title: Transcriptomic profile of circulating monocyte subsets in active versus latent tuberculosis

city: La Jolla

first: Julie

last: Burel

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

summary: Tuberculosis (TB) is responsible for the majority of mortality and morbidity associated with infectious diseases worldwide. The characterization of exact molecular components of immune response associated with protection against TB may help design more effective therapeutic interventions. In this study, we aimed to characterize the immune signature of monocyte subsets associated with active versus latent infection with Mycobacterium tuberculosis. Transcriptomic profiling using RNA sequencing was performed on classical (CD14+CD16-), intermediate (CD14+CD16+) and non-classical (CD14-CD16+) monocytes isolated from individuals with active TB (at diagnosis and 2 months post treatment), latent TB, as well as from TB negative healthy controls. Overall, we found specific gene signatures for each monocyte subset that could successfully discriminate between individuals with active TB at diagnosis, treated active TB, latent TB and healthy controls.

overall_design:
RNA-sequencing of sorted classical (CD14+CD16-), intermediate (CD14+CD16+) and non-classical (CD14-CD16+) monocytes from cryopreserved PBMC of individuals with active tuberculosis collected a diagnosis (and for some individuals an additional sample collected at 2 months post treatment), individuals with latent tuberculosis infection (IGRA+) and tuberculosis negative healthy controls (IGRA-).

***RAW DATA not provided for the following Samples due to patient privacy concerns***
GSM5611833-GSM5611903, GSM5611936-GSM5612008, GSM5612039-GSM5612093

first: Gregory

last: Seumois

first: Alessandro

last: Sette

first: Bjoern

last: Peters

first: Pandurangan

last: Vijayanand


title: Transcriptomic profile of single-cell sorted CD14+ monocytes from 6 PBMC samples of individuals with active tuberculosis

status: Public on Jan 02 2023

city: San Diego

first: Ashu

last: Sethi

state: CA

department: Health Sciences

country: USA

institute: La Jolla Institute for Immunology

type: Expression profiling by high throughput sequencing

summary: Previous studies suggest that monocytes are an important contributor to tuberculosis (TB)-specific immune signatures in blood. Here we carried out  single-cell profiling of classical CD14+CD16- and intermediate CD14+CD16+ monocytes  in paired blood samples of active TB (ATB) patients at diagnosis and end-treatment. At diagnosis, ATB patients displayed upregulation of interferon signaling genes that significantly overlapped with previously reported blood TB signatures in both CD14+ subsets. In ATB diagnosis, we identified additional transcriptomic and functional changes in intermediate CD14+CD16+ monocytes, such as the upregulation of inflammatory and MHC-II genes, and increased capacity to activate T cells, reflecting overall increased activation in this population. Single-cell transcriptomics revealed that distinct subsets of intermediate CD14+CD16+ monocytes were responsible for each gene signature, indicating significant functional heterogeneity within this population. Finally, we observed that transcriptomic changes in CD14+ monocytes were transient, as they were no longer observed in the same ATB patients mid-treatment, suggesting they are associated with disease resolution.

overall_design: Single-cell RNA sequencing of sorted CD14+ monocytes from 6 PBMC samples of individuals with active tuberculosis (4 samples at diagnosis, 2 paired samples at end of treatment, 6 months after diagnosis). Each sample was stained with  a distinct Total-seq antibody prior sorting for hashtag demultiplexing post-sequencing.


title: Multi-modal analysis of human Plasma-cells

city: Nijmegen

first: Jessie

middle: van

last: Buggenum

address: Heyendaalseweg 135

country: Netherlands

institute: Radboud University

summary: Plasma cells are key components of humoral immunity by secreting antibodies and providing protection against pathogens. These cells can be of IgM, IgA, or IgG subclass and migrate to class-specific niches. Localization and rareness of plasma cells make it challenge to define subclass-specific molecular hallmarks. Here, we describe how in-vitro differentiation of peripheral B-cells results in antibody-secreting plasma cells. Using a single-cell multi-modal sequencing approach (RAID) we find subclass-specific hallmark transcriptional profiles, surface protein expression and signaling pathway activation.

overall_design: Isolated B-cells from three (anonymous healthy) donors were subjected to the differentiation protcol. Final samples was split into two: one for live immunostaining and a second for fixation and intracellular immunostaining.

middle: A

last: van Buggenum


title: Identification of a forkhead box protein transcriptional network induced in human neutrophils in response to inflammatory stimuli

city: Montreal

first: Aiten

last: Ismailova

state: Quebec

address: 3655 Promenade Sir William Osler

country: Canada

institute: McGill University

summary: We performed the first RNAseq analysis of human primary neutrophils exposed to lipopolysaccharide which revealed a robustly enhanced transcriptional network driven by forkhead box (FOX) transcription  factors.

overall_design: Comparative gene expression profiling anaysis of RNAseq data for primary human neutrophils treated with vehicle or 1µg/ml LPS for 6 hours. Differential analysis was conducted using edgeR.

first: Reyhaneh

last: Salehi-Tabar

first: Vassil

last: Dimitrov

first: Babak

last: Memari

first: Camille

last: Barbier

first: John

middle: H

last: White


title: Wnt inhibitors reduce the unfolded protein response and enhance bortezomib-induced cell death in multiple myeloma

status: Public on Jan 01 2023

city: Utrecht

first: Victor

last: Peperzak

state: Utrecht

address: Heidelberglaan 100

department: Center for Translational Immunology

institute: UMC Utrecht

summary: Dysregulation of the Wnt pathway is involved in pathogenesis of many types of carcinomas and associated with certain hematological cancers, including multiple myeloma (MM). Several studies reported that MM plasma cells carry a functional Wnt/β-catenin signaling pathway that promotes cell survival. Despite new and successful treatment options, MM remains incurable due to clinical, genetic and transcriptomic heterogeneity, which ultimately results in therapy resistance and relapse. We examined the therapeutic potential of targeting the Wnt pathway in patient-derived MM cells. Our results demonstrate that inhibition of tankyrase (TNKSi) and inhibition of porcupine (PORCi), two established methods to block the Wnt pathway in other cell types and malignancies, promotes cell death of primary MM cells. Single-cell RNA sequencing showed that inhibition of Wnt signaling is likely effectuated via downregulation of genes involved in the unfolded protein response (UPR). Combining TNKSi and PORCi with bortezomib resulted in a potent killing of primary MM cells, demonstrating that inhibitors of Wnt signaling might be considered as therapeutic targets in future anti-myeloma combinatorial strategies.

overall_design: Transcriptome analysis by single-cell RNA sequencing of viable CD38+CD138+ primary MM cells of samples MM09-MM13 after 72 hours of exposure to a combination of 20 μM tankyrase inhibitor (TNKSi) XAV939 and 5 μM porcupine inhibitor C59, or untreated control cells, in the presence of IL-6 and APRIL.

first: Ingrid

last: Spaan

first: Niels

last: van Nieuwenhuijzen


title: Dendritic cells direct circadian anti-tumor immune responses

status: Public on Dec 31 2022

city: Geneva

first: Chen

last: Wang

address: 1, rue Michel Servet

country: Switzerland

institute: University of Geneva

summary: To evaluate the rhythmicity of DCs after tumor inoculation

overall_design: We perform bulk sequencing of CD11C+ MHCII high cells in dLN

first: Christoph

last: Scheiermann


title: Regulation of T cell exhaustion and PD-1 targeted immunotherapy by mTOR during chronic viral infection

city: Cincinnati

first: Koichi

last: Araki

state: Ohio

address: 240 Albert Sabin Way, Room S8.544

department: Division of Infectious Diseases

institute: Cincinnati Children's Hospital Medical Center

summary: RNA-Sequence data of stem-like and TIM3+ differentiated CD8 T cells generated in rapamycin treated mice

overall_design: Gene expression profilng by high throughput sequencing

first: Satomi

last: Ando


title: PFKFB3 overexpression in monocytes of patients with colon but not rectal cancer programs pro-tumor macrophages and is indicative for higher risk of tumor relapse [GeoMx]

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

address: Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia

country: Russia

institute: Tomsk State University

summary: Circulating monocytes are main source for tumor-associated macrophages (TAMs) that control tumor growth, angiogenesis, metastasis and therapy resistance. We raised the questions how monocyte programming is affected by growing tumors localized in colon and rectal sections, and how treatment onsets affect monocyte programming in the circulation. Patients with rectal cancer and colon cancer were enrolled in the study. Spatial transcriptomic analysis was applied using GeoMX DSP-NGS. The key transcriptional difference between monocytes of patients with colon and rectal cancer was increased expression of PFKFB3, activator of glycolysis that is currently considered as therapy target for major solid cancers. PFKFB3-expressing monocyte-derived macrophages massively infiltrated tumor in colon. Nanostring technology identified correlation of PFKFB3 with amount and tumor-promoting properties of TAMs in colon but not in rectal cancer.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: The study included patients with colorectal adenocarcinoma with morphologically verified diagnosis, treated in the Department of abdominal oncology, Cancer Research Institute of Tomsk National Research Medical Center (Tomsk, Russia). The study was carried out according to Declaration of Helsinki (from 1964, revised in 1975 and 1983) and was approved by the local committee of Medical Ethics of Tomsk Cancer Research Institute (15 May 2019, the approval No. 6/1); all patients signed informed consent for the study. FFPE samples (5 μm) were taken from 5 untreated patients with colon cancer and 5 NAC-treated patients with rectal cancer to perform spatially resolved RNA profiling via NanoString GeoMx digital spatial profiling (DSP). We used the Cancer Transcriptome Atlas (CTA) panel designed for comprehensive profiling of tumor biology, the tumor microenvironment, and the immune response

first: Marina

last: Patysheva

first: Pavel

last: Iamshchikov

first: Elena

last: Kazakova

first: Anna

first: Militsa

last: Rakina

first: Evgeniya

last: Grigoryeva

last: Tarasova

first: Sergei

last: Afanasiev

first: Natalia

last: Bezgodova

first: Artem

last: KIselev

first: Alexey

last: Dobrodeev

first: Dmitriy

last: Kostromitskiy

first: Nadezhda

last: Cherdyntseva

first: Julia

last: Kzhyshkowska


title: LncRNA LIMp27 regulates the DNA damage response through p27 in p53-defective cancer cells

city: Callaghan

first: Ting

last: La

state: NSW

address: University Drive

country: Australia

institute: UON

summary: P53 inactivation occurs in about 50% human cancers, where p53-driven p21 activity is devoid and p27 becomes essential for the establishment of the G1/S checkpoint upon DNA damage. Here, we show that the E2F1-responsive lncRNA LIMp27 selectively represses p27 expression and contributes to proliferation, tumorigenicity, and treatment resistance in p53-defective colon adenocarcinoma (COAD) cells. LIMp27 competes with p27 mRNA for binding to cytoplasm-localized hnRNA0, which otherwise stabilizes p27 mRNA leading to cell cycle arrest at G0/G1 phase. In response to DNA-damage, LIMp27 is upregulated in both wild-type and p53-muant COAD cells, whereas cytoplasmic hnRNPA0 is only increased due to translocation from the nucleus in p53-mutant COAD cells. High LIMp27 expression is associated with poor survival of p53-mutant but not wide-type p53 COAD patients. These results uncover a lncRNA mechanism that promotes p53-defective cancer pathogenesis and suggest that LIMp27 may constitute a target for the treatment of such cancers.

overall_design: To dissect the mechanism through which LIMp27 promotes p53-mutant COAD cell proliferation, we compared the transcriptomes of WiDr cells with and without LIMp27 knockdown using two different siRNAs for 24 hours.

first: Xu

middle: D

last: Zhang

first: Lei

last: Jin


title: Expression Profiles of Long Non-Coding RNAs and Messenger RNAs in a Rat Model of Spinal Cord Injury

city: Nanchang

first: Jian

last: Cao

state: Jiangxi

address: 1 Minde Road, East Laker District, Nanchang, Jiangxi, China

department: orthopaedics

country: China

institute: The Second Affiliated Hospital of Nanchang University

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

summary: Spinal cord injury (SCI) is a serious disorder of the central nervous system with a high disability rate. Long non-coding RNAs (lncRNAs) are reported to mediate many biological processes. The aim of this study was to explore lncRNA and mRNA expression profiles and functional networks after SCI.We identified 5465 differentially expressed lncRNAs (DE lncRNAs) and 8366 differentially expressed mRNAs (DE mRNAs) in the SCI group compared with the sham group (fold change >2.0, P<0.05). Four genes were confirmed by real-time PCR which were consistent with the microarray data. GSEA analysis showed that most marked changes occurred in pathways related to immune inflammation and nerve cell function, including cytokine-cytokine receptor interaction (rno04060), TNF signaling pathway (rno04668), neuroactive ligand-receptor interaction (rno04080)，and GABAergic synapse (rno04727). Enrichment analysis identified 30 signaling pathways, including those associated with inflammation and the immune response. A total of 40 key lncRNAs were identified using the SVM-RFE algorithm. A key lncRNA-mRNAs co-expression network was generated for 230 951 lncRNA-mRNA pairs with half showing positive correlations. Several key DE lncRNAs were predicted to have “cis” or “trans”-regulated target genes. The transcription factors, Sp1, JUN, and SOX10, may regulate the interaction between XR_001837123.1 and ETS 1. In addition, five pairs of ceRNA regulatory sequences were identified.

overall_design: 6 male SD rats were randomly divided into two groups, including 3 in spinal cord injury group and 3 underwent the same laminectomy procedure without subsequent damage to the spinal cord. Rats were anesthetized at 3 days post-SCI, and the T10 spinal cord segments centered on and enclosing the injured site were collected. Microarray analysis was performed to investigate the lncRNA and mRNAs expression patterns in rat spinal cord three days after SCI.


title: Comprehensive profile and contrastive analysis of circular RNA in cervical squamous carcinoma and adenocarcinoma

city: Beijing

first: Hongxue

last: Luo

state: China

address: Department of Ob/Gyn, Peking University People's Hospital, Beijing, PR China

institute: Peking university people's hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
To contrastively analyze the expression pattern of circRNAs in cervical squamous carcinoma, adenocarcinoma and adenosquamous carcinoma variants.
CircRNAs expression in cervical squamous carcinoma, adenocarcinoma and adenosquamous carcinoma tissues together with the adjacent normal tissues were profiled by high-throughput RNA sequencing.

overall_design: Comparative circRNAs expression profiling analysis of RNA-seq data for three cervical cancer variants.


title: Caspase-10 affects PBC pathogenesis

city: Seoul

first: Yeongun

last: Lee

state: State...

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei university

summary: The loss of functional caspase-10 promotes inflammatory cell death in macrophages and a fibrotic response of hepatic stellate cells, which may affect the pathogenesis of PBC.

overall_design: To explore the role of caspase-10, we performed RNA-seq using samples from caspase-10 or caspase-8 KO U937 macrophages, upon immune stimulation such as that with lipopolysaccharide (LPS), TNF-α, or Z-VAD+cycloheximide+TNF-α (ZCT).

first: Minjeong

last: Cho

first: Sohee

last: Dho


title: Gene expression of colorectal cancer cells treated with Celastrol or compound 19-048

city: Shanghai

first: Hao

address: No.555 Zuchongzhi Road

department: Chemical Biology

institute: Shanghai Institute of Materia Medica

summary: As a terpenoids natural product isolated from the plant Thunder God Vine, Celastrol is widely studied for its pharmacological activities, including anti-tumor activities. However, the clinical application of Celastrol is strictly limited due to its severe side effects. Without identification and validation of the target protein of Celastrol, it is difficult to determine whether its anti-tumor activities and side effects are due to inhibition of the same protein. Using a new computational tool we have developed for target discovery, peroxiredoxin I (PRDX1) was identified as the ROS-manipulating target protein of Celastrol. High-resolution crystal structure revealed the unique binding mode of Celastrol with PRDX1, via covalent reaction to the catalytic Cys-173 residue of PRDX1. New derivative compound named 19-048 with improved potency against PRDX1 and selectivity towards PRDX2~PRDX6 were synthesized. Both Celastrol and compound 19-048 effectively suppressed the proliferation of colorectal cancer cells. While these anti-tumor efficacy was significantly diminished on xenograft nude mice bearing PRDX1 knock-down colorectal cancer cells. Several downstream genes of p53 were dramatically up-regulated in the presence of Celastrol and compound 19-048. Our findings reveal that the side effects of Celastrol could be reduced via structural modification, and PRDX1 inhibition is promising for the treatment of colorectal cancer.

overall_design: transcriptome RNA sequencing in colorectal cancer HCT116 and SW620 cells in the presence or absence of Celastrol and Compound 19-048

first: Hongfang

last: Zhao

first: Heng

last: Xu

first: Cheng


title: The impact of G9a-inhibitors in T-cell and Treg differentiation [ATAC-seq]

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

summary: As methyltransferase G9a has been implicated in immune cell differentiation we have assessed the role of G9a enzymatic inhibitors (UNC0642) in the differentiation of human naïve T-cells under different stimulation conditions.

overall_design: Examined average binding profiles representing open chromatin state at ATAC peaks associated human naïve T cells, regulatory T cells, T helper 17 cells and naïve T cells differentiated in the presence of of UNC0642 2uM concentration.

first: Guilherme

middle: P

last: Ramos

first: Michelle

middle: M

last: Gonzalez

first: Mary

middle: R

last: Sagstetter

first: Feda

last: Hamdan

first: Zhifu

last: Sun

first: Zhenqing

last: Ye

first: William

last: Faubion Jr


title: Fibroblast heterogeneity revealed by single cell sequencing in healthy and atherosclerotic arteries

city: Edinburgh

first: Ian

last: McCracken

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

summary: Specific markers and in-depth analysis of adventitial fibroblast heterogeneity are underexplored. Using single-cell RNA-sequencing of enriched fraction of adventitial mesenchymal cells, we defined and quantified novel markers in healthy murine adventitia. PHATE dimensionality reduction and subsequent clustering characterized heterogeneity, predicting three novel differentiation trajectories. Gene ontology (GO) analysis supported divergent functional profiles, related to vascular development, antigen presentation and collagen fibril organization. Vascular pathologies, including ageing and hypercholesterolemia, differentially affected trajectory presence in vivo. We validated increased presence of the trajectory with collagen gene ontology prior to plaque development, and its association with increased adventitial collagen accumulation, while trajectory presence diminished in advanced atherosclerosis. Fibroblast trajectory gene-sets were also observed in human advanced atherosclerosis, where aforementioned trajectory negatively correlated to detrimental plaque traits. We have therefore unveiled the basis for fibroblast heterogeneity in health and vascular pathologies, and our data suggest that trajectory regulation will be instrumental for trajectory-specific interventions.

overall_design: Characterisation of adventitial fibroblast heterogeneity from aorta of LDLR-ko mice on chow or high cholesterol diet using single cell RNA sequencing.

first: Kim

last: van Kuijk

first: Renée

last: Tillie

first: Sebastiaan

middle: J

last: Asselberghs

first: Ruud

middle: W

last: Schreur

first: Richard

middle: S

last: Taylor

first: Christoph

last: Kuppe

first: Han

first: Ross

last: Dobie

first: Prakesh

last: Ramachamdran

first: Marion

last: Gijbels

first: Lieve

last: Temmerman

first: Julien

last: Luyten

first: Heidi

last: Noels

first: Pieter

last: Goossens

first: John

last: Wilson-Kanamori

first: Leon

last: Schurgers

first: Phoebe

last: Kirkwood

first: Barend

middle: E

last: Mees

first: Erik

middle: L

last: Biessen

first: Neil

middle: C

last: Henderson

first: Rafael

last: Kramann

first: Andrew

last: Baker

first: Judith

last: Sluimer


title: Transcription profiling of ALK-rearranged cell lines resistent and sensitive to crizotinib

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: In this study we have analysed the transcription profile of ALK rearranged cell lines (COST, DEL, JB6, KARPAS, SR786, SUPM2, TS). The analysis was done on untreated cell lines and on the te same cell lines surviving to progressive increasing addition of crizotinib to the culture medium. Crizotinib concentration was progressively increased to reach a final concentration of 1 μM. The resulting pool of resistant cells (designated crizotinib-resistant (CR)) were maintained in RPMI with 10% FBS containing 0.5-1 μM crizotinib.

overall_design: Seven ALK rearranged cell lines, which became resistent to crizotinib, were compared at transcription level with the corresponding untreated cell lines.

first: Cristina

last: Mastini

first: Marco

last: Campisi

first: Enrico

last: Patrucco

first: Antonio

last: Ferreira

first: Carlotta

last: Costa

first: Chiara

last: Ambrogio

first: Giulia

last: Germena

first: Cinzia

last: Martinengo

last: Mura

first: Silvia

last: Peola

first: Maddalena

last: Arigoni

first: Martina

last: Olivero

first: Nina

last: Prokoph

first: Laurence

last: Brugieres

first: Birgit

last: Geoerger

first: Suzanne

last: Turner

first: Luca

last: Mologni

first: Rocco

last: Piazza

first: Carlo

last: Gambacorti-Passerini

first: Valeria

last: Chiono

first: Roger

last: Kamm

first: Emilio

last: Hirsch

first: Jon

last: Aster

first: Claudia

last: Voena

first: Roberto

last: Chiarle


title: The impact of G9a-inhibitors in T-cell and Treg differentiation

first: Asha

last: Nair

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

overall_design: Refer to individual Series


title: Lung response to multi-walled carbon nanotube exposure in rats.

city: Morgantown

first: Christina

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

summary: The projected increase in the production and use of nanomaterials is expected to result in a corresponding increase in human exposure, potentially resulting in significant morbidity and mortality. Currently, the lung toxicity of multi-walled carbon nanotubes (MWCNT), a prototype nanomaterial, was investigated in a rat model. The rats were exposed by whole-body inhalation to air (controls) or MWCNT (6 hours/day, 3 days) to result in cumulative doses of 180, 90, 45, 22.5, or 11.25 mg/m3. Lung toxicity and gene expression profiles were determined in the lungs of the control and MWCNT exposed rats one day following termination of the exposures. Moderate lung histological changes, indicative of toxicity, were detected in rats exposed to MWCNT at doses > 45 mg/m3. Changes in toxicity parameters including, lactate dehydrogenase (LDH) activity, oxidant production, cell counts of phagocytes, and cytokine levels were detected in the bronchoalveolar lavage of rats exposed to > 22.5 mg/m3 MWCNT, compared with the air controls. Lung gene expression profiling detected differences in transcript levels (fold change >1.5 and FDR p<0.05) of several genes in the rats exposed to >22.5 mg/m3 MWCNT, compared with the controls. The changes in lung toxicity and gene expression profiles exhibited a dose-response to the MWCNT administered in the rats.

overall_design: Approximately 3 months old male Fischer rats (Charles River Laboratories, Wilmington, MA) were used in this study, conducted in an AAALAC International approved animal facility (NIOSH, Morgantown, WV) following a protocol approved by the NIOSH Animal Care and Use Committee. Rats were housed in groups of 3 rats/cage. The rats (n=6) were exposed by whole-body inhalation to MWCNT (6 hours/day, 3 days) to result in cumulative doses of 180, 90, 45, 22.5, or 11.25 mg/m3. Separate groups of rats (n=6) exposed simultaneously to filtered air served as the controls. One day following termination of exposure to air or multi-walled carbon nanotubes, the rats were euthanized, and lung gene expression profiles determined by RNA sequencing.

first: Tina

last: Sager

first: Pius

last: Joseph


title: Single nucleus analysis of early onset dementia caused by DAP12 deficiency reveals a unique DAP12-independent microglia response at late stage of disease

city: Saint Louis

first: Yingyue

last: Zhou

state: Missouri

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,, Pathology and Immunology

department: Pathology and Immunology

institute: Washington University in St. Louis

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: TET2 guards against unchecked BATF3-induced CAR T cell expansion [RNA-seq]

status: Public on Dec 30 2022

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: Comparing transcriptional profiles of TET2 deficent hyper-proliferative CAR T cells and unedited CAR T cells

overall_design: Unedited and TET2-edited human CAR T cells were sorted from spleen (NSG mice) at day 90 and compared via RNA-seq

first: Nayan

last: Jain

first: Zeguo

last: Zhao

first: Michel

last: Sadelain


title: The impact of G9a-inhibitors in T-cell and Treg differentiation [RNA-Seq]

overall_design: Human naïve T cells obtained from healthy donors were differentiated in vitro in the presence of UNC0642 2uM concentration. Cells were treated with anti-CD3 and anti-CD28 stimulation in the presence or not of regulatory T cell cytokines (IL-2 and TGF-b).

first: Guilherme

last: Ramos

first: William

last: Faubion

first: Feda

last: Hamdam


title: TET2 guards against unchecked BATF3-induced CAR T cell expansion


title: TET2 guards against unchecked BATF3-induced CAR T cell expansion [ATAC-seq]

summary: Comparing genome accessibility profiles (ATACseq) of TET2 deficent hyper-proliferative CAR T cells and unedited CAR T cells

overall_design: Unedited and TET2-edited human CAR T cells were sorted from spleen (NSG mice) at day 90 and compared via ATAC-seq


title: Effect of iron depletion on gene expression of NCOA4-deficient and control HT22 hippocampal neuron cells

first: Moon-Suhn

last: Ryu

address: 50 Yonsei-ro, Seodaemun-gu

department: Food and Nutrition

institute: Yonsei University

summary:
To determine the physiological roles of NCOA4 and NCOA4-mediated ferritinophagy in hippocampal neurons, NCOA4 was depleted using siRNA and desferrioxamine (DFO; 100 µM, 24 h) was added to restrict iron availability.
Cells were treated for NCOA4 depletion, iron restriction, or both, and then the transcriptome profiles acquired from RNA-seq were compared with those of control (scramble siRNA-treated) cells.

overall_design: Comparative gene expression profiling of control HT22 cells and those deficient of NCOA4, iron, or both (n = 3 biological replicates per group)

first: Emily

middle: F

last: Bengson

first: Michael

middle: K

last: Georgieff


title: Molecular mechanisms of cannabinoid type II receptor agonists in a mouse model of psychological stress-induced cardiac injury revealed by whole transcriptomic analysis

first: cheng

last: qin

address: No.28 Fuxing Road

department: Department of Cardiology

institute: Chinese People's Liberation Army General Hospital and Medical School of Chinese People's Liberation Army

summary:
To investigate the mechanisms of chronic psychological stress-induced cardiac injury and the protective mechanisms of cannabinoid type II agonists in a model of psychological stress-induced cardiac injury
We constructed a mouse chronic psychological stress model based on a chronic unpredictable stress pattern. Mice were randomly divided into control, case (psychological stress group), and treatment groups (post-stress with the cannabinoid type II receptor agonist JWH133) to begin a 3-week psychological stress procedure, and cardiac tissue was subsequently removed for whole-transcriptome sequencing

overall_design: We removed heart tissue from the control, disease and treatment groups for whole transcriptome sequencing

first: Cheng

last: Qin

first: Feng

last: Cao


title: Longitudinal study of nasopharyngeal carcinoma tissue

city: Bangkok

first: Tavan

last: Janvilisri

address: 272 Rama 6 Road

department: Department of Biochemistry, Faculty of Science

country: Thailand

institute: Mahidol University

summary: To attempt to understand the NPC pathogenesis, the tissues of NPC at diagnosis, first relapse, and second relapse were included into this study.

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 15 NPC samples was used to acquire expression profiles.

first: Noppadol

last: Larbcharoensub

first: Warut

last: Tulalamba


title: Aqueous microRNA profiling in age-related macular degeneration and polypoidal choroidal vasculopathy by next-generation sequencing

status: Public on Dec 29 2022

city: Daegu

first: Areum

last: Jeong

address: 170 Hyunchungro, Nam-gu

department: Ophthalmology

institute: Yeungnam University College of Medicine

summary: To investigate the roles of microRNAs in the aqueous humor of patients with typical age-related macular degeneration and polypoidal choroidal vasculopathy using next-generation sequencing.

overall_design: Comparative microRNA profiling analysis of next-generation sequencing data for aqueous humor of patients with age-related macular degeneration and polypoidal choroidal vasculopathy, and eyes of normal controls.

first: Yeong

last: Choi

first: Soon

last: Cha

first: Min

last: Sagong


title: Effect of PMA/Ionomycin mediated T cell activation on Jurkat Tat gene expression

status: Public on Dec 28 2022

city: Vancouver

first: Ivan

last: Sadowski

state: British Columbia

address: 2350 Health Sciences Mall

institute: University of British Columbia

summary: To investigate gene regulation in response to T cell activation. We then performed gene expression profiling analysis using data obtained from RNA-seq of cell lines stimulated by PMA and Ionomycin.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Jurkat Tat cells either untreated or stimulated with PMA/Ionomycin.

first: Riley

last: Horvath


title: A single-cell atlas reveals heterogeneity of meningeal immunity in a mouse model of Methyl CpG binding protein 2 deficiency

first: Huiping

last: Li

address: Wanyuan Road 399

institute: Children's hospital of Fudan university

summary: Methyl CpG binding protein 2 (MeCP2) is a DNA methylation reader protein, and mutations in MeCP2 are the major cause of Rett syndrome (RTT). Increasing evidence has shown that dysregulated immunity and chronic subclinical inflammation are linked to MeCP2 deficiency and contribute to RTT development and deterioration. The meninges surrounding the central nervous system (CNS) contain a wide repertoire of immune cells that participate in immune surveillance of the CNS and influence brain functions. However, the characterization and role of meningeal immunity in CNSs with MeCP2 deficiency remain poorly understood. We applied a single-cell sequence to profile Mecp2 deficient meningeal immune cells from the dura mater, which has been reported to have the most numerous meningeal immune cells in homeostasis. The data showed that the meninges of Mecp2-null mice contained the same diverse immune cell populations as control mice and showed an up-regulation of immune-related processes. B cell populations were great larger in Mecp2-null mice than in control mice, and the expression of genes coding for immune globulins was remarkably higher. For T cells, Mecp2 deficient meninges were more enriched in cytotoxic CD8+ T cells than in the control. With increased interferon-γ transcription in T and natural killer cells, meningeal macrophages showed less suppression and were more active in Mecp2 deficiency mice. Our study provides novel insights into meningeal immunity, which is a less studied aspect of neuroimmune interactions in Mecp2 mutated diseases and offers an essential resource for comparative analyses and data exploration for a better understanding of the functional role of meningeal immunity in RTT.

overall_design: For Mecp2-null mice, we pooled dura from three individual mice, and the experiments were repeated 2 times. For WT mice, we pooled the dura from two and three individual mice in two repeated experiments.

first: Weijun

last: Feng

first: Xiu

last: Xu

first: Meixin

last: Hu


title: Effect of depletion of TFII-I or TRIM24 on Jurkat T cell activation.

summary:
To investigate the cooperative function TFII-I and TRIM24 in the regulation of T cell activation regulated genes, we established Jurkat Tat cells in which TFII-I was depleted by shRNA and TRIM24 was knocked out by CRISPR-Cas9.
We then performed gene expression profiling analysis using data obtained from RNA-seq of cell lines stimulated by PMA and Ionomycin.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C3H10T1/2 cells and its KD derivatives (shKDM4D, shNFIB, and shMLL1).


title: Arbitrary Ca2+-dependent expression data from mouse vascular endothelial cells

city: Nagoya

first: Koichi

last: Inoue

state: Aichi

address: 1 Kawasumi Mizuho-cho, Mizuho-ku

department: Department of Integrative Anatomy

country: Japan

institute: Nagoya City University School of Medical Sciences

summary:
Gene expression depending on artbtary Ca2+ elevation in mouse vascular endothelial cells
We used microarrays to detail the global programme of gene expression relatd  to putative Ca2+- increase.

overall_design: Mouse vascular endothelial cells, F2 (Toda et al, 1990, Cancer Res 50:5526-5530), were transfected with hBACCS2, an optogenetic tool which induces intracellular Ca2+ elevation using blue light (wave length: 470 nm), and blue light was applied on and off for 4 hours. Those cells were then collected,  followed by RNA extraction and hybridization on Affymetrix microarrays. A negative control cells did not have hBACCS2.

first: Takatoshi

last: Ueki

first: Tomoyasu

last: Yamanaka

first: Mitsuhito

last: Mase


title: Transcriptomic profiling of young and old rhesus macaques vaccinated with DNA/ALVAC+gp120

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

summary: The development of an effective vaccine to protect against HIV acquisition will be greatly bolstered by in-depth understanding of the innate and adaptive responses to the virus. We report here that the efficacy of DNA/ALVAC/gp120/alum vaccines, based on V2-specific antibodies mediating apoptosis of infected cells (V2-ADCC), is complemented by efferocytosis, a cyclic AMP (cAMP)-dependent antiphlogistic engulfment of apoptotic cells by CD14+ monocytes. Central to vaccine efficacy is the engagement of the CCR2+/CCL2 axis and tolerogenic dendritic cells producing IL-10 (DC-10). Durable epigenetic reprogramming in CD14+ cells of the cyclic AMP/CREB pathway and increased levels of miRNA-139-5p, a negative regulator of expression of the cAMP-specific phosphodiesterase PDE4D, in extracellular vesicles correlated with vaccine efficacy. These data posit that efferocytosis, through the prompt and effective removal of apoptotic infected cells, contributes to vaccine efficacy by decreasing inflammation and maintaining tissue homeostasis.

overall_design: Thirteen young and seventeen old rhesus macaques were vaccinated with a DNA/ALVAC+gp120 vaccine. Whole blood were collected 5 hours pre-vaccination and 24 hours after the last immunization (week 12). In total, the dataset comprises of 60 samples.

first: Massimiliano

last: Bissa

first: Genoveffa

last: Franchini

first: Rafick

last: Sekaly


title: Huwe1 supports B-cell development, B-cell-dependent immunity, somatic hypermutation and class switch recombination by regulating proliferation

status: Public on Dec 23 2022

city: Amsterdam

first: Heinz

last: Jacobs

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

summary: The development and differentiation of B cells is intimately linked to cell proliferation and the generation of diverse immunoglobulin gene (Ig) repertoires. The ubiquitin E3 ligase HUWE1 controls proliferation, DNA damage responses, and DNA repair, including the base excision repair (BER) pathway. These processes are of crucial importance for B-cell development in the bone marrow, and the germinal center (GC) response, which results in the clonal expansion and differentiation of B cells expressing high affinity immunoglobulins. Here, we re-examined the role of HUWE1 in B-cell proliferation and Ig gene diversification, focusing on its involvement in somatic hypermutation (SHM) and class switch recombination (CSR). B-cell-specific deletion of Huwe1 resulted in impaired development, differentiation and maturation of B cells in the bone marrow and peripheral lymphoid organs. HUWE1 deficiency diminished SHM and CSR by impairing B-cell proliferation and AID expression upon activation in vitro and in vivo, and was unrelated to the HUWE1-dependent regulation of the BER pathway. Interestingly, we found that HUWE1-deficient B cells showed increased mRNA expression of Myc target genes upon in vitro activation despite diminished proliferation. Our results confirm that the E3 ligase HUWE1 is an important contributor in coordinating the rapid transition of antigen naïve, resting B cells into antigen-activated B cells and regulates mutagenic processes in B cells by controlling AID expression and the post-transcriptional output of Myc target genes.

overall_design: Three biological replicates from WT and Huwe1;Mb1cre B cells isolated from muise spleens. RNA was either directly taken from B cells of unimmunized mice or after simulation of B cells for three days with LPS+CD40+IL4+IgD-Dextran

first: Aldo

last: Spanjaard

first: Maria

last: Stratigopoulou

first: Daniël

last: de Groot

first: Paul

last: van den Berk

first: Matilda

last: Ayidah

first: Chantal

last: Stappenbelt

first: Joyce

last: Catsman

first: Muhammad

last: Aslam

first: Iris

middle: N

last: Pardieck

first: Maaike

last: Kreft

first: Ramon

last: Arens

first: Jeroen

last: Guikema


title: Transcriptomic analysis of the upper lip and primary palate development in mouse

status: Public on Dec 25 2022

first: Sini

last: Cai

address: Badachu #33 road

institute: Palate of plastic surgery hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: To better investigate the genetic regulation of upper lip and primary palate development

overall_design: lambdoidal junction tissues of mice from embryonic days 10.5, 11.5 and 12.5,three key developmental stages, were selected for RNA sequencing


title: Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples

city: Solna

first: Ludvig

middle: Ale

last: Larsson

state: Stockholm

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: SciLifeLab

summary: Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of unbiased SRT methods targeting the polyA tail of mRNA, relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available SRT assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), an SRT workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we demonstrate the RRST protocol on tissue sections collected from five challenging tissue types, including: human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyzed 52 tissue sections and our results demonstrate that RRST is a versatile, powerful, and reproducible protocol for FF specimens of different qualities and origins.

overall_design: Gene expression profiiles of spatially resolved transcriptomics data generated from degraded or challenging samples

first: Zaneta

last: Andrusivova

first: Reza

last: Mirzazadeh


title: SC-beta vs SC-EC +/- IFN-G

city: Cambridge

first: Dario

last: Gerace

address: 7 Divinity Ave

institute: Harvard University

summary: The goal of this study was to identify transcriptional changes in SC-beta and SC-endothelial cells pre and post IFN-gamma stimulation. Specifically, to characterize the differential expression of immune cell ligands in these cells with respect to a partial inflammatory stimulus.

overall_design: SC-beta and SC-endothelial cells were differentiated from hESCs, enriched and treated with IFN-G. RNA-sequencing and differential gene expression analysis was performed.

first: Douglas

last: Melton


title: Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes

city: Munich

first: Karin

last: Hrovatin

address: Ingolstädter Landstraße 1

department: Institute of Computational Biology

country: Germany

institute: Helmholtz Munich

summary:
Mouse pancreatic islet scRNA-seq integrated atlas encompassing different ages, sexes, chemical stress leading to dedifferentiation, and diabetes models with corresponding treatments.

Two datasets (sub-series) were newly generated for the atlas.

overall_design:
The atlas integrates data from nine studies and 56 samples with over 300,000 pancreatic islet cells, including over 100,000 beta cells, across different conditions (sex, age, chemical stress, diabetes status). The atlas object with raw and processed expression, annotations, and integrated embedding is contained in GSE211799_adata_atlas.h5ad.gz. Two datasets newly generated for the atlas are in sub-series.
We mapped an external dataset (GSE137909), not contained in the atlas, on top of the atlas and provide the integrated latent embedding  in GSE211799_adata_referenceMapping_GSE137909.h5ad.gz

In both anndata integration objects we describe individual anndata fields under uns key field_descriptions.

Code associated with the manuscript: https://github.com/theislab/mm_pancreas_atlas_rep

cellxgene portal entry: https://cellxgene.cziscience.com/collections/296237e2-393d-4e31-b590-b03f74ac5070

first: Aimée

last: Bastidas-Ponce

first: Luke

last: Zappia

first: Mostafa

last: Bakhti

first: Maren

last: Büttner

first: Ciro

last: Sallino

first: Michael

last: Sterr

first: Anika

last: Böttcher

first: Adriana

last: Migliorini

first: Heiko

last: Lickert

first: Fabian

last: Theis


title: ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs

city: Seattle

first: Chia-Lin

last: Wei

state: WA

address: 3720 15th Ave NE

department: The Northwest Genomics Center (NWGC)

institute: University of Washington

summary: Here, we report a new strategy that combines in situ nuclear proximity ligation and transposase digestion, called ChIATAC, for highly efficient mapping of chromatin interactions between open chromatin loci simultaneously from lower input cells.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: ChIATAC: S2 (50k cells), 3 technical replicates; GM12878 (50k ~ 1k cells), 2 technical replicates; CD4+ T cells (50k cells), 2 technical replicates.

first: Haoxi

last: Chai

first: Harianto

last: Tjong

first: Yijun

last: Ruan

first: Chia


title: Class switch towards non-inflammatory, spike-specific IgG4 antibodies after repeated SARS-CoV-2 mRNA vaccination [CITE-Seq]

status: Public on Dec 22 2022

city: Erlangen

first: Simon

last: Schaefer

state: Bavaria

address: Glueckstr. 6

department: Genetics

institute: FAU Erlangen

summary: RNA vaccines are efficient preventive measures to combat the SARS-CoV-2 pandemic. High levels of neutralizing SARS-CoV-2-antibodies are an important component of vaccine-induced immunity. Shortly after the initial two mRNA vaccine doses, the IgG response mainly consists of the pro-inflammatory subclasses IgG1 and IgG3. Here, we report that several months after the second vaccination, SARS-CoV-2-specific antibodies were increasingly composed of non-inflammatory IgG4, which were further boosted by a third mRNA vaccination and/or SARS-CoV-2 variant breakthrough infections. IgG4 antibodies among all spike-specific IgG antibodies rose on average from 0.04% shortly after the second vaccination to 19.27% late after the third vaccination. This induction of IgG4 antibodies was not observed after homologous or heterologous SARS-CoV-2 vaccination with adenoviral vectors. Single-cell sequencing and flow cytometry revealed substantial frequencies of IgG4-switched B cells within the spike-binding memory B-cell population (median 14.4%; interquartile range (ICR) 6.7-18.1%) compared to the overall memory B-cell repertoire (median 1.3%; ICR 0.9-2.2%) after three immunizations. Importantly, this class switch was associated with a reduced capacity of the spike-specific antibodies to mediate antibody-dependent cellular phagocytosis and complement deposition. Since Fc-mediated effector functions are critical for antiviral immunity, these findings may have consequences for the choice and timing of vaccination regimens using mRNA vaccines, including future booster immunizations against SARS-CoV-2.

overall_design: We performed single-cell RNA sequencing (scRNA seq) of spike-specific B cells from four selected donors 210 days after the second or 10 days after the third Comirnaty dose. We combined this technology to CITE-sequencing to obtain measurements of surface proteins and the transcriptome and to enable HTO HASH-sequencing in order to demultiplex data sets.

first: Pascal

last: Irrgang

first: Juliane

last: Gerling

first: Katharina

last: Kocher

first: Dennis

last: Lapuente

first: Philipp

last: Steininger

last: Habenicht

first: Monika

last: Wytopil

first: Stephanie

last: Beileke

last: Schäfer

first: Jahn

last: Zhong

first: George

last: Ssebyatika

first: Thomas

last: Krey

first: Valeria

last: Falcone

first: Christine

last: Schülein

first: Antonia Sophia

last: Peter

first: Krystelle

last: Nganou-Makamdop

first: Hartmut

last: Hengel

first: Jürgen

last: Held

first: Christian

last: Bogdan

first: Klaus

last: Überla

first: Kilian

last: Schober

first: Thomas H.

last: Winkler

first: Matthias

last: Tenbusch


title: Class switch towards non-inflammatory, spike-specific IgG4 antibodies after repeated SARS-CoV-2 mRNA vaccination [scRNA-Seq]

first: Simon

last: Schaefer

overall_design: We performed single-cell RNA sequencing  (scRNA seq) of spike-specific B cells from four selected donors 210 days after the second or 10 days after the third Comirnaty dose.

first: Pascal

last: Irrgang

first: Juliane

last: Gerling

first: Katharina

last: Kocher

first: Dennis

last: Lapuente

first: Philipp

last: Steininger

last: Habenicht

last: Wytopil


title: Class switch towards non-inflammatory, spike-specific IgG4 antibodies after repeated SARS-CoV-2 mRNA vaccination

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

overall_design: Refer to individual Series


title: Superenhancer-activation of KLHDC8A Drives Glioma Ciliation and Hedgehog signaling

city: La Jolla

first: Derrick

last: Lee

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Glioblastoma ranks among the most aggressive and lethal of all human cancers, with poor responses to all therapeutic modalities. Self-renewing, highly tumorigenic glioblastoma stem cells (GSCs) contribute to therapeutic resistance and maintain cellular heterogeneity. Identification of GSC vulnerabilities may provide novel therapeutic targets for treating glioblastoma. Here, we interrogated superenhancer landscapes of primary glioblastoma specimens and patient-derived GSCs, revealing a kelch domain-containing gene (KLHDC8A) with a previously unknown function as an epigenetically driven oncogene. Targeting KLHDC8A decreased GSC proliferation, reduced sphere formation, induced apoptosis, and impaired in vivo tumor growth. Transcription factor control circuitry analyses revealed that the master transcriptional regulator SOX2 contributes to KLHDC8A expression. Mechanistically, KLHDC8A functions in the assembly of primary cilia via interactions with Chaperonin-containing TCP1 (CCT) and establishes a platform for a critical stem-specific signaling node through the Hedgehog pathway. Furthermore, we identified that Hedgehog and Aurora B/C Kinase signaling are complementary in GSCs, and dual inhibition synergistically inhibits GSC proliferation. Collectively, superenhancers enrich for essential mediators of cellular identity and offer a novel regulatory mechanism whereby promotion of ciliogenesis establishes and maintains a core GSC signaling node via the Hedgehog pathway, potentially offering insights into therapeutic vulnerabilities for glioblastoma treatment.

overall_design: Two glioma stem cell models were treated with a non-targeting shRNA or one of two shRNAs targeting KLHDC8A and profiled by RNA-sequencing. Two replicates were used for analysis

first: Jeremy

last: Rich


title: A bioengineered tridimensional substrate designed for mesenchymal stem cells culture: whole transcriptomic analysis

city: Milano

first: Carolina

last: Testa

address: Piazza Leonardo da Vinci 32

institute: Politecnico di Milano

summary: In this work we aimed to evaluate how the three-dimensionality of an engineered scaffold, concieved to emulate the stem cell niche, can influence the whole gene expression profile of mesenchymal stem cells. We performed a differential expression analysis, comparing the transcriptome of MSCs grown in 3D Nichoids with that of MSCs grown on 2D Nichoids, a structure with the same grid geometry, except for the overall tickness which allows a spreading expansion of cells. We found a total of 603 differentially expressed genes that were used also for functional enrichment analysis.

overall_design: Total RNA extracted from rBMSCs cultured on 3D Nichoid (n=3) and 2D Nichoid (n=3) after 4 days of culture

first: Stefania

last: Oliveto

first: Emanuela

last: Jacchetti

first: Francesca

last: Donnaloja

first: Chiara

last: Martinelli

first: Pietro

last: Pinoli

first: Roberto

last: Osellame

first: Giulio

last: Cerullo

first: Stefano

last: Ceri

last: Biffo

first: Manuela

middle: T

last: Raimondi


title: Ikaros family proteins redundantly regulate temporal patterning in the developing mouse retina

city: Montreal

first: Awais

last: Javed

state: Quebec

address: 110 Avenue des Pins

institute: IRCM

summary: Temporal identity factors regulate competence of neural progenitors to generate specific cell types in a time-dependent manner, but how they operate remains poorly defined. In the developing mouse retina, the Ikaros zinc-finger transcription factor Ikzf1 regulates production of early-born cell types, except cone photoreceptors. In this study we show that, during early stages of retinal development, another Ikaros family protein, Ikzf4, functions redundantly with Ikzf1 to regulate cone photoreceptor production. Using CUT&RUN and functional assays, we show that Ikzf4 binds and represses genes involved in late-born rod photoreceptor specification, hence favoring cone production. At late stages, when Ikzf1 is no longer expressed in progenitors, we show that Ikzf4 re-localizes to target genes involved in gliogenesis and is required for Müller glia production. We report that Ikzf4 regulates Notch signaling genes and is sufficient to activate the Hes1 promoter through two Ikzf GGAA-binding motifs, suggesting a mechanism by which Ikzf4 may influence gliogenesis. These results uncover a combinatorial role for Ikaros family members during nervous system development and provide mechanistic insights on how they temporally regulate cell fate output.

overall_design: RNA-seq and CUT&RUN analysis of Ikzf1 misexpressed in late stage RPCs and Ikzf4 CUT&RUN analysis of E14 and P0 retinas.

first: Pedro

last: Santos-Franca

first: Pierre

last: Mattar

first: Allie

last: Cui

first: Fatima

last: Kassem

first: Michel

last: Cayouette


title: The role of altered lipid composition and distribution in liver fibrosis revealed by multimodal nonlinear optical microscopy

city: Beijing

first: Juan

last: Liu

address: No 168, Litang Road

institute: Beijing Tsinghua Changgung Hosptial

summary: To reveal the involved gene regulatory pathways, we carried out RNA-seq transcriptomics analysis on the cells treated with or without PA, treated with PA+OA and PA+BMS.

overall_design:
con: HepaRG without treated for 4h.
PA: HepaRG were treated with 400μM deuterium-labeled palmitate acid (PA) for 4h.
PA+OA: HepaRG were treated with 400μM PA and 200μM oleic acid (OA) for 4h
PA+BMS: HepaRG were treated with 50μM BMS-309403 (BMS) for 24 h during concomitant incubation with 400μM PA for 4 h.

first: Hao

last: Jia

first: Yunfang

last: Wang

first: Shuhua

last: Yue


title: BRPF1 co-occupies with H3K4me3 and H3K23ac in human ESCs essential to pluripotency [RNA-Seq]

status: Public on Dec 21 2022

city: Guangzhou

first: Cong

last: Zhang

state: Guangdong Province

address: No. 190 Kaiyuan Avenue, Huangpu District

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Post-translational modifications (PTMs) on histones play essential roles in cell fate decisions during development. However, how these PTMs are recognized and coordinated remains to be fully illuminated. Here, we show that BRPF1, a multi-histone binding module protein, is essential to maintain pluripotency in human embryonic stem cells (ESCs). BRPF1, H3K4me3 and H3K23ac substantially co-occupy the active and stemness genes in hESCs. BRPF1 deletion impairs H3K23ac and leads to pluripotency exit and closed chromatin accessibility on stemness genes. Deletion of the N terminal or PHD-zinc knuckle-PHD (PZP) modules completely impairs BRPF1 to maintain hESC pluripotency while PWWP module deletion only partially impact its functions. Together, we reveal that the multi-histone binding module protein, BRPF1 co-ordinates the crosstalk between different histone modifications to maintain the pluripotency in hESCs.

overall_design: RNA-seq analysis revealed a distinct transcriptome profile between wild type (WT) and BRPF1knock-out in hESCs

first: Huaisong

last: Lin

first: Yongli

last: Shan

first: Guangjin

last: Pan


title: BRPF1 co-occupies with H3K4me3 and H3K23ac in human ESCs essential to pluripotency [ChIP-seq]

overall_design: We performed the ChIP-Seq assay to study FLAG(BRPF1), H3K4me3 and H3K27me3 location of the triple-FLAG knock-in(KI) into BRPF1 locus in hESCs. In addition, we studied H3K4me3 binding of BRPF1knock-out (D12) in hESCs


title: Gene expression of cAMP-relevant genes in T cell subsets

city: Hamburg

first: Roberta

last: Kurelic

address: Martinistrasse 52

department: Institute of Experimental Cardiovascular Research

institute: UKE

summary: Analysis of gene expression level of cAMP-relevant genes in non-activated murine conventional (Tcon) and regulatory T cell (Treg) subsets

overall_design: NanoString panel specially designed to perform analysis on a gene-level essential to delineate diverse expression patterns among potential targets driving higher basal levels of Treg compared to Tcon subset

first: Jana

last: Sonner

first: Nina

last: Kursawe

first: Elisabeth

last: Kraemer


title: BRPF1 co-occupies with H3K4me3 and H3K23ac in human ESCs essential to pluripotency [ATAC-seq]

overall_design: We performed the ATAC-seq assay in WT and BRPF1-/- hESCs cultured at two different culture time points (Day 12 and Day 30)


title: BRPF1 co-occupies with H3K4me3 and H3K23ac in human ESCs essential to pluripotency


title: Mycobacterium avium subsp. paratuberculosis antigens induce cellular immune responses in cattle

city: Lincoln

first: Paul

last: Maclean

address: Cnr Springs Road and Gerald Street

country: New Zealand

institute: AgResearch NZ LTD

summary: Mycobacterium avium subspecies paratuberculosis (MAP) causes chronic progressive granulomatous enteritis leading to diarrhea, weight loss, and eventual death in ruminants. Commercially available vaccines provide only partial protection against MAP infection and can interfere with the use of current diagnostic tests for bovine tuberculosis in cattle. In the current study, we characterized immune responses in calves to vaccines containing either MAP fusion protein particles (MAP antigens Ag85A202-347-SOD1-72 -Ag85B173-330-74F1-148+669-786 as a fusion), recombinant MAP (rMAP) fusion protein or commercially available Silirum(R) vaccine.

sample_organism:
Bos taurus
other sequences

overall_design: Thirty-two Holstein-Friesian cattle, 2-3 months old were sourced from a commercial farm with no history of JD. Prior to the trial, the cattle (n = 32) tested negative for reactivity to protein purified derivative from Mycobacterum avium (PPDA) (Prionics, Schlieren-Zurich, Switzerland) in the whole-blood interferon-g (IFN-g) assay were selected from a larger group of animals (n = 45). Thirty-two calves were divided randomly into 4 vaccine groups of 8 animals. The cattle were grazed on pasture in a separate paddock during the trial. RNA was prepared from the antigen-stimulated leukocytes before vaccination (week 0) and after vaccination (weeks 6, 9 and 12 of the study) and analyzed using PlexSet-24 consisting of probes specific to 21 immune response genes and 3 reference genes

first: Sandeep

last: Gupta

first: Tania

last: Wilson

first: Bernd

last: Rhem

first: Axel

last: Heiser

first: Bryce

last: Buddle

first: Neil

last: Wedlock


title: Microarray analysis in TRIM40-overexpressing HT-29 cells

city: Seoul

first: Sujin

last: Kang

address: 50, Yonsei-ro, Seodaemun-gu

department: Department of Systems Biology

institute: Yonsei University

summary: To identify the differentially expressed genes by TRIM40 overexpression in intestinal cells

overall_design: Microarray using total RNAs extracted in Control and TRIM40-overexpressing HT-29 cells


title: Cross-species single-nuclei transcriptome atlas of dorsal root ganglion sensory neurons [humanDRG]

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: OMNI Bx, gRED

institute: Genentech Inc

summary: Sensory neurons of the dorsal root ganglion (DRG) play a crucial role in maintaining tissue homeostasis by sensing and initiating responses to stimuli. While most preclinical studies of DRGs are conducted in rodents, much less is known about the mechanisms of sensory perception in primates. We generated a transcriptome atlas for mouse, guinea pig, cynomolgus monkey, and human DRGs using a framework that implements a common laboratory workflow (i.e sequencing technologies, laboratory protocols, and sample archival methods) and multiple data-integration approaches to generate accurate cross-species mappings of sensory neuron subtypes.

overall_design: Fresh or frozen DRG tissues from mouse, guinea pig, cynomologus monkey and human were collected and nuclei were isolated with FACS or density-gradient centrifugation and analyzed with snRNA-seq.

first: Min

last: Jung

first: Michelle

last: Dourado

first: Lorena

last: Riol-Blanco

first: David

last: Hackos


title: Cross-species single-nuclei transcriptome atlas of dorsal root ganglion sensory neurons [mouseDRG]


title: Cross-species single-nuclei transcriptome atlas of dorsal root ganglion sensory neurons [gpDRG]


title: Cross-species single-nuclei transcriptome atlas of dorsal root ganglion sensory neurons [cynoDRG]


title: Analysis of total RNA transcriptome in TRIM40 overexpressing HT-29 cells [RNA-seq]

summary: To investigate the novel function TRIM40 in intestinal epithelial cells, we established TRIM40 overexpressing HT-29 cells

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq
Comparative gene expression profiling analysis of RNA-seq data for TRIM40 overexpression and control vector expressing HT-29 cells (Mock, Myc-TRIM40).


title: Analysis of TRIM40 induced gene profiles in intestinal cells


title: Cross-species single-nuclei transcriptome atlas of dorsal root ganglion sensory neurons

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus
Cavia porcellus

overall_design:
Refer to individual Series

mousegpcynohumanDRG.rds: Integrated Seurat object with DRG subtype annotations (downsampled).


title: Gene Regulatory Network Reconfiguration in Direct Lineage Reprogramming

status: Public on Dec 20 2022

city: Saint Louis

first: Samantha

last: Morris

address: 660 S Euclid Ave

institute: Washington University School of Medicine

summary: In direct lineage reprogramming, transcription factor (TF) overexpression reconfigures Gene Regulatory Networks (GRNs) to convert cell identities between fully differentiated cell types. We previously developed CellOracle, a computational pipeline that integrates single-cell transcriptome and epigenome profiles to infer GRNs. CellOracle leverages these inferred GRNs to simulate gene expression changes in response to TF perturbation, enabling network re-configuration during reprogramming to be interrogated in silico. Here, we integrate CellOracle analysis with lineage tracing of fibroblast to induced endoderm progenitor (iEP) conversion, a prototypical direct lineage reprogramming paradigm. By linking early network state to reprogramming success or failure, we reveal distinct network configurations underlying different reprogramming outcomes. Using these network analyses and in silico simulation of TF perturbation, we identify new factors to coax cells into successfully converting cell identity, uncovering a central role for the AP-1 subunit Fos with the Hippo signaling effector, Yap1. Together, these results demonstrate the efficacy of CellOracle to infer and interpret cell-type-specific GRN configurations at high resolution, providing new mechanistic insights into the regulation and reprogramming of cell identity.

overall_design: For lineage tracing, scRNA-seq was performed for CellTagged in vitro reprogramming MEFs at multiple time points to allow longitudinal lineage tracing. For Fos-Yap1 experiments, scRNA-seq was performed for reprogramming iEPs on Day 20

first: Kenji

last: Kamimoto

first: Mohd

last: Adil

first: Kunal

last: Jindal

first: Christy

last: Hoffmann

first: Wenjun

last: Kong

first: Xue

last: Yang


title: Gene expression profile at single cell level of hepatocytes from livers of ad libitum fed (AL) and intermitently fasted (IF) mice.

city: Stanford

first: Roel

last: Nusse

address: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: Hepatocytes are considered as a heterogenous cell population in the liver. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of hepatocytes in livers under different feeding conditions.

overall_design: Hepatocytes from ad libitum fed or intermittently fasted mice were isolated and analyzed using scRNAseq.

first: Yan

first: Abby

last: Sarkar


title: Local light signalling at the leaf tip drives remote differential petiole growth through auxin-gibberellin dynamics

city: Utrecht

first: Ronald

last: Pierik

address: Padualaan 8

institute: Utrecht University

summary: Arabidopsis plants transfer information from the leaf tip to the petiole base to induce adaptive upward leaf movement upon neighbour detection through Far-Red light enrichment in the leaf tip. To determine how a distally derived signal can specifically regulate growth in the abaxial petiole we analysed the transcriptome in the leaf tip and abaxial-adaxially split petiole sections during the first hours of far-red enrichment.

overall_design: Wild-type Arabidopsis plants were exposed to white light control or white light + Far-Red for five hours. Samples were taken at timepoints ranging from 40 - 300 minutes after the start of treatment. The harvested samples were the leaf tip, abaxial petiole base and adaxial petiole base. There were 4 biological replicates, each consisting of material from selected leaves of 13 plants.

first: Jesse

last: Küpers

first: Basten

last: Snoek


title: Spatial transcriptomics of post-mortem lung tissue from COVID-19 donors

city: Berlin

first: Anja

middle: Erika

last: Hauser

address: Charitéplatz 1

department: Rheumatology and Clinical Immunology

institute: Charité - Universitätsmedizin and DRFZ

summary: Visualization of gene expression in lung tissue was performed using Visium spatial gene expression kits (10x Genomics) following the manufacturer`s protocol. The four capture areas in a 10x Genomics Visium Gene Expression slide consist of 5000 spots with DNA oligos for mRNA capture that have a unique spatial barcode and a unique Molecular Identifier (UMI). Each spot has 55 µm diameter and can therefore capture mRNA from 1 to 10 cells. We report the spatially resolved transcriptome of 3 control lung samples from non-COVID-19-related pneumonia donors and 9 COVID-19 lung samples analyzed with the 10x Visium platform.

overall_design: Control (n=3) and COVID-19 lung samples (n=9) from donors categorized based on disease durations (acute n=3, chronic n=3, prolonged n=3) were cut into 10μm sections using a MH560, cryotome (ThermoFisher, Waltham, Massachusetts, USA), and mounted on 10X Visium slides, which were pre-cooled to −20°C. The sections were fixed in pre-chilled methanol for 30 min, stained with CD45-AF647, CD31-AF594 and DAPI for 30min and imaged using an LSM 880 confocal microscope (Zeiss). The sections were then permeabilized for 10 minutes and spatially tagged cDNA libraries were constructed using the 10x Genomics Visium Spatial Gene Expression 3’ Library Construction V1 Kit. Tissue sections from the same fresh frozen human lung samples used for MELC and snRNA-seq were analyzed by ST.

first: Anna

last: Pascual-Reguant

first: Juliane

last: Liebeskind

first: Ralf

last: Köhler

first: Ronja

last: Mothes


title: Single-cell transcriptomes and T Cell receptors of vaccine-expanded Apolipoprotein B-specific T cells

first: Klaus

last: Ley

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: Atherosclerotic cardiovascular diseases are the major cause of death worldwide. CD4 T cells responding to Apolipoprotein B (ApoB),  the core protein of most lipoproteins, have been identified as critical disease modulators. In healthy individuals, ApoB-reactive  (ApoB+) CD4 T cells are mostly regulatory T cells (Tregs), which exert anti-inflammatory effects. Yet, they may obtain  pro-inflammatory features and thus become proatherogenic. Evidence from animal studies suggests that vaccination against  certain major histocompatibility complex (MHC) II-binding ApoB peptides induces an expansion of ApoB+ Tregs and thus confers  atheroprotection. To date, in-depth phenotyping of vaccine-expanded ApoB+ T cells has not yet been performed. To this end, we  vaccinated C57BL/6J mice with the ApoB-peptide P6 (ApoB978-993 TGAYSNASSTESASY) and performed single-cell RNA sequencing of  tetramer-sorted P6+ T cells. P6+ cells were clonally expanded (one major, two minor clones) and formed a transcriptional cluster  distinct from clusters mainly containing non-expanded P6+ and P6- cells. Transcriptomic profiling revealed that most expanded P6+  cells had a strong Treg signature and highly expressed genes mediating suppressive function. Yet, some expanded P6+ cells only had  a residual Treg signature and expressed genes related to T helper 1 (TH1) cells, which are proatherogenic. Modeling the T cell  receptor (TCR) and P6:MHC‐II interaction showed that only 3 amino acid residues in each the α and β chain contact the P6 peptide in  the MHC-II groove and thus determine the specificity of this TCR to P6. Our data begin to reveal the vaccination-induced response  to an ApoB epitope.

overall_design: Single-cell RNA sequencing of tetramer-sorted P6+ T cells

first: Felix

last: Nettersheim

first: Yanal

last: Ghosheh

first: Holger

last: Winkels

first: Kouji

last: Kobiyama

first: Christopher

last: Durant

first: Sujit

last: Armstrong Suthahar

first: Simon

last: Brunel

first: Payel

last: Roy

first: Thamotharampillai

last: Dileepan

first: Marc

last: Jenkins

first: Dirk

last: Zajonc


title: Comprehensive expression analysis with cell-type-specific transcriptome in ALS-linked mutant SOD1 mice

city: Nagoya

first: Koji

last: Yamanaka

address: Furo-cho, Chikusa-ku

department: Neuroscience and Pathobiology

institute: Research Institute of Environmental Medicine, Nagoya University

summary: Non-cell autonomous mechanisms are involved in the pathogenesis of amyotrophic lateral sclerosis (ALS), an adult neurodegenerative disease characterized by selective motor neuron loss. While the emerging role of glial cells in ALS has been noted, the detailed cell-type-specific role of glial cells has not been clarified. Here, we examined mRNA expression changes using microarrays of the spinal cords of three distinct lines of mutant superoxide dismutase (SOD) 1 transgenic mice, an established ALS model. Our analysis used a transcriptome database of component cell types in the central nervous system (CNS), as well as SOD1G93A cell-type transcriptomes. More than half of the differentially expressed genes (DEGs) were highly expressed in microglia, and enrichment analysis of DEGs revealed that immunological reactions were profoundly involved and some transcription factors were upregulated. Our analysis focused on DEGs that are highly expressed in each cell type, as well as chemokines, caspases, and heat shock proteins. Disease-associated microglial genes were upregulated, while homeostatic microglial genes were not, and galectin-3 (Mac2), a known activated microglial marker, was predicted to be ectopically expressed in astrocytes in mutant SOD1 mice. In mutant SOD1 mice, we developed a prediction model for the pathophysiology of different cell types related to TREM2, apolipoprotein E, and lipoproteins. Our analysis offers a viable resource to understand not only the molecular pathologies of each CNS constituent cell type, but also the cellular crosstalk between different cell types under both physiological and pathological conditions in model mice for various neurodegenerative diseases.

overall_design: We isolated total RNA from lumbar spinal cords (SOD1-G37R: 3 samples, SOD1-WT: 3 samples, SOD1-G85R: 3 samples, and non-transgenic littermates: 3 samples) for the gene expression analysis and compared paired excessive dismutase activity (SOD1-G37R vs. SOD1-WT) or paired normal dismutase activity (SOD1-G85R vs. non-transgenic littermates).

first: Hirofumi

last: Yamashita

first: Okiru

last: Komine

first: Noriko

last: Fujimori-Tonou


title: Identification of transcriptomic signatures for differentiation of CD4+ T cell subsets

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

institute: KAZUSA DNA Research Institute

summary: To investigate transciprtomic landscape changes during the Th cell activation induced by Th cell-specific cytokines, we stimulated naïve CD4+ T cells  with immobilized anti-TCR mAb and anti-CD28 mAb for 48 hours under Th0, Th1, Th2, Th17, or Treg cell culture conditions.

overall_design: We then performed gene expression profiling analysis of RNA-seq data for naïve CD4+ T cells, Th0, Th1, Th2, Th17, and Treg cells (n=4 per group)

first: Ryo

last: Konno

first: Satoru

last: Yokoyama

first: Yusuke

last: Kawashima

first: Yoshinori

last: Hasegawa

first: Osamu

last: Ohara

last: Endo


title: Convergent abnormalities in striatal gene networks in human cocaine use disorder and mouse cocaine administration models

status: Public on Dec 19 2022

city: New York

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Cocaine use disorder (CUD) is an intractable syndrome, and rising overdose death rates represent a significant public health crisis that exacts tremendous personal and financial costs on patients and society. Sharp increases in cocaine use drive the urgent need for better mechanistic insight into this chronic relapsing brain disorder that currently lacks effective treatment options. To investigate the transcriptomic changes involved, we conducted RNA sequencing on two striatal brain regions that are heavily implicated in CUD, the nucleus accumbens and caudate nucleus, from postmortem brains of subjects with CUD and matched control subjects. Weighted gene co-expression analyses identified CUD-specific gene networks enriched in ionotropic receptors and associated with lowered neuroinflammation, contrasting the proinflammatory responses found in opioid use disorder. Integration of comprehensive transcriptomic datasets from mouse cocaine self-administration models revealed evolutionarily conserved gene networks in CUD that implicate especially D1 medium spiny neurons as drivers of cocaine-induced plasticity.

overall_design: We performed RNA sequencing (RNAseq) on both the ventral (NAc) and dorsal (CN) striatum from postmortem tissue of persons with CUD and matched control subjects. We combined differential gene expression and network-based approaches to provide an integrative and unbiased characterization of transcriptional signatures triggered by chronic cocaine use across the striatum. Our analyses revealed a profound overlap between CUD-specific transcriptome changes in the NAc and CN, introducing the downregulation of neuroinflammatory processes, and upregulation of synaptic transmembrane transporters and ionotropic receptors.

first: Philipp

last: Mews

first: Ashley

last: Cunningham

first: Deborah

last: Mash

first: Eric

last: Nestler


title: Genome-wide characterization of mitochondrial DNA methylation in human brain

city: Exeter

first: Darren

middle: Mark

last: Soanes

address: RILD Building, RD&E Hospital Wonford, Barrack Road

department: College of Medicine and Health

institute: University of Exeter

type: Methylation profiling by high throughput sequencing

summary: Here, we present a novel approach to interrogate the mitochondrial DNA (mtDNA) methylome at single base resolution using targeted bisulfite sequencing. We applied this method to investigate mitochondrial DNA methylation patterns in post-mortem superior temporal gyrus and cerebellum brain tissue from seven human donors. We show that mitochondrial DNA methylation patterns are relatively low but conserved, with peaks in DNA methylation >5% at a number of sites and higher levels of methylation at non-CpG compared to CpG sites. We identify a number of loci that show differential DNA methylation patterns associated with age, sex and brain region. Finally we validate differences between cortical and cerebellar mitochondrial DNA methylation patterns using data previously generated using methylated DNA immunoprecipitation sequencing.

overall_design: We used a customized, targeted bisulfite sequencing method to assess mitochondrial DNA methylation at single nucleotide resolution in isolated mitochondrial DNA from matched cortex (superior temporal gyrus [STG]) and cerebellum [CER] brain tissue from seven donors free of neurodegenerative disease, including three males and four females.

first: Matthew

last: Devall

first: Adam

last: Smith

first: Katie

last: Lunnon


title: Genome-wide DNA binding mapping of ZFP266 with DamID-Seq in mouse embryonic fibroblasts

city: Edinburgh

first: Keisuke

last: Kaji

state: Midlothian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

institute: University of Edinburgh

summary: We used DamID-Sequencing of a DAM-ZFP266 fusion protein and DAM only control to identify binding sites for ZFP266 in mouse embryonic fibroblasts (MEFs). We identified >15,000 ZFP266 binding sites which are significantly enriched for SINEs and AP-1 complex transcription factor motifs.

overall_design: DamID-Sequencing to identify binding sites of ZFP266 in MEFs

first: Daniel

last: Kaemena

first: James

last: Ashmore


title: mRNA Sequencing of control and Zfp266 KO mouse embryonic fibroblasts, intermediate reprogramming cells, iPSCs and ESCs

summary: We performed bulk mRNA sequencing of either control or Zfp266 KO mouse embryonic fibroblasts (MEFs), intermediate reprogramming populations, iPSCs and ESCs. We reveal enhanced and early upregulation of pluripotent and ESC associated genes in Zfp266 KO reprogramming populations.

overall_design: Examination of gene expression changes in Zfp266 KO conditions in reprogramming, MEFs and pluripotent cells


title: Expression data from cardiac myofibroblasts treated with siControl or siVgll3

city: Fukuoka

first: Michio

last: Nakaya

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Pharmacology and Toxicology

institute: Kyushu University Graduate School of Pharmaceutical Science

summary:
VGLL3 promotes the expression of collagens in cardiac myofibroblasts
Fibrosis is occurred various organs and there has been reported that fibrosis contributes about 45% of all mortalities in the developed countries. In fibrosis, extracellular matrix such as collagens is mainly produced by myofibroblasts. In this time, we knocked down VGLL3 in cardiac myofibroblasts by using siRNA.

overall_design: Gene expression (RNA-seq) of cardiac myofibroblasts treated with siVgll3 or siControl


title: Mex3a RIP-seq

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

summary: Neural stem cells (NSCs) in the adult mammalian subependymal zone maintain a glial identity and the developmental potential to generate neurons during the lifetime. Production of neurons from these NSCs is not direct but follows an orderly pattern of cell progression which allows the gradual increase in pro-neural factors needed for neuronal fate. Although little is known about how stemness is molecularly balanced with the acquisition of the cell competence for neuronal differentiation along the lineage, regulated translation of existing transcripts is a potential mechanism to avoid the critical challenge posed by genes that encode proteins with conflicting functions, i.e. self-renew or differentiate. Here, we identify MEX3A as a post-transcriptional regulator of a set of stemness-associated transcripts at critical transitions in the subependymal neurogenic lineage. MEX3A regulates a quiescence-related RNA signature in activated NSCs that is needed for the return to quiescence, playing a role in the long-term maintenance of the NSC pool. Furthermore, it is required for the repression of the same program at the onset of neuronal differentiation. Our data indicate that MEX3A acts via a number of downstream targets to function as a pivotal regulator of adult mammalian neurogenesis.

overall_design: In order to identify MEX3A target RNAs, endogenous MEX3A was immunoprecipitated in FLAG-tagged NSC cultures (Mex3aFLAG/FLAG). Wild-type cultures from the same background that did not express the knock-in FLAG sequence were used as controls for nonspecific binding. 2-3 biological replicates for both the FLAG-tagged and the wild-type cultures were used and the IP was performed both with crosslinked and non-crosslinked samples.

first: Ana

last: Domingo-Muelas

first: Pere

last: Duart-Abadía

last: Jordán-Pla

first: Jose

last: Morante-Redolat

first: Isabel

last: Farinas


title: Role of Zfp266

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

overall_design: Refer to individual Series


title: Expression data from cardiac myofibroblasts culutured on plastic plates or in suspension

summary: Identification of the genes whose expresion levels are changed by the various culture conditions in cardiac myofibroblasts

overall_design: 3 different samples (1-3) mixed with hearts from three plates, respectively; “adherent” myofibroblasts (1) “non-adherent” myofibroblasts (2), and “re-adherent” myofibroblasts (3); A comparison between adherent, non-adherent and re-adherent myofibroblasts

first: Hitoshi

last: Kurose

first: Chikashi

last: Yoshimura


title: Expression data from mouse heart three days after myocardial infarction

city: Kumamoto

first: Soken

last: Tsuchiya

address: 5-1 Oe-honmachi, Chuo-ku

institute: Kumamoto University

summary: Identification of the genes whose expresion levels are changed by the operation of myocardial infarction in C57BL/6J mice

overall_design: 2 different samples (1-2) mixed with hearts from three mice, respectively; sham-operated mouse hearts (1) and myocardial infarcted mouse hearts (2) at the three days after the operations; A comparison between sham-operated and infarcted mouse hearts


title: Chromatin accessibility assay in Zfp266 Wt and KO cells, in mouse embryonic fibroblasts and at 72 hours of OSKM reprogramming

summary: We used Omnni-ATAC-Sequencing to generate chromatin accessibility maps of the genome in Zfp266 KO and Wt control cells, both in mouse embryonic fibroblasts (MEFs) and at an early stage of reprogramming (72 hours after OSKM induction by the addition of doxycycline). We found distinct loci become more open when Zfp266 is knocked out, so called More Open Regions (MORs) and these regions significantly overlap with B1 SINEs in both MEFs and reprogramming cells. In MEFs, Zfp266 KO MORs are strongly enriched for AP-1 complex transcription factor binding motifs.  In reprogramming, we show Zfp266 KO MORs contain motifs for KLF,SOX and OCT transcription factor families centrally enriched in the summit of ATAC peaks, while overlapping B1 SINEs are excluded from the centre of MORs and instead are located adjacent to OSK binding motifs.

overall_design: Examination of chromatin accessibility in MEFs and cells that have undergone 72 hours reprogramming in both Zfp266 Wt and Zfp266 KO conditions


title: Adipose-derived mesenchymal stem cells inhibit JNK-mediated mitochondrial retrograde pathway to alleviate acetaminophen-induced acute liver injury

status: Public on Dec 17 2022

city: Hang Zhou

first: Yelei

last: Cen

address: Yuhangtang Road No.388,Zhejiang Province,P.R.China

institute: Zhejiang University

summary: Acetaminophen (APAP) is the major cause of drug-induced liver injury, with limited treatment options. APAP overdose invokes excessive oxidative stress that triggers mitochondria-to-nucleus retrograde pathways, contributing to APAP-induced liver injury (AILI). Mesenchymal stem cell therapy is a promising tool for acute liver failure. Therefore, the purpose of this study is to investigate the beneficial effects of adipose-derived mesenchymal stem cell (AMSC) therapy on AILI and reveal the potential therapeutic mechanisms. C57BL/6 mice are used as the animal model and AML12 normal murine hepatocytes as the cellular model of APAP overdose. Immunohistochemical staining, western blotting, immunofluorescence staining, and RNA sequencing assay are used for assessing the efficacy and validating mechanisms of AMSC therapy. We found AMSC therapy effectively ameliorated AILI, while delayed AMSC injection lost its efficacy related to the c-Jun N-terminal kinase (JNK)-mediated mitochondrial retrograde pathways. We further found that AMSC therapy inhibited JNK activation and mitochondrial translocation, reducing APAP-induced mitochondrial damage. The down-regulation of activated Ataxia telangiectasia mutated (ATM) and DNA damage response proteins in AMSC treated mice liver indicated AMSC blocked the JNK-ATM pathway. Overall, AMSC may be an effective treatment for AILI by inhibiting JNK-ATM mitochondrial retrograde pathway, which improves APAP-induced mitochondrial dysfunction and liver injury.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NC, APAP overdosed-mice and AMSC-treated mice.

first: Yanning

last: Liu

first: Guohua

last: Lou


title: Disome profiling of rocaglamide A treatment in HEK293FT cells

city: Beijing

first: Xuerui

last: Yang

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

summary: For the past decade, extensive studies of translation have produced a vast amount of ribosome profiling data, an insightful resource for mining of critical details about the dynamics of translation regulation under various biological contexts. Previously, Rocaglamide A (RocA), an anti-tumor heterotricyclic natural compound, has been shown to selectively inhibit translation initiation of a large group of mRNA species by clamping eukaryotic translation initiation factor 4A (eIF4A) onto poly-purine motifs in the 5’ un-translational regions (5’UTRs). However, re-analysis of the previous ribosome profiling datasets revealed an unexpected shift of the ribosome occupancy pattern during early translation elongation upon RocA treatment in various types of cells, for a specific group of mRNA transcripts without poly-purine motifs over-presented in their 5’UTRs. Such perturbation of the translation elongation dynamics can be attributed to the blockage of translating ribosomes due to the binding of eIF4A to the poly-purine sequence in coding sequences. This new mode of action of RocA, which is complementary to the canonical function inhibiting translation initiation, selectively interfere with the translation of the genes involved in fundamental processes such as ATP synthase, mitochondrial respiratory chain complex, et al. In summary, re-analyses of previous ribosome profiling data has revealed the complete dual modes of RocA in blocking translation and thus underlying the potent anti-tumor effect

overall_design: Comparative distribution of the disome protected fragments under RocA and DMSO treatment based on disome profiling data analyses.

first: Fajin

last: Li

first: Jianhuo

last: Fang

first: Yifan

last: Yu


title: IFN gamma signaling in cytotoxic T cells restricts antitumor responses by inhibiting the maintenance and clonality of intra-tumoral stem-like T cells

status: Public on Dec 16 2022

city: Oxford

first: Audrey

last: Gerard

address: Roosevelt Dr.

institute: The Kennedy Institute of Rheumatology

overall_design: C57Bl6 WT mice and CD8-IFNgRKO mice were engrafted with the melanoma cell line B16 expressing OVA. CD3+ CD8+ T cells were isolated by Fluorescence-activated cell sorting (FACS)  from the tumor and draining lymph node after 12 days and subjected to scRNA and scTCR sequencing.

last: Gérard

first: Vivian

last: Lau

first: Lada

middle: A

last: Koneva

first: Stephen

last: Sansom


title: An NPAS4:NuA4 complex couples synaptic activity to DNA repair [END-Seq]

city: BOSTON

first: ELIZABETH

last: POLLINA

state: MA

address: 220 LONGWOOD AVENUE, GOLDENSON 405

department: Neurobiology

institute: HARVARD MEDICAL SCHOOL

summary: Neuronal activity is critical for adaptive circuit remodeling but poses an inherent risk to the stability of the genome across the long lifespan of post-mitotic neurons.   Whether neurons have acquired specialized genome protection mechanisms that enable them to withstand decades of potentially damaging stimuli during periods of heightened activity is not known. Here we identify the first example of a neuronal-specific DNA repair mechanism via a new form of the NuA4/TIP60 chromatin modifier that assembles in activated neurons around the inducible, neuronal-specific transcription factor NPAS4. We purify this complex directly from the brain and demonstrate its function in eliciting activity-dependent changes to neuronal transcriptomes and neuronal circuitry. NPAS4:NuA4 binds at fragile regulatory regions that undergo neuronal activity-induced DNA double-strand breaks and recruits additional DNA repair machinery to stimulate the repair of these sites. Gene regulatory elements bound by the NPAS4:NuA4 complex are partially protected from age-dependent accumulation of somatic mutations. Impaired NPAS4:NuA4 signaling leads to a cascade of cellular defects including dysregulated transcriptional responses to activity, loss of control over neuronal inhibition, and genome instability, culminating in reduced longevity at the organismal level. In addition, mutations in several components of the NuA4 complex are reported to lead to neurodevelopmental disorders and autism. Together, these findings identify a neuronal-specific complex that couples neuronal activity directly to genome preservation and whose disruption may contribute to developmental disorders, neurodegeneration and aging.

overall_design: Primary cortical neurons were infected with shRNAs targeting members of NuA4:Tip60 complex or with a non-targeting control shRNA and stimulated for 0,2 hours with 55 mM KCl.  Experiments were performed in duplicate and infected with a targeting shRNA.

first: Elizabeth

last: Pollina

first: Daniel

last: Gilliam

first: Michael

last: Greenberg


title: CagA-specific gastric CD8+ tissue-resident T cells control Helicobacter pylori during the early infection phase

city: München

first: Maximilian

middle: Richard

last: Koch

address: Trogerstr. 30

department: Inst. for med. Micobiology

institute: TUM

summary: Infection with Helicobacter pylori strongly impacts global health by causing chronic gastritis, ulcer disease and gastric cancer. Although extensive research into the strong immune response against this persistently colonizing bacterium exists, the specific role of CD8+ T cells remains elusive. We comprehensively characterize gastric H. pylori-specific CD8+ T cell responses in mice and humans. We define CD8+ T cell populations bearing a tissue-resident memory (TRM) phenotype, which infiltrate the gastric mucosa shortly after infection and mediate pathogen control by executing antigen-specific effector properties. These induced CD8+ TRM cells show a skewed T cell receptor beta chain usage and are specific for CagA, the distinctive oncoprotein injected by H. pylori into host cells. As the infection progresses, we observe a loss of the TRM phenotype and replacement of CD8+ by CD4+ T cells, indicating a shift in the immune response during the chronic infection phase. Our results point towards a hitherto unknown role of CD8+ T cell response in this bacterial infection, which may have important clinical implications for treatment and vaccination strategies against H. pylori.

overall_design: Gastric CD8+ TRM cells defined by the expression of TCRb, CD8b, CD69 and CD103 as well as control splenic memory T cells defined by the expression of TCRb, CD8b, CD27 and CD44 were isolated from 4 mice infected for 28 days with the H. pylori strain PMSS1. The respective organs were pooled after the creation of single cell suspension, then from each population 10000 cells were sorted for each sample (technical replicates) and bulk RNA-Seq was performed of all samples.

first: Ruolan

last: Gong

first: Verena

last: Friedrich

first: Veronika

last: Engelsberger

first: Lorenz

last: Kretschmer

first: Andreas

last: Wanisch

first: Sebastian

last: Jarosch

first: Anna

last: Ralser

first: Bob

last: Lugen

last: Quante

last: Vieth

first: Riccardo

last: Vasapolli

first: Chirstian

last: Schulz

first: Veit

last: Buchholz

first: Dirk

middle: H

last: Busch

first: Raquel

last: Mejías-Luque

first: Markus

last: Gerhard


title: Sequence determinants of dsRNA processing by DICER [Massively Parallel Assay]

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

institute: Seoul National University

summary: RNA silencing relies on specific and efficient processing of dsRNA by DICER which produces microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, our current knowledge of DICER’s specificity is restricted to the secondary structures of its substrates: a dsRNA than 22 bp with a 2-nt 3′ overhang. We recently found evidence pointing to additional sequence-dependent determinant(s) beyond these features. To systematically interrogate the features of precursor miRNAs (pre-miRNAs), we carried out massively parallel assays with over a million pre-miRNA variants. Our analyses revealed a highly conserved cis-acting element, termed the “GYM” motif (paired G, paired pyrimidine, and mismatched C or A) at the cleavage site, which strongly promotes processing at a specific position. We find that the C-terminal double-stranded RNA binding domain (dsRBD) of DICER recognizes the GYM motif. Mutation of the dsRBD alters pre-miRNA cleavage sites and impairs processing in a motif-dependent fashion, which in turn affects the miRNA repertoire in cells. Consistently, integrating the GYM motif into short hairpin RNA (shRNA) or Dicer substrate siRNA (DsiRNA) potentiates RNA interference.

overall_design: AQ-seq (bias-minimized sRNA-seq) libraries were constructed as described in our previous study (Kim et al., 2019).

first: Young-Yoon

last: Lee

first: V


title: Sequence determinants of dsRNA processing by DICER [Rescue Experiment]

overall_design: AQ-seq (bias-minimized sRNA-seq) libraries were constructed using total RNAs as described in our previous study (Kim et al., 2019).


title: Sequence determinants of dsRNA processing by DICER


title: An NPAS4:NuA4 complex couples synaptic activity to DNA repair [snRNA-seq]

first: ELIZABETH

last: POLLINA

summary: Neuronal activity is critical for adaptive circuit remodeling but poses an inherent risk to the stability of the genome across the long lifespan of post-mitotic neurons. Whether neurons have acquired specialized genome protection mechanisms that enable them to withstand decades of potentially damaging stimuli during periods of heightened activity is not known. Here we identify the first example of a neuronal-specific DNA repair mechanism via a new form of the NuA4/TIP60 chromatin modifier that assembles in activated neurons around the inducible, neuronal-specific transcription factor NPAS4. We purify this complex directly from the brain and demonstrate its function in eliciting activity-dependent changes to neuronal transcriptomes and neuronal circuitry. NPAS4:NuA4 binds at fragile regulatory regions that undergo neuronal activity-induced DNA double-strand breaks and recruits additional DNA repair machinery to stimulate the repair of these sites. Gene regulatory elements bound by the NPAS4:NuA4 complex are partially protected from age-dependent accumulation of somatic mutations. Impaired NPAS4:NuA4 signaling leads to a cascade of cellular defects including dysregulated transcriptional responses to activity, loss of control over neuronal inhibition, and genome instability, culminating in reduced longevity at the organismal level. In addition, mutations in several components of the NuA4 complex are reported to lead to neurodevelopmental disorders and autism. Together, these findings identify a neuronal-specific complex that couples neuronal activity directly to genome preservation and whose disruption may contribute to developmental disorders, neurodegeneration and aging.

overall_design: Single-nucleus RNA-seq was performed in the hippocampus of Npas4fl/fl or Tip60fl/fl infected with AAVs expressing wither Cre-mCherry or DelCre-GFP.  DelCre is a nuclease-deficient Cre that cannot excise and so mice are wild-type for the gene of interest.  Nuclei were collected from 2 independent mice for Npas4fl/fl datasets and 3 mice in Tip60fl/fl datasets.

first: Elizabeth

last: Pollina

first: Daniel

last: Gilliam

first: Michael

last: Greenberg


title: An NPAS4:NuA4 complex couples synaptic activity to DNA repair [RNA-seq]

overall_design: Primary cortical neurons were infected with shRNAs targeting members of NPAS4:NuA4 complex or with a non-targeting control shRNA and stimulated for 0,2, or 6 hours with 55 mM KCl.  Experiments were performed in triplicate and 2 independent shRNAs were used to knockdown Tip60 or Ep400. In addition, we include RNA-seq data from hippocampal tissue isolated at 0, 2 or 10 hours post low dose KA stimulation to induce neuronal activity. These datasets were collected from the same tissue as sBLISS-seq datasets.


title: Epigenetic control of cellular cross-talk defines organ fate and function

city: Toronto

first: Tae-Hee

state: Ontario

address: 686 Bay St.

department: Development and Stem Cell Biology

institute: The Hospital for Sick Children

summary: Investigation of the transcriptional and chromatin-accessibility effects of Eed knockout in the developing mouse stomach and intestinal mesenchyme using RNA-seq and ATAC-seq.

overall_design: ATAC-seq and RNA-seq from mesenchyme of E13.5 Stomach and Intestine in WT and EED-KO mice. N=2 replicates per condition/tissue/experiment.

first: TaeHee

first: Ryan

last: Smith

first: Minggao

last: Liang