title: LncRNA Tuna is activated in cadmium-induced placental insufficiency and drives the NRF2-mediated oxidative stress response.

status: Public on May 31 2023

city: RALEIGH

first: Dereje

last: Jima

address: 850 Main Campus Drive

department: CHHE

institute: NCSU


title: Combinatorial targeting of a novel MET/EMT network components by macroH2A variants safeguards cell identity [RNA-seq]

status: Public on Jun 21 2023

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

type: Expression profiling by high throughput sequencing

summary: The establishment and maintenance of cellular identity rely upon the precise coordination of regulatory pathways culminating to the proper execution of cell type-specific gene expression programs. Generation of induced pluripotent stem cells (iPSCs) from highly specialized cell types provides an excellent model system to study how cells maintain their stability through the functional interplay of transcription factors and chromatin structure, and how they can change identity, especially in the context of disease. Previous studies have shown that chromatin structure safeguards cell identity by acting as a barrier to reprogramming. Here, we investigated the mechanisms of how the histone variant macroH2A inhibits reprogramming by interfering with the mesenchyme to epithelial transition, a step that is a prerequisite for reprogramming of mouse embryonic fibroblasts. We found that each of the macroH2A isoforms regulates the expression of defined sets of genes, whose overall function is to stabilize the mesenchyme phenotype, thus resisting reprogramming. We identified a novel gene network (MSCN, mesenchyme network) composed of 63 macroH2A-regulated genes encoding proteins of the extracellular matrix, cell membrane, cytoplasmic signal integrators and the transcriptional regulators Id2 and Snai2, all of which can function as key controllers of the mesenchyme phenotype. Functional studies including ChIP-seq and KD experiments using any one of the individual macroH2A isoforms revealed an isoform-specific combinatorial targeting of the genes that reconstruct the MSCN. Our findings established that the combinatorial macroH2A targeting of the MSCN components safeguards cell identity and demonstrated its pivotal role in maintaining the differentiated cell phenotype by generating robustness in gene expression programs to resist cellular reprogramming.

overall_design: RNAseq

last: Thanos

first: Dimitrios


title: LncRNA Tuna is activated in cadmium-induced placental insufficiency and drives the NRF2-mediated oxidative stress response [human Jeg3]

state: NC

country: USA

summary: Cadmium (Cd) is a toxic heavy metal found throughout the environment and one of the top ten toxicants of major public health concern identified by the World Health Organization.InuteroCd exposure causes fetal growth restriction, malformation, and spontaneous abortion; however, the mechanisms by which Cd impacts these outcomes are poorly understood. Cd accumulates in the placenta, suggesting that these negative outcomes may be a consequence of disrupted placental function and placental insufficiency. To understand the impact of Cd on gene expression within the placenta, we developed a mouse model of Cd-induced fetal growth restriction through maternal consumption of CdCl2 and performed RNA-seq on control and CdCl2 exposed placentae. The top differentially expressed transcript was the Tcl1Upstream Neuron-Associated (Tuna) long non-coding RNA, which was up-regulated over 25-fold in CdCl2 exposed placentae. Tuna has been shown to be critical for neural stem cell differentiation. However, within the placenta, there is no evidence that Tuna is normally expressed or functional at any developmental stage. To determine the spatial expression of Cd-activated Tuna within the placenta, we used in situ hybridization as well as placental layer-specific RNA isolation and analysis. Both methods confirmed the absence of Tuna expression in control samples and determined that Cd-induced Tuna expression is specific to the junctional zone. Since many lncRNAs regulate gene expression, we hypothesized that Tunaforms part of the mechanism of Cd-induced transcriptomic changes. To test this, we over-expressed Tuna in cultured choriocarcinoma cells and compared gene expression profiles to those of control and CdCl2 exposed cells. We demonstrate significant overlap between genes activated byTunaoverexpression and genes activated by CdCl2 exposure, with enrichment in the NRF2-mediated oxidative stress response. Herein we analyze the NRF2 pathway and show that Tuna increases NRF2/NRF2 both at the transcript and protein levels. Tuna drives increased NRF2 target gene expression, a result that is abrogated with the use of an NRF2 inhibitor, confirming that Tuna activates oxidative stress response genes through this pathway. This work identifies the lncRNA Tuna as a potential novel player in Cd-induced placental insufficiency.

overall_design: 4 replicates of Jeg-3 cells exposed to 0 micromolar CdCl2, 4 replicates of Jeg-3 cells exposed to 5 micromolar CdCl2, 4 replicates of Jeg-3 cells over-expressing GFP,  replicates of Jeg-3 cells over-expressing Tuna

first: Mark

middle: D

last: Simmers

first: Yoshiaki

last: Tsuji

first: Michael

last: Cowley


title: LncRNA Tuna is activated in cadmium-induced placental insufficiency and drives the NRF2-mediated oxidative stress response [mouse]

overall_design: 4 placentas from dams exposed to 0 ppm CdCl2; 4 placentas from dams exposed to 50 ppm CdCl2. Each placenta is from a different dam.


title: Deep dynamical modelling of developmental trajectories with temporal transcriptomics

status: Public on Jul 06 2023

city: London

first: Rory

middle: James

last: Maizels

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Deep dynamical modelling of developmental trajectories with temporal transcriptomics [SPECIES_MIXTURE_DATA]

summary: Developmental cell fate decisions are dynamic processes driven by the complex behaviour of gene regulatory networks. A challenge in studying these processes using single-cell genomics is that the data provides only a static snapshot with no detail of dynamics. Metabolic labelling and splicing can provide time-resolved information, but current methods have limitations. Here, we present experimental and computational methods that overcome these limitations to allow dynamical modelling of gene expression from single-cell data. We developed sci-FATE2, an optimised metabolic labelling method that substantially increases data quality, and profiled approximately 45,000 embryonic stem cells differentiating into multiple neural tube identities. To recover dynamics, we developed velvet, a deep learning framework that extends beyond instantaneous velocity estimation by modelling gene expression dynamics through a neural stochastic differential equation system within a variational autoencoder. Velvet outperforms current velocity tools across quantitative benchmarks, and predicts trajectory distributions that accurately recapitulate underlying dataset distributions while conserving known biology. Velvet trajectory distributions capture dynamical aspects such as decision boundaries between alternative fates and correlative gene regulatory structure. Using velvet to provide a dynamical description of in vitro neural patterning, we highlight a process of sequential decision making and fate-specific patterns of developmental signalling. Together, these experimental and computational methods recast single-cell analyses from  descriptions of observed data distributions to models of the dynamics that generated them, providing a new framework for investigating developmental gene regulation and cell fate decisions.

overall_design: ES cells from human and mouse mixed together and sequenced with sci-RNA-seq. This data is used to measure doublet rate by detecting mouse-human hybrid cells.

middle: J

first: Daniel

last: Snell

first: James

last: Briscoe


title: IgE produced in Food Allergy Is Dependent Upon IL-4 Derived from T Follicular Regulatory Cells

status: Public on May 01 2023

city: Indianapolis

first: Qiang

last: Chen

state: IN

address: 332/333 RESEARCH II, 950 W Walnut Street

department: Microbiology and Immunology

institute: Indiana University School of Medicine

summary: It has been reported that T follicular regulatory (TFR) cells promote IgE in a food allergy model but suppress IgE in a house dust mite (HDM)-induced airway inflammation model. To understand the differential roles of TFR cells in different models, mice were sensitized with peanut plus cholera toxin (PCT) (i.g.) or challenged with HDM (i.n.). TFR cells were sorted from these mice, total RNA was extracted and used for RNA-seq. Naive mice were used as additional control.

overall_design: bulk RNA-seq of TFR cells from draining lymph nodes from naïve, PCT-sensitized, and HDM-challenged mice

first: Alexander

last: Dent


title: Molecular barcodes and single cell transcriptomics to map graft diversity and lineage of human DA neurons in a rat xenograft model of Parkinson’s Disease

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

summary: Human pluripotent stem cells (PSCs) differentiated into dopamine (DA) neurons via a ventral floor plate intermediate provide an unlimited cell source for cell replacement therapy for Parkinson’s disease (PD). However, histology and scRNA-seq profiling of resulting grafts in in vivo models have revealed that seemingly homogenous cell preparations give rise to heterogenous grafts not only made up of dopamine neurons. Here, we used single nuclei RNA-seq combined with molecular barcode tracing delivered to the PSC-derived DA progenitors both in vitro and in vivo to show that three cell types (neurons, astrocytes and vascular leptomeningeal cells, VLMCs) make up the cellular composition of the grafts and that these cell types all share a common progenitor.  Additionally, barcoding proliferative cells in vivo 1 month after transplantation, showed that a fraction of the cells retained their multipotent potential also after transplantation. Single-cell chromatin accessibility and RNA expression paired maps identified seemingly subtle chromatin accessibility differences among progenitors supporting their homogeneity, and together with the tracing data shows that the PSC-derived floor plate cells used for transplantation are tri-potent, giving rise to dopamine neurons, astrocytes and VLMCs.

overall_design:
Single-nuclei RNA-seq of stem cell derived midbrain grafts
-------------------------------------------
Authors state "Due to privacy concerns we are unable to submit raw data and has hence only uploaded count matrices."

first: Malin

last: Parmar


title: Transcriptomic analysis and cellular responses to nanoscale zero-valent iron in green microalga Raphidocelis subcapitata

status: Public on Jun 06 2023

city: Liberec

first: Alena

last: Sevcu

state: Liberec

address: Bendlova 1409/7

department: Applied Biology

country: Czech Republic

institute: Technical University of Liberec

summary: Nanoscale zero valent iron (nZVI) is used to remediate aquifers polluted by organochlorines or heavy metals and was also suggested to eliminate harmful algal blooms. nZVI can therefore affect microorganisms in the vicinity of the application area, including microalgae. However, studies on early transcriptomic effects of microalgae after exposure to nZVI are rare. Here, we described the early physiological and transcriptomic response of the freshwater ecological indicator green microalga, Raphidocelis subcapitata ATCC 22662, to 100 mg/L of reactive nZVI and non-reactive nano-magnetite (nFe3O4). The combined effect of shading and the release of total iron from nZVI posed a short-term inhibition effect leading to 15 % of deformed cells and cytosol leakage, while cells viability increased after 24 h. nZVI triggered a more pronounced transcriptomic response with (7380 differentially expressed genes [DEGs]) compared to nFe3O4 (4601 DEGs) after 1 h. nZVI, but not nFe3O4 increased the expression of genes function in DNA repair and replication, while deactivated carbohydrate-energy metabolisms, mitochondria signaling, and transmembrane ion transport. This study highlights an early fate assessment of algal cells under nZVI and nFe3O4 exposure using next-generation risk assessment methods and will serve as valuable information for safe and sustainable application of nZVI in water remediation.

overall_design:
To evaluate the toxicity effect in R. subcapitata posed by 100 mg/L nZVI and nFe3O4 at transcriptomic level
To identify and characterize the expression of different genes during the exposure of nZVI and nFe3O4 at different time points (1 h and 4 h).
To identify metabolic pathways changed after the exposure of nZVI and nFe3O4

first: Cheryl

last: Yeap


title: Transcriptomic profiling of DU4475 cells in 3D cell culture matrices and suspension

status: Public on Apr 05 2023

city: Espoo

first: Maria

last: Heilala

address: Puumiehenkuja 2

country: Finland

institute: Aalto University

summary: The extracellular matrix (ECM)-regulated phenotypic plasticity is crucial for metastatic progression of triple negative breast cancer (TNBC). To investigate the effect of matrix cues on phenotypic plasticity, we embedded triple negative DU4475 cells from suspension culture into mechanically tunable fibrin gels or basement membrane extract (Matrigel). Cells in suspension culture and matrix cultures showed divergent gene expression profiles, with specific gene expression signatures depending on the biochemical composition and stiffness of the matrix.

overall_design: DU4475 cells were embedded into soft fibrin (10 mg/mL), stiff fibrin (30 mg/mL) or Matrigel. RNA-seq analysis was performed after culturing DU4475 cells in the matrices for one week. Cells maintained in liquid suspension provided a reference for native cell phenotype. Three replicates were done for each condition.

first: Aino

last: Peura

first: Pauliina

last: Munne


title: Pathogen dynamics and discovery of novel viruses and enzymes by deep nucleic acid sequencing of wastewater

status: Public on Apr 13 2023

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: Nucleic acids in wastewater provide a rich source of data for detection and surveillance of microbes. We have longitudinally collected 116 RNA samples from a wastewater treatment plant in Berlin/Germany, from March 2021 to July 2022, and 24 DNA samples from May to July 2022. We tracked human astroviruses, enteroviruses, noroviruses and adenoviruses over time to the level of strains or even individual nucleotide variations, showing how detailed human pathogens can be observed using wastewater. For respiratory pathogens, a broad enrichment panel enabled us to detect waves of RSV, influenza, or common cold coronaviruses in high agreement with clinical data. By applying a profile Hidden Markov Model-based search for novel viruses, we identified more than 100 thousand novel transcript assemblies likely not belonging to known virus species, thus substantially expanding our knowledge of virus diversity. Phylogenetic analysis is shown for bunyaviruses and parvoviruses. Finally, we identify Hundreds of novel protein sequences for CRISPR-associated proteins such as Transposase B, a class of small RNA-guided DNA editing enzymes. Taken together, we present a longitudinal and deep investigation into wastewater-derived genomic sequencing data that underlines the value of sewage surveillance for public health, planetary virome research, and biotechnological potential.

overall_design: Raw influx from Berlin/Germany wastewater treatment plants was collected over a time period from May 2021 to July 2022, total RNA and (from May 2022 to July 2022) total DNA extracted and subjected to high-throughput sequencing.

first: Chris

last: Lauber

first: Artür

last: Manukyan

first: Aylina

last: Deter

first: Claudia

last: Quedenau

first: Luiz

middle: G

last: Teixeira Alves

first: Stefan

last: Seitz

first: Janine

last: Altmüller

first: Markus

last: Landthaler


title: RNAseq profiling of defined immunocyte subsets from human blood, healthy volunteers

status: Public on Mar 20 2023

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: In the context of the Human Cell Atlas, the ImmGen consortium generated reference profiles by bulk RNAseq on finely sorted populations of immunocytes from human blood, healthy volunteers.

overall_design: Specific cell populations were sorted by flow cytometry to high purity (2 rounds of sorting, 1,000 cells/sample), as biological duplicates. The cells profiled according to the ImmGen ULI low-input (SmartSeq2) protocol.

first: Angela

last: Magnuson

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Suppressed cellular senescence mediated by T-box3 in aged gastric epithelial cells may contribute to aging-related carcinogenesis

status: Public on Mar 22 2023

city: Sendai

first: Naoki

last: Asano

state: Miyagi

address: 1-1 Seiryo-machi, Aoba-ku

department: Division of Gastroenterology

country: Japan

institute: Tohoku University Graduate School of Medicine

summary:
Aging is a risk factor of carcinogenesis in various organs, and abnormal aging of the stem cells is considered responsible for carcinogenesis. Recent advances in organoid culturing system have made it viable to investigate mini organs developed from tissue stem cells. In this study, we aimed to investigate the implications of aging stem cells for gastric carcinogenesis. We found that gastric organoids of aged mice grew larger in size and proliferated vigorously compared to that of young mice. To elucidate the mechanism involved in this difference, we extracted the total RNA from the organoids and subjected it to microarray analysis, which revealed that the expression of transcription factor T-box 3 (Tbx3) was enhanced in aged gastric organoids. Further studies showed that this enhanced Tbx3 expression suppressed cellular senescence and enhanced proliferation.
We utilized microarray analysis to find out the gene responsible for restraining cellular senescence in aged gastric organoids.

overall_design: Gastric organoids were established from young and aged murine stomachs. Total RNA was extracted from the organoids and was subjected to microarray analysis.

first: Akio

last: Takeuchi

first: Akira

last: Imatani


title: Identification and isolation of hematopoietic stem and progenitor cell populations (scRNA-seq)

status: Public on Mar 03 2023

city: Bethesda

first: Jens

last: Lichtenberg

state: MD

address: 49 Convent Dr 3A19

department: National Human Genome Research Institute

institute: National Institutes of Health

summary: Single cell RNA sequencing of 37,501 cells representing four independently isolated hematopoietic stem and progenitor populations from mouse bone marrow

overall_design: Single cell transcriptional profiling using the 10X Genomics platform was performed on 10,882 Lineage-depleated SCA1+ KIT+ cells, 12,185 common myeloid progenitors, 8,064 granulocyte/monocyte progenitors, and 6,370 megakaryocyte/erythroid progenitors independently isolated from normal mouse bone marrow

first: Elisabeth

middle: F

last: Heuston

first: David

middle: M

last: Bodine


title: Identification and isolation of hematopoietic stem and progenitor cell populations

type: Genome binding/occupancy profiling by high throughput sequencing


title: Transcriptional alteration in the treatment of MDA-MB-231 cells using BITC and/or ZA

city: Pittsburgh

first: Shivendra

middle: V.

last: Singh

state: PA

address: 5117 Centre Avenue, UPMC HCC Research Pavilion Suite 2.32A

institute: University of Pittsburgh

summary: We report differential gene expression changes by benzyl isothiocyanate (BITC) and/or zoledronic acid (ZA) in MDA-MB-231 human breast cancer cell line

overall_design: Examinine the transcriptome regulated by BITC and/or ZA in the MDA-MB-231 human breast cancer cell line

middle: V


title: Identification and isolation of hematopoietic stem and progenitor cell populations (ATAC-seq)

summary: Accessible chromatin profiling profiling of four common myeloid progenitor subpopulations prospectively isolated from mouse bone marrow

overall_design: The assay for transposase-accessible chromatin (ATAC-Seq) was performed on C10, C11, C17, and C3 common myeloid progenitor subpopulations defined by single cell transcriptional profiling and clustering and prospectively isolated in duplicate from mouse bone marrow.


title: Dynamic interplay between sortilin and syndecan-1 has a role in the metabolic switch during prostate cancer progression

status: Public on Aug 21 2023

city: Adelaide

first: Nick

last: Warnock

state: South Australia

address: UniSA Bradley Building, North Terrace

department: Centre for Cancer Biology

country: Australia

institute: SA Pathology

summary: Prostate cancer development and progression relies on the programming of glucose and lipid metabolism, and this involves alterations in androgen receptor expression and signalling. Androgen deprivation therapy (ADT) provides short-term efficacy for patient treatment, but inevitably promotes a castration-resistant phenotype with poor prognosis. Defining the molecular mechanism that underpins this metabolic programming will have direct significance for prostate cancer patients who have poor expected outcomes and/or receive ADT. Here we show that there is a dynamic balance between sortilin and syndecan-1 that reports on different metabolic phenotypes. Sortilin, enhances glucose metabolism by regulating GLUT1 and GLUT4, while binding progranulin and lipoprotein lipase (LPL) to limit lipid metabolism. In contrast, syndecan-1 interacts with LPL and β3 integrin, to promote lipid metabolism and this process is upregulated in androgen-insensitive cells. We report a hitherto unappreciated molecular mechanism for prostate cancer, which has significance for disease progression and how ADT may promote castration-resistant prostate cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PC3 versus LNCaP cells and for LNCaP cells treated with dihydrotestosterone (DHT) vs vehicle (0.01% ethanol).

first: Joanna

last: Lazniewska

first: Ian

middle: R

last: Johnson

first: Courtney

last: Moore

first: Douglas

middle: A

last: Brooks


title: Crac analysis of the Bud22 ribosome biogenesis factor

status: Public on Apr 30 2023

city: Heidelberg

first: Ed

last: Hurt

address: Im Neuenheimer Feld 328

department: BZH

institute: Biochemie Zentrum Heidelberg

summary:
Bud22 binds to the 5´domain of 18S rRNA and U14 snoRNA

Grant Number: BA 2316/2-1
German Research Foundation (DFG)
Grantee: Jochen,,Baßler

overall_design: 2 samples

first: Jochen

last: Baßler

first: Maximilian

last: Eivaskhani

first: Olga

last: Beine-Golovchuk

first: Ruth

last: Kunze


title: Interferon regulates stem cell output via post-transcriptional repression of Sox2 independent of its antiviral function in the brain

status: Public on Jan 13 2023

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

institute: German Cancer Research Center


title: AhR alters essential transcriptional regulators driving osteogenic differentiation of multipotent mesenchymal stem cells

status: Public on Feb 08 2023

first: Dereje

last: Jima

summary: Differentiation of multipotent mesenchymal stem cells into bone-forming osteoblasts requires strict coordination of transcriptional pathways. Aryl hydrocarbon receptor (AhR) ligands, such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), have been shown to alter osteoblast differentiation in vitro and bone formation in multiple developmental in vivo models. The goal of the present study was to establish a global transcriptomic landscape during early, intermediate, and apical stages of osteogenic differentiation in vitro in response to TCDD exposure. Human bone-derived mesenchymal stem cells (hBMSC) were cultured in growth media (GM), osteogenic differentiation media (ODM), or osteogenic differentiation media containing 10 nM TCDD (ODM+TCDD), thus enabling a comparison of the transcriptomic profiles of undifferentiated, differentiated, and differentiated -TCDD-exposed hBMSCs, respectively. In this test system, exposure to TCDD attenuated differentiation of hBMSCs into osteoblasts as evidenced by reduced alkaline phosphatase activity and mineralization. At various timepoints, we observed altered expression of genes that play a role in the Wnt, FGF, BMP/TGF-β developmental pathways, as well as pathways related to extracellular matrix organization and deposition. Reconstruction of gene regulatory networks with the iDREM analysis revealed modulation of transcription factors (TF) including POLR3G, NR4A1, RDBP, GTF2B, POU2F2 and ZEB1, which may putatively influence osteoblast differentiation and the requisite deposition and mineralization of bone extracellular matrix. We demonstrate that the combination of RNA-Seq data in conjunction with the iDREM regulatory model, captures the transcriptional dynamics underlying mesenchymal stem cell differentiation under different conditions in vitro. Model predictions are consistent with existing knowledge and provides a new tool to identify novel pathways and transcription factors that may facilitate a better understanding of the osteoblast differentiation process, perturbation by exogenous agents, and potential intervention strategies targeting those specific pathways.

overall_design: TCDD alters essential transcriptional regulators of osteogenic differentiation in multipotent mesenchymal stem cells

first: AtLee

middle: T

last: Watson

first: Aldo

middle: C

last: Baez

last: Reif

first: Jun

last: Ding

first: Seth

middle: W

last: Kullman


title: Gene expression profile at single cell level of pancreatic islets cells from mice fed with regular or high fat diet for 6 weeks after weaning.

status: Public on Jan 23 2023

city: New York

first: Friederike

last: Dündar

state: New York

address: 1300 York Ave

department: Physiology & Biophysics

institute: Weill Cornell Medicine

summary: We have assessed the single-cell transcriptomes of pancreatic islets in a mouse model of obesity and glucose intolerance in order to characterize the cellular and molecular perturbations induced by obesity that lead to T2D.

overall_design: C57BL/6J wild-type mice  were fed a regular chow diet (RD, N=4) or a 60% high fat diet (HFD, N=5) (Research Diets) for 6 weeks after weaning. Mouse pancreatic islets were isolated by perfusion of the pancreases with CIzyme (VitaCyte) through the common hepatic duct and digested at 37°C for 17 minutes. After gradient-based separation using Histopaque-1077 (Sigma), islets were then hand-picked to avoid exocrine contamination. For details of the analyses, see https://github.com/abcwcm/RubioNavarro_Pancreas

first: Alfonso

last: Rubio-Navarro

first: Nicolás

last: Gómez-Banoy

first: Lisa

last: Stoll

first: Alex

last: Mawla

first: Lunkun

last: Ma

first: Nathalia

last: Montoya-Oviedo

first: Paul

last: Zumbo

first: Moritz

last: Reiterer

first: Norihiro

last: Imai

first: Ankit

last: Gilani

first: Boris

last: Yang

first: Eric

last: Cortada

first: Angie

last: Chong

first: David

middle: E

last: Cohen

first: Shuibing

last: Chen

first: Jingli

last: Cao

first: Geoffrey

middle: S

last: Pitt

first: Mark

middle: O

last: Huising

first: Doron

last: Betel

first: James

last: Lo


title: Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression

status: Public on Jan 01 2023

first: Xin

last: Wang

address: 300 Longwood Ave,

institute: Boston children's hospital

summary: In response to DNA double strand damage, ongoing transcription is inhibited to facilitate accurate DNA repair while transcriptional recovery occurs after DNA repair is complete. However, the mechanisms at play and identity of the transcripts being regulated in this manner are unclear. In contrast to the situation following UV damage, we found that transcriptional recovery after ionizing radiation (IR) occurs in a manner independent of the HIRA histone chaperone. Sequencing of the nascent transcripts identified a programmed transcriptional response, where certain transcripts and pathways are rapidly downregulated after IR, while other transcripts and pathways are upregulated. Specifically, most of the loss of nascent transcripts occurring after IR is due to inhibition of transcriptional initiation of the highly transcribed histone genes and the rDNA. To identify factors responsible for transcriptional inhibition after IR in an unbiased manner, we performed a whole genome gRNA library CRISPR / Cas9 screen. Many of the top hits in our screen were factors required for protein neddylation. However, at short times after inhibition of neddylation, transcriptional inhibition still occurred after IR, even though neddylation was effectively inhibited. Persistent inhibition of neddylation blocked transcriptional inhibition after IR, and it also leads to cell cycle arrest. Indeed, we uncovered that many inhibitors and conditions that lead to cell cycle arrest in G1 or G2 phase also prevent transcriptional inhibition after IR. As such, it appears that transcriptional inhibition after IR occurs preferentially at highly expressed genes in cycling cells.

overall_design: Comparative nascent transcripts profiling analysis of RNA-seq data for Abl pre-B cells before and after irradiation, with two biological replicates

first: Zulong

first: Xinlei

last: Gao

first: Nina

last: Arslanovic

first: Kaifu

first: Jessica

last: Tyler


title: Single-Cell 10x RNA Sequencing of old and young wildtype and interferon receptor knockout mice

first: Ana

last: Martin-Villalba

summary: Sequence neural stem cells and related cells of the ventricular-subventricular zone in wildtype mice and mice lacking interferon receptors across ages.

overall_design: 10x RNA sequencing of subventricular zones and other related tissues from two mice from all combinations of old, young and wildtype (TiCY) as well as ifnagrko (TiCY).

first: Santiago

last: Cerrizuela

first: Jooa

last: Hooli


title: RiboSeq of Interferon-β treated neural stem cells

summary: Neural stem cells were treated with vehicle or Interferon-β for different treatment lengths. Ribosome protected RNA and total RNA were extracted and sequenced

overall_design: Neural stem cells were treated with vehicle or Interferon-β for different treatment lengths in 4 replicates. Ribosome protected RNA and total RNA were extracted, SmartSeq libraries were prepared and samples were sequenced.

first: Maxim

last: Skabkin

first: Damian

last: Carvajal Ibanez

first: Manuel

last: Göpferich


title: Gene expression analysis of human spinal cord astrocyte culture on collagen I/decellularized spinal cord matirx(DSCM) hydrogel [bulk RNA-seq]

status: Public on Dec 31 2022

city: Guangzhou

first: Sheng

last: Zhang

state: None Selected

address: 132 Waihuan West Road, Guangzhou Science Park, Luogang District

country: China

institute: School of Materials Science and Engineering, Sun Yat-sen University

summary:
To further verify the effect of DSCM and COLI on cell fate  regulation of ASCs, bulk RNAseq assays were implemented using human spinal cord derived primary astrocytes (hspASCs).
We then performed gene expression profiling analysis using data obtained from RNA-seq of hspASC culture on COLI/DSCM hydrogel.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hspASC under COLI/DSCM condition.

first: Xiao


title: Cancer cells enter an adaptive persistence to survive radiotherapy and repopulate tumor 2

status: Public on Jan 06 2023

city: Shanghai

first: Yucui

last: Zhao

state: Please Select

address: No. 650 Xinsongjiang Road, Hongkou District, Shanghai

department: cancer center

institute: Shanghai general hospital

summary: Tumor cell repopulation represents a critical factor in the failure of radiotherapy. Analogous to the concept of “drug-tolerant persistence (DTP)” in stress of chemo- or targeted therapy, here, we show that cancer cells enter a “radiation-tolerant persistence (RTP)” to survive radiotherapy and repopulate tumor. These RTP cells exhibit a distinct phenotype characterized by enlargement of cell sizes and nucleus, complex karyotype, cell cycle arrest and engagement of quiescence. A fraction of RTPs unexpectedly give birth to mitotic-competent progeny cells via a viral budding-mimicking cell division. To gain insight into the molecular mechanisms how RTPs generating progenies and repopulating tumors, we applied single cell SMART RNA-sequencing and 10x RNA-sequencing to different status of human colorectal cancer cells HCT116 before and exposed to irradiation. For the first time, we profiled two transitional transcriptional waves throughout budding process and characterized two gene panels associated with budding of RTPs, illustrating the therapeutic potential for blocking tumor repopulation after radiation.

overall_design: We performed single cell SMART RNA-seq of isolated unirradiated cells, RTPs, budding RTPs, budded progenies and repopulated cells. Furthermore, we performed 10× single cell RNA-seq (mixture of unirradiated cells, irradiated cells and progenies)

first: Tingting

last: Lu

first: Yanqian

last: Wen

first: Jiahui

last: Fan

first: Yongyong

last: Shi

first: Qian

last: Huang


title: Decellularized Spinal Cord Matrix Manipulate Glial Niche Alteration via Serglycin Mediated Signalling Pathway

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

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Refer to individual Series


title: Cancer cells enter an adaptive persistence to survive radiotherapy and repopulate tumor


title: APC and P53 mutations synergize to create a therapeutic vulnerability to NOTUM inhibition in advanced colorectal cancer [scRNA-seq]

city: Philadelphia

first: Joshua

middle: .H

last: Rhoades

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: We thought the immediate effects of APC inactivation may represent unexplored therapeutic vulnerabilities in later stages of advanced colorectal adenocarcinoma. We performed transcriptome profiling of epithelial colon organoids immediately after APC inactivation and cross-referenced gene expression changes to the transcriptomes of several mouse models of colon cancer, including colon tumors in an inflammation-induced CRC model (AOM-DSS), a model of familial adenomatous polyposis (FAP, the Apcmin mouse), and an implantation-based model of metastatic adenocarcinoma using Apc/Trp53/KrasG12D/Smad4 quadruple-mutant tumor organoids15 (APKS tumoroids). Of the roughly 150 genes whose expression is acutely induced upon APC loss and remains elevated in these colon cancer models.

overall_design: We did single cell RNA sequencing analysis to show common molecular changes from 3 different tumor models compared to normal adjacent tissue.

first: Christopher

last: Lengner

first: Ning

last: Li

first: Yuhua

last: Tian

middle: H


title: Repairing growth of a genome-reduced strain using adaptive laboratory evolution and targeted gene knock-in

status: Public on Dec 20 2022

city: La Jolla

first: Cameron

last: Lamoureux

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

summary: We profiled growth of an evolved version of the genome reduced E. coli strain DGF-298 in various growth conditions. We used RNA-seq to compare this strain's growth to the parent wild-type strain. We also profiled the transcriptional effect of adding in a removed gene predicted by models to have a positive impact on growth (aldA).

overall_design: Growth of E. coli was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation.

first: Sebastien

last: Rodrigue


title: APC and P53 mutations synergize to create a therapeutic vulnerability to NOTUM inhibition in advanced colorectal cancer.


title: Dynamic brain cell changes after middle cerebral artery occlusion revealed by massive single cell RNAseq

city: Los Angeles

first: Weihong

last: Ge

address: 635 Charles E Young Dr South 355

institute: UCLA

summary: We used 10XGenomics Single Cell 3' Droplet-based single cell approach to profile adult mouse cortical brain cells after middle cerebral artery occlusion.

overall_design: Single brain cells were isolated and profiled from two brain regions (both ipsilateral perilesional regions and its coresponding contralateral regions ) and 4 different time points after MCAO (4hrs, 1 day, 3 days and 7 days). Moreover, single cells from 3 uninjured mice coresponding regions were also being profiled.

first: Yi

last: Sun


title: CDK8/19 inhibition plays an important role in pancreatic β-cell induction from human iPSCs

status: Public on Dec 08 2022

city: Fujisawa

first: Kensuke

last: Sakuma

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

institute: Orizuru Therapeutics, Inc.

summary: In this study, we demonstrate that we can obtain human iPSC-derived pancreatic islet-like cells (iPICs) with comparable transcriptomic profile by using a combination of an ALK5 inhibitor and a CDK8/19 inhibitor, instead of utilizing ALK5 inhibitor II.

overall_design: The iPICs were generated from the human iPSC line Ff-I14-s04 based on our previous report (Hiyoshi et al., Scientific Reports 2022). The ALK5 inhibitor II in the protocol was replaced with an ALK5 inhibitor, a CDK8/19 inhibitor and their combinations.

first: Noriko

last: Tsubooka-Yamazoe

first: Kiyohiro

last: Hashimoto

first: Nozomu

last: Sakai

first: Shinya

last: Asano

first: Saori

last: Watanabe-Matsumoto

first: Takeshi

last: Watanabe

first: Bunnai

last: Saito

first: Hirokazu

last: Matsumoto

first: Hikaru

last: Ueno

first: Ryo

last: Ito

first: Taro

last: Toyoda


title: Coordinated local overexpression of complement induced by interferon gamma in myositis

first: Iago

last: Pinal-Fernandez

state: MARYLAND

address: 50 South Drive, Room 1142, Building 50, MSC 8024

department: NIAMS

institute: NIH

summary: Complement proteins are deposited in the muscles of patients with myositis. However, the local expression and regulation of complement genes within myositis muscle have not been well characterized. In this study, bulk RNA sequencing (RNAseq) analyses of muscle biopsy specimens revealed that complement genes are locally overexpressed and correlate with markers of myositis disease activity, including the expression of interferon-gamma (IFN𝛾)-induced genes. Single cell and single nuclei RNAseq analyses showed that most local expression of complement genes occurs in macrophages, fibroblasts, and satellite cells, with each cell type expressing different sets of complement genes. Biopsies from immune-mediated necrotizing myopathy patients, who have the lowest levels of IFN𝛾-induced genes, also had the lowest complement gene expression levels. Furthermore, data from cultured human cells showed that IFN𝛾 upregulates complement expression in macrophages, fibroblasts, and muscle cells. Taken together, our results suggest that in myositis muscle, IFN𝛾 coordinates the local overexpression of complement genes that occurs in several cell types.

overall_design: Gene expression profiling analysis of RNA-seq data for patients with different types of myositis (DM, AS, IMNM, IBM) and histologically normal muscle biopsies (NT).

first: Andrew

middle: L

last: Mammen


title: PIP4K2B is mechanoresponsive and controls heterochromatin-driven nuclear softening through UHRF1

status: Public on Feb 11 2023

city: Milano

first: Paolo

last: Maiuri

address: via Adamello 16

country: Italy

institute: IFOM

summary: Phosphatidylinositol-5-phosphate (PtdIns5P)-4-kinases (PIP4Ks) are stress-regulated phosphoinositide kinases able to phosphorylate PtdIns5P to PtdIns(4,5)P2. In cancer patients their expression is typically associated with bad prognosis. Among the three PIP4K isoforms expressed in mammalian cells, PIP4K2B is the one with more prominent nuclear localization. Here, we unveil the role for PIP4K2B as mechanosensor. PIP4K2B protein level, indeed, strongly decreases in cells growing on soft substrates. Its direct silencing or pharmacological inhibition, mimicking cell response to soft, triggers a concomitant reduction of the epigenetic regulator UHRF1 and induces changes in nuclear polarity, nuclear envelope tension and chromatin compaction. This substantial rewiring of the nucleus mechanical state drives YAP cytoplasmic retention and impairment of its activity as transcriptional regulator, finally leading to defects in cell spreading and motility. Since YAP signalling is essential for initiation and growth of human malignancies, our data suggest that potential therapeutic approaches targeting PIP4K2B could be beneficial in the control of the altered mechanical properties of cancer cells.

overall_design:
RNA-seq, 3 replicates per condition , 3 conditions (sh_Ctrl, sh_2B, Soft), 1 cell line.

Data is available under CC BY 4.0 license.

This project was supported by Italian Association for Cancer Research (AIRC) Investigator Grant (Paolo Maiuri, #24976) and individual fellow- ship (Fabrizio A. Pennacchio, #23966). Alessandro Poli's work was founded by Fondazione Umberto Veronesi Post-doctoral fellowships (#000359) and Short-EMBO Fellowship (#8386). Polish National Science Centre grant founded Paulina Nastaly (#2020/39/D/NZ3/00882).

first: Alessandro

last: Poli

first: Fabrizio

last: Pennacchio

first: Paulina

last: Nastaly

first: Andrea

last: Ghisleni

first: Michele

last: Crestani

first: Francesca

last: Pramotton

first: Fabio

last: Iannelli

first: Galina

last: Beznoussenko

first: Alexander

last: Mironov

first: Valeria

last: Panzetta

first: Sabato

last: Fusco

first: Bhavwanti

last: Sheth

last: Netti

first: Dimos

last: Poulikakos

first: Aldo

last: Ferrari

first: Nils

last: Gauthier

first: Nullin

last: Divecha


title: Decellularized Spinal Cord Matrix Manipulate Glial Niche Alteration via Serglycin Mediated Signalling Pathway [scRNA-seq]

first: Sheng

last: Zhang

summary: The decellularized spinal cord matrix (DSCM) provides the advantage in the translational potential for microenvironment replacement therapies to repair spinal cord injury (SCI) However, the cell type alteration in the SCI repairing niche is undefined. Using single cell transcriptome and bulk RNA-seq analysis, we showed that DSCM regulated cell fate changes in niches related to the multicellular model. This work opens the door for understanding the SCI repairing from a tissue niche perspective.

overall_design: We evaluated and compared the cells migrated out from spinal cord slice, hspASCs, and ECs under DSCM and Collagen I (COLI) culture conditions using organotypic model and human hspASC-hEC co-culture model.

first: Xiao


title: APC and P53 mutations synergize to create a therapeutic vulnerability to NOTUM inhibition in advanced colorectal cancer [bulk RNA-seq]

first: Joshua

last: Rhoades

summary: We report that inactivation of the APC tumor suppressor results in dramatic activation of the NOTUM carboxylesterase, which has potent tumor suppressive activity in APC-null adenomatous epithelium.  During progression to adenocarcinoma, APC and TP53 mutations (usually coincident in advanced CRC) synergize, converting NOTUM to an obligate oncoprotein.  We provide evidence that the Jekyll-and-Hyde behavior of NOTUM results from its differential activity upon enzymatic targets Glypicans 1 and 4 in early vs. late-stage disease, respectively.  Ultimately, we demonstrate that small molecule inhibition of NOTUM activity in a mouse model of metastatic colon cancer is sufficient to arrest primary tumor growth and metastatic colonization.  Thus, the extracellular carboxylesterase NOTUM represents a novel therapeutic vulnerability in advanced colorectal adenocarcinomas.

overall_design: Infected A and AP organoid with sh-Ctrl or sh-Notum virus and puro selected for 3 days and do bulk RNA sequencing

first: Christopher

middle: J

last: Lengner

first: Ning

last: Li

first: Yuhua

last: Tian


title: The miR-497~195 cluster suppresses cell cycle regulators and in vivo leukemia growth in B-cell precursor Acute Lymphoblastic Leukemia [expression]

status: Public on Dec 09 2022

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

institute: University of Padova

summary: Despite considerable improvements in the treatment of B-cell precursor acute lymphoblastic leukemia (BCP-ALL), relapse is still associated with poor prognosis. We previously found that the risk for early relapse can be predicted by the rapid engraftment of patient-derived blasts transplanted into NOD/SCID mice. In search for the cellular and molecular profile associated with this phenotype, we investigated the expression of microRNAs (miRNAs) in different engraftment phenotypes and patient outcomes. We found miR-497~195 high expression in patient-derived xenograft samples with slow engraftment, derived from patients with favorable outcome. In contrast, epigenetic repression and low expression of these miRNAs was observed in rapidly engrafting samples, which were associated with early relapse. Overexpression of miR-497~195 in patient-derived cells suppressed in vivo engraftment of leukemia cells and considerably prolonged recipient survival by inhibition of regulators of cell cycle progression. As key factors for the entry in S phase were downregulated upon miR-497~195 overexpression, we identified CDK4/CCND3 mediated control of G1/S transition as a principal mechanism for miR-497~195 mediated suppression of leukemia progression in BCP-ALL. Thus, the association of the miR-497~195 cluster expression with outcome in BCP-ALL, and the importance of these miRNAs in counteracting the development of ALL in vivo indicate the relevance of the involved pathways as potential targets for therapeutic intervention.

overall_design: BCP-ALL cell transduced with empty vector (N=5) and with miR-497~195 (N=4)

first: Elena

last: Boldrin

first: Enrico

last: Gaffo

first: Judith

last: Boer

first: Salih

last: Demir

first: Julia

last: Zinngrebe

first: Felix

last: Seyfried

first: Rainer

last: Claus

first: Christoph

last: Plass

first: Monique

middle: D

first: Klaus-Michael

last: Debatin

first: Geertruy

last: Kronnie

first: Lüder

last: Meyer


title: Arginase 1 expression by macrophages promotes Cryptococcus neoformans proliferation and invasion into brain microvascular endothelial cells.

status: Public on Nov 30 2022

city: Klong-luang

first: Pornpimon

last: Angkasekwinai

state: Patumthani

country: Thailand

institute: Thammasat University

summary: Cryptococcal meningoencephalitis caused by C. neoformans infection is the most common cause of death in HIV/AIDS patients. Macrophages are recognized as key players in promoting the growth, proliferation, and dissemination of Cryptococcus. However, macrophage-derived factors that underlie these pathogenic responses remain unclear. Thus, the aim of this study is to investigate the permissive factors of macrophages that support the pathogenicity of Cryptococcus infection. We generated mRNA expression profiles of alveolar macrophage isolated from BALB/c mice intranasally treated with PBS or infected with C. neoformans H99 at 7 and 14 days postinfection and performed a comparative transcriptomic analysis to investigate the transcriptomic changes of macrophages during infection. Alveolar macrophages isolated from C. neoformans-infected mice showed dynamic gene expression patterns which were altered from a protective M1-like cells to a pathogenic M2-like phenotype. Interestingly, Arg1, encoded for enzyme arginase-1, was a predominant up-regulated gene observed in alveolar macrophages after infection at 14 days and the activation of macrophage arginase activity is required for the development of M2 macrophages that supports cryptococcal growth, proliferation, and dissemination.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of alveolar macrophage during C. neoformans infection

first: Adithap

last: Hansakon

first: Chumpol

last: Ngamphiw

first: Sissades

last: Tongsima


title: RNA-seq of evolved strains from Acinetobacter baumannii NCCP 16007

status: Public on Nov 16 2022

city: Seongbuk-gu

first: sohyeon

last: yun

address: Anam-ro 145

country: South Korea

institute: laboratory of molecular environmental microbiology

summary: Comparison for gene expression of Acinetobacter  baumannii NCCP 16007 by evolved strains

overall_design: Control(WT) and 2 sample (EAB1, and EAB2)

first: Sohyeon

last: Yun


title: The proto-oncogene TCL1A deregulates mitotic checkpoint transition and genomic stability in CLL

status: Public on Nov 14 2022

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

institute: University of Cologne (UoC), Germany

summary:
Upregulation of the proto-oncogene TCL1A is causally implicated in various B- and T-cell malignancies. High-level TCL1A correlates with aggressive disease features and inferior clinical outcomes. However, molecular and cell-biological consequences of TCL1A dysregulation are not fully elucidated.
To analyze if TCL1A’s oncogenic activity depends on its subcellular localization, we transduced murine hematopoietic stem cells and progenitor cells (HSC/HPC) with three different human TCL1A variants, being wild type, membrane-localized myristoylated (myr) TCL1A, and TCL1A fused to a nuclear localization signal (nls). All three groups developed mostly B-cell leukemias/lymphomas and less frequently CD4/CD8 double-positive or double-negative T-cell leukemia/lymphomas. Mice transplanted with cells expressing nls-hTCL1A had a significantly shorter survival in comparison to mice harboring wt TCL1A. Gene set enrichment analysis of gene expression profiling data from B-cell tumors identified nuclear pathways including DNA repair, cell cycle, and mitotic spindle to be enriched in the nls-hTCL1A over the hTCL1A cohort.

overall_design: Primary hematopoietic stem cells (HSC)/hematopoietic progenitor cells (HPC) were isolated from tibias and femurs of B6-SJL mice carrying the differential Ptprca pan leukocyte marker CD45.1. Cells were depleted of lineage-committed cells using a Lineage Cell Depletion Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Cells were retrovirally transduced in vitro with MP91-EGFP, -hTCL1A, -myr-hTCL1A, or -nls-hTCL1A. C57BL/6 recipient mice were irradiated with a split dose of 5.5Gy each, with 24 hours between doses, using a BIOBEAM 2000 Cs-137 chloride gamma irradiator (Eckert & Ziegler, Berlin, Germany). One hour after the last dose, 1x10^6 transduced cells were transplanted into each recipient mouse. The development of leukemias was monitored by flow cytometry analysis of blood samples. Gene expression profiles (GEP) were performed on B-cell tumor samples (>70% tumor cell content) from spleens of hTCL1A (n=3), myr-hTCL1A (n=3), and nls-hTCL1A recipient mice (n=3) and EGFP control mice (CD19+GFP+ cells at day 100, n=3). Analyses were performed on an Affymetrix Mouse Gene 1.0 ST Array.

first: Kathrin

last: Warner

first: Sebastian

last: Newrzela

first: Marco

last: Herling


title: Effect of LUCAT1 depletion in THP-1 monocytes on gene expression

status: Public on Nov 01 2022

city: Worcester

first: Katherine

last: Fitzgerald

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: Umass Chan Medical

summary: To investigate the effect of LUCAT1 depletion on gene expression after stimulation with LPS or infection with Sendai virus, RNA-seq on THP-1 control guide RNA and LUCAT1-deficient cells after stimulation.

overall_design: LUCAT1-deficient cells were generated using CRISPR/Cas9 system and cells transduced with a non-targeting guide RNA were used as a control. Two independent experiments per treatment and per genotype were performed.

first: Tim

last: Vierbuchen


title: High resolution ribosome profiling reveals gene-specific details of UGA recoding in selenoprotein biosynthesis

status: Public on Nov 02 2022

city: Bonn

first: Ulrich

last: Schweizer

state: NRW

address: Nussallee 11

department: Institut für Biochemie und Molekularbiologie

institute: Universitätsklinikum Bonn

summary: SECIS binding protein 2 (SECISBP2) increases the efficiency of recoding of UGA codons as selenocysteine (Sec) during translation of mRNAs containing a selenocysteine insertion sequence (SECIS) in the 3’-untranslated region. Using ribosomal profiling, we have previously studied selenoprotein translation in hepatocyte-specific Secisbp2-deficient mouse liver and neuron-specific Secisbp2-mutant mouse brain. The use of organs carries the limitation of cellular heterogeneity with cells still expressing wild-type SECISBP2 that might potentially confound analyses and conclusions. To address this concern, we studied a haploid human HAP1 cell line carrying a non-functional SECISBP2 protein. These cells are still capable of metabolically incorporating 75Se into selenoproteins. We performed ribosomal profiling, and show that the efficiency of UGA recoding is gene-specific in SECISBP2- deficient cells. Analysis of ribosomes with UGA either at the A-site or the P-site revealed in a transcript-specific manner that SECISBP2 helps to recruit tRNASec and stabilizes mRNA. We propose a new measure to assess UGA/Sec read-through at codon resolution in all selenoproteins, i.e. the proportion of ribosomes carrying UGA in the P-site, pUGA. An additional, new observation is frame- shifting occurring after the UGA/Sec codon in GPX1, SELENOF, and SELENOW in HAP1 cells, a finding corroborated by reanalysis of neuron-specific Secisbp2-mutant brains.

overall_design: Ribosome profiling and 3'-mRNA-sequencing of HAP1 Cell samples from 2 SECISBP2 KO replicates and 2 WT replicates

first: Simon

last: Bohleber

first: Wenchao

last: Zhao

first: Noelia

last: Fradejas Villar


title: Cancer cells enter an adaptive persistence to survive radiotherapy and repopulate tumor 1

first: Yucui

first: Tingting

last: Lu

first: Yanqian

last: Wen

first: Jiahui

last: Fan

first: Yongyong

last: Shi

first: Qian

last: Huang


title: The imprinted gene Zac1 regulates steatosis in developmental cadmium-induced non-alcoholic fatty liver disease

status: Public on Oct 21 2022

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

summary:
Background and Aims:
Cadmium (Cd) exposure in adulthood is associated with non-alcoholic fatty liver disease (NAFLD), characterized by steatosis, inflammation, and fibrosis. NAFLD is the leading type of chronic liver disease, resulting in $103 billion per year in medical costs and affecting 30 % of the adult US population. Diagnosis of NAFLD is occurring at increasingly younger ages, with up to 20 % of adolescents and young adults currently affected, suggesting that susceptibility to NAFLD may be programmed by the environment during early life. However, the role of developmental Cd exposure in programming NAFLD and the underlying mechanisms remain unclear. We have proposed that imprinted genes are strong candidates for connecting the early life environment and later disease.
Approach and Results:
We established a hybrid mouse model of developmental Cd exposure in which dams were exposed to 0 or 50 ppm CdCl2 five weeks prior to mating until their offspring reached postnatal day (PND) 10. CdCl2 exposure is associated with histological, biochemical, and molecular signatures of hepatic steatosis and fibrosis in juvenile mice. Using RNA-seq, we show that the Imprinted Gene Network (IGN), including its regulator Zac1, is up-regulated and over-represented among differentially expressed genes, consistent with a role in developmental Cd-induced NAFLD. In support of this, we show that hepatocyte-specific over-expression of Zac1 is sufficient to drive lipid accumulation in vitro.
Conclusions:
Our findings demonstrate that developmental CdCl2 exposure is sufficient to program NAFLD in later life, and with our previous work, establish Zac1 and the IGN as key regulators of prosteatotic and profibrotic pathways, two of the major pathological hallmarks of NAFLD

overall_design: Liver mRNA profiles from PND0 and PND21 mice exposed to 0 or 50 ppm CdCl2 from gestation through PND10

first: Sierra

last: Riegl

first: Cassie

last: Starnes

first: Marine

last: Baptissart

first: Anna

last: Diehl

first: Scott

last: Belcher

first: Michael

last: Cowley


title: Post-transcriptional regulation in cranial neural crest cells expands developmental potential [II]

status: Public on Oct 25 2022

city: Houston

first: Rachel

last: Keuls

state: TX

address: One baylor plaza, Alkek N1020

institute: Baylor College of Medicine

summary: Developmental potential is progressively restricted after germ layer specification during gastrulation. However, cranial neural crest cells challenge this paradigm, as they develop from anterior ectoderm yet give rise to both mesodermal derivatives of the craniofacial skeleton and ectodermal derivatives of the peripheral nervous system. How cranial neural crest cells differentiate into multiple lineages is poorly understood. Here, we demonstrate that cranial neural crest cells possess a transient state of increased chromatin accessibility; and that the earliest premigratory neural crest are biased towards either a neuronal or ectomesenchymal fate, with each lineage expressing distinct factors from the pluripotent state. We profile the spatiotemporal emergence of each neural crest population and demonstrate that the ectomesenchymal lineage forms prior to the neuronal progenitors. Expression of the pluripotency microRNA family miR-302 is maintained in cranial neural crest cells and genetic deletion leads to precocious specification of the ectomesenchymal lineage. We find that miR-302 directly targets Sox9 to slow the timing of ectomesenchyme induction and regulates multiple genes involved in chromatin condensation to maintain accessibility for neuronal differentiation. Loss of mir-302 results in reduced chromatin accessibility in the neuronal progenitor lineage of neural crest and a reduction in peripheral neuron differentiation. Our findings reveal a post-transcriptional mechanism governed by miRNAs from pluripotency as an important mechanism to expand developmental potential of cranial neural crest.

overall_design: E7.5 TS11d 0s whole embryo, E8.25 TS12a 3s cranial region, E8.5 TS13 8-12s cranial region, and E9.5 TS15 26-28s cranial region were harvested for single cell mRNA and single cell ATAC sequencing using a 10X Genomics chromum controller

first: Ronald

last: Parchem


title: Time course mRNA-seq of in vitro decidualization of the T-HESC model

status: Public on Sep 28 2022

city: Cambridge

first: Lajos

last: Kalmar

address: Tennis Court Road

institute: MRC Toxicology Unit, University of cambridge

summary: We analyze by mRNA seq the in vitro decidualization of an immortalized human endometrial stromal cell line (T-HESC). As shown in our previous morphologic analysis (Anelli et al., Traffic 2022) T-HESC undergo a dramatic rearrangement (also at the mRNA level) of the entire the secretory pathway.

overall_design: The experimental design consist in a duplicate of samples collected at eight different timepoints (0, 6, 18, 24, 36, 48, 72, 144 hrs) after initiation of the in vitro decidualization protocol.

first: Ritwick

last: Sawarkar

first: Barbara

last: Hummel

first: Eelco

last: Van Anken

first: Roberto

last: Sitia

first: Tiziana

last: Anelli

first: Paola

last: Panina

first: Daniele

last: Pittari


title: TFH and TFR cells with different timing of peanut sensitizations

status: Public on Jun 28 2022

city: Indianapolis

first: Qiang

last: Chen

state: IN

address: 332/333 RESEARCH II, 950 W Walnut Street

department: Microbiology and Immunology

institute: Indiana University School of Medicine

summary: Peanut-specific IgE is present with peanut sensitizations at day 1 an day 8, while is absent with peanut sensitizations at day 1 and day 3. Since TFH and TFR cells are import in regulating antibody response in germinal center, we would like to know the different in TFH and TFR cells between D1D3 and D1D8 peanut sensitizations.

overall_design: TFH cells from D1D3 and D1D8 with four samples for each group. TFR cells from D1D3 and D1D8 with four samples for each group.

first: Alexander

last: Dent


title: A method to investigate muscle target-specific transcriptional signatures of single motor neurons

status: Public on Jul 29 2022

city: Basel

first: Patrick

last: Tschopp

address: Vesalgasse 1

department: Department of Environmental Sciences

country: Switzerland

institute: University of Basel

summary: To investigate target-specific transcriptional signatures of single motor neurons, here we combine ex-ovo retrograde axonal labelling in mid-gestation chicken embryos with manual isolation of individual fluorescent cells and Smart-seq2 single-cell RNA-sequencing. We validate our method by injecting the EMR and FDQ wing muscles and harvest a total of 50 fluorescently labeled cells, in which we detect upto 10000 transcribed genes. Additionally, we present visual cues and cDNA metrics predictive of sequencing success.

overall_design: SMART-seq2 single neuron RNA-seq of manually picked motor neurons identified by axonal backfill from EMR and FDQ muscles of Day 9  chicken embryos.

first: Bianka

last: Berki

first: Fabio

last: Sacher

first: Antoine

last: Fages

first: Maëva

last: Luxey


title: Long non-coding RNA profile of the intracranial artery in the patients with Moyamoya disease

status: Public on Jul 03 2022

city: Showa-ku, Nagoya

first: Kinya

last: Yokoyama

state: Aichi

address: Tsurumai 65

department: Neurosurgery

institute: Nagoya University Hospital

summary: We collected microsamples of the middle cerebral artery (MCA) from MMD patients (n = 21)  and control patients (n = 11). Using microarray experiments, the profile of lncRNAs expression in MCA were compared between groups and differentially expressed lncRNAs (fold change > 2, q < 0.05) were identified. In addition, the neighboring coding gene whose transcription can be regulated in cis by the identified differentially expressed lncRNAs were investigated, and applied to Gene Ontology analysis for predicting those biological functions.  We detected 308 differentially expressed lncRNAs (fold change > 2, q < 0.05), including 306 up-regulated and 2 down-regulated lncRNAs in the MCA from the MMD patients. As for the prediction of biological function, Gene Ontology analyses with possible coding genes whose transcription are regulated in cis by the identified differentially expressed lncRNAs suggested the involvement in antibacterial humoral response, T cell receptor signaling pathway, positive regulation of cytokine production, and branching involved in blood vessel morphogenesis. Quantitative polymerase chain reaction demonstrated a similar lncRNAs expression to the microarray experiments.

overall_design:
During surgery, micro-samples of MCA from the patients with Moyamoya desease (MMD, n=21), internal carotid artery aneurysm (IA, n=4), and epilepsi (EPI, n=5) were collected.

GSE189993 includes re-used Samples from GSE141022 and GSE157628.

first: Fumiaki

last: Kanamori

first: Takashi

last: Mamiya


title: Gene expression profiles in the hippocampus of the Rp58 hetero-KO and the control wild-type mice in adulthood and old age.

status: Public on Jul 16 2022

city: Tokyo

first: Tomoko

last: Tanaka

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

summary: The early onset of microglia activation in the Rp58 hetero-KO mice raised the possibility that chronic inflammation in the brain was induced by mutation even in the early life stage. To test this possibility, we examined gene expression profiles in the hippocampus of the Rp58 hetero-KO and the control wild-type mice in adulthood and old age months. Among the genes whose expression level was down-regulated in the aged wild-type mice, 341 genes were down-regulated in the adulthood Rp58 hetero-KO mice when both were compared with the adulthood wild-type mice. Conversely, the expression levels of 103 genes were up-regulated both in the adulthood Rp58 hetero-KO and the aged wild-type mice. In the pathway enrichment analysis, these 103 up-regulated genes included Cxcl10, Oas2, Oas1a, and Oasl2, which are associated with a pathway of immune response interferon gamma action on extracellular matrix and cell differentiation.

overall_design: The experiment was performed using three independent total RNA samples from each group.

first: Haruo

last: Okado

first: Yasumasa

last: Nishito


title: Endocrine and molecular factors of increased female reproductive performance in mice

status: Public on Aug 30 2022

first: Ulrich

last: Schweizer

summary: Will be edited in future

overall_design: 3' Poly(A) RNA-sequencing of N = 5 Ctl and FL1 mice ovaries in Estrous and Diestrous

first: Carolin

last: Ludwig

first: Simon

last: Bohleber

first: Marten

last: Michaelis


title: Transcriptomics of Toxoplasma gondii sporulating oocysts

status: Public on Jun 20 2022

city: Zurich

first: Chandra

last: Ramakrishnan

address: Winterthurerstrasse 266a

department: Institute of Parasitology

institute: University of Zurich

summary: Toxoplasma gondii is an apicomplexan parasite that approximately infects one third of the human population worldwide. When sporulated oocysts that are shed in the faeces of infected felids are accidentally ingested through contaminated food or water, sporozoites can infect the intestine of the intermediate host. Upon this infection, the fast replicating tachyzoites then disseminate overall the body and can cross the blood-brain, blood-retina or the blood-placenta barrier. Eventually, immune pressure will lead to differentiation into the slow replicating bradyzoites that are contained within tissue cysts for life. Despite the importance of sporulation for transmission, the process is not yet understood. We therefore exploited Illumina Next-Generation RNA-Sequencing to analyse the transcriptome of oocysts in the process of sporulation and compared it to unsporulated and sporulated oocysts. We thus identified genes that are highly specific to the sporulation process and that may be involved in the formation of sporozoites.

overall_design: Oocysts were enriched from cat faeces using sucrose flotation and CsCl gradient. Unsporulated were preserved in QIAzol at -80 °C until RNA extraction. To initiate sporulation, oocysts were re-suspended in 2% sulphuric acid. Sporulating oocysts were harvested 8 h after re-suspension in sulphuric acid and stored in QIAzol at -80 °C. Fully sporulated oocysts were harvested 8 days after initiation of sporulation and were stored as the samples above. Total RNA was extracted, enriched for mRNA and subjected to RNA-Sequencing using the Illumina HiSeq 4000 system. Differential gene expression was assessed by DESeq2.

first: Jessica

last: Bader

first: Marc

last: Schmid

first: Adrian

middle: B

last: Hehl


title: miR-148a-3p and DDX6 functional link promotes survival of myeloid leukemia cells

status: Public on Jun 07 2022

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Post-transcriptional regulation of genes is heavily dependent on the action of miRNAs. miRNAs take part in various cellular processes and have been shown to be crucial in oncogenesis. Identification of miRNA targets is crucial for understanding its functions in different cellular contexts. miR-148a-3p is highly expressed in HCT116 cells and several other cell lines. However, the studies about mRNA targetting activitiy of this miRNA was limited. In this study, we aimed at identifying target repotoire of miR-148a-3p by using HCT116 DROSHA-KO model. We found several genes that are under miR-148a-3p regulation, including several reported targets. We next found the negative association between miR-148a-3p and DDX6, one of the identified gene, in leukemia. We examined DDX6 functions in this cancer and showed that the depletion of DDX6 helps impair leukemia cell growth, promote apoptosis and increase survival rate of transplanted mice. We then identified that DDX6 functions to suppress TXNIP, a well known tumor suppressor in leukemia and various types of cancer. Our findings uncovered the regulation axis between miR-148a-3p/DDX6/TXNIP in leukemia which provides molecular mechanism basis for therapeutic treatment directions.

overall_design: mRNA sequencing and small RNA sequencing

first: Maryam

last: Ghashghaei

first: Cong-Truc

last: Le

first: Marty

last: Yue

first: Haya

last: Shalaan

first: Tuan-Anh

last: Nguyen

first: P

last: Vu


title: Blood expression profiling of an adult inflammatory bowel disease cohort

status: Public on Sep 16 2022

city: new york city

first: Carmen

last: argmann

state: NY

address: 1425 Madison Avenue

institute: MSSM

summary: Inflammatory Bowel Disease (IBD) is a progressive disease of the gut and consists of two types, Crohn’s Disease (CD) and Ulcerative Colitis (UC). It is a complex disease involving genetic, microbial, and environmental factors. The incidence of IBD is steadily increasing and current therapeutic options are plateauing. Thus treatments are evolving to 1. deeper levels of remission from clinical to endoscopic and histologic normalization and 2. Embrace novel targets or drug combinations. We explored whole transcriptome data generated in blood specimens sampled from a large cohort of adult IBD and control subjects to provide 1. a granular, objective and sensitive molecular measures of disease activity in the gut and 2. Novel molecular mechanisms and biomarkers underlying IBD pathology.

overall_design: The Mount Sinai Crohn's and Colitis registry (MSCCR) is a prospective cross-sectional cohort consisting of adult IBD patients and controls. Blood RNA sequencing (RNA-Seq) data were generated on whole blood sampled at the time of the participant’s endoscopy visit which also included detailed clinical, histological and endoscopic assessments.

last: Argmann

first: Mayte

last: Suárez-Fariñas

first: Ruixue

last: Hou

first: Aritz

last: Irizar


title: Snrpb, the gene mutated in CCMS, is haploinsufficient and required for proper splicing and morphogenesis

status: Public on Jun 15 2022

city: Montreal

first: Loydie

last: Jerome-Majewska

state: QC

address: 1001 Decarie Blvd EM0.2210

department: Pediatrics

country: Canada

institute: McGill University Health Centre Glen Site

summary:
Purpose: Heterozygous mutations in SNRPB, an essential core component of the five small  ribonucleoprotein particles of the spliceosome, are responsible for  craniofacial and rib defects in patients with Cerebrocostomandibular Syndrome  (CCMS). However, why the mutations in SNRPB causes tissue specific CCMS abnormalities  such as craniofacial defects are unknown. We hypothesize that splicing of tissue  specific transcripts required for craniofacial development is disrupted due to  SNRPB deficiency, during embryonic development. The purpose of the study was to  identify those developmentally important transcripts that are dysregulated due  to Snrpb mutation.
Methods: We mated Snrpbloxp mice that we have  developed with commercially available Wnt-1-Cre2 transgenic mice to remove  one allele of Snrpb from neural crest cells. The mutant (Snrpb \ncc+/-)  embryos showed craniofacial abnormalities at E9.5 and onward. We collected  morphologically normal embryos at E9.0 for both Snrpb wildtype and Snrpbncc+/-  mutants. We pooled two embryo heads of similar somites for each genotype and  extracted the RNA for RNAseq.
Results: We found that Snrpbncc+/-  mutants show aberrant splicing that includes both increased exon skipping and  intron retention. A strong tendency  towards increased exon skipping and intron inclusion in the mutant samples were  observed; there were more SE (273 in Het versus 83 in WT) and RI (191 in Het  versus 21 in WT). We identified 13 transcripts required for  craniofacial development or stem cell development with significant increases in  exon skipping including Smad2, Rere and Pou2f1. From pathway  analysis of differentially expressed genes, we found they were associated with the spliceosome and  the P53-pathway. We also found an increase in splicing of two P53  regulator, Mdm2 and Mdm4.
Conclusions: We propose that abnormal splicing underlies  the defects found in Snrpbncc+/-mutant embryos. We confirmed  differential splicing of the P53 regulators, Mdm2 and Mdm4  and identified several transcripts important for craniofacial development which  were abnormally spliced in Snrpbncc+/- embryos.

overall_design: Neural crest cell-specific Snrpb embryos’ mRNA profiles of E9.0 heterozygous (Snrpbncc+/-) mice

last: A. Jerome-Majewska

first: Sabrina

last: Shameen Alam

first: Shruti

last: Kumar

first: Marie-Claude

last: Beauchamp

first: Eric

last: Bareke

first: Alexia

last: Boucher

first: Nadine

last: Nzirorera

first: Reinnier

last: Padilla

first: Si

last: Zhang

first: Jacek

last: Majewski


title: Identification of differentially expressed genes in the bone marrow microenvironment of mice with leukemia

city: Mainz

first: Pablo

last: Llavona

state: Rhineland-Palatinate

address: Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4

institute: IMB

summary: To identify the genes that are differntially expressed in the bone marrow microenvironment of mice with leukemia we isolated total RNA from primary stromal cells sorted from mice with chronic or acute myeloid leukemia.

overall_design: Comparative gene expression profiling analysis by microarray ofstromal cells isolated from the bone marrow of mice with chronic (3 replicats) or acute (3 rplicates) myeloid leukemia.

first: Minciacchi

last: Valentina R.

first: Karantanou

last: Christina

first: Zaneti

last: Costanza

first: Kumar

last: Rahul

first: Thomasberger

last: Nathalie

first: Llavona

last: Pablo

first: Krack

last: Theresa

first: Bankov

last: Katrin

first: Meister

last: Melanie

first: Hartmann

last: Sylvia

first: Maguer-Satta

last: Véronique

first: Lefort

last: Sylvian

first: Putyrski

last: Mateusz

first: Ernst

last: Andreas

first: Meduri

last: Eshwar

first: Krause

last: Daniela S.


title: Genome Wide Transcriptome Analysis of tef (Eragrostis tef) Under Long-Term Low Calcium Stress

status: Public on Sep 23 2022

first: Dereje

last: Jima

summary: Calcium (Ca2+) is one of the essential mineral nutrients for plant growth and development. However, the effects of long-term Ca2+ deficiency in orphan crops such as tef (Zucc.) Trotter] which accumulate high levels of Fe in the grains remained unknown. Tef is a staple crop for nearly 70 million people in East Africa, particularly Ethiopia and Eritrea. It is rich in mineral nutrients (Ca+2, Fe, Zn and Mn), vitamins and essential amino acids.  In this study, tef plants were grown in hydroponic solution containing optimum (1 mM) or low (0.01 mM) Ca2+ and plant growth parameters and whole genome transcriptome were analyzed. Ca+2-deficient plants exhibited symptoms including leaf necrosis, leaf curling, and growth stunting. Ca2+ deficiency significantly decreased root and shoot Ca+2, potassium (K) and copper content in both root and shoots while it significantly increased root iron (Fe2+) content, suggesting the role of Ca2+ in the uptake and/or translocation of these minerals. Transcriptomic analysis using RNA-seq revealed that members of Ca2+ channels including the cyclic nucleotide-gated channels (CNGC) and glutamate receptor-like channels (GLRs), Ca2+-transporters, Ca2+-binding proteins (CBP) and Ca2+-dependent protein kinases (CDPK) were differentially regulated by Ca+2 treatment. Moreover, several Fe/metal transporters including members of vacuolar Fe transporters (VIT), yellow stripe-like (YSL), natural resistance-associated macrophage protein (NRAMP) and oligo-peptide transporters (OPT) were differentially regulated between shoot and root in response to Ca2+ treatment.  Taken together, our findings suggest that Ca2+ deficiency affects plant growth and mineral accumulation by regulating the transcriptomes of several transporters and signaling genes.

overall_design: N = 4 SAMPLES PER TREATMENT GROUP

first: Ayalew

last: Ligaba-Osena

first: Mohammad

last: Salehin

first: Muhammad

last: Numan

first: Xuegeng

last: Wang

first: Sang-Chul

last: Choi

first: Louis-Mari

last: Bobay

first: Wanli

last: Guo


title: Effect of depletion of ANXA2 and ANXA5 on gene expression in primary murine mesenchymal stromal cells

status: Public on Jun 14 2022

first: Pablo

last: Llavona

summary: To investigate the effects of ANXA2 or ANXA5 depletion on gene expression in primary mesenchymal stromal cells we compared the gene expression profile of sorted mesenchymal stromal cells from the bone marrow of normal wildtype, ANXA2 knockout or ANXA5 knockout mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mesenchymal stromal cells isolated from the bone marrow of normal wildtype C57/BL6 mice (4 replicates), ANXA2 KO C57/BL6 mice (3 replicates) and ANXA5 KO C57/BL6 mice (4 replicates).

first: Valentina

last: Minciacchi

first: Christina

last: Karantanou

first: Costanza

last: Zaneti

first: Rahul

last: Kumar

first: Nathalie

last: Thomasberger

first: Theresa

last: Krack

first: Katrin

last: Bankov

first: Melanie

last: Meister

first: Sylvia

last: Hartmann

first: Véronique

last: Maguer-Satta

first: Sylvian

last: Lefort

first: Mateusz

last: Putyrski

first: Andreas

last: Ernst

first: Eshwar

last: Meduri

first: Daniela

last: Krause


title: Transcriptome-wide N6-methyladenosine modification profiling in patients with recurrent implantation failure (RIF)

status: Public on Oct 16 2022

city: Lanzhou

first: Wenxin

last: Gao

state: 甘肃

address: East west road no. 1

institute: Lanzhou university

summary:
Purpose:using m6A modified RNA immunoprecipitation sequence (m6A-seq), to establish the m6A methylation transcription profiles in recurrent implantation failure (RIF).
Methods: GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) was used to construct RNA libraries for IP and input samples by following the manufacturer's instructions. The library quality was evaluated using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina 6000).
Result:using m6A modified RNA immunoprecipitation sequence (m6A-seq),  methylated sites in mRNA,lncRNA and circRNA are identified.
Conclusions: Our study revealed the m6A methylation landscape by MERIP sequencing.

overall_design: Comparative gene expression profiling analysis of MeRIP-seq data for middle secretory phase endometrium in recurrent implantation failure and  control. (subjects referred to women, who were pregnant in the next cycle after sampling, underwent IVF/ICSI-ET due to fallopian tube or male factors, and less than 2 fresh or frozen embryos were transferred.)

first: Ting

last: Wang

first: Lili

last: Zhang

first: Yidan

last: Liu

first: Feng

last: Yue

first: Xiaoling

last: Ma

first: Lin


title: Paired human colon and tumor biopsies

status: Public on Feb 21 2022

city: Philadelphia

first: Patrick

last: Lundgren

state: PA

address: 302 Johnson Pavilion, 3610 Hamilton Walk

institute: University of Pennsylvania

overall_design:
Paired human colon and tumor biopsies were obtained and made into single cell suspensions. Cells were encapsulated into droplets and libraries prepared using the 10X Genomics platform and libraries sequenced on an Illumina NextSeq
***Raw data are being deposited in dbGaP due to patient privacy concerns***

first: Maayan

last: Levy

first: Christoph

last: Thaiss

first: Oxana

last: Dmitrieva-Posocco


title: Gene expression profile at single cell level of breast cancer patient-derived xenograft models using SMART-seq and MULTI-seq

status: Public on Aug 12 2022

city: San Francisco

first: Juliane

last: Winkler

address: 513 Parnassus Avenue

department: Department of Cell and Tissue Biology

institute: University of California, San Francisco

summary: We profiled the tumor heterogeneity of individual primary tumor of breast cancer using a set of patient derived xenograft models with different metastatic potentials. This data set gives insights into the transcriptional tumor heterogeneity and how these are changing in regard to varying metastatic phenotypes.

overall_design: Live human tumor cells from breast tumor and matched metastatic lung tissues of patient-derived xenograft models were isolated using Fluorescence-activated cell sorting (FACS) based on the human specific CD298 antibody and pooled, captured and processed in microfluidics droplets via 10x Genomics using MULTI-Seq protocol.

first: Angela

last: Pisco

first: Spyros

last: Darmanis

first: Andrei

last: Goga


title: Integrative small and long RNA-omics analysis of human healing and non-healing wounds discovers cooperating microRNAs as therapeutic targets

status: Public on Mar 06 2022

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

institute: Karolinska Institutet

summary: Due to microRNAs' (miRs) important functions and high potential for disease diagnosis and therapy, increasing efforts have been put to understand their role in wound repair and identify targetable miRs for wound treatment. However, lack of knowledge about miR-mediated gene expression in human wound tissues hinders the recognition of clinically relevant miRs. Here we profiled genome-wide miR and mRNA expression by RNA-sequencing in the same set of samples from human normal acute wounds and chronic non-healing venous ulcers (VU). By integrative analysis of miR and mRNA omics, we unraveled miR-mediated gene regulatory networks specifically associated with different phases of wound repair or VU. We also identified transcriptional factors and miR arm switching events underpinning the dynamically changed miR expression. In this study, we focused on not only a few top changed miRs, but also the miRs with their targetome enriched in the VU gene signature, such as miR-34a-5p, miR-34c-5p, miR-218-5p, miR-7704, miR-424-5p, miR-450-5p, miR-517b-3p, miR-96-5p, and miR-516b-5p. We confirmed these miRs' targetome in human keratinocytes and fibroblasts using microarrays and demonstrated their functional relevance to VU pathology.

overall_design: Twenty tissue samples from four groups (each N = 5), including Skin, Wound1, Wound7 and VU, were prepared for small RNA (miRNA-seq) and mRNA (mRNA-seq) library construction, respectively.

middle: X

last: Landén

first: Pehr

last: Sommar

first: Zhuang

first: Letian


title: Context-specific translation arrest by evernimicin, an inhibitor of tRNA accommodation

status: Public on Apr 15 2022

city: Chicago

first: Kyle

last: Mangano

state: Illinois

address: 900 S Ashland Ave, MBRB Rm 3056

institute: University of Illinois at Chicago

summary: Antibiotics of the orthosomycin class bind at a distinct site on the large subunit of the bacterial ribosome not used by any other known protein synthesis inhibitor. Structural and biochemical in vitro studies suggested that orthosomycins should block accommodation of aminoacyl-tRNAs in the ribosomal A-site arresting the ribosome at the start codons of the genes. However, the mode of action of orthosomycins in the living cell remains unknown. Here, to get a general and unbiased view of the mode of action of orthosomycin antibiotics, we carried out genome-wide ribosome profiling analysis in Escherichia coli cells exposed to evernimicin, one of the most active antibiotics of this class. Our in vivo data, supported by the analysis of evernimicin action upon in vitro translation of a variety of mRNAs, argue that orthosomycins preferentially inhibit translation elongation and act in a context specific manner. We show that evernimicin predominantly arrests translation when the ribosome needs to accommodate Pro-tRNA or Leu-tRNA in the A site while polymerizing specific amino acid sequences. We further show that the discovered context specificity of orthosomycins is exploited for the programmed translation arrest that apparently regulates resistance to these antibiotics.

overall_design: Ribosome profiling of E. coli imp4213 cell cultures treated with evernimicin were compared to untreated cultures to study the mechanism of translation inhibition

first: James

last: Marks

first: Dorota

last: Klepacki

first: Chayan

last: Kumar Saha

first: Gemma

last: Atkinson

first: Nora

last: Vázquez-Laslop

first: Alexander

last: Mankin


title: Integrated analysis of lncRNA-miRNA-mRNA ceRNA Network elucidates the molecular interactome

status: Public on May 18 2022

city: Karaj

first: Abolfazl

last: Bahrami

address: Daneshgah

department: Biology

country: Iran

institute: University of Tehran

summary: This study constructed a ceRNA network consisting of lncRNA–miRNA–mRNA based on lncRNA-mRNA and miRNA-mRNA interactions. Our objective was to investigate functional modules and hub differentially expressed genes, miRNAs and lncRNAs on different traits.

overall_design: 12 pooled samples; 6 control, 6 treatment differential expression analysis.

first: Mohamed

last: Mohammadi

first: Ali

last: Hasankhani


title: Mammalian PERIOD2 regulates H2A.Z incorporation into chromatin to orchestrate circadian negative feedback [Mnase-seq]

status: Public on Feb 17 2022

city: Lyon

first: Kiran

last: Padmanabhan

address: 32-34 avenue Tony Garnier

department: IGFL

country: France

institute: ENS-Lyon

type: Methylation profiling by high throughput sequencing

summary: We report the interdependance of PERIOD and H2A.Z to orchestrated the circadian negative feedback. H2A.Z is required for the circadian rhythm, it allows the binding of Bmal1 and PERIOD2 to the chromatin. And reciprocally, PERIOD2 aid H2A.Z deposition by interacting with the specific chaperone YL1.

overall_design: RNA-seq and Mnase-seq between wildtype and period triple KO or H2A.Z double KO MEF cells

first: Kevin

last: Tartour

first: Francesca

last: Andriani

first: Eric

last: Folco


title: Mammalian PERIOD2 regulates H2A.Z incorporation into chromatin to orchestrate circadian negative feedback

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

overall_design: Refer to individual Series


title: Identification and isolation of hematopoietic stem and progenitor cell populations (RNA-seq)

status: Public on Mar 03 2023

city: Bethesda

first: Jens

last: Lichtenberg

state: MD

address: 49 Convent Dr 3A19

department: National Human Genome Research Institute

country: USA

institute: National Institutes of Health

summary: Transcriptional profiling of four common myeloid progenitor subpopulations prospectively isolated from mouse bone marrow

overall_design: Bulk RNA sequencing was performed on C10, C11, C17, and C3 common myeloid progenitor subpopulations defined by single cell transcriptional profiling and clustering and prospectively isolated in duplicate from mouse bone marrow.

first: Elisabeth

middle: F

last: Heuston

first: David

middle: M

last: Bodine


title: Mammalian PERIOD2 regulates H2A.Z incorporation into chromatin to orchestrate circadian negative feedback [Mnase-Seq]

overall_design: Mnase-seq between wildtype and period triple KO or H2A.Z double KO MEF cells


title: H3K27me3 regulates macrophage cytokine transcription and impacts on Collagen Induced Arthritis

status: Public on Mar 11 2022

city: Qingdao

first: zhao

last: zhan

state: Shandong

address: No.23 HongKong East Road,Laoshan District

department: School of Medicine and Pharmacy

institute: Ocean University of China


title: Zac1 and the Imprinted Gene Network program juvenile NAFLD in response to maternal metabolic syndrome [AML12]

status: Public on Feb 14 2022

city: RALEIGH

first: Dereje

last: Jima

address: 850 Main Campus Drive

institute: NCSU

summary: Background and Aims  Within the next decade, non-alcoholic fatty liver disease (NAFLD) is predicted to become the most prevalent cause of childhood liver failure in developed countries. Predisposition to juvenile NAFLD can be programmed during early life in response to maternal metabolic syndrome (MetS), but the underlying mechanisms are poorly understood. We hypothesized that imprinted genes, defined by expression from a single parental allele, play a key role in maternal MetS-induced NAFLD, due to their susceptibility to environmental stressors and their functions in liver homeostasis. We aimed to test this hypothesis and determine the critical periods of susceptibility to maternal MetS.    Approach and Results  We established a mouse model to compare the effects of MetS during prenatal and postnatal development on NAFLD. Postnatal but not prenatal MetS exposure is associated with histological, biochemical and molecular signatures of hepatic steatosis and fibrosis in juvenile mice. Using RNA-seq, we show that the Imprinted Gene Network (IGN), including its regulator Zac1, is up-regulated and over-represented among differentially expressed genes, consistent with a role in maternal MetS-induced NAFLD. In support of this, activation of the IGN in cultured hepatoma cells by over-expressing Zac1 is sufficient to induce signatures of profibrogenic transformation. Using chromatin immunoprecipitation, we demonstrate that Zac1 binds the TGF-β1 and COL6A2 promoters, forming a direct pathway between imprinted genes and well-characterized pathophysiological mechanisms of NAFLD. Finally, we show that hepatocyte-specific over-expression of Zac1 is sufficient to drive fibrosis in vivo.  Conclusions  Our findings identify a novel pathway linking maternal MetS exposure during postnatal development to the programming of juvenile NAFLD, and provide support for the hypothesis that imprinted genes play a central role in metabolic disease programming.

overall_design: Cultured mouse hepatocytes (AML12 cells) were transfected with over-expression constructs containing either the Zac1 or EGFP open reading frames and the resulting global transcriptional changes were analyzed by RNA-seq after 24h.

first: Marine

last: Baptissart

first: Christine

last: Bradish

first: Brie

last: Jones

first: Evan

last: Walsh

first: Jesse

last: Tehrani

first: Vicmarie

last: Marrero-Colon

first: Sanya

last: Mehta

first: She

last: Oh

first: Anna

last: Diehl

first: Tiffany

last: Fougeray

first: Hervé

last: Guillou

first: Michael

last: Cowley


title: OCT4 has an atheroprotective role in endothelial cells by preventing metabolic and phenotypic dysfunction

status: Public on Apr 02 2022

city: Cleveland

first: Olga

last: Cherepanova

state: OH

address: 9500 Euclid Ave

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic

summary: Until recently, the pluripotency factor OCT4 was believed to be dispensable in adult somatic cells. However, our recent studies provided clear evidence that OCT4 has a critical atheroprotective role in smooth muscle cells (SMC). Here, we demonstrate that OCT4 controls endothelial cell (EC) phenotypic modulation in atherosclerosis.  We establish a new atheroprotective function for OCT4, in that EC-specific Oct4 knockout resulted in increased lipid and LGALS3+ cell accumulation, and altered plaque characteristics consistent with decreased plaque stability. A combination of single-cell RNA sequencing and EC-lineage-tracing studies revealed increased EC activation, endothelial-to-mesenchymal transitions, plaque neovascularization, and mitochondrial dysfunction in the absence of OCT4. We show that ATP transporter, ABCG2, is a direct target of OCT4 in EC, and establish for the first time that the OCT4/ABCG2 axis maintains EC metabolic homeostasis by regulating intracellular heme accumulation and related reactive oxygen species production, which, in turn, contributes to atherogenesis. These results provide the first direct evidence that OCT4 has a protective metabolic function in EC, and identifies vascular OCT4 and its signaling axis as a potential target for novel therapeutics.

overall_design: Comparison of wild-type and Oct4 knockout aortic and lung endothelial cells sorted from EC lineage tracing Apoe knockout mice after 5 week of Western diet feeding

first: Junchul

last: Shin

first: Svyatoslav

last: Tkachenko

first: Malay

last: Chaklader

first: Connor

last: Pletz

first: Kanwardeep

last: Singh

first: Gamzey

last: Bulut

first: Young-min

last: Han

first: Kelly

last: Mitchell

first: Richard

middle: A

last: Baylis

first: Andrey

last: Kuzmin

first: Bo

last: Hu

first: Justin

last: Lathia

last: Stenina-Adognravi

first: Eugene

last: Podrez

first: Tatiana

last: Byzova

first: Gary

middle: K

last: Owens


title: Single cell RNA-seq on kidneys of mice with inactivated hepatocellular Mdm2.

status: Public on Feb 01 2022

city: Glasgow

first: Tom

last: Bird

address: Switchback Road

country: United Kingdom

institute: Beatson Insistute for Cancer Research

summary: In our study we aimed to characterise the effects of p53-induced liver senescence on murine kidneys. We induced liver senescence in 8-12 weeks old male mice by compromising hepatocellular Mdm2 functionality through systemic administration of the AAV8-TBG-Cre viral vector (ΔMdm2Hep mice). We observed transmision of the senescent phenotype from the senescent liver to the genetically unmanipulated kidney. To further elucidate the mechanisms that mediate this transmission phenotype and to characterise its effects on the kidney, we performed single-cell RNA sequencing (scRNA-seq) on the kidneys of 3 ΔMdm2Hep and 3 control mice. We observed the upregulation of several signalling pathways in specific renal cell compartments (e.g. TGFβ in the tubular compartment and JAK-STAT in the mesenchymal compartment). Our results show that liver senescence has a different effect on the renal transcriptome depending on the cellular compartment.

overall_design: This experiment contains 6 biological samples of kidney cells from mice with an AAV8-TBG-Cre that excises the floxed Mdm2 exons 5 and 6 in the liver (n=3 mice, Cre group) or AAV8-TBG-Null empty vector (n=3 mice) which does not affect the mentioned exons (control/Null group). 4 days post AAV injection the mice were culled and their kidneys were harvested. Cell viability and concentration were determined using the Trypan Blue assay. 20,000- 40,000 cells were loaded on a 10x Chromium chip (1 sample per lane). Cleanup, reverse transcription, cDNA amplification and library preparation were performed using the Chromium Single cell 3’ Reagent Kits (v3) as per the manufacturer’s instructions. The samples were sequenced in the Illumina NextSeq500 using the 2x150bp kit with the following read length parameters: 26bp Read1 - cell barcode and UMI, 8bp I7 index - sample index, 98bp Read2 - transcript read. Each biological sample has mutlple raw fastq files, corresponding to different reads or index (e.g. R1, R2, I1) and to different lanes used for sequencing (e.g. L001, L002, etc...).

first: Maria

last: Terradas-Terradas

first: Christos

last: Kiourtis

first: Thomas

first: Ya-Ching

last: Hsieh


title: Zac1 and the Imprinted Gene Network program juvenile NAFLD in response to maternal metabolic syndrome

first: Dereje

last: Jima

summary:
Background and Aims

Within the next decade, non-alcoholic fatty liver disease (NAFLD) is predicted to become the most prevalent cause of childhood liver failure in developed countries. Predisposition to juvenile NAFLD can be programmed during early life in response to maternal metabolic syndrome (MetS), but the underlying mechanisms are poorly understood. We hypothesized that imprinted genes, defined by expression from a single parental allele, play a key role in maternal MetS-induced NAFLD, due to their susceptibility to environmental stressors and their functions in liver homeostasis. We aimed to test this hypothesis and determine the critical periods of susceptibility to maternal MetS.

Approach and Results

We established a mouse model to compare the effects of MetS during prenatal and postnatal development on NAFLD. Postnatal but not prenatal MetS exposure is associated with histological, biochemical and molecular signatures of hepatic steatosis and fibrosis in juvenile mice. Using RNA-seq, we show that the Imprinted Gene Network (IGN), including its regulator Zac1, is up-regulated and over-represented among differentially expressed genes, consistent with a role in maternal MetS-induced NAFLD. In support of this, activation of the IGN in cultured hepatoma cells by over-expressing Zac1 is sufficient to induce signatures of profibrogenic transformation. Using chromatin immunoprecipitation, we demonstrate that Zac1 binds the TGF-β1 and COL6A2 promoters, forming a direct pathway between imprinted genes and well-characterized pathophysiological mechanisms of NAFLD. Finally, we show that hepatocyte-specific over-expression of Zac1 is sufficient to drive fibrosis in vivo.

Conclusions

Our findings identify a novel pathway linking maternal MetS exposure during postnatal development to the programming of juvenile NAFLD, and provide support for the hypothesis that imprinted genes play a central role in metabolic disease programming.

overall_design: Liver mRNA profiles from PND21 mice exposed to maternal MetS during prenatal development only (MetS-Ct), postnatal development only (Ct-MetS), throughout development (MetS-MetS) or never (Ct-Ct)

first: Marine

last: Baptissart

first: Christine

last: Bradish

first: Brie

last: Jones

first: Evan

last: Walsh

first: Jesse

last: Tehrani

first: Vicmarie

last: Marrero-Colon

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