots was compared to control roots expressing GFP. Nodules of A17, dnf1-2, R108 and nin-16 at 15 days post inoculation were used for transcriptional analysis.

first: Jian

last: Feng

first: Katharina

last: Schiessl


title: GluN3A-NMDA receptors constrain protein synthesis and memory by limiting synaptic GIT1/mTORC1 assembly

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

country: Spain

institute: CSIC-Instituto de Neurociencias de Alicante

summary: Protein synthesis has been implicated in learning and memory, but regulatory mechanisms operating at the synaptic level have not been identified yet. Here we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mTOR kinase and Raptor that couple synaptic stimuli to mTORC1-dependent protein synthesis; and identify non-conventional NMDA receptors containing GluN3A subunits as key negative regulators of GIT1’s binding to mTOR. GluN3A removal enables GIT1/mTOR complex formation, switches on mTORC1-dependent synthesis of plasticity proteins and enhances memory. The memory enhancement becomes evident with light training and can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood. Notably, unlike the memory enhancement seen after global manipulations of translation, GluN3A deletion does not compromise memory flexibility or extinction. These findings identify a novel regulatory mechanism whereby GIT1/GluN3A interactions set local modes of protein synthesis and gate memory formation, offering a potentially selective target for cognitive enhancement.

overall_design: mRNA profiles from DIV14 cortical primary cultured neurons expressing exogenous GFP-GluN3A or GFP in basal conditions or upon a 1h treatment with BDNF 100ng/ml or Bicuculine 50uM.

first: María

last: Conde-Dusman

first: Angel

last: Barco

first: Isabel

last: Pérez-Otaño


title: Vaccine-elicited CD4 T cells prevent the deletion of antiviral B cells in chronic infection

first: Carolyn

last: King

address: Hebelstrasse 28

summary: CD4 T cells responses induced by LM61 immunization are heterogeneous in phenotype. The majority consists of Th1 cells, but there is also a consistent population of Tfh-differentiated cells and a minor population of Treg cells. Tfh-differentiated cells, alongside Th1 cells expand upon LCMV challenge.

overall_design: LCMV GP66-77-specific CD4 T cells were analyzed on day 9  after LM61 immunization. Additional mice were given KL25HL B cell transfer and LCMV challenge on day 9 after LM61 immunization and GP66-77-specific CD4 T cells were analyzed on day 14. To control for the impact of LM61 pre-immunization on the differentiation of GP66-77-specific CD4 T cell responses upon LCMV challenge, an additional group of mice was given wildtype LM on day 0 instead of LM61.

first: Kerstin

last: Narr

first: David

last: Schreiner

first: Daniel

middle: D

last: Pinschewer


title: EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma [ChIP-seq]

city: Memphis

first: Brian

last: Abraham

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: Gene expression is regulated by promoters and enhancers marked by histone H3-lysine-27 acetylation (H3K27ac), which is established by the paralogous histone acetyltransferases (HATs), EP300 and CBP. These enzymes display overlapping regulatory roles in untransformed cells, but less characterized roles in cancer cells. We demonstrate that the majority of high-risk pediatric neuroblastomas (NB) depend on EP300, whereas CBP has a limited role. EP300 controls enhancer acetylation by interacting with TFAP2?, a transcription factor member of the lineage-defining transcriptional core regulatory circuitry (CRC) in NB. To disrupt EP300, we developed a proteolysis-targeted-chimaera (PROTAC) compound termed ?JQAD1? that selectively targets EP300 for degradation. JQAD1 treatment causes loss of H3K27ac at CRC enhancers and neuroblastoma apoptosis, with limited toxicity to untransformed cells where CBP compensates. Comparing HAT inhibition and EP300-specific degradation, we identified a non-catalytic role for EP300 in promoting MYCN expression and repression of apoptosis.

overall_design: ChIP-Seq targeting histone acetyltransferases and associated acetylated histones in neuroblastoma cell lines

first: Adam

last: Durbin

first: Tingjian

last: Wang

first: Virangika

last: Wimalasena

first: Mark

last: Zimmerman

first: Deyao

last: Li

first: Neekesh

middle: V

last: Dharia

first: Luca

last: Mariani

first: Noha

middle: A

last: Shendy

first: Stephanie

last: Nance

first: Anand

last: Patel

first: Ying

last: Shao

first: Maya

last: Mundada

first: Lily

last: Maxham

first: Paul

last: Park

first: Logan

last: Sigua

first: Ken

last: Morita

first: Amy

last: Conway

first: Amanda

middle: L

last: Robichaud

first: Antonio

last: Perez-Atayde

first: Melissa

last: Bikowitz

first: Taylor

last: Quinn

first: Olaf

last: Wiest

first: John

last: Easton

first: Ernst

last: Schönbrunn

first: Martha

last: Bulyk

first: Kimberly

last: Stegmaier

first: A

last: Look

first: Jun

last: Qi


title: EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma [ChIP-rx]

first: Brian

middle: J

last: Abraham

first: Adam

last: Durbin

first: Tingjian

last: Wang

first: Virangika

last: Wimalasena

first: Mark

middle: W

last: Zimmerman

first: Deyao

last: Li

first: Neekesh

last: Dharia

first: Luca

last: Mariani

first: Noha

last: Shendy

first: Stephanie

last: Nance

first: Anand

last: Patel

first: Ying

last: Shao

first: Maya

last: Mundada


title: Inhibiting the KIT-Src pathway to ensure differentiation of hematopoietic progenitor requires ARID4B [ChIP-seq]

city: Miami

first: Karoline

last: Briegel

state: FL

address: 1600 NW 10th Ave

department: Surgery

institute: University of Miami

summary: Hematopoiesis is maintained by a highly regulated and hierarchical system, whereas aberrant control of hematopoiesis is the underlying cause of severe hematological diseases. Here, we demonstrate the indispensable role of ARID4B in fetal hematopoiesis that recruits Ezh2 to transcriptionally downregulate the expression of KIT during erythroid cell differentiation. Functional analyses reveal that the aberration of Arid4b inhibits fetal hematopoiesis at the multipotent progenitors (MPPs) stage, which reactivates the KIT-Src-family kinase (Src) pathway and leads to pre-mature erythroblast proliferation. The differentiation defect caused by ARID4B aberration could be counteracted by the Src inhibitor PP2 or by KIT knockdown. In summary, we identify ARID4B as a master regulator in the KIT-Src pathway, thus providing a fundamental insight in hematopoiesis and stem cell regulation.

overall_design: K562 cells were used for ChIP, library preparation, sequencing, and initial data analysis. ChIP assays were performed using the anti-ARID4B antibody. Input DNA was used for control.

first: In

middle: C

last: Young

first: Sung

middle: T

last: Chuang

first: Ray

last: Wu

first: Mei

middle: Y


title: Inhibiting the KIT-Src pathway to ensure differentiation of hematopoietic progenitor requires ARID4B [RNA-seq]

overall_design: mRNA profiles of control and ARID4B knockout K562 cells were generated by RNA sequencing.


title: Control of cellular translation by endogenous RNA G-quadruplex structures

first: Sergio

last: Martínez Cuesta

address: 1 Francis Crick Avenue

department: Data Sciences and Quantitative Biology, Discovery Sciences

country: United Kingdom

institute: AstraZeneca

summary: Four-stranded G-quadruplex (G4) structures form guanine-rich tracts, but their role in RNA biology remains poorly defined. Herein, we first delineate the presence of endogenous RNA G4s in the human cellular transcriptome by proxy of their binding to interacting proteins, DHX36, GRSF1 and DDX3X. We then demonstrate that a sub-population of these RNA G4s are reliably detected as folded structures in cross-linked cellular lysates using the G4 structure-specific antibody BG4. The 5' UTRs of protein-coding mRNAs show significant enrichment in such folded RNA G4s, particularly within mRNA for ribosomal proteins. As G4s in ribosomal mRNA are evolutionarily conserved in higher vertebrates this points to a common mode for translational co-regulation mediated by RNA G4 structures. Supporting this we find that G4-stabilising small molecules inhibit the translation of ribosomal protein mRNA and significantly down-regulate cellular translation.

overall_design:
DHX36 and GRSF1 iCLIP in combination with BG4 crosslinked RIP for mapping cellular RNA G4s. Polysome profiling experiments to detect alterations in translation.
RNA-seq experiments in HEK293FT cells expressing the tagged proteins DHX36 WT and GRSF1

first: Dhaval

last: Varshney

last: Martinez Cuesta

first: Barbara

last: Herdy

first: Ummi

last: Abdullah

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: H3K27 tri-methylation signature in CML CD34+ cells

status: Public on Nov 08 2021

city: Milwaukee

first: Michael

last: Deininger

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Versiti Blood Research Institute

summary: This study compares the epigenetic signatures of CD34+ cells from chronic phase chronic myeloid leukemia (CML) samples and blast phase CML samples v.s. normal CD34+ cells from cord blood and adult bone marrow samples. H3K27me3 genomic loci were detected by ChIP-seq.

overall_design: 3 CD34+ cell samples from 3 chronic phase CML patients and 2 CD34+ cell samples from 2 blast phase CML patients were compared to normal controls (3 CD34+ cell samples from 3 cord blood donors and 2 CD34+ cell samples from 2 adult bone marrow donors).

first: Helong

last: Zhao

first: Anthony

last: Pomicter

first: Anna

last: Eiring

first: Anca

last: Franzini

first: Jonathan

last: Ahmann

first: Jae-Yeon

last: Hwang

last: Senina

first: Bret

last: Helton

first: Siddharth

last: Iyer

first: Dongqing

last: Yan

first: Jamshid

last: Khorashad

first: Matthew

last: Zabriskie

first: Anupriya

last: Agarwal

first: Hannah

last: Redwine

first: Amber

last: Bowler

first: Phillip

last: Clair

first: Shannon

last: McWeeney

first: Brian

last: Druker

first: Jeffrey

last: Tyner

first: Derek

last: Stirewalt

first: Vivian

middle: G

last: Oehler

first: Sooryanarayana

last: Varambally

first: Kristofer

last: Berrett

first: Jeffery

last: Vahrenkamp

first: Jason

last: Gertz

first: Katherine

last: Varley

first: Jerald

middle: P

last: Radich


title: EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma

last: Abraham

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

overall_design: Refer to individual Series


title: Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide phosphodiesterase (CNPase) in Salmonella Typhimurium 14028s (Salmonella) II.

first: Emily

last: Weinert

summary: The impact of 2',3'-cyclic nucleotide phosphodiesterase (CNPase) on global gene expression in Salmonella was investigated by heterologous expression of mammalian CNPase in a strain containing a deletion of the 'rna' gene. 'rna' encodes an endoribonuclease capable of hydrolyzing RNA into 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) such that deletion of 'rna' drastically reduces 2',3'-cNMPs presence to undetectable levels. Expression of CNPase in this strain allowed any effects of CNPase unrelated to 2',3'-cNMPs to be observed.

overall_design: Global transcript levels in a 'rna' deletion strain of Salmonella expressing CNPase were compared to levels in control cells with the same deletion expressing a catalytically inactive variant of CNPase in order to identify cellular processes modulated by CNPase that are unrelated to  2',3'-cyclic nucleotide monophosphates.

first: Benjamin

last: Fontaine

first: Jennifer

last: Kurasz

first: Yashasvika

last: Duggal

first: Shikha

middle: S

last: Chauhan

first: Nick

last: Marotta

first: Anna

last: Karls


title: Ferroptosis Induction in Multiple Myeloma Cells Triggers an Epigenomic Stress Response Associated with DNA Repair and Cellular Senescence

city: Wilrijk

first: Emilie

last: Logie

state: Antwerp

address: Universiteitsplein 1

department: Biomedical Sciences

institute: University of Antwerp

summary: Acquired and primary therapy resistance remain a major hurdle in clinical treatment of multiple myeloma (MM). Despite the availability of broad spectrum anti-cancer drugs, most MM patients eventually relapse and become refractory to current treatments. Therefore, we explored whether therapy-resistant MM cells are sensitive to ferroptosis induction, an iron-catalyzed mode of cell death associated with increased lipid peroxidation. In this study, we exposed glucocorticoid-resistant MM1R and glucocorticoid-sensitive MM1S cells to ferroptosis inducers RSL3 and evaluated their transcriptional changes via RNA sequencing. Compared to untreated controls, ferroptotic RSL3-treated cells displayed a significant upregulation of genes involved in inflammation, kinase signaling, cellular stress, and cell death pathways. Pre-treatment with ferroptosis inhibitor Fer-1 partly reverted these RSL3-induced transcriptional changes and revealed that especially genes involved in metal binding, nuclear receptor signaling, chromatin remodeling, and gene transcription regulation are pivotal for ferroptosis induction. Overall, these findings suggest that ferroptosis effectively targets MM1 cells and that RSL3-mediated ferroptosis triggers similar oxidative stress and cell death pathways in both MM1R and MM1S cells, irrespective of their glucocorticoid-sensitivity status.

overall_design: RNA sequencing of Glucocorticoid-sensitive (MM1S) and - resistant (MM1R) multiple myeloma cell lines treated with ferroptosis inducer RSL3, with or without pre-treatment with ferroptosis inhibitor ferrostatin-1 (Fer-1).

first: Bart

last: Cuypers

first: Kris

last: Laukens

first: Wim

last: Berghe


title: Developmental regulation by miR-29 specifies age-related differences in the CD8+ T cell immune response

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University


title: Developmental regulation by miR-29 specifies age-related differences in the CD8+ T cell immune response (Mouse scRNA-Seq)

summary: Neonates are highly susceptible to repeat infection and respond poorly to vaccination; these attributes derive from intrinsic differences between neonatal and adult naïve CD8+ T cells. In contrast to adult cells, naïve neonatal cells exhibit a greatly limited ability to differentiate into memory cells, a fundamental property of their adult counterparts.  Here, we describe the role of the miR-29 microRNA in naïve T cells, focusing on age-related differences in miR-29 expression and the consequences of these differences in adult and neonatal cells, from mice and humans. In adults, high expression of miR-29 licenses naïve cells towards eventual memory cell fates; whereas neonatal naïve cells, which lack high expression of miR-29, are predisposed towards effector cell fates in response to an infection. Multiple lines of evidence support this model, including analysis of a mouse model deficient in miR-29, which we examine with adoptive transfer experiments to define the functional consequences of reduction of miR-29, together with genomic assays to define the regulatory impact of miR-29. Adult miR 29 deficient naïve CD8+ T cells cell are primed for activation and therefore secrete elevated levels of cytolytic molecules, and express transcription factors at levels associated with effector cell differentiation; moreover, these cells exhibit an altered CD8+ T cell memory repertoire, akin to that of neonatal CD8+ T cells. Importantly, we use a method that exploits extracellular vesicles as a delivery vehicle with which to modulate levels of miR-29 in neonatal and adult naïve T cells, examining both human and mouse cells. For example, increasing miR 29 expression in mouse naïve neonatal CD8+ T cells significantly improved the memory response during infection, concomitant with alterations to the chromatin landscape characteristic of cells primed for memory differentiation. Delivery of miR-29 antagomirs to human adult naïve CD8+ T cells was sufficient to induce the adult cells to adopt phenotypes and gene expression signatures normally found in cells present in newborns.  This study establishes miR-29 as a key conserved regulator in naïve CD8+ T cells, and by adjusting levels of miR-29, has the potential to underlie therapeutic strategies for controlling the balance of effector versus memory fates in human T cells.

overall_design: single cell mRNA profiles of adult CD8+ T cells, neonatal CD8+ T cells and adult CD8+ T cells with miR-29 gene knocked out.

first: Kristel

last: Yee Mon

first: Ciarán

last: Daly

first: Hongya

last: Zhu

first: Luyen

last: Vu

first: Norah

last: Smith

first: Ravi

last: Patel

first: Minh

last: Le

first: David

last: Topham

first: Kristin

last: Scheible

first: Kondwani

last: Jambo

first: Brian

last: Rudd


title: Exploration of human lung resident immunity and response to respiratory viral infection in a humanized mouse model

city: Changchun

first: Cong

last: Fu

state: Jilin

address: NO.17  Xinmin Street

institute: The First Hospital of Jilin University

summary: There is an urgent need for humanized mouse models of viral respiratory diseases to study immunopathogenesis and therapeutic interventions. Although mice with a functional human immune system (HIS) permit analysis in real time of human immune responses in vivo, evolutionary divergences preclude their usefulness for studies of respiratory viruses that do not infect mouse lungs. Here, we sought to use HIS mice with human lung tissue xenografts (referred to as HISL mice) to address this issue. The grafted human lung tissue was found survived for over 30 weeks, maintained histologically normal structure, and populated with human tissue-resident immune cells, including CD11c+ DCs and CD4+ and CD8+ tissue-resident memory T cells (TRMs). HISL mice showed a marked expansion of TRMs and generation of viral antigen-specific T cells in the human lung xenografts, and production of antiviral IgM and class-switched IgG antibodies upon infection of the human lung xenograft by H1N1 influenza viruses. RNA-seq analysis on H1N1-infected and control human lung xenografts identified a total of 5089 differentially expressed genes (DEGs) with enrichments for genes involved in respiratory tract and lung diseases, viral infections and associated immune responses. Furthermore, prophylactic viral exposures resulted in protection against subsequent lethal challenge by intranasal viral inoculation, leading to reduced disease severity and mortality. This study supports the usefulness of this preclinical model in exploring the immunopathology and therapies of respiratory viral diseases.

overall_design: human lung tissue xenografts mRNA profiles of H1N1 infected HISL mouse and PBS injected HISL mouse.

first: Yixin

last: Wang

first: Lei

first: Xue

first: Siyao

last: Zuo

first: Chang

last: Shu

first: Jin

last: He

first: Yong-Guang

last: Yang

first: Zheng

last: Hu

first: Shucheng

last: Hua


title: Developmental regulation by miR-29 specifies age-related differences in the CD8+ T cell immune response (Mouse ATAC-Seq)

first: Andrew

last: Grimson

overall_design: Profiling chromatin landscape of true naïve(TN) and virtual memory(VM) adult CD8+ T cells, neonatal CD8+ T cells and neonatal CD8+ T cells with miR-29 levels induced.

first: Kristel

last: Yee Mon

first: Ciarán

last: Daly

first: Hongya

last: Zhu

first: Luyen

first: Norah


title: Developmental regulation by miR-29 specifies age-related differences in the CD8+ T cell immune response (Mouse RNA-Seq)

overall_design: mRNA profiles of true naïve(TN) and virtual memory(VM) adult CD8+ T cells, neonatal CD8+ T cells and neonatal CD8+ T cells with miR-29 levels induced.

last: Vu

last: Smith

first: Ravi

last: Patel

first: Minh

last: Le

first: David

first: Kristin

first: Kondwani

first: Brian


title: Developmental regulation by miR-29 specifies age-related differences in the CD8+ T cell immune response (Human RNA-Seq)

overall_design: mRNA profiles of adult CD8+ T cells, neonatal CD8+ T cells, adult CD8+ T cells with miR-29 levels reduced and neonatal CD8+ T cells with miR-29 levels induced.

last: Topham

last: Scheible

last: Jambo

last: Rudd


title: TNF plays a crucial role in inflammation by signaling via T cell TNFR2

status: Public on Nov 06 2021

city: Bethesda

first: Jonathan

last: Ashwell

state: MD

address: Room 3002, Bldg. 37, 9000 Rockville Pike

department: Laboratory of Immune Cell Development

institute: NIH


title: Human Reproduction is Regulated by Retrotransposons derived from Ancient Hominidae-Specific Viral Infections

status: Public on Nov 07 2021

first: Xinyu

last: Xiang

overall_design: Refer to individual Series.


title: TNF plays a crucial role in inflammation by signaling via T cell TNFR2 [bulkRNA-seq]

summary: TNF regulates the inflammatory cytokine secretion from CD4+ T cells in vitro.

overall_design: In vitro experiment (Bulk seq): Naïve CD4+ T cells from WT or Tnfr2-/- mice were isolated from spleen and stimulated with anti-CD3/CD28 for 3 days in the presence of the different combinations of cytokines (WT: TNF+TGF-β, Tnfr2-/-: TNF+TGF-β; WT: IL-6+TGF-β) followed by bulk RNA sequence. Each experimental condition was done triplicates and analyzed.

first: M

last: Alam

first: Nathan

last: Wong

first: Yu

last: Fan

first: J


title: TNF plays a crucial role in inflammation by signaling via T cell TNFR2 [scRNA-seq]

summary: Identification of differentially expressed genes between WT and Tnfr2-/- CD4+ T cells in Experimental autoimmune encephalomyelitis (EAE).

overall_design: Identification of differentially expressed genes between WT and Tnfr2-/- CD4+ T cells infiltrated in the spinal cord after immunization with MOG(35-55). Cells were asolated at day 15 of the immunization.


title: Interactions between Verticillium longisporum and plant terpenes

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

institute: Swedish University of Agricultural Sciences

summary: Plant roots secrete secondary metabolites to sense the enviroment around them. Among them, terpenes play a prominent role. Terpenes can have either fungistatic or fungicide action. However, their exact role in plant-host interactions is not fully understood. Verticillium longisporum is a soilborne pathogen causing disease in Brasicacae plants. In this project we investigated the transcriptomic changes of this species upon exposure to the β-pinene monoterpene in different time points 0hpi, 8hpi, 24hpi and 24hpi.

overall_design: 12 Verticillium longisporum RNA samples upon exposure to β-pinene monoterpene in different time points 0, 8,24 and 48hpi

first: Georgios

last: Tzelepis

last: Hodén

first: Mukesh

last: Dubey

first: Raimondas

last: Mozuraitis

first: Vahidehalsadat

last: Rafieebanadaki

first: Alessandra

last: Ruffino

first: Anna

last: Törnkvist


title: Androgens increase excitatory neurogenic potential in human brain organoids

city: Cambridge

first: Madeline

last: Lancaster

state: Cambridgeshire

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

summary: The biological basis of male-female brain differences has been difficult to elucidate in humans. The most striking morphological difference is size, with males having on average a larger brain than females; yet a mechanistic understanding of how this difference arises remains to be elucidated. Here, we use brain organoids to demonstrate that while sex chromosomal complement has no observable effect on neurogenesis, sex steroids, namely androgens, lead to increased proliferation of cortical progenitors and an increased neurogenic pool. Transcriptomic analysis and functional studies demonstrate downstream effects on HDAC activity and mTOR pathway. Finally, we show that androgens specifically increase neurogenic output of excitatory neuronal progenitors, while inhibitory neuronal progenitors are not increased. These findings uncover a hitherto unknown role for androgens in regulating excitatory neuron number and represent a first step towards understanding the origin of human sex-related brain differences.

overall_design: Bulk and single-cell RNA sequencing was performed on organoids treated with sex steroid hormones and subjected to differential gene expression analysis.

first: Iva

last: Kelava

first: Alex

last: Kalinka


title: SF3B1 mutant-induced missplicing of MAP3K7 causes anemia in myelodysplastic syndromes

city: NewYork

first: Zhaoqi

last: Liu

state: New York

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

institute: Columbia university

summary: SF3B1 is the most frequently mutated RNA splicing factor in cancer, including in ~25% of myelodysplastic syndromes (MDS) patients. SF3B1-mutated MDS, which is strongly associated with ringed sideroblast morphology, is characterized by ineffective erythropoiesis, leading to severe, often fatal, anemia. However, functional evidence linking SF3B1 mutations to the anemia described in MDS patients harboring this genetic aberration is weak, and the underlying mechanism is completely unknown. Using isogenic SF3B1 wild-type and mutant cell lines, normal human CD34 cells and MDS patient cells, we define a previously unrecognized role of the kinase MAP3K7, encoded by a known mutant SF3B1-targeted transcript, in controlling proper terminal erythroid differentiation, and show how MAP3K7 missplicing leads to the anemia characteristic of SF3B1-mutated MDS, although not to ringed sideroblast formation. We found that p38 MAPK is deactivated in SF3B1 mutant isogenic and patient cells and that MAP3K7 is an upstream positive effector of p38 MAPK. We demonstrate that disruption of this MAP3K7-p38 MAPK pathway leads to premature downregulation of GATA1, a master regulator of erythroid differentiation, and that this is sufficient to trigger accelerated differentiation, erythroid hyperplasia and ultimately apoptosis. Our findings thus define the mechanism leading to the severe anemia found in MDS patients harboring SF3B1 mutations.

overall_design: 4 human cell line samples: K562_SF3B1 K700E and wild-type knock-in controls

first: Yen

middle: K

last: Lieu


title: scRNAseq demonstrates distinct transcriptional response to IL-1B in mIDH2 cells as compared to wtIDH cells

status: Public on Nov 05 2021

city: Nashville

first: Paul

middle: Brent

last: Ferrell

state: TN

address: 777 Preston Research Bldg., 2220 Pierce Ave.

department: Medicine

institute: Vanderbilt University Medical Center

summary: We report the results of scRNA sequencing of parental and  mIDH2R140Q TF-1 cell lines following exposure to PBS (control) and IL-1B. We obtained 1 million cells of each cell line for each condition and incubated them with either PBS or IL-1B. Following treatment, cells were processed using previously described inDrop protocols (Wolock et al., 2019 Cell Reports). Samples were split into 3,000 single-cell transcriptomes and one library per sample was prepared and sequenced on NextSeq 500. Data was prepared for analysis as described in our methods and gene expression was normalized and quantified. Gene set enrichment, differential gene expression and UMAP visualization was performe dusing SEurat 3.0. Ultimately, we compared the cellular response of parental and mIDH2 cells to IL-1B and our results indicate that mIDH2 cells have augmented expression of NF-κB target transcripts .  This component of our study demonstrates a dynamic response of  both cell lines to IL-1B with an exaggerated response seen in mIDH2 cells.

overall_design: Examination of impact of mIDH2R140Q mutation on IL-1B responsiveness in TF-1 cell lines

first: Kathryn

middle: I

last: Sunthankar

middle: B


title: Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes

city: San Francisco

first: Kenneth

last: Lim

state: CA

department: Psychiatry

institute: UCSF

summary: Deleterious genetic variants in POGZ, which encodes the chromatin regulator Pogo Transposable Element with ZNF Domain protein, are strongly associated with autism spectrum disorder (ASD). Although it is a high confidence ASD risk gene, the neurodevelopmental functions of POGZ remain unclear. Here we reveal the genomic binding of POGZ in the developing forebrain at euchromatic loci and gene regulatory elements (REs). We profile chromatin accessibility and gene expression in Pogz-/- mice and show that POGZ promotes the active chromatin state and transcription of clustered synaptic genes. We further demonstrate that POGZ forms a nuclear complex and co-occupies loci with ADNP, another high-confidence ASD risk gene, and provide evidence that POGZ regulates other neurodevelopmental disorder risk genes as well. Our results reveal a neurodevelopmental function of an ASD risk gene and identify molecular targets that may elucidate its function in ASD.

overall_design: ATAC-seq, and ChIP-seq, and RNA-seq in POGZ knockout and wildtype telencephalic tissues at E13.5.  CUT&RUN for POGZ, ADNP, and HP1gamma in E13.5 wildtype mouse telencephalic tissue.

first: Eirene

last: Markenscoff-Papadimitriou

first: Fadya

last: Binyameen

first: Sean

last: Whalen

first: James

last: Price

first: Athena

middle: R

last: Ypsilanti

first: Rinaldo

last: Catta-Preta

first: Emily

last: Pai

first: Xin

last: Mu

first: Duan

last: Xu

first: Katherine

last: Pollard

last: Nord

first: Matthew

last: State

first: John

last: Rubenstein


title: Krencik NPCs, iAstros, Chemogenetic iAstros, OptoNeurons

city: Houston

first: Robert

last: Krencik

state: TX

address: 6670 Bertner Ave.

department: Neurosurgery

institute: Houston Methodist

summary: RNAseq for comparison of human pluripotent stem cell-derived neural subtypes containing genetic-encoded tools.

overall_design: The purpose of this study was to validate cellular identify of neural subtypes and to assess the consequence of Gq-based chemogenetic activation of astrocytes over time. All cells are from the same parental human pluripotent stem cell line (WT-C11) and all samples were extracted from cell cultured as a monolayer on matrigel in the same basal media formulation.

first: Caroline

last: Cvetkovic


title: Selection of cashmere fineness functional genes by translatomics

city: Shenyang

first: yu

last: zhang

address: Dongling Street

institute: Shenyang Agricultural University

summary: Cashmere fineness is an important index to evaluate cashmere quality. Liaoning Cashmere Goat (LCG) has a large cashmere production and long cashmere fiber. But the fineness is not enough,improving the fineness of cashmere is an important problem.Therefore, it is important to find genes involved in cashmere fineness that can be used in future in future endeavors aiming to improve this phenotype. With the continuous advancement of research, the regulation of cashmere fineness has made new development through high-throughput sequencing and genome-wide association analysis. It has been found that translatomics can identify genes associated with phenotypic traits. Through a translatomic analysis, the skin tissue of LCG sample groups differing in cashmere fineness was sequenced by Ribo-seq. With this data, we identified 529 differentially expressed genes between the sample groups among the 27197 expressed genes(expressed,not co-expressed). From these, 343 genes were up-regulated in the fine LCG group in relation to the coarse LCG group and 186 down-regulated in the same relationship.Through GO enrichment analysis and KEGG enrichment analysis of differential genes, the biological functions and pathways of differential genes can be found. In the GO enrichment analysis, 491 genes were significantly enriched, and the functional region was mainly in the extracellular region. In the KEGG enrichment analysis, the enrichment of human papillomavirus infection pathway was the most. We found that COL6A5 gene may affect cashmere fineness. The characteristics and expression analysis of COL6A5 gene may play an important role in the study of LCG cashmere fineness.

overall_design: The genes affecting cashmere fineness were screened by translatomics in three coarse and three fine Liaoning cashmere goats.

first: zhang

last: yu