title: CF (1565) vs CFTR-corrected (1564) iPSC_airway at ALI

summary: Platform: iPSC-derived airway plated on 2D-air liquid interface through basal cell intermediate. Purpose of experiment: To examine the role of mutant CFTR on IPSC-derived airway epithelium (ie. immune dysregulation; dysregulated calcium channel signaling etc). Description of samples:Typical phenotype CF F508del (1565) and syngeneic CFTR-corrected (1564) iPSCs- derived airway epithelium at D90 (D15 CD47hi/CD26lo; replated in 3DMG cultured in 210DCIY x 2 weeks, single-cell passaged and cultured in PNExPlus+dual smad media in 3D, s/p 2 NGFR sorts, cultured at air-liquid interface at 2D)

overall_design: iPSCs- derived airway epithelium from CF and CFTR-corrected syngeneic line, at D90 (D15 CD47hi/CD26lo; replated in 3DMG cultured in 210DCIY x 2 weeks, single-cell passaged and cultured in PNExPlus+dual smad media in 3D,  s/p 2 NGFR sorts, cultured at air-liquid interface at 2D)


title: CF vs CFTR-corrected hiPSC-airway at ALI

status: Public on Mar 02 2023

city: Boston

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

country: USA

institute: Center for Regenerative Medicine, Boston University

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effects of metformin and its metabolite guanylurea on fathead minnow (Pimephales promelas) reproduction

status: Public on Mar 03 2023

city: Durham

first: Weichun

last: Huang

state: NC

address: 109 TW Alexander Dr

department: ORD

institute: US EPA

summary: Metformin, along with its biotransformation product guanylurea, are commonly observed in municipal wastewaters and subsequent surface waters. Previous studies in fish have identified metformin as a potential endocrine active compound but there are inconsistencies in the literature with regard to effects. To further investigate the potential reproductive toxicity of metformin and guanylurea to fish, a series of experiments were performed with reproductively mature fathead minnows (Pimephales promelas). First, explants of mature fathead minnow ovary tissue were exposed to 0.001-100 µM metformin or guanylurea  to investigate whether they can directly perturb steroidogenesis. Second, spawning pairs of fathead minnows were exposed to metformin (0.41, 4.1, 41 µg/L) or guanylurea (1.0, 10, 100 µg/L) for 23 d to assess impacts on reproduction. Lastly, male fathead minnows were exposed to 41 µg/L metformin, 100 µg/L guanylurea, or a mixture of both compounds, with samples collected over a 96 h time course to investigate potential impacts to the hepatic transcriptome or metabolome. Neither metformin or guanylurea effected  estradiol or testosterone by ovary tissue exposed in vitro. In the 23 d exposure, neither compound significantly impacted transcription of endocrine-related genes in male liver or gonad, circulating steroid concentrations in male or female fish, or fecundity of spawning pairs. In the 96 h time course, 100 µg guanylurea/L elicited more differential gene expression than 41 µg metformin/L , and showed the greatest impacts after 96 h. A number of DEGs up-regulated after 24 h were subsequently down-regulated after 96 h, demonstrating time-dependent impacts of guanylurea on the liver. Overall, metformin and guanylurea did not elicit effects consistent with reproductive toxicity in adult fathead minnows at environmentally relevant concentrations. Where effects were identified using ‘omics approaches, guanylurea induced greater impacts than metformin.

overall_design: Male fathead minnows were exposed to 41 µg/L metformin, 100 µg/L guanylurea, or a mixture of both compounds, with samples collected over a 96h time course to investigate transcriptome responses from exposure

first: Mary

middle: J

last: See

first: Adam

middle: D

last: Biales

first: Brett

middle: R

last: Blackwell

first: Gerald

middle: T

last: Ankley

first: Jenna

middle: E

last: Cavallin

first: Alexander

last: Cole

first: Timothy

middle: W

last: Collette

first: Drew

last: Ekman

first: Rachel

middle: N

last: Hofe

first: Kathleen

middle: M

last: Jensen

first: Michael

last: Kahla

first: Ashley

last: Kittelsonc

first: Shannon

last: Romanod

first: Quincy

last: Tengd

first: Charlene

middle: B

last: Tilton

first: Daniel

middle: L

last: Villeneuve


title: RB1 depleted pluripotent stem cell retinal organoids recapitulate state cell transitions of retinoblastoma development

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

summary: Retinoblastoma (Rb) is a childhood cancer of the developing retina that begins in utero in response to bi-allelic inactivation of RB1 or MYCN amplification, accounting for up to 1% of all tumours in infancy. To gain insights into the transcriptional events of each state cell transition during Rb development, we developed two Rb models via retinal organoid differentiation of RB1 depleted human embryonic stem cell line (RB1-null hESCs) and RB1patient-specific induced pluripotent (iPSC) line harbouring RB1 biallelic mutation (c.2082delC). Both models were characterised by RB1 depletion and a significant increase in the fraction of proliferating cone precursors (RXRγ+Ki67+), which were defined as cell of origin for Rb by the single cell RNA-Seq analysis. The RB1 depleted retinal organoids displayed similar features to Rb tumours including mitochondrial cristae aberration and rosette-like structures and were able to undergo cell growth in an anchorage-independent manner, indicative of cell transformation in vitro. The patient-specific iPSC model displayed an enhanced reduction of amacrine, horizontal and retinal ganglion cells and an accelerated loss of cone photoreceptor markers during transition towards retinoma and Rb, compared to RB1-null hESC. In both models, the Rb cells of origin, intermediate retinoma and/or Rb cells expressed retinal ganglion and horizontal cell in addition to cone markers, a novel finding, which should help to better identify and eradicate these cells within the tumour mass. Application of Melphalan, Topotecan and TW-37 led to a significant reduction in the fraction of proliferating cone precursors, validating the suitability of these in vitro models for testing novel therapeutics for Rb.

overall_design: Study of two Rb models developed via retinal organoid differentiation of RB1 depleted human embryonic stem cell line (RB1-null hESCs) and RB1patient-specific induced pluripotent (iPSC) line harbouring RB1 biallelic mutation (c.2082delC)

first: Agata

last: Rozanska

last: Queen

first: Joseph

last: Collin

first: Darin

last: Zerti

first: Birthe

last: Dorgau

first: Tracey

last: Davies

first: Jumana

last: Al-Aam

first: David

last: Steel

first: Nissim

last: Benvenist

first: Lyle

last: Armstrong

first: Manoj

last: Parulekar

first: Jonathan

last: Coxhead

first: Rafiqul

last: Hussain

first: Rodrigo

last: Cerna-Chavez


title: Comparative analysis of transcriptomic changes induced by zearalenone and bisphenol A in human ovarian cancer cells [microRNA_seq]

city: Debrecen

first: Melinda

last: Szilágyi-Bónizs

address: Egyetem tér 1

department: Human Genetics

country: Hungary

institute: University of Debrecen

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study we compared the effect of zeralenone (ZEA; mycotoxin) and bisphenol A (BPA; plastic additive) to the global microRNA expression of human ovarian cells with the effect of physiological estradiol (E2). For this purpose we applied the PEO1 human ovarian cell line that was treated with 10 nM ZEA, 100 nM BPA and 10 nM E2. MicroRNA expression was compared by microRNA sequencing (Illumina NextSeq 500).

overall_design: The PEO1 human epithelial ovarian cell line was treated with 10 nM E2, 10 nM ZEA and 100 nM BPA. Total RNA was isolated 8 h-s after the treatment.

last: Szilágyi

first: Éva

last: Márton

first: Alexandra

last: Varga

first: András

last: Penyige

first: Zsuzsanna

last: Birkó

first: István

last: Balogh

first: Bálint

last: Nagy


title: RNA sequencing of in vivo sorted Trem2 mutant MDSCs and WT MDSCs

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

overall_design: Examination of the differences between Trem2 mutant MDSCs and WT MDSCs in genes and pathways

first: Troiani

last: Martina

first: Alimonti

last: Andrea


title: Functionally distinct promoter classes initiate transcription via different mechanisms [PRO-Seq]

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

summary: To identify the functional contribution to transcription of various promoter-bound proteins we have endogenously tagged select proteins with an auxin-inducible degron and measured nascent transcription with PRO-seq 6 hours after their depletion

overall_design: Endogenously tagged AID cell lines were created using CRISPR/Cas9 in Drosophila S2 cells constitutively expressing OsTir ligase. PRO-seq was performed 3, 6 or 12 hours after auxin addition

first: Leonid

last: Serebreni

first: Lisa-Marie

last: Pleyer


title: ITK Degradation to Block T-cell Receptor Signaling and Overcome Therapeutic Resistance in T-Cell Lymphomas

status: Public on Mar 01 2023

city: Guangzhou

first: Wenchao

last: Wu

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District,

country: China

institute: Sun Yat-sen University Cancer Center

summary: IL-2-inducible T cell kinase (ITK) is essential for T cell receptor (TCR) signaling and plays an integral role in T-cell proliferation and differentiation. Unlike the ITK homolog BTK, no inhibitors of ITK are currently FDA approved. In addition, recent studies have identified mutations within BTK that confer resistance to both covalent and non- covalent inhibitors. Here, as an alternative strategy, we report the development of BSJ-05-037, a potent and selective heterobifunctional degrader of ITK. BSJ-05-037 displayed enhanced anti-proliferative effects relative to its parent inhibitor BMS- 509744, blocked the activation of NF-kB/GATA-3 signaling and increased the sensitivity of T cell lymphoma cells to cytotoxic chemotherapy both in vitro and in  vivo. In summary, targeted degradation of ITK is a novel approach to modulate TCR signal strength that could have broad application for the investigation and treatment of T cell-mediated diseases.

overall_design: NSG mice were xenografted with H9 cells and treated with vehicle control or BSJ-05-037 (50 mg/kg I.P., Q.O.D) for for 14 days.

first: Baishan

last: Jiang

first: Sam

last: Amaka

first: Nicholas

last: Donaldson


title: A monoclonal Trd chain supports the development of the complete set of functional γδ T cell lineages (VDJ)

city: Erlangen

first: Simon

last: Schaefer

state: Bavaria

address: Glueckstr. 6

department: Genetics

country: Germany

institute: FAU Erlangen

summary: The clonal selection theory describes the key features of adaptive immune responses of B and T cells. For αβ T cells and B cells antigen recognition and selection principles are known at a detailed molecular level. The precise role of the antigen receptor in γδ T cells remains less well understood. To better understand the role of the γδ T cell receptor (TCR), in particular its specificity for thymic selection of γδ T cells and for γδ T cell biology in general, we generated a novel orthotopic TCRδ transgenic mouse model. We demonstrate a multi-layered functionality of γδ TCRs and diverse roles of CDR3δ-mediated selection during γδ T cell development. Whereas epithelial populations using Vγ5 or Vγ7 chains are affected to only minor extend in their biology in the presence of a single TCRδ chain, pairing with Vγ1 positively selects subpopulations of γδ T cells with distinct programs in several organs, thereby distorting the repertoire.  In conclusion, our data support dictation of developmental tropism together with adaptive-like recognition principles in a single antigen receptor.

overall_design: Murine γδ T cells were isolated from the spleen via Fluorescence-activated cell sorting (FACS) according to the presence of CD3 and γδTCR and the absence of αβTCR, B220 and CD11c, and analyzed using scRNAseq for transcriptome and V(D)J repertoire analysis.

first: Anne

last: Hahn

first: Lisa

last: Vogg

first: Stefanie

last: Brey

last: Schneider

last: Schäfer

first: Ralph

last: Palmisano

first: Anna

last: Pavlova

first: Inga

last: Sandrock

first: Likai

last: Tan

first: Alina

middle: S

last: Fichtner

first: Immo

last: Prinz

first: Sarina

last: Ravens

first: Thomas

middle: H

last: Winkler


title: A monoclonal Trd chain supports the development of the complete set of functional γδ T cell lineages (NGS)

first: Andrea


title: A monoclonal Trd chain supports the development of the complete set of functional γδ T cell lineages (GEX)


title: Gene expression based molecular test as diagnostic aid for the differential diagnosis of psoriasis and eczema in formalin fixed and paraffin embedded tissue, microbiopsies and tape strips

city: Freiburg

last: Eyerich

address: Breisacher Straße 153

department: Department of Dermatology and Venereology

institute: University of Freiburg

summary: Development of a real-time PCR based molecular classifier to distinguish psoriasis from eczema in FFPE-fixed skin samples and evaluation of the use of minimally invasive microbiopsies and tape strips for molecular diagnosis.

overall_design: Performing gene expression analysis using data obtained from RNA-seq of macrobiopsies and microbiopsies of eczema and psoriasis patients

first: Felix

last: Fischer

first: Anais

last: Doll

first: Deniz

last: Uereyener

first: Sophie

last: Roenneberg

first: Christina

last: Hillig

first: Lucca

last: Weber

first: Verena

last: Hackert

first: Martin

last: Meinel

first: Ali

last: Farnoud

first: Peter

last: Seiringer

first: Jenny

last: Thomas

first: Philipp

last: Anand

first: Larissa

last: Graner

first: Franziska

last: Schlenker

first: Roland

last: Zengerle

first: Manja

last: Jargosch

first: Fabian

last: Theis

first: Carsten

last: Schmidt-Weber

first: Tilo

last: Biedermann

first: Michael

last: Howell

first: Kristian

last: Reich

last: Menden

first: Natalie

last: Garzorz-Stark

last: Lauffer


title: Dynamic Activity in cis-Regulatory Elements of Leukocytes Identifies Transcription Factor Activation and Stratifies COVID-19 Severity in ICU Patients

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego


title: A monoclonal Trd chain supports the development of the complete set of functional γδ T cell lineages

first: Simon

last: Schaefer


title: RNA sequencing of BM-derived senescent MDSCs treated or not with Romidepsin

first: Andrea

last: Alimonti

overall_design: Examination of the differences between  BM-derived senescent MDSCs treated or not with Romidepsin

first: Troiani

last: Martina

first: Alimonti

last: Andrea


title: A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy (EPIC)

city: Grand Rapids

first: Hyo Sik

last: Jang

state: Michigan

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: We designed a Phase II clinical trial testing the combination of guadecitabine (DNMTi) and atezolizumab (anti-PD-L1) with the goal to re-stimulate the immune mediated anticancer effects of immune checkpoint inhibitors (ICI) in metastatic urothelial carcinoma patients who were resistant to prior ICI treatment. No RECIST criteria responses were observed, however, patients could be separated into those with either progressive or stable disease outcomes. Analysis of the tumors did not show substantial DNA hypomethylation in the tumor or the upregulation of viral mimicry after two cycles of combination treatment. We did, however, observe that the therapy associated with immune activation of circulating immune cells and abundance of tumor-infiltrating CD8 T cells within the tumor, which were correlated with a longer survival outcome. Our results suggest that further studies to target the reprogramming of T cells with alternate methodologies may be of benefit in this disease setting.

overall_design: DNA methylation EPIC array data was generated from tumor needle biopsies from patients in this clinical trial.

first: H

first: Peter

middle: A

last: Jones

first: Elizabeth

last: Plimack

first: Ryan

last: Burgos


title: A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy (NGS)

type: Genome variation profiling by high throughput sequencing

overall_design: Total RNA-seq, whole exome sequencing, and whole exome sequencing data was generated from tumor needle biopsies from patients in this clinical trial.


title: Impact of sequential exposures to allergens and ultrafine particles on human bronchial epithelial BEAS-2B cells at the air liquid interface

city: Munich

first: Elias

middle: Josef

last: Zimmermann

address: Gmunder Str. 37

department: Comprehensive Molecular Analytics

institute: Helmholtz Zentrum Munich

summary: BEAS-2B cells, at air liquid interface, were exposed to birch pollen extract or house dust mite extract in a cloud chamber and, later, to UFP rich combustion aerosols in an in vitro exposure system. As control the same exposure was performed without allergen containing extracts. The goal was to understand the effect of allergenic pre-exposure to a UFP rich combustion aerosol exposed cells and their effect on allergic sensitization, using an established model that mimics more closely real life exposures.

overall_design: For the subsequent exposure, BEAS-2B cells, at air-liquid interface, were exposed to 30mg/ml birch pollen extract or 25µg/ml house dust mite extract and after 4 h or 24 h to UFP rich combustion aerosol for 2 h. The cells were seeded in 24mm Transwells 72 h before UFP exposure and kept at liquid interface conditions for 48 h before UFP exposure. Effect of subsequent exposure were referenced against cells exposed to clean air and PBS. Two replicates were performed for control and one for each allergen extract as well as incubation time between exposures.

first: Joana

last: Candeias

first: Nadine

last: Gawlitta

first: Christoph

last: Bisig

first: Stephanie

last: Binder

first: Jana

last: Pantzke

first: Svenja

last: Offer

first: Narges

last: Rastak

first: Stefanie

last: Bauer

first: Anja

last: Huber

first: Evelyn

last: Kuhn

first: Jeroen

last: Buters

first: Thomas

last: Groeger

first: Sebastian

last: Oeder

first: Mathilde

last: Delaval

first: Sebastiano

last: DiBucchianico

first: Ralf


title: Influenza-specific effector memory B cells predict long-lived antibody responses to vaccination in humans [Rep-Seq]

city: Birmingham

first: Alexander

last: Rosenberg

state: AL

address: 1720 2nd Avenue South, Suite 276/11

institute: University of Alabama at Birmingham

summary: BCR repertoire sequencing data from influenza vaccinated subjects.

overall_design: Three healthy subjects had blood drawn at various time points following IM influenza vaccine. Cells were sort purified to obtain naive B cells, plasmablasts, flu (HA) specific memory B cells (FcRL5+ and FcRL5neg) and IgD negative memory B cells. Donor 1 had HA-specific memory B cells for 7 and 14 days post vaccine; Donor 2 had HA-specific memory B cells 7 days post vaccine; Donor 3 had HA-specific memory B cells 14 and 28 days post vaccine. All donors had IgD negative memory B cells 120 days post vaccine, naive B cells for either 7 or 14 days post vaccine and plasmablasts 7 days post vaccine in years 1 and 2. These samples were used for repertoire analysis by deep sequencing.

first: Anoma

last: Nellore

first: Esther

last: Zumaquero

first: Christopher

last: Scharer

middle: F

last: Fucile

last: Tipton

first: Rodney

middle: G

last: King

first: Tian

last: Mi

first: Betty

last: Mousseau

first: John

last: Bradley

first: Fen

last: Zhou

first: Stuti

last: Mutneja

first: Paul

last: Goepfert

first: Jeremy

last: Boss

first: Troy

last: Randall

first: Ignacio

last: Sanz

first: Frances

last: Lund


title: A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy

first: Hyo Sik

last: Jang


title: Atypical Neurofibromas reveal distinct epigenetic features with proximity to benign peripheral nerve sheath tumor entities

city: Hamburg

first: Catena

last: Kresbach

address: Martinistrasse 52

institute: Research Institute Children‘s Cancer Center Hamburg

type: Methylation profiling by genome tiling array

summary: Unsupervised hierarchical clustering and t-SNE analysis indicated that 36/40 ANF cluster separately from MPNST and instead close to the benign tumor entities. Of these 36 tumors, 23 ANF formed a molecularly distinct cluster in proximity to schwannomas. Tumors from this cluster had frequent heterozygous or homozygous loss of CDKN2A/B and significantly more lymphocyte infiltration than MPNST, schwannomas, and NF. Few ANF clustered closely with neurofibromas, schwannomas, or MPNST, raising the question, whether diagnosis based on histological features alone might pose a risk to both over- and underestimate the aggressiveness of these lesions.

overall_design: 40 samples of histologically diagnosed atypical neurofibromas, ANNUBPs and low grade MPNST from 40 individuals were analyzed. All samples passed the detection p-value cut-off of <0.01.

first: Ulrich

last: Schüller


title: Hepatocyte Smoothened Activity Controls Susceptibility to Insulin Resistance and Nonalcoholic Fatty Liver Disease [scRNA-Seq]

first: Anna Mae

last: Diehl

address: 905 S LaSalle St

institute: Duke University

summary:
Nonalcoholic fatty liver disease (NAFLD) is strongly associated with insulin resistance (IR), but little is known about the key genetic driver that links these two disorders.
We aimed to elucidate the mechanism by which Smoothened (Smo), a G-protein coupled receptor, contributes to pathogenesis of NAFLD and IR.

overall_design: We used Smoflox/flox mice in combination with AAV8-TBG-Cre which enables genetic disruption of Smo in mature hepatocytes selectively. Adult Smoflox/flox mice were treated with AAV vectors for 7 days. Their livers were analyzed by histology, immunoblots, qPCR and single-cell RNA sequencing. We also performed RNA sequencing of 368 liver samples from controls and patients with NAFLD to assess the association of Smo expression with liver inflammation and fibrosis.

first: Tianyi

last: Chen

first: Anna


title: Hepatocyte Smoothened Activity Controls Susceptibility to Insulin Resistance and Nonalcoholic Fatty Liver Disease

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Hepatocyte Smoothened Activity Controls Susceptibility to Insulin Resistance and Nonalcoholic Fatty Liver Disease [RNA-Seq]


title: NFIC1 suppresses migration and invasion of breast cancer cells through interferon-mediated Jak-STAT pathway

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

summary: NFIC1, the longest isoform of NFIC, is essential for the regulation on spatiotemporal expressions of drug-metabolizing genes in liver. However, the role of NFIC1 in breast cancer is not clear. Here we showed that increased expression of NFIC1 suppressed the migration and invasion of MCF-7 cells. The activation of interferon-associated Jak-STAT pathway was enhanced with NFIC1 overexpression. NFIC1 overexpression upregulated the expression of IFNB1, IFNL1, IFNL2 and IFNL3. Treatment with Jak-STAT pathway inhibitors, Filgotinib or Ruxolitinib, reversed the suppressive effects of NFIC1 overexpression on migration and invasion. In addition, we found that MX1 and MX2 were the target genes of NFIC1- activated Jak-STAT pathway, which mediated the migration and invasion of MCF-7 cells. These results demonstrated that NFIC1 inhibited the migration and invasion in MCF-7 cells through interferon mediated activation of Jak-STAT pathway, indicating that Jak-STAT pathway might be a potential therapeutic target for preventing breast cancer metastasis.

overall_design: Total RNA obtained from MCF7 cells transiently transfected with pcDNA3.1 (Control) or pcDNA3.1-NFIC1 (NFIC1).

first: Jing

last: Zhang

first: Mingyue

last: Fan

first: Chanjuan

last: Jin

first: Zhaoying

last: Wang

first: Yutong

last: Yao

first: Yueru

last: Shi

first: Youzhong

last: Wan


title: circRNA expression in db/db mouse

city: Wuhan

first: Qiong

last: Yuan

address: Huangjiahu Road 2#

institute: Wuhan University of Science and Technology

summary: This research was detected the differentially expressed circular RNAs in the heart tissues of WT mouse and db/db mouse. We have completed the circRNA Arraystar mouse V.2 analysis of the 3 wt mouse and 3 db/db mouse age 3 month. Whole heart tissue RNA samples were collected and then were digested with RNAse R. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar?s standard protocols.

overall_design:
Different circRNA expression in the heart tissues of db/db mouse compared with wt group
3 samples for control group (C1-C3) and 3 samples for db/db group (d1-d3)


title: Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications

city: Warsaw

first: Adria-Jaume

last: Roura

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Glioblastoma (GBM, WHO grade IV) is an aggressive, primary brain tumor. Despite gross surgery and forceful radio- and chemotherapy, survival of GBM patients did not improve over decades. Several studies reported transcription deregulation in GBMs but regulatory mechanisms driving overexpression of GBM-specific genes remain largely unknown. Transcription in open chromatin regions is directed by transcription factors (TFs) that bind to specific motifs, recruit co-activators/repressors and a transcriptional machinery. Identification of GBM-related TFs-gene regulatory networks may reveal new, targetable mechanisms of gliomagenesis.

overall_design: We predicted TFs-regulated networks in GBMs in silico and intersected them with putative TF binding sites identified in accessible chromatin in human glioma cells and GBMs. The Cancer Genome Atlas and gliomaAtlas datasets (DNA methylation, H3K27 acetylation, transcriptomic profiles) were explored to elucidate TFs-gene regulatory networks and effects of the epigenetic background

first: Paulina

last: Szadkowska

first: Kasia

last: Poleszak

first: Karolina

last: Stepniak

first: Michal

last: Dabrowski

first: Aleksandra

last: Ellert-Miklaszewska

first: Kamil

last: Wojnicki

first: Iwona

last: Ciechomska

first: Bozena

last: Kaminska

first: Bartosz

last: Wojtas


title: Duodenal Mucosal Barrier in Functional Dyspepsia [miRNA]

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

summary:
Epithelial Barrier and Leaky Gut in Dyspepsia
Running title: Epithelial Barrier and Leaky Gut in Dyspepsia
Context: Some studies suggest that FD is associated with ex vivo duodenal epithelial micro-inflammation and barrier impairment; the pathogenesis of these findings is unclear. miRNAs reduce expression of epithelial barrier genes and have been postulated to increase epithelial permeability in irritable bowel syndrome.
New findings: Compared to controls, there is reduced mRNA expression of several barrier proteins (zona occludin-1), increased expression of several miRNAs (eg, miR-142-3p) that suppress the genes for barrier proteins in FD. However, mucosal eosinophils, intraepithelial lymphocytes, and mast cells, ex- and in vivo permeability (urinary lactulose and mannitol excretion) were not significantly different in FD.
Impact: Patients with FD do not have a leaky gut syndrome.

overall_design: We compared the duodenal mucosal gene expression and miRNAs, in vivo permeability (lactulose-mannitol excretion for 2h after ingestion), ex vivo assessments (transmucosal resistance [TMR], FITC-dextran flux, and basal ion transport), and duodenal histology (light and electron microscopy) in patients with FD and controls.

first: Sushmitha

last: Puthanmadhom Narayanan

last: O’Brien

first: Pritha

last: Chanana

first: Mayank

last: Sharma

first: Anshuman

middle: C

last: Desai

first: Thomas

last: Smyrk

first: Rondell

middle: P

last: Graham

first: Madhusudan

last: Grover

first: Adil

last: Bharucha


title: Duodenal Mucosal Barrier in Functional Dyspepsia

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

overall_design: Refer to individual Series


title: Duodenal Mucosal Barrier in Functional Dyspepsia [mRNA]

middle: R


title: Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus. [ChIP-seq II]

city: Shanghai

first: yonghu

last: wu

address: 800# Dongchuan Road

institute: Shanghai JiaoTong University

summary: By CRISPR/Cas9 DNA-fragment editing, in conjunction with chromosome conformation capture,  ChIP-seq and RNA-seq technology, we studied CRISPR single cell clones of duplicated CBS-containing enhancers or promoters in the Pcdhα gene cluster. We found that CTCF plays an essential role in determining promoter choice and enhancer selection. In addition, the choices mediated by CTCF is based on the chromatin loops formed between forward-reverse convergent CBS pairs with the proximal one dominant.

overall_design: ChIP-seq, 4C-seq and RNA-seq experiments were performed on both wildtype and DNA-fragment editting cell lines (mE1 insertion, mE2 insertion and ac1 repeat). For ChIP-seq experiments, Binding patterns of CTCF and Cohesin complex(showed by Rad21) as well as histone modification marker H3K27ac were examined. For 4C-seq experiments, the 3D chromatin conformations of several viewpoints were captured by 4C (Circular Chromatin Conformation Capture) method, in duplicate.  For RNA-seq experiments, the mRNA  profiles of these cell lines were generated by deep sequencing, in duplicate.

first: Yonghu

last: Wu

first: Zhilian

last: Jia

first: Xiao

last: Ge


title: Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus. [RNA-seq]


title: Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus


title: Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus. [ChIP-seq I]


title: RNA Polymerase IV sensitises the chromatin via histone modifications modulating protein coding genes [sRNA-Seq]

status: Public on Feb 28 2023

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

summary: Knock down of RNA polymerase IV in rice caused pleiotropic reproductive defects. We investigated the molecular effects of loss of pol IV in different rice tissues by profiling sRNA and mRNA transcriptomes, DNA methylomes, histone modifications and degradome sequencing. These analyses revealed the multifaceted roles of RNA polymerase IV in bringing about regulation of protein coding genes.

overall_design: We profiled sRNAs in the WT and pol IV kd tissues from pre-emerged panicle, anther and endosperm tissues to estimate the effect of loss of pol IV the the sRNA transcriptome.

last: Padubidri

first: Vivek

last: Sundar

first: Swetha

last: Chenna


title: RNA Polymerase IV sensitises the chromatin via histone modifications modulating protein coding genes [RNA-Seq]

overall_design: We performed RNA seq analyses to look at the expression of the genes in WT and pol IV kd pre-emerged panicle and anther tissues.


title: Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus. [4C-seq]


title: RNA Polymerase IV sensitises the chromatin via histone modifications modulating protein coding genes [MethylC-Seq]

type: Methylation profiling by high throughput sequencing

overall_design:
We have performed MethyC-Seq to profile the DNA methylation status genomewide from the WT and pol IV kd pre-emerged panicle tissue.
We have performed MethyC-Seq to profile the DNA methylation status genomewide from the WT and pol IV kd vegetative leaf tissue.


title: RNA Polymerase IV sensitizes the chromatin via histone modifications modulating protein coding genes [Degradome]

overall_design: We have performed degradome sequencing in the pre-emerged panicle of Wt and pol IV kd plants to profile the differences in the post transcriptional silencing mechanism of RNA silencing upon loss of pol IV.


title: RNA Polymerase IV sensitizes the chromatin via histone modifications modulating protein coding genes [ChIP-Seq]

overall_design:
Histone H3 PTMs (H3K4me3, H3K9me2 and H3K27me3), Pol II ChIP and total H3 were profiled genomewide using ChIP seq employing commercially available validated antibodies in the pre-emerged panicle tissues of green house grown WT and pol IV kd plants.
Histone H3K9me2 and Pol II ChIP were profiled genomewide using ChIP seq employing commercially available validated antibodies in the pre-emerged panicle tissues of green house grown WT and pol IV kd plants.


title: RNA Polymerase IV sensitises the chromatin via histone modifications modulating protein coding genes


title: Expression data from cancer cells and fibroblasts populations

status: Public on Feb 27 2023

city: Shreveport

first: Ana-Maria

last: Dragoi

state: Louisiana

address: 1501 Kings Hwy, Molecular and Cellular Physiology Room 4-208

institute: LSU-Health Shreveport

summary:
Epithelial-to-mesenchymal transition is a complex process that occurs in development and cancer metastasis. We show that EMT plasticity occurs in cancer cells when co-culture with fibroblasts.
We used microarrays to detail the global program of gene expression in the H69 small-cell lung carcinoma line when in direct contact with CCD8 fibroblasts.

overall_design: H69 and CCD8 cells from control (CT), indirect (INS), and direct (MIX) contact were sorted for RNA extraction and hybridization on Affymetrix microarrays. All samples were collected from one time-point (72h).


city: ShangHai

first: Lijun

last: Wang

state: China

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary: The Ten-eleven translocation (TET) family of dioxygenases can mediate cytosine demethylation by catalyzing the oxidation of 5-methylcytosine (5mC). TET-mediated DNA demethylation controls the proper differentiation of embryonic stem cells and TET proteins display functional redundancy during early gastrulation. However, it is unclear if TET proteins have functional significance in mammalian skeletal development. Here, we report that Tet deficiency in mesoderm mesenchymal stem cells results in severe defects of bone development. The existence of any single Tet gene allele can support early bone formation, suggesting a potential functional redundancy of TET proteins. Integrative analyses of RNA-seq, Whole Genome Bisulfite Sequencing (WGBS) and Assay for Transposase-Accessible Chromatin (ATAC-seq) demonstrate that TET-mediated demethylation increases the chromatin accessibility of target genes by RUNX2 and facilities RUNX2-regulated transcription. In addition, TET proteins interact with RUNX2 through their catalytic domain to regulate cytosine methylation around RUNX2 binding region. The catalytic domain is indispensable for TET proteins to regulate RUNX2 transcription activity on its target genes and to regulate bone development. These results demonstrate that TET proteins function redundantly to regulate RUNX2 activity via dual mechanisms and maintain skeletal homeostasis.

overall_design: Gene expression profiles with WT and Tet KO osteoblasts, three repeats.

first: Weiguo

last: Zou

first: Wanlu

last: Liu

first: Xiuling

last: You

first: Dengfeng

last: Ruan


title: Transcriptomic characterization of control and drug-treated APOB-mutant organoids to study steatosis-resolving drug effects

status: Public on Feb 23 2023

city: Utrecht

first: Delilah

last: Hendriks

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We treated APOB-mutant organoids with different anti-NAFLD drug candidates that were effective at resolving steatosis. To understand the mechanisms of drug action and adverse drug effects we performed bulk RNA-sequencing on drug-treated and vehicle-treated APOB mutant organoids.

overall_design: APOB-mutant organoids, 2 clonal lines from 2 different donors, were treated with the respective drug (ACCi, FASi, DGAT2i, FXRa, or hFGF19) or vehicle (control) for 7 days. Thereafter, organoids were harvested for RNA extraction.

first: Hendriks

last: Delilah

first: Artegiani

last: Benedetta

first: Clevers

last: Hans


title: CD4+ T cell calibration of antigen-presenting cells optimizes antiviral CD8+ T cell immunity

city: Bonn

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

institute: University Hospital Bonn

summary:
Antiviral CD8+ T cell immunity depends on the integration of various
contextual cues, but how antigen-presenting cells (APCs) consolidate these
signals for decoding by T cells remains unclear. Here, we describe gradual
interferon-α/interferon-β (IFNα/β)-induced transcriptional adaptations
that endow APCs with the capacity to rapidly activate the transcriptional
regulators p65, IRF1 and FOS after CD4+ T cell-mediated CD40 stimulation.
While these responses operate through broadly used signaling components,
they induce a unique set of co-stimulatory molecules and soluble mediators
that cannot be elicited by IFNα/β or CD40 alone. This response is critical
for the acquisition of antiviral CD8+ T cell effector function, and its activity
in APCs from individuals infected with severe acute respiratory syndrome
coronavirus 2 correlates with milder disease. These observations uncover a
sequential integration process whereby APCs rely on CD4+ T cells to select
the innate circuits that guide antiviral CD8+ T cell responses.

overall_design: Examination of IFN-aA and a-CD40 signaling in BM-derived cDC1

first: Elise

last: Gressier

first: Jonas

last: Schulte-Schrepping

first: Paul

last: Whitney

first: Annabell

last: Bachem

first: Lev

last: Pretrov

first: Katharina

last: Hochheiser

first: Michele

last: Clarke

first: Maike

last: Kreutzenbeck

first: Sarah

last: Gabriel

first: Wolfgang

last: Kastenmüller

first: Christian

last: Kurts

first: Axel

last: Kallies

middle: J

last: Hertzog

first: Eicke

last: Latz

first: Thomas

last: Gebhardt

first: Leif

last: Sander

first: Joachim

last: Schultze

middle: V

first: Sammy

last: Bedoui

first: Jasper

last: Spitzer

first: Tomislav

last: Kostevc

first: Alexandru

last: Odainic

first: Carolin

last: van de Sandt

first: Oanh

last: Nguyen

last: Ashhurst

first: Linden

last: Gearing

first: Tina

last: Meischel

first: Marie

last: Greyer

last: Londrigan

first: Katherine

last: Kedzierska

first: Michael

last: Chopin

first: Jan

last: Schroeder

first: Birgit

last: Sawitzki

first: Anna

last: Brumhard

first: Paula

last: Stubbemann

first: Benedikt

last: Obermayer

first: Kayla

last: Wilson

first: Clare

last: Oates

first: Yu-Chen

last: Chen

first: Kristen


title: Cerebellar Transcriptomic Analysis in a Chronic Plus Binge Mouse Model of Alcohol Use Disorders Demonstrate Ethanol Induced Neuroinflammation and Altered Glial Gene Expression

city: Little Rock

first: Stephanie

middle: D

last: Byrum

state: Arkansas

address: 501 Jack Stephens Dr, Jackson T. Stephens Bldg 4th floor

institute: University of Arkansas for Medical Sciences

summary: Alcohol use disorders (AUD) are one of the most common preventable mental health disorders and can result in pathology within the CNS, including the cerebellum. Cerebellar alcohol exposure during adulthood has been associated with disruptions in proper cerebellar function. However, the mechanisms regulating ethanol-induced cerebellar neuropathology are not well understood. High-throughput next generation sequencing was performed to compare control versus ethanol treated adult C57BL/6J mice in a chronic plus binge model of AUD. Mice were euthanized, cerebella were microdissected, RNA was isolated, and RNA-sequencing was performed. Down-stream transcriptomic analyses revealed significant changes in gene expression and global biological pathways in control versus ethanol treated mice that included pathogen-influenced signaling pathways and cellular immune response pathways.  Microglial associated genes showed a decrease in homeostatic molecules and an increase in molecules associated with chronic neurodegenerative diseases, while astrocyte associated genes showed an increase in molecules associated with acute injury.  Oligodendrocyte lineage cell genes showed a decrease in molecules associated with both early-stage progenitors as well as mature myelinating oligodendrocytes.   These data provide new insight into the mechanisms by which ethanol induces cerebellar neuropathology and alterations to the immune response in AUD.

overall_design: Compare gene expression of control vs. ethanol treated adult C57BL/6J mice, in a chronic plus binge model of alcohol use disorder (AUD), using RNAseq data.

first: Kalee

last: Holloway

first: Marissa

last: Pinson

first: James

last: Douglas

first: Tonya

last: Rafferty

first: Cynthia

last: Kane

first: Rajesh

last: Miranda

first: Paul

last: Drew


title: ALL-tRNAseq enables robust tRNA profiling in tissue samples

status: Public on Feb 24 2023

city: Amsterdam

first: Chantal

last: Scheepbouwer

address: De Boelelaan 1117

department: Neurosurgery

institute: VU University Medical Center

summary: Transfer RNAs (tRNAs) are small adaptor RNAs essential for mRNA translation. Alterations in the cellular tRNA population can directly affect mRNA decoding rates and translational efficiency during cancer development and progression. To evaluate changes in the composition of the tRNA pool, multiple sequencing approaches have been developed to overcome reverse transcription blocks caused by the stable structures of these molecules and their numerous base modifications. It remains however unclear whether current sequencing protocols faithfully capture tRNAs existing in cells or tissues. This is specifically challenging for clinical tissue samples that often present variable RNA qualities. For this reason, we developed ALL-tRNAseq, which combines the highly processive MarathonRT and RNA demethylation, for the robust assessment of tRNA expression, together with a randomized adapter ligation strategy prior to reverse transcription, to assess tRNA fragmentation levels in both cell lines and tissues. Incorporation of tRNA fragments not only informed on sample integrity, but also significantly improved tRNA profiling of tissue samples. Our data showed that our profiling strategy effectively improves classification of oncogenic signatures in glioblastoma and diffuse large B-cell lymphoma tissues, particularly for samples presenting higher levels of RNA fragmentation, further highlighting the utility of ALL-tRNAseq for translational research.

overall_design: Development of a high-throughput sequencing technology that is useful to explore relative mature tRNA abundance and to simultaneously assess tRNA integrity in cell lines as well as clinical tissue samples.

first: Ernesto

last: Aparicio-Puerta

first: Michael

last: Hackenberg

first: Danijela

last: Koppers-Lalic


title: Fungal plant pathogen “mutagenomics” reveals tagged and untagged mutations in Zymoseptoria tritici and identifies SSK2 as key morphogenesis and stress-responsive virulence factor

status: Public on Feb 25 2023

city: Harpenden

first: Daniel

last: Smith

state: Hertfordshire

address: West Common

department: IDE

institute: Rothamsted Research

summary: 'Mutagenomics' is a combination approach of random mutagenesis, phenotypic screening, and whole-genome re-sequencing to uncover all tagged and untagged mutations linked with phenotypic changes in an organism. In this study, we performed a mutagenomics screen on the wheat pathogenic fungus Zymoseptoria tritici for altered morphogenetic switching and stress sensitivity phenotypes using Agrobacterium-mediated “random” T-DNA mutagenesis (ATMT).  Biological screening identified four mutants which were strongly reduced in virulence on wheat. Whole genome re-sequencing defined the positions of the T-DNA insertion events and revealed several unlinked mutations potentially also affecting gene functions. Remarkably, two independent reduced virulence mutant strains, with similarly altered stress sensitivities and aberrant hyphal growth phenotypes, were found to have distinct loss of function mutations in the ZtSSK2 MAPKKK gene. One mutant strain had a direct T-DNA insertion affecting the N-terminus of the predicted protein, whilst the other possessed an unlinked frameshift mutation towards the C-terminus. We used genetic complementation to restore both strains' wild-type (WT) function (virulence, morphogenesis, and stress response). We demonstrated that ZtSSK2 has a non-redundant function with ZtSTE11 in virulence through the biochemical activation of the stress-activated HOG1 MAPK pathway. Moreover, we present data suggesting that SSK2 has a unique role in activating this pathway in response to specific stresses. Finally, dual RNAseq-based transcriptome profiling of WT and SSK2 mutant strains revealed many HOG1-dependent transcriptional changes in the fungus during early infection and suggested that the host response does not discriminate between WT and mutant strains during this early phase. Together these data define new genes implicated in the virulence of the pathogen and emphasise the importance of a whole genome sequencing step in mutagenomic discovery pipelines.

sample_organism:
Triticum aestivum
Zymoseptoria tritici IPO323

overall_design: Dual RNA sequencing on total RNA extracted from wheat leaves infected with  a Z. tritici wild type IPO323 or an IPO323 mutant (4-124, NCBI:SAMN33272755) at two time points, 6hpi and 24hpi.  5 sample leaves were pooled into each technical replicate and there were 3 technical replicates for each treatment time point.

first: Hannah

last: Blyth

first: Robert

last: King

first: Carlos

last: Bayon

first: Tom

last: Ashfield

last: Walpole

first: Eudri

last: Venter

first: Rumiana

last: Ray

first: Kostya

last: Kanyuka

first: Jason

last: Rudd


title: Rapamycin-Induced Feedback Activation of mRNA Translation in Pancreatic Cancer

status: Public on Feb 21 2023

city: Bronx

first: Kamini

last: Singh

state: NY

address: 1300 Morris Park Ave, Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: We report mTOR inhibitor Rapamycin's specific and genome-wide effect on mRNA translation. Using ribosome footprinting in pancreatic cancer cells that lack 4EBP1 expression we establish the effect of mTOR-S6-dependent mRNA translation, and identify translation programs activated following mTOR inhibition.

overall_design: We performed ribosome footprinting and RNA sequencing on six samples of PANC1 cells: three control DMSO-treated biological replicates and three biological replicates collected 60 minutes after 50nM Rapamycin treatment. Control samples are labeled as 'CT', and Rapamycin-treated samples as 'RAPA'. Data from ribosome protected RNA are labeled as 'RF', and from total RNA as 'RNA'.

first: Trang

middle: U

last: Nguyen

first: Harrison

last: Hector

first: Eric

middle: N

last: Pederson

first: Jianan

last: Lin

first: Zhengqing

last: Ouyang

first: Hans

last: Wendel


title: Spatiotemporal Regulation of Cholangiocarcinoma Growth and Dissemination by Peritumoral Myofibroblasts in a Vcam1-dependent Manner

status: Public on Feb 22 2023

city: Memphis

first: Liqin

last: Zhu

state: TN

address: 262 Danny Thomas Place

department: Pharmacy and Pharmaceutical Sciences

institute: St. Jude Children’s Research Hospital

summary: Intrahepatic cholangiocarcinoma (iCCA) is characterized by its highly desmoplastic stroma. Myofibroblasts (MFs) are present both within the tumor mass (intratumoral MFs, iMFs) and at the tumor border (peritumoral MFs, pMFs). Using a spheroid-based coculture system, we show that the initial iCCA-pMF contact is growth suppressive to the tumor cells. However, prolonged iCCA-pMF interaction elicits significant tumor cell invasion and dissemination. We find that vascular cell adhesion molecule-1 (Vcam1) level is elevated in tumor cells in contact with pMFs but low in disseminated tumor cells both in vitro and in vivo. A gene regulatory network analysis of mouse and patient iCCA tumors and Vcam1 knockout (Vcam1KO) demonstrate a heavy involvement of Vcam1 in epithelial-to-mesenchymal transition. While Vcam1KO has only a limited impact on tumor cell growth in their monoculture, Vcam1KO spheroids exhibit instant dissemination and a severe growth defect when cocultured with pMFs. When transplanted into the liver, Vcam1KO iCCA cells show a similar increase in dissemination but a significant defect in establishing primary and metastatic tumors. Incomplete blocking of Vcam1 in vivo reduces the size but increase the number of metastatic lesions. Overall, our study shows a spatiotemporal regulation of iCCA growth and dissemination by pMFs in a Vcam1-dependent manner.

overall_design: Two Vcam1KO single-cell clones were generated (Vcam1KO1 and Vcam1KO2) to identify the direct downstream targets of Vcam1 by RNA-seq.

first: Cheng

last: Tian

first: Liyuan

last: Li

first: Qingfei

last: Pan

first: Beisi

last: Xu

first: Yizhen

first: Li

last: Fan

first: Anthony

last: Brown

first: Michelle

last: Morrison

first: Kaushik

last: Dey

first: Jun

last: Yang

first: Jiyang

last: Yu

first: Evan

last: Glazer


title: Bromocriptine inhibits proliferation in eutopic endometrium from women with adenomyosis

city: Münster

first: Eberhard

last: Korsching

state: NRW

address: Niels-Stensen-Str. 14

department: Inst. of Bioinformatics

institute: University of Muenster

summary:
Objective: Bromocriptine treatment has been shown to reduce menstrual bleeding and pain in women with adenomyosis in a pilot clinical trial. The underlying mechanism contributing to the treatment effect is however unknown. This study was to explore the effect of bromocriptine on the proliferation and migration properties of the endometrium in women with adenomyosis, by assessing cellular and molecular changes after six months of vaginal bromocriptine treatment.
Methods: Endometrial specimens were collected during the proliferative phase from women with adenomyosis (n=6) before (baseline) and after six months of vaginal bromocriptine treatment. Immunohistochemistry was used to determine changes in the protein expression of Ki67 in the endometrium. Primary endometrial stromal cells isolated at baseline were expanded in vitro and exposed to different doses of bromocriptine to determine the optimal half-maximum inhibitory concentration (IC50) using CellTiter-Blue® Cell Viability Assay. Cell proliferation was assessed by bromodeoxyuridine ELISA assay and Ki67 gene expression was checked by real-time PCR. The migratory ability of endometrial stromal cells was determined by wound healing and transwell migration assays. Small RNA sequencing was applied on tissues collected from women with adenomyosis before and after bromocriptine treatment to identify differentially expressed micro RNAs. Bioinformatic methods were used for target gene prediction and the identification of biological pathways.
Results: Vaginal bromocriptine treatment reduced the Ki67 protein expression in the endometrium of women with adenomyosis and did not change the prolactin mRNA expression and protein concentration of prolactin in endometrial tissues. Bromocriptine significantly inhibited the proliferative and migrative abilities of endometrial stromal cells derived from women with adenomyosis in vitro. Moreover, small RNA sequencing revealed 27 differentially expressed micro RNAs (miRNAs) between the endometrium of women with adenomyosis before and after six months of vaginal bromocriptine treatment. KEGG pathway analysis on targeted genes of 27 miRNAs showed that several signaling pathways associated with cell proliferation and apoptosis were enriched after treatment.
Conclusion: Bromocriptine treatment exhibits an anti-proliferative effect in the endometrium of women with adenomyosis in vivo and in vitro. Bromocriptine might inhibit the proliferation of endometrial tissue in adenomyosis in part through the regulation of dysregulated microRNAs and proliferation-associated signaling pathways.

overall_design: Compare the expression of microRNAs in endometrium from women with adenomyosis before and after treatment with Bromocriptine. Samples included are paired (before and after treatment).

first: Caroline

last: Frisendahl

first: Yiqun

last: Tang


title: Gene expression during transdifferentiation of bovine ear fibroblasts into adipocytes induced by small molecule compounds

city: Guangxi

first: ben

last: huang

address: NO.100. DAXUE EAST RD, Nanning

institute: School of Animal Science and Technology, Guangxi University

summary: To investigate the molecular mechanism of small molecule compound-induced transdifferentiation of bovine fibroblasts into adipocytes, we established direct conversion of bovine ear fibroblasts (BearFs) into the chemically-induced adipocytes (CiADCs) using three Small Molecular Compound.

overall_design:
We performed gene expression profiling analysis using data obtained from RNA-seq of 3 stages induced adipocytes at three time points
Cells at the end of  0 day,3 day and 6 day were analyzed by RNA-seq.

first: Longfei

last: Sun

first: Ben

last: Huang


title: Nutlin-3a induced changes in the transcriptome of parental and RFX7-/- U2OS cells

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: RNA-seq from parental and RFX7-/- U2OS cells treated with Nutlin-3a or DMSO control

overall_design: Parental U2OS and two distinct RFX7-/- clones of U2OS were treated with 10µM Nutlin-3a or DMSO control for 24h

first: Konstantin

last: Riege

first: Steve

last: Hoffmann


title: Longitudinal multi-omics analysis of Bordetella pertussis Tohama I fermentation

city: Lyon

first: Paul

last: Anziani

address: 40 avenue Tony Garnier

country: France

institute: Bioaster

summary: A longitudinal multi-omics analysis was carried out over a 26-hour small-scale fermentation of B. pertussis. Fermentations were performed in batch mode and under culture conditions intended to mimic industrial processes.

overall_design: Longitudinal gene expression profiling analysis of RNA-seq data, during a 26-hour small scale fermentation of B. pertussis. Samples were in biological triplicates and library were prepared in triplicates

first: Jérémie

last: Becker

first: Charlotte

last: Mignon

first: Nadège

last: Arnaud-Barbe

first: Virginie

last: Courtois

first: Marie

last: Izac

first: Romain

last: Pizzato

first: Joséphine

last: Abi-Ghanem

first: Viet-Dung

last: Tran

first: Magali

last: Sarafian

first: Andrei

last: Bunescu

first: Dominique

last: Garnier

first: Eric

last: Abachin

first: Geneviève

last: Renauld-Mongénie

first: Cyril

last: Guyard


title: Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-Coding Genes

status: Public on Feb 20 2023

city: Xiamen

first: Fan

last: Gao

state: Fujian

address: 668 Jimei Road

institute: Huaqiao University

summary: The human genome encodes a multitude of different noncoding transcripts that have been tra-ditionally separated on the basis of their lengths into long (>200 nt) or small (<200 nt) noncoding RNAs. The functions, mechanisms of action, and biological relevance of the vast majority of both long and short noncoding transcripts remain unknown. However, according to the functional understanding of the known classes of long and small noncoding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Nevertheless, direct evidence of functionality is lacking for most noncoding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we developed a high-throughput assay to test the functionality of sncRNAs by overexpressing them in human cells. Surprisingly, we found that a significant fraction (>40%) of unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small noncoding transcriptome can harbor multiple func-tional transcripts that warrant future studies.

overall_design: Nine samples sRNA-seq and twenty samples DNA-seq data used in this study.


title: Simultaneous inhibition of PPAR-γ and mTORC1 enables GM-CSF to induce the differentiation of monocytes into highly immunogenic dendritic cells

city: Buenos Aires

first: Fernando

last: Erra Diaz

address: Paraguay 2155 , 11th floor

department: Immunology

country: Argentina

institute: Universidad de Buenos Aires - The Jackson Laboratory

summary: Monocytes can differentiate into macrophages or dendritic cells. When treated with granulocyte-macrophage colony-stimulating factor (GM-CSF) monocytes differentiate into macrophage-like cells. Here, we report that pharmacological blockade of the nuclear receptor PPARγ in monocytes turns GM-CSF into a potent inducer of dendritic cell (Mo-DC) differentiation. Remarkably, simultaneous blockade of PPARγ and mTORC1 in the presence of GM-CSF promoted the differentiation of Mo-DCs with a stronger phenotypic stability and immunogenic profile when compared with canonical Mo-DCs differentiated by treatment with GM-CSF and IL-4. Moreover, and in contrast with the observations made with GM-CSF and IL-4, blockade of PPARγ and mTORC1 was shown to be able to induce the differentiation of monocyte-derived macrophages (Mo-Macs) into Mo-DCs. Transcriptional profiling performed at either early time points, as well as at the end of the differentiation process, revealed marked differences in the gene expression signature between Mo-DCs induced by GM-CSF and IL-4 and Mo-DCs induced by GM-CSF in the presence of PPARγ and/or mTORC1 inhibitors, thus suggesting diverging differentiation pathways. Our observations might contribute, not only to a better understanding of the mechanisms involved in Mo-DCs differentiation but also to improving the efficacy of both, DC vaccines and therapies focusing on the modulation of myeloid cell functions.

overall_design: Human monocytes were isolated from buffy coats obtained from healthy individuals using negative selection (RosetteSep™ Human Monocyte Enrichment Cocktail , StemCell) and cultured (1M/ml in RPMI1640 + 10% FBS) for either 8 hours or 5 days in the presence of a) GM-CSF (50ng/ml) alone, to induce MoMac differentiation, or in combination with b) IL4(30ng/ml) , c) Temsirolimus 50nM , d) GW9662 (10uM) or e) Temsirolimus 50nM + GW9662 (10uM), to induce MoDC differentiation.  RNAseq was performed after 8h of culture to analyze the early transcriptional profile of monocytes treated with the different experimental conditions (4 donors). Also , RNA was extracted from FACS sorted CD1a+ CD16-  MoDCs obtained after 5 days of culture in the presence of GM-CSF + IL4 (GMIL4-MoDC) , GM-CSF + Temsirolimus (GMT-MoDC) , GM-CSF + GW9662 (GMGW-MoDC) and GM-CSF + GW9662 + Temsirolimus (GMTGW-MoDC), in order to compare their transcriptional profile (3 donors).

first: Asa

last: Thibodeau

first: Duygu

last: Ucar

first: Jorge

last: Geffner


title: Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-coding Genes II

summary: Human genome encodes a multitude of different non-coding transcripts that have been traditionally separated based on their lengths into long or small non-coding RNAs. The vast majority of both long and short non-coding transcripts are not annotated and their functions, mechanisms of action and biological relevance remain unknown. However, based on the functional understanding of the known classes of long and small non-coding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Still, direct evidence of functionality is lacking for most non-coding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we have developed a high-throughput assay to test functionality of sncRNAs based on overexpressing them in human cells. Surprisingly, we found that a significant fraction (> 40%) unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small non-coding transcriptome can harbor multiple functional transcripts that warrant future studies.

overall_design: Functional analysis of novel small non-coding (snc) RNAs found in human K562 cell line.

first: Philipp

last: Kapranov


title: Single-Cell RNA sequencing reveals the immune microenvironment and signaling networks in cystitis glandularis

status: Public on Feb 18 2023

city: Changsha

first: Zhou

last: Tailai

address: Xiangya street, Changsha,

institute: Central South University

summary: Cystitis glandularis (CG) is a common chronic bladder hyperplastic disease. The current lack of unified diagnosis and treatment criteria makes it essential to comprehensively describe the inflammatory immune environment in CG research. Here, we performed scRNA-sequencing in CG patients for the first time, in which four inflamed tissues as well as three surrounding normal bladder mucosa tissues were included. Specifically, we isolated 18,869 cells to conduct bioinformatic analysis and performed immunofluorescence experiments. Our genetic results demonstrate that CG does not have the classic chromosomal variation observed in bladder tumors, reveal the specific effects of TNF in KRT15 epithelial cells, and identify a new population of PIGR epithelial cells with high immunogenicity. In addition, we confirmed the activation difference of various kinds of T cells during chronic bladder inflammation and discovered a new group of CD27-Switch memory B cells expressing a variety of immunoglobulins. Our study reveals, for the first time, the different kinds of cell subgroups in CG and provides the necessary basis for the clinical treatment of cystitis glandularis.

overall_design: We performed scRNA-sequencing in cystitis glandularis patients for the first time, in which four inflamed tissues as well as three surrounding normal bladder mucosa tissues were included.

first: Tailai

last: Zhou

first: Hengxin

last: Chen

first: Yinzhao

last: Wang

first: Sijie

last: Wen

first: Pinghong

last: Dao

first: Yuhang

first: Minfeng


title: Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar

city: Geraardsbergen

first: An

last: Vanden Broeck

address: Gaverstraat 4

country: Belgium

institute: Research Institute for Nature and Forest

summary: Insights into the forces that shape the plant methylome contribute to the understanding of the evolutionary significance of epigenetic diversity in plants. Previous research has mainly focused on herbaceous annual plants but it is currently unclear how much epigenetic variation is stably induced in long-lived woody perennials. There is also a need to demonstrate the role of parental environments and epigenetic variation on fitness. : We present detailed methylome analyses of the long-lived Lombardy poplar, Populus nigra cv. ‘Italica‘ Duroi. Trees of this widespread clonal cultivar descended from a common ancestor at least two centuries ago. We analyzed genome-wide methylomes of in total 29 pooled and individual DNA-samples. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts over at least two years and across vegetatively produced generations. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context.

overall_design: We selected plant material for whole genome bisulfite sequencing (WGBS) that was described and verified as the ‘true’ Lombardy poplar previously (doi.org/10.5061/dryad.2gf700), thus representing one single genotype. We used DNA samples of individual plants to investigate the stability of the epigenome during a growing season and across vegetatively reproduced generations.  The DNA samples from individual plants included i) DNA-samples from F1-ramets collected from Lombardy poplars located in Hungary, Italy, Spain and the UK, respectively, and ii) DNA-samples from second generation vegetative offspring (F2-ramets), propagated from the former F1-ramets). All ramets were grown in a common greenhouse environment in Geraardsbergen, Belgium (lat. 50,77635°, lon. 3.881007°) .

first: Tim

last: Meese

first: Pieter

last: Verschelde

first: Karen

last: Cox

first: Berthold

last: Heinze

first: Dieter

last: Deforce

first: Ellen

last: De Meester

first: Filip

last: Van Nieuwerburgh


title: Effects of Dlx2 Overexpression on the Genome of Maxillary Process in Early Embryo of Mice [CUT&Tag]

status: Public on Feb 17 2023

city: Shanghai

first: Jian

last: Sun

address: Quxi Road No.500

institute: Shanghai Ninth People's Hospital

summary: Transcription factor Dlx2 plays an important role in craniomaxillofacial development. Overexpression or null mutation can lead to craniomaxillofacial malformation in mice. Although some in vivo or in vitro experiments have explored part information about the mechanism of Dlx2 regulation, there is still a lack of complete description. Using a mouse model that can stably overexpress Dlx2 in neural crest cells, the authors conducted bulk RNA-Seq, scRNA-Seq and CUT&Tag on the early maxillary processes of mice, and comprehensively described the effects of Dlx2 overexpression on the early development of maxillary processes. Bulk RNA-Seq results showed that Dlx2 had greater interference on nerve development at E10.5, and gradually affected bone development at E12.5. ScRNA-Seq proved that overexpression of Dlx2 did not change the differentiation type of mesenchymal cells during this development process, but it would restrict the proliferation of cells and make mesenchymal cells differentiate prematurely, thus limiting the development of maxillary. CUT&Tag suggested that this regulatory process is closely related to Notch signaling pathway, and MNT and RUNX2, as direct downstream regulatory target genes of Dlx2, also play a very critical role.

overall_design: Cleavage under targets and segmentation (CUT&Tag) was performed on the maxillary process of E12.5 mice, the possible binding sites of DLx2 were analyzed, and the downstream target genome was searched by combining with bulk RNA Seq data.

first: Qian

last: Bian

first: Xudong


title: Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-coding Genes I

first: Fan

last: Gao

first: Philipp

last: Kapranov


title: Dp(10)2Yey mouse model of Down syndrome exhibits aberrant cognition, hippocampal-prefrontal neural dynamics and cytoarchitecture

city: London

first: Elizabeth

last: Fisher

state: London

address: Queen Square

institute: University College London

summary: The Dp(10)2Yey mouse carries a ~2.3 Mb intra-chromosomal duplication of mouse chromosome 10 (Mmu10) that makes it an essential model for aspects of Down syndrome (DS, trisomy 21). Specifically, these animals carry extra copies of Mmu10 genes that are homologous to those on human chromosome 21 (Hsa21). Here, we report spatial memory impairment and anxiety-like behaviour in this model alongside altered neural activity in the medial prefrontal cortex (mPFC) and hippocampus (HPC). Specifically, Dp(10)2Yey DS mice showed impaired spatial alternation associated with increased ripple activity in mPFC during the period of memory consolidation, and reduced mobility in a novel environment accompanied by reduced theta-gamma phase-amplitude coupling in HPC. Finally, we found alterations in the number of interneuron subtypes in mPFC and HPC that may contribute to the observed phenotypes and highlight potential approaches to ameliorate the effects of human trisomy 21.

overall_design: Hippocampal cells from the Dp(10)2Yey mouse and wildtype littermates were dissociated and analysed by scRNAseq

last: Cleverley

first: Rifdat

last: Aoidi

first: Miriam

last: Sopena


title: Effects of Dlx2 Overexpression on the Genome of Maxillary Process in Early Embryo of Mice [OE Bulk RNA-seq]

overall_design: Using a Dlx2 overexpression mouse model, the authors conducted bulk RNA Seq on the maxillary process of E10.5 mice, analyzed the impact of Dlx2 overexpression on genome expression, and compared it with the existing data of E12.5 mouse maxillary process in GEO database.

last: Wang


title: Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells [scRNA-Seq 2]

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

summary: Reconstitution of germ cell fate from pluripotent stem cells provide the opportunities to understand the molecular underpinning of germ cell development. Here, we established a several culture methods of induced pluripotent stem cells (iPSCs) in common marmoset (Callithrix jacchus, cj), which stably propagate in an undifferentiated state. Notably, iPSCs cultured on feeder layer in the presence of a WNT signaling inhibitor upregulate genes related to ubiquitin-dependent protein catabolic process and acquire permissive state that readily differentiate into primordial germ cell-like cells (PGCLCs) bearing immunophenotypic and transcriptomic similarities to pre-migratory cjPGCs. Induction of cjPGCLCs accompanies transient upregulation of mesodermal genes and culminate in establishing primate-specific transcriptional network similar to humans and cynomolgus monkeys. Moreover, cjPGCLCs can be expanded in monolayer while retaining cellular state. Upon co-culture with mouse testicular somatic cells, these cells acquire DDX4+ early prospermatogonia-like state. Our findings provide a framework for understanding and reconstituting germ cell development in marmoset in vitro, which serve as an comparative tool and foundation for a preclinical model for human in vitro gametogenesis.

overall_design: Harvest marmoset iPSC and PGCLCs aggregates, and run single cell RNA-seq

first: Keren

last: Cheng

first: Yasunari

last: Seita

first: Kotaro

last: Sasaki


title: Effects of Dlx2 Overexpression on the Genome of Maxillary Process in Early Embryo of Mice [WT Bulk RNA-seq]

overall_design: The authors conducted bulk RNA Seq on the maxillary process of E10.5 wildtype mouse and Dlx2 overexpression mouse, analyzed the impact of Dlx2 overexpression on genome expression, and compared it with the existing data of E12.5 mouse maxillary process in GEO database.


title: Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells [bisulfite-seq]

overall_design: Harvest marmoset cjiPSC on feeder with IWR1, d4 cjPGCLCs and extension culture of cjPGCLCs at day30 and make bisulfite sequencing libraries to estimate the overall DNA methylation levels.


title: Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells [bulk RNA-seq]

overall_design: CjiPSCs cultured in the presence or absence of feeders, in the presence or absence of IWR1, were collected. Extension culture of cjPGCLCs were collected at day 30.


title: Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells [scRNA-seq]

overall_design: Harvest marmoset embryonic day 50 embryo, and run single cell RNA-seq.

first: John

last: McCarrey

first: Nomesh

last: Yadu

first: Ian

last: Cheeseman

first: Alec

last: Bagwell

first: Sean

last: Vargas

first: Christopher

last: Navara

first: Brian

last: Hermann


title: Microbiota-derived tryptophan catabolites mediate the chemopreventive effects of statins on colorectal cancer III

first: Ji-Xuan

last: Han

address: 145 Middle Shandong Road

institute: Renji Hospital, Shanghai Jiao-Tong University School of Medicine

summary: Epidemiological studies have indicated an association between statin use and reduced incidence of colorectal cancer (CRC), and work in preclinical models has demonstrated a potential chemopreventive effect. Statins are also associated with reduced dysbiosis in the gut microbiome, yet the role of the gut microbiome in the protective effect of statins in CRC is unclear. Here we validated the chemopreventive role of statins by retrospectively analysing a cohort of patients who underwent colonoscopies. This was confirmed in preclinical models and patient cohorts, and we found that reduced tumour burden was partly due to statin modulation of the gut microbiota. Specifically, the gut commensal Lactobacillus reuteri was increased as a result of increased microbial tryptophan availability in the gut after atorvastatin treatment. Our in vivo studies further revealed that L. reuteri administration suppressed colorectal tumorigenesis via the tryptophan catabolite, indole-3-lactic acid (ILA). ILA exerted anti-tumorigenic effects by downregulating the IL-17 signalling pathway. This microbial metabolite inhibited T helper 17 cell differentiation by targeting the nuclear receptor, RAR-related orphan receptor γt (RORγt). Together, our study provides insights into an anti-cancer mechanism driven by statin use and suggests that interventions with L. reuteri or ILA could complement chemoprevention strategies for CRC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lamina propria cells from Apc Min/+ mice treated with vehicle control or atorvastatin

first: Zhi-Hang

last: Tao

first: Ji-Lin

first: Hua

last: Xiong

first: Ying-Xuan

last: Chen

first: Jing-Yuan

last: Fang


title: Microbiota-derived tryptophan catabolites mediate the chemopreventive effects of statins on colorectal cancer II

overall_design: Comparative gene expression profiling analysis of RNA-seq data for epithelial cells from Apc Min/+ mice treated with vehicle control or atorvastatin

last: Wang


title: Microbiota-derived tryptophan catabolites mediate the chemopreventive effects of statins on colorectal cancer I

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Th17 cells (Vehicle control, ILA, GSK805, GSK805+ILA).


title: Effects of Dlx2 Overexpression on the Genome of Maxillary Process in Early Embryo of Mice [scRNA-seq]

first: Jian

last: Sun

overall_design: Using a Dlx2 overexpression mouse model, the authors conducted bulk RNA Seq on the maxillary process of E10.5 mice, analyzed the impact of Dlx2 overexpression on genome expression, and compared it with the existing data of E12.5 mouse maxillary process in GEO database. Single cell RNA sequencing (scRNA Seq) was performed on the maxillary process of E12.5 mice, and the effects of overexpression of Dlx2 on cell population, cell cycle and developmental trajectory were analyzed. Cleavage under targets and segmentation (CUT&Tag) was performed on the maxillary process of E12.5 mice, the possible binding sites of DLx2 were analyzed, and the downstream target genome was searched by combining with bulk RNA Seq data.

first: Bian

last: Qian

first: Xudong


title: Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells

first: keren

last: cheng

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

overall_design: Refer to individual Series


title: Effects of Dlx2 Overexpression on the Genome of Maxillary Process in Early Embryo of Mice

status: Public on Feb 15 2023


title: mRNA expression and translation regulated by the prion-like domain of Ilf3 in the mouse amygdala under chronic stress

city: Okazaki

first: Akira

last: Yamashita

address: Nishigonaka 38, Myodaiji

country: Japan

institute: National Institute for Basic Biology

summary: Prion-like domain (PrLD) is a class of intrinsically disordered regions. Although its propensity to form condensates has been studied in the context of neurodegenerative diseases, the physiological role of PrLD remains unclear. Here, we investigated the physiological role of PrLD in NFAR2, generated by a splicing variant of the Ilf3 gene. Removal of the PrLD in mice affected the chronic water immersion and restraint stress (WIRS)-sensitive nuclear localization of NFAR2 in the amygdala, a fear-related brain region. Since NFAR2 regulates transcription and translation in the nucleus and cytoplasm, respectively, we investigated the effects of the PrLD deletion and WIRS on gene expression using RNA-seq and ribosome profiling.

overall_design: RNA-seq and ribosome profiling in the amygdala from Ilf3+/+ and Ilf3∆PrLD/∆PrLD mice under WIRS and control conditions

first: Yuichi

last: Shichino

first: Mari

last: Mito

first: Shinichi

last: Nakagawa

first: Shintaro

last: Iwasaki

first: Nobuyuki

last: Shiina


title: Metabolic maturation of neonatal hearts driven by γ-linolenic acid in maternal milk [ATAC-seq]

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

country: Spain

institute: CNB-CSIC

summary: The goal of this study was to compare the epigenetic landscape of perinatal hearts of cardiomyocyte-specific RXRab-deficient (edKO) and WT mice, to identify differential chromatin dynamics that are controlled by TF RXRa and RXRb.

overall_design: The chromatin accessibility profiles of WT and edKO perinatal hearts mice were generated using individual P0 hearts as individual biological replicates. Transposition was performed using Tn5 enzyme (Illumina), applying size selection. Sequencing was performed in duplicate using 2×50 HiSeq 3000 (Illumina) and with an average of 25 million paired-end reads per sample.

first: A

last: Paredes

first: M


title: Loss of mammalian glutaminase orthologs impairs sperm function in C. elegans

first: qifei

last: liang

address: Medical building, 1239 Siping Road

department: Medical college

institute: Tongji University

summary: The decline in sperm function is a major cause of human male infertility. Glutaminase, a mitochondrial enzyme that catalyzes the hydrolysis of glutamine to generate glutamate, takes part in many diverse biological processes such as neurotransmission, metabolism, and cellular senescence. Here we report a role of glutaminase in regulating sperm function. By generating a triple mutant that harbors a loss-of-function allele for each of all three mammalian glutaminase orthologs, we found that glutaminase gene activity is required for optimal C. elegans sperm function. Tissue-specific gene manipulations showed that germline glutaminase activity plays an important role. Moreover, transcriptional profiling and antioxidant treatment suggested that glutaminase promotes sperm function by maintaining cellular redox homeostasis. As maintaining a low level of ROS is crucial to human sperm function, it is very likely that glutaminase plays a similar role in humans and therefore can be a potential target for treating human male infertility.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type and glna knockout L4 stage hermaphrodite nematodes.

first: Qifei

last: Liang

first: Haiyan

last: Yang

first: Zhifei

last: Zhang

first: Jialin

last: Zheng

first: Zhao

last: Qin


title: Metabolic maturation of neonatal hearts driven by γ-linolenic acid in maternal milk [H3K27ac ChIP-seq]

summary: The goal of this study was to compare the cistrome profile of H3K27ac (ChIP-seq) of perinatal hearts of cardiomyocyte-specific RXRab-deficient and WT mice, in order to identify genomic regions that are differentially activated by TF RXRa and RXRb.

overall_design: P0 hearts from wild type (WT) and cardiomyocyte-specific RXRab-/- (edKO) newborns were collected and analyzed. Individual P0 hearts were considered as individual biological replicates. Prior to cardiac tissue homogenization, each heart was sequentially fixed with DSG and FA. Chromatin was extracted and then sheared using a Covaris sonicator. Immunoprecipitation was performed with the corresponding antibody and Dynabeads A. Input was obtained by keeping a 10% total chromatin.


title: Microbiota-derived tryptophan catabolites mediate the chemopreventive effects of statins on colorectal cancer

first: Ji-Xuan

last: Han


title: Metabolic responses in blood-stage malaria parasites associated with increased and decreased sensitivity to PfATP4 inhibitors

status: Public on Feb 14 2023

city: Frederick

first: Shivendra

last: Tewari

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute

summary: Spiroindolone and pyrazoleamide antimalarial compounds target Plasmodium falciparum P-type ATPase (PfATP4) and induce disruption of intra-cellular Na+ homeostasis. Recently, a PfATP4 mutation was discovered that confers resistance to a pyrazoleamide while increasing sensitivity to a spiroindolone. To understand the different cellular accommodation to PfATP4 disruptions, we examined biochemical and metabolic adaptations that underlie this seemingly contradictory response of P. falciparum to sublethal concentrations of each compound. We used a genetically engineered P. falciparum Dd2 strain (Dd2A211V) carrying an Ala211Val (A211V) mutation in PfATP4 to identify metabolic adaptations associated with the mutation that results in decreased sensitivity to PA21A092 (a pyrazoleamide) and increased sensitivity of KAE609 (a spiroindolone). We first identified sublethal doses of PA21A092 and KAE609 causing substantial reduction (30-70%) in Dd2A211V parasite replication. At this sublethal dose of PA21A092 (or KAE609), we collected metabolomic and transcriptomic data during the first intraerythrocytic developmental cycle (IDC). Finally, we integrated the time-resolved data with a whole-genome metabolic network model of P. falciparum to characterize antimalarial-induced physiological adaptations. We found that sublethal treatment with PA21A092 caused significant (p < 0.001) alterations in the abundances of 91 Plasmodium gene transcripts whereas only 21 transcripts were significantly altered due to sublethal treatment with KAE609. In the metabolomic data, we found a substantial alteration (fourfold) in the abundances of carbohydrate metabolites in the presence of either compounds. The estimated rates of macromolecule syntheses between the two antimalarial-treated conditions were also comparable, except for the rate of lipid synthesis. A closer examination of parasite metabolism in the presence of either compound indicated statistically significant differences in enzymatic activities associated with synthesis of phosphatidylcholine, phosphatidylserine, and phosphatidylinositol. Our results suggest that malaria parasites activate protein kinases via phospholipid-dependent signaling in response to the ionic perturbation induced by the Na+ homeostasis disruptor PA21A092. Therefore, we hypothesize that targeted disruption of phospholipid signaling in PA21A092-resistant parasites could be a means to block the emergence of resistance to PA21A092.

overall_design: PfDd2-A211V parasites were cultured, in quadruplicate, for 48 hours in the presence of sublethal doses of KAE609 (cipargamin drug) and PA21A092 (a pyrazoleamide compound). We collected samples every eight hours for transcriptomic profiling. The samples associated with timepoint 8 (Rep 2) of KAE609 cultures, and timepoint 32 and 40 (Rep 3) of PA21A092 cultures were lost during the hybridization process.

first: Rubayet

last: Elahi

first: Bobby

last: Kwan

first: Krithika

last: Rajaram

first: Suyash

last: Bhatnagar

first: Amanda

last: Dziedzic

first: Anne

middle: E

last: Jedlicka

first: Jaques

last: Reifman

first: Sean

middle: T

last: Prigge

first: Akhil

middle: B

last: Vaidya

first: Anders

last: Wallqvist


title: Metabolic maturation of neonatal hearts driven by γ-linolenic acid in maternal milk [RXR ChIP-seq]

first: Mercedes

last: Ricote

summary: The goal of this study was to compare the cistrome profile of RXR (ChIP-seq) of perinatal hearts of cardiomyocyte-specific RXRab-deficient and WT mice, in order to identify genomic regions which are directly controlled by TF RXRa and RXRb.

first: A

last: Paredes

first: M


title: Natural killer cell transcriptomics following vaccinia virus infection of mice

status: Public on Feb 13 2023

city: Cambridge

first: Brian

last: Ferguson

address: Tennis Court Road

department: Department of Pathology

institute: University of Cambridge

summary: RNA-seq analysis identified differentially regulated genes in purified NK cells isolated from naïve mice or those vaccinated with vaccinia virus. DEGs were compared with

overall_design: Splenic NK cells were isolated by FACS from black 6 mice at day 0, day 1.5 and day 6.5 following intradermal inncoulation of mice with vaccinia virus strain Western Reserve. RNAseq was carried out on RNA extracted from these cells

first: Geoffrey

middle: L

last: Smith

first: Delphine

last: Depierreux


title: Identification of lncRNA–miRNA–mRNA networks in circulating exosomes as potential biomarkers for systemic sclerosis

city: Bao Tou

first: Tiantian

last: Ding

address: No 41, Linyin Road, Kundulun district, Baotou

institute: The First Affiliated Hospital of Baotou Medical College

summary: This study aimed to analyze potential biomarkers for systemic sclerosis (SSc) by constructing lncRNA–miRNA–mRNA networks in circulating exosomes (cirexos).

overall_design: Differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) in SSc cirexos were screened using high-throughput sequencing and detected with real-time quantitative PCR (RT-qPCR). Differentially expressed genes (DEGs) were analyzed using the DisGeNET, GeneCards, GSEA4.2.3, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Receiver operating characteristic (ROC) curves, correlation analyses, and a double-luciferase reporter gene detection assay were used to analyze competing endogenous RNAs (ceRNAs) networks and clinical data.

first: Xiaolin

last: Sun

first: Baoyue

last: Wang

first: Yongfu


title: Expression data from WT and Elektra (Slfn2 mutant, loss of function) homozygous hematopoietic multipotent progenitor cells extracted from mice.

status: Public on Feb 09 2023

city: Lund

first: Sarah

last: Warsi

address: BMC, Sölvegatan 17

country: Sweden

institute: Lund University

summary:
In this study we investigated the effect of Slfn2 loss of function in the murine hematopoietic system. We chose to evaluate gene expression differences in multipotent progenitors, as this population was found to be diminshed in elektra homozygous mice, additionally the MPP population also displayed increased cell cycling compared to wildtype and increased apoptosis. Abstract from associated publication copied in below, from Warsi et al. 2022 Schlafen2 is a regulator of quiescence in adult murine hematopoietic stem cells, published in Haematologica. DOI 10.3324/haematol.2021.279799
Even though hematopoietic stem cells (HSCs) are characterized by their ability to self-renew and differentiate, they primarily reside in quiescence. Despite the immense importance of this quiescent state, its maintenance and regulation is still incompletely understood. Schlafen2 (Slfn2) is a cytoplasmic protein known to be involved in cell proliferation, differentiation, quiescence, interferon response, and regulation of the immune system. Interestingly, Slfn2 is highly expressed in primitive hematopoietic cells. To investigate the role of Slfn2 in the regulation of HSCs we have studied HSC function in the elektra mouse model, where the elektra allele of the Slfn2 gene contains a point mutation causing loss of function of the Slfn2 protein. We found that homozygosity for the elektra allele caused a decrease of primitive hematopoietic compartments in murine bone marrow. We further found that transplantation of elektra bone marrow and purified HSCs resulted in a significantly reduced regenerative capacity of HSCs in competitive transplantation settings. Importantly, we found that a significantly higher fraction of elektra HSCs (as compared to WT HSCs) were actively cycling, suggesting that the mutation in Slfn2 increases HSC proliferation. This additionally caused an increased amount of apoptotic stem and progenitor cells. Taken together, our findings demonstrate that dysregulation of Slfn2 results in a functional deficiency of primitive hematopoietic cells, which is particularly reflected by a drastically impaired ability to reconstitute the hematopoietic system following transplantation and an increase in HSC proliferation. This study thus identifies Slfn2 as a novel and critical regulator of a dult HSCs and HSC quiescence.

overall_design: MPPs (LSK CD48- CD150-) were sorted from c-kit enriched mouse bone marrow using FACS. Samples were frozen at -80 in RLT buffer and sent to KFB (Regenburg, Germany) for RNA extraction and hybridization on Affymetrix microarrays. Cells were sorted from four Elektra homozygous C57Bl/6 mice and four WT control mice (littermates). Please see further information in the associated pubilcation by Warsi et al. 2022.

first: Shamit

last: Soneji

first: Stefan

last: Karlsson


title: Microbiota exploring in CAVD: the potential fil rouge from aortic valve calcification to infiltrating bacteria

status: Public on Feb 08 2023

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Comparing bacteriota between calcified aortic valves

overall_design: Total DNA was extracted from cardiac valve of 20 patients suffering from CAVD, amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

first: matteo

last: ramazzotti

first: amedeo

last: amedei

first: lavinia

last: curini

first: leandro

last: di gloria


title: Arginase 1 deletion in myeloid cells decreases immune suppression and tumor formation in pancreatic cancer

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

country: USA

institute: University of Michigan

summary: We deleted Arginase 1 in myeloid cells in a spontaneous pancreatic cancer mouse model. We sequenced the spontaneous pancreatic tumor generated by an 11-month-old KF mouse (Ptf1aFlpO/+;KrasFrt-STOP-Frt-G12D/+) and an 11-month-old KFCA mouse (Ptf1aFlpO/+;KrasFrt-STOP-Frt-G12D/+;LysMcre;Arg1f/f). Single cell RNA sequencing revealed macrophage reprogramming and increase CD8+ T cell infiltration upon deletion of Arginase 1 in myeloid cells.

overall_design: This 10X Genomics single cell RNA sequencing repository includes raw and processed data files from a KF and KFCA pancreatic tumor. Single cell cDNA libraries were prepared and sequenced at the University of Michigan Advanced Genomics Core using the 10x Genomics platform. The sample was run using 50 paired-end cycle reads on NovaSeq 6000 (Illumina) to a depth of 100,000 reads. Alignment was performed by the University of Michigan Advanced Genomics Core. Parameters include Cell Ranger version 4.0.0 (default settings) with an initial expected cell count of 10,000.

first: Rosa

last: Menjivar

first: Katelyn

last: Donahue


title: Ginsenoside CK improves cognitive impairment

status: Public on Feb 10 2023

city: Changchun

first: Qing

last: Yang

address: Boshuo Road

institute: Changchun University of Chinese Medicine

summary:
Alzheimer's disease (AD) is a neurodegenerative disease and is the most common form of dementia, cognitive dysfunction is a pre-AD manifestation, followed by progressive deterioration in behavior and mood, CK has good pharmacological activity, inhibit neuronal damage associated with Aβ and improve learning memory in mice through its antioxidative properties.
We used microarrays to detail the regulation of brain tissue genes in cognitively impaired mice by ginsenoside CK.

overall_design: Brain tissues of mice in the Control, Model, and CK group were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Li


title: The OSUMMER lines: a series of ultraviolet-accelerated NRAS-mutant mouse melanoma cell lines syngeneic to C57BL/6

status: Public on Feb 11 2023

city: Columbus

first: Christin

last: Burd

state: Ohio

address: 460 West 12th Avenue

department: Molecular Genetics

institute: Ohio State University Wexner Medical Center

summary: The Ohio State University-Moffitt Melanoma Exposed to Radiation (OSUMMER) cell lines are generated in vivo in TN61R mice following a single dose of UVB radiation. These cell lines are meant to serve as a model of Nras driven melanoma.

overall_design: Comparative gene expression profiling analysis via bulk RNAseq of the OSUMMER cell lines

first: Murphy

last: Brandon

first: Jensen

last: Daelin

first: Tiffany

last: Arnold

first: Renan

last: Aguilar-Valenzuela

first: Jase

last: Hughes

first: Valentina

last: Posada

first: Kimberly

last: Nguyen

first: Vi

last: Chu

first: Kenneth

middle: Y

last: Tsai

first: Craig

first: Burd

last: Christin


title: Single-cell transcriptome profiling reveals developmental trajectory and transcriptional regulatory networks of mouse maxillary prominence

first: Qian

last: Bian

state: Shanghai

address: Pudong New District, Jinzun Rd, No.115

department: Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: During embryonic development of vertebrates, neural crest- derived mesenchymal cells within the maxillary prominences undergo precisely coordinated proliferation and differentiation to give rise to a series of craniofacial structures, such as tooth and secondary palate. However, the transcriptional regulatory networks underpinning such an intricate process have not been fully elucidated. Here we combined bulk and single-cell RNA-Seq to comprehensively characterize the transcriptome dynamics during mouse maxillary development from embryonic day (E) 10.5 to 14.5. We identified mesenchymal cell populations that represent different developmental states and inferred their developmental trajectory, demonstrating that a cell fate divergence toward the palatal versus dental mesenchyme lineage occurs at E11.5. We further identified the core transcriptional regulators associated with maxillary cell fate transitions and deduced the gene regulatory networks directed by these factors. We further demonstrated that Foxp1 regulates genes involved in skeletal and cartilage development and is required for efficient osteogenesis. Collectively, our study provides rich resources and important insights for achieving a systems level understanding of craniofacial morphogenesis and abnormality.

overall_design: Single cell RNA-Seq of E10.5, E11.5, E12.5, E14.5 mouse embryonic maxillary prominence tissue.

first: Jian

last: Sun

first: Xudong

last: Wang

first: Nayoung

last: Ha