title: Estrogen receptor alpha regulates uterine epithelial lineage specification and homeostasis

city: Pullman

first: Kimberly

last: Davenport

state: WA

address: 100 Dairy Rd

department: Animal Science

institute: Washington State University

summary: Postnatal development of the uterus involves specification of undifferentiated epithelium into uterine-type epithelium. That specification is regulated by stromal-epithelial interactions as well as intrinsic cell-specific transcription factors and gene regulatory networks. This study utilized mouse genetic models of Esr1 deletion, endometrial epithelial organoids (EEO), and organoid-stromal co-cultures to decipher the role of Esr1 in uterine epithelial development. Organoids derived from wild-type (WT) mice developed a normal single layer of columnar epithelium. In contrast, EEO from Esr1 null mice developed a multilayered stratified squamous type of epithelium with basal cells. Co-culturing Esr1 null epithelium with WT uterine stromal fibroblasts inhibited basal cell development. Of note, estrogen treatment of EEO-stromal co-cultures and Esr1 conditional knockout mice increased basal epithelial cell markers. Collectively, these findings suggest that Esr1 regulates uterine epithelium lineage plasticity and homeostasis and loss of ESR1 promotes altered luminal-to-basal differentiation driven by ESR1-mediated paracrine factors from the stroma.

overall_design: This study utilized mouse genetic models of Esr1 deletion, endometrial epithelial organoids (EEO), and organoid-stromal co-cultures to decipher the biological role of Esr1 in uterine morphogenesis

first: Jason

last: Rizo

first: Wipawee

last: Winuthayanon

last: Spencer

first: Andrew

last: Kelleher


title: PD-L1 positive astrocytes attenuate inflammatory functions of PD 1 positive microglia in models of autoimmune neuroinflammation

status: Public on Aug 02 2023

city: Erlangen

first: Mathias

last: Linnerbauer

address: Schwabachanlage 6

department: Neurology

country: Germany

institute: University Hospital Erlangen

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Circular RNA sequencing of P0 and P2 generation chondrocytes

city: Hangzhou

first: shuying

last: shen

state: Zhejiang

address: 3 East Qingchun Road

department: Department of Orthopaedic Surgery

country: China

institute: Sir Run Run Shaw Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose: Circular RNA sequencing was used to find out differentially expressed CircRNAs between P0 generation samples and P2 generation samples. Method: chondrocyte CircRNAs profiles of P0 generation samples and P2 generation samples were analyzed.

overall_design: We collected three human knee joint samples and primary chondrocytes were cultured. Then, all three P0 genaration chondrocyte were culture into P2 generation. At last, three P0 generation samples and three P2 generation samples were collected

first: Shuying

last: Shen


title: Post-transcriptional regulation of Ribosome Biogenesis during differentiation

status: Public on Aug 03 2023

city: Durham

first: Marcos

last: Morgan

address: 111 TW Alexander Dr

country: USA

institute: NIEHS


title: A methanotrophic bacterium to enable direct methane capture for climate mitigation

city: Seattle

first: Erin

last: Wilson

address: 185 E Stevens Way NE

department: The Paul G. Allen School of Computer Science & Engineering

institute: University of Washington

summary: We report here a methanotroph, Methylotuvimicrobium buryatense 5GB1C, that consumes methane at 500ppm at rates several times higher than any previously published. Analyses of bioreactor-based performance and RNAseq based transcriptomics suggest that this superior ability to utilize low methane is based at least in part on an extremely low non-growth associated maintenance energy and on a 5-fold higher methane specific affinity than previous reports.

overall_design: M. buryatense 5GB1C cultures were grown with 500 ppm or 1000 ppm methane at steady state. Specific growth rates were 0.009 and 0.02 h-1, respectively. RNA samples were collected after three-generation growth.

first: Lian

last: He

first: Joseph

middle: D

last: Groom

middle: H

first: Janette

last: Fernandez

first: Michael

last: Konopka

first: David

middle: A

last: Beck

first: Mary

middle: E

last: Lidstrom


title: Let-7 enhances murine anti-tumor CD8 T cell responses by promoting memory and antagonizing terminal differentiation

city: Amherst

first: Leonid

last: Pobezinsky

state: MA

address: 661 N Pleasant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts Amherst

summary: The success of the CD8 T cell-mediated immune response against infections and tumors depends on the formation of a long-lived memory pool, and the protection of effector cells from exhaustion. The advent of checkpoint blockade therapy has significantly improved anti-tumor therapeutic outcomes by reversing CD8 T cell exhaustion, but fails to generate effector cells with memory potential. Here, using in vivo mouse models, we show that let-7 microRNAs determine CD8 T cell fate, where maintenance of let-7 expression during early cell activation results in memory CD8 T cell formation and tumor clearance. Conversely, let-7-deficiency promotes the generation of a terminal effector population that becomes vulnerable to exhaustion and cell death in immunosuppressive environments and fails to reject tumors. Mechanistically, let-7 restrains metabolic changes that occur during T cell activation through the inhibition of the PI3K/AKT/mTOR signaling pathway and production of reactive oxygen species, potent drivers of terminal differentiation and exhaustion. Thus, our results reveal a role for let-7 in the time-sensitive support of memory formation and the protection of effector cells from exhaustion. Overall, our data may suggest a strategy in developing next-generation immunotherapies by preserving the multipotency of effector cells rather than enhancing the efficacy of differentiation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for T cells (naïve, activated, or CTLs) on either a WT, Lin28b transgenic, or Let-7 transgenic background (n=3 for each sample group).

first: Alexandria

middle: C

last: Wells

first: Kaito

last: Hioki

first: Constance

last: Angelou

first: Elena

middle: L

last: Pobezinskaya


title: Acute murine cytomegalovirus infection boosts cell-type specific response and lipid metabolism changes in infant mice liver

city: Hefei

first: Tingyue

last: Zhou

address: Huangshan road

institute: USTC

summary: Human cytomegalovirus (HCMV) infection in infants cause severe diseases, such as neonatal hepatitis. However, the single-cell dimensional description of the immune cell alteration during the first virus exposure process in infants, remains poorly understood. The hepatocytes play an essential role in metabolic homeostasis and detoxification. The Concomitant Effects of CMV infection on liver lipid metabolism in infants are still unclear. Here, using single-cell RNA-sequencing, we found MCMV can infect most cell types of infant mice liver, changing the number of immune cells. MCMV infection increases proliferating CD8 effector T cells and a subset of Nos2+ monocytes, which may play important roles in the early anti-viral process. Furthermore, MCMV infection subvert the protein expression profile of lipid metabolism in hepatocytes. Overall, our data provide insights as to how the immune system response to MCMV infection during the early stage of infection, and the impact of infection on lipid metabolism in infant mice hepatocytes.

overall_design: Infant mice were infected by MCMV and livers were subjected to scRNA-seq.

first: Anmin

last: Wang


title: Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells [RNA-seq]

city: Padua

first: Irene

last: Zanin

state: Italy

address: Via Gabelli 63

department: Molecular Medicine

country: Italy

institute: University of Padua

summary: i-Motifs (iMs) are four-stranded DNA structures that form at cytosine (C)-rich sequences and in acidic conditions in vitro. However, their formation and distribution in cells is still under debate. Here we performed CUT&Tag sequencing using the anti-iM antibody iMab and showed that iMs form within the human genome in live cells. We mapped native iMs in two different human cell lines and recovered C-rich sequences that were confirmed to fold into iMs in vitro. We found that iMs in cells are mainly present at actively transcribing gene promoters and that their abundance and distribution are specific to each cell type. iMs with both long and short C-tracts were recovered, further extending the relevance of iMs throughout the genome. By simultaneously mapping G-quadruplexes (G4s), four-stranded structures that form at guanine-rich regions, and comparing the results with iMs, we proved that the two structures can form in independent genomic regions; however, when both iMs and G4s are present in the same genomic tract, their formation is favored. Our findings support the in vivo formation of iM structures and provide new insights into their interplay with G4s as new regulatory elements in the human genome.

overall_design: RNA-seq analysis of HEK293T (ATCC #CRL-3216)

first: Emanuela

last: Ruggiero

first: Giulia

last: Nicoletto

first: Sara

last: Lago

first: Ilaria

last: Maurizio

last: Gallina

middle: N

last: Richter


title: Trained immunity transplant (TITR) bulk RNA-seq libraries of HSCs

city: Houston

first: Bailee

last: Kain

state: Texas

address: 1102 Bates Avenue

institute: Baylor College of Medicine

summary:
Purpose: To evaluate whether methylation changes occuring upon M. avium infection correlate with transcriptional alterations in trained HSCs, we reisolated CD45.2 untrained vs. trained HSCs (LK CD150+CD48–) from transplanted mice one-month after M. avium challenge to generate bulk RNA-Seq libraries. We compared both libraries to a library from HSCs of WT donor mice following primary M. avium infection. This comparison revealed changes in global transcription in trained HSCs after M. avium challenge compared to primary infection, with the untrained set serving as the irradiation and transplant control.
Methods: 10,000-50,000 HSCs (CD45.1/CD45.2 KL CD150+ CD48-) into HBSS from naive or 1-month infected WT/transplanted mice (n=10-12 per group). DNA and RNA were isolated with the NucleoSpin ® RNA Plus XS kit (Macherey Nagel). RNA-seq libraries were prepared using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio Usa). Illumina NovaSeq SP was used for sequencing with a paired-end sequencing length of 10bp. Samples were sequenced at Admera Health using an Illumina HiSeq 2x150 at sequencing depth of ~40 million reads. FASTQ files were preprocessed using HTS stream (https://github.com/ibest/HTStream) and the clean FASTQ file were aligned using STAR. Differential expression (DE) analysis of gene expression was performed using Limma-Voom. False discovery rate (FDR)<0.05 was considered statistically significant. Further analysis was completed using Illumina Basespace packages and programs (deSeq2) We performed gene ontology analysis for differentially expressed genes with q value of <0.05. Gene set enrichment analysis (GSEA, Broad Institute and UC San Diego) was completed using normalized gene counts as previously described ((Subramanian et al., 2005). Results were visualized using Tidyverse packages in R. Comparison of differentially expressed gene lists and generation of Venn diagrams were generated using the GeneVenn webtool. Biological process and molecular function gene ontology analysis of differentially expressed genes found in bulk RNA-seq datasets were completed using GENEONTOLOGY of the Mus musculus database (Ashburner et al., 2000; Gene Ontology, 2021).
Results:The gene expression profile of M. avium-challenged untrained HSCs was compared to that of control infected animals . Next, the gene expression profile of trained HSCs was compared to the same untransplanted controls to detect transcriptional changes potentiated by training. This analysis revealed many more genes (670) upregulated upon secondary infection in the trained population compared to untrained (255). GO analysis of the trained HSPC gene signature showed that there was an enrichment in pathways related to G protein-coupled receptor signaling, cellular adhesion, cell differentiation, immunity, and autophagy . Strikingly, gene set enrichment analysis (GSEA) of the genes uniquely upregulated upon infectious challenge in the trained HSPCs aligned with enhanced metabolism — glycolysis, oxidative phosphorylation, and fatty acid metabolism — genes that are reportedly rewired in macrophages in other trained immunity models (Figure 4C). Pathways related to transcription and translation were also upregulated in trained HSPCs (Supplemental Figure 4C). On the other hand, untrained HSPCs primarily upregulated chemokine responses and immune response pathways, as we previously reported. Together, these analyses reveal trained versus untrained HSPCs have differing responses to infection at 1 month post-challenge compared to untransplanted controls. When directly comparing untrained versus trained gene expression, those with a primary infectious exposure (untrained HSPCs) upregulated immune response pathways while trained cells upregulated metabolic pathway genes. We speculate that relatively lower immune response pathways in trained HSPCs may reflect greater control of infection in the host, enabling the cells to prioritize other cellular pathways.
Conclusions: Upregulation of metabolism and gene regulation pathways in trained HSPCs that have been rechallenged with M. avium may reflect greater control of infection and improved immunity within the host compared to untrained controls.

overall_design: Comparison of transcriptomic profiles following transplant, prior immune stimulation (training) of HSPCs, and chronic bacterial infection to further understand impact of HSPC trained immunity

first: Brandon

last: Tran

first: Duy

middle: T

last: Le

first: Katherine

middle: Y

last: King


title: Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells

type: Genome binding/occupancy profiling by high throughput sequencing


title: Temporal transcriptome in Pou5f3, Nanog and  Sox19b mutant zebrafish embryos

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

institute: University of Freiburg

summary: To understand the role of Pou5f3, Sox19b and Nanog during zebrafish zygotic genome activation, RNA-seq  time-series for single, double and triple maternal-zygotic (MZ) zebrafish mutants for Pou5f3, Nanog,  Sox19b, as well as the wild-type.

overall_design: RNA samples were collected at eight time points: 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6 hours post-fertilization (hpf). For the mutants MZspg (Pou5f3), MZsox19b, MZnanog, MZsox19bspg and MZsox19bnanog and four biological replicates of the wild-type the single-end 50 bp sequencing was performed with the depth 35M reads per sample. For the mutants  MZnanogspg, MZtriple (triple mutant for Pou5f3, Sox19b and Nanog) and for six biological replicates of the wild-type paired-end 150 bp sequencing was performed with 58M reads per sample.

first: Meijiang

last: Gao


title: Early-adulthood spike in protein translation drives aging via juvenile hormone/germline signaling

status: Public on Aug 01 2023

first: Andrew

middle: M

last: Pickering

state: tx

address: 6431 Fannin St

institute: UTHealth Houston

summary: Protein translation (PT) declines with age in invertebrates, rodents, and humans1-6. It has been assumed that elevated PT at young ages is beneficial to health and PT ends up dropping as a passive byproduct of aging. In Drosophila, we show that a transient elevation in PT during  early-adulthood exerts long-lasting negative impacts on aging trajectories and proteostasis in later-life. Blocking the early-life PT elevation robustly improves life-/health-span and prevents age-related protein aggregation, whereas transiently inducing early-life PT surge in long-lived fly strains abolishes their longevity/proteostasis benefits. The early-life PT elevation triggers proteostatic dysfunction, silences stress responses, and drives age-related functional decline via juvenile hormone-lipid transfer protein axis and germline signaling. Our findings suggest that PT is adaptively suppressed after early-adulthood, alleviating later-life proteostatic burden, slowing down age-related functional decline, and improving lifespan. Our work provides a novel theoretical framework for understanding how lifetime PT dynamics shape future aging trajectories.

overall_design: Flies were treated with cycloheximide and collected at either day 0 or day 2

first: Harper

last: Kim


title: Janus nanoparticles targeting extracellular polymeric substance achieve flexible elimination of drug-resistant biofilms

city: Beijing

first: Liu

last: Zhiwen

address: NO.15 Of North Three-ring East Road,Chao Yang District

institute: Beijing University of Chemical Technolgoy

summary: Safe and efficient antibacterial materials are urgently needed to combat drug-resistant bacteria and biofilm-associated infections. The rational design of nanoparticles for flexible elimination of biofilms by alternative strategies remains challenging. Herein, we propose the fabrication of Janus-structured nanoparticles targeting extracellular polymeric substance to achieve dispersion or near-infrared (NIR) light-activated photothermal elimination of drug-resistant biofilms, respectively. Asymmetrical Janus-structured dextran-bismuth selenide (Dex-BSe) nanoparticles are fabricated by a facile strategy to exploit synergistic effects of both components. The biocompatible dextran domain with the maximum exposure endows the Janus nanoparticles with biofilm penetration, targeting, and dispersion functions. Interestingly, Janus Dex-BSe nanoparticles realize enhanced dispersal of biofilms over time compared with dextran nanoparticles while the underlying molecular mechanisms are further revealed by RNA-sequencing transcriptomics analysis. Alternatively, taking advantage of the preferential accumulation of nanoparticles at infection sites, the self-propelled active motion induced by the unique Janus structure enhances the photothermal killing effect under NIR light irradiation, thereby eradicating the biofilm. Given these favorable features, the antibiofilm activity of Janus Dex-BSe against methicillin-resistant Staphylococcus aureus (MRSA) was first validated in vitro. More importantly, the flexible application of Janus Dex-BSe nanoparticles for biofilm removal or NIR-triggered eradication in vivo was demonstrated by MRSA-infected mouse excisional wound model and abscess model, respectively. The currently developed Janus nanoplatform holds great promise for the efficient elimination of drug-resistant biofilms in diverse antibacterial scenarios.

overall_design: To investigate the function of BS, Dex and DexBS in the regualtion of S. aureus biofilms, We evaluate the gene expression of S. aureus biofilms after treated by Ctrl, BS, Dex,DexBS through RNA-Seq. We then performed gene expression profiling analysis using data obtained from RNA-Seq of different treated S. aureus.

first: Zhiwen

last: Liu

first: Kangli

last: Guo


title: Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells [CUT&Tag]

last: Zanin

overall_design: i-motifs and G-quadruplex analysis in HEK293T (ATCC #CRL-3216) and WDLPS (ATCC #CRL-3043) through CUT&Tag method

last: Ruggiero


title: Hepatic SREBP signaling requires SPRING to govern systemic lipid metabolism in mice and humans

city: Amsterdam

first: Noam

last: Zelcer

address: Meibergdreef 9

department: Medical BIochemistry

country: Netherlands

institute: AMC

summary: The sterol regulatory element binding proteins (SREBPs) are transcription factors that govern cholesterol and fatty acid metabolism. Owing to their central role in controlling hepatic lipid and lipoprotein metabolism their activity is tightly coordinated, and accordingly dysregulation of the SREBP pathway is associated with development of dyslipidemia and non-alcoholic fatty liver disease. Using a suite of genome-wide genetic screens we have recently identified SPRING (C12ORF49) as a novel post-transcriptional regulator of SREBP activation in vitro. Our previous work demonstrated that constitutive ablation of Spring in mice is embryonically lethal. Here we show that inducible global deletion of Spring is also untolerated, and therefore to interrogate the physiological role of SPRING in controlling hepatic lipid metabolism we developed liver-specific Spring knockout mice (LKO). Liver transcriptomics and proteomics analysis revealed severely attenuated SREBP signaling in livers and in hepatocytes of LKO mice, which was associated with marked effects on both plasma and hepatic lipid levels. In plasma, total cholesterol levels were dramatically reduced in both male and female LKO mice, apparent in both the LDL and HDL fractions, while triglyceride levels remained largely unaffected. In liver, loss of Spring diminished cholesterol and triglyceride biosynthesis resulting in decreased hepatic cholesterol and triglyceride content. This coincided with reduced secretion of VLDL into the circulation. Consistent with diminished hepatic de novo lipogenesis, LKO mice were protected from developing hepatosteatosis when challenged with a fructose-rich diet. Supporting the significance of our findings in mice, we identified common and rare SPRING genetic variants that are strongly associated with circulating HDL-c and ApoA1 levels in humans. Collectively, our study positions SPRING as a core component of hepatic SREBP signaling, and consequently of systemic lipid metabolism in mice and humans.

overall_design: We compared the hepatic gene expression profile of Ctrl mice to mice lacking hepatic expression of Spring (SPRING LKO). This was done in livers of fasted (20 h fasting; n Ctrl = 8; n LKO = 9) and refed (20h fasting followed by 4 h refeding; n Ctrl = 9; n LKO = 8) mice the as transition from the fasted to the fed state is accompanied by acute reprogramming of hepatic gene expression and induction of the SREBP-regulated pathway.

first: Sebastian

last: Hendrix

first: Aldo

last: Jongejan


title: SHIELD: A platform for high-throughput screening of barrier DNA elements in human cells

city: Stanford

first: Meng

last: Zhang

state: California

address: 443 Via Ortega

institute: Stanford

summary: Chromatin boundary elements contribute to the partitioning of mammalian genomes into topological domains to regulate gene expression. Certain boundary elements are adopted as DNA insulators for safe and stable transgene expression in mammalian cells. These elements, however, are ill-defined and less characterized in the non-coding genome, partially due to the lack of a platform to readily evaluate boundary-associated activities of putative DNA sequences. Here we report SHIELD (Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains), a novel platform tailored for the high-throughput screening of barrier-type DNA elements in human cells. SHIELD takes advantage of the high specificity of serine integrase at heterochromatin, and exploits the natural heterochromatin spreading inside LADs for the discovery of potent barrier elements. We adopted SHIELD to evaluate the barrier activity of 1000 DNA elements in a high-throughput manner and identified 8 novel elements with barrier activities comparable to the core region of cHS4 element. SHIELD should greatly facilitate the discovery of novel barrier DNA elements from the non-coding genome in human cells.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: To screen the potential barrier activity of DNA elments in a high-throughout manner, we adopted the landing-pad strategy. We first generated a chassis cell line (HCT116) by inserting the landing pad at epigenetically highly repressive LAD loci. Then we integrated pooled reporter plasmids at the selected loci via integrase-mediated recombination. The reporter plasmid carried the EGFP reporter gene flanked by candidate DNA elements. Each DNA element was barcoded with its own sequence. Strong barrier activity would lead to higher EGFP expression at the repressive loci. Following reporter integration, we sorted polyclonal cells based on EGFP expression levels using FACS, extracted the genomic DNA from each population, amplifed genomic DNA with primers targeting the candidate DNA, and performed NGS analysis of the amplicon to determine the relative abundance of each element in the corresponding population. The abundance of a given DNA element in the sorted population determined by NGS would reflect its relative barrier activity.

first: Mary

last: Ehmann

first: Srija

last: Matukumalli

first: Aashutosh

middle: G

last: Boob

first: David

last: Gilbert

first: Huimin

last: Zhao


title: The DEAD-box RNA helicase Ded1 is a translation-elongation factor

city: Paris

first: N.

middle: Kyle

last: Tanner

state: Ile de France

address: 13 rue Pierre et Marie Curie

department: Microbial Gene Expression

country: France

institute: Université de Paris-Cité & CNRS

summary: DEAD-box RNA helicases are ATP-dependent RNA binding proteins and RNA-dependent ATPases that possess weak, nonprocessive unwinding activity in vitro, but they can form long-lived complexes on RNAs when the ATPase activity is inhibited. Ded1 is a yeast DEAD-box protein, the functional ortholog of mammalian DDX3, that is considered important for the scanning efficiency of the 48S pre-initiation complex ribosomes to the AUG start codon. We used a modified PAR-CLIP technique, which we call quicktime PAR-CLIP (qtPAR-CLIP) to crosslink Ded1 to 4-thiouridine-incorported RNAs in vivo using UV light centered at 365 nm. The irradiation conditions are largely benign to the yeast cells and to Ded1, and we are able to obtain a high efficiency of crosslinking under physiological conditions. We find that Ded1 forms crosslinks on the open reading frames of many different mRNAs, but it forms the most extensive interactions on a relatively few mRNAs, and particularly on mRNAs encoding certain ribosomal proteins and translation factors. Under glucose-depletion conditions the crosslinking pattern shifts to mRNAs encoding metabolic and stress-related proteins, which reflects the altered translation. These data are consistent with Ded1 functioning in the regulation of translation elongation, perhaps by pausing or stabilizing the ribosomes through its ATP-dependent binding.

overall_design: Identify the RNA substrates of the yeast DEAD-box helicase Ded1 using a modified PAR-CLIP protocol

first: Yeter-Alat

last: Hilal

first: Belgareh-Touzé

last: Naïma

first: Huvelle

last: Emmeline

first: Banroques

last: Josette

first: Tanner

last: N Kyle


title: Thinking out of the box to evaluate the performance of engineered SOX17 in pluripotency reprogramming (ATAC-Seq)

city: hong kong

first: Haoqing

last: Hu

address: No.21 Pokflam road, L412

institute: The University of Hong Kong

summary: The SOX17 triple-mutant SOX17FNV is a more potent inducer of pluripotency than wild-type SOX2 for unknown features outside its DNA binding high mobility group box domain. Using an inducible reprogramming system, we verified that wild-type SOX17 is not capable to induce pluripotency but SOX17FNV outperforms SOX2 in mouse and human. In mature pluripotent stem cells, SOX17FNV can fully replace SOX2 without compromising self-renewal and pluripotency despite considerable sequence variation. Binding assays using full length proteins expressed in mammalian cells show that SOX17FNV and SOX17 co-bind OCT4 more tightly than SOX2 albeit with switched preferences for composite DNA motifs. Through the systematic analyses of domain deletions, we found that the N-terminus is dispensable for the reprogramming activity of SOX17FNV whilst the C-terminus encodes for essential as well as superfluous domains. Domains have non-additive and partially compensatory effects suggesting that versatile multivalent interaction drive transactivation and reprogramming. We define a minimal SOX17FNV (miniSOX) that can support reprogramming without loss in activity enabling payload reduction within reprogramming cassettes. The definition, functional evaluation and utilisation of potent effector domains that are optimised to pioneer cell fate transition will open up new avenues to enhance cellular reprogramming and stem cell engineering with synthetic transcription factors.

overall_design: We analyzed the chromatin accessibility profiles of SOX2 and SOX17FNV rescued 2TS22C mouse ESC cell lines. Cells cultured in 2i serum/Lif medium were analyzed in this study.

first: Ralf

last: Jauch


title: Thinking out of the box to evaluate the performance of engineered SOX17 in pluripotency reprogramming

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus


title: Tumor-associated monocytes promote mesenchymal transformation through EGFR signaling in glioma

city: HONG KONG

first: Jiguang

last: WANG

address: clear water bay, HKUST

institute: HKUST

summary: The role of brain immune compartments in glioma evolution remains elusive. We profiled immune cells in glioma microenvironment and the matched peripheral blood from 11 patients at a single-cell level. Notably, glioblastoma exhibits specific infiltration of certain blood-originated monocytes expressing EGFR ligands including EREG and AREG, coined as tumor-associated monocytes (TAMo). TAMo infiltration is mutually exclusive with EGFR alterations (P = 0.019), while co-occurring with mesenchymal subtype (P = 4.7x10-7) and marking worse prognosis (P = 0.004 and 0.032 in two independent cohorts). Evolutionary analysis of initial-recurrent glioma pairs and single-cell study of a multi-centric glioblastoma reveals remarkable association between elevated TAMo and glioma mesenchymal transformation. Further analysis identifies FOSL2 as a master regulator of TAMo. The roles of FOSL2-EREG/AREG-EGFR signaling axis in promoting glioma invasion were verified experimentally. Collectively, we have identified TAMo in tumor microenvironment and revealed its driving role in activating EGFR signaling to shape glioma evolution.

overall_design:
The GB or peripheral blood cell suspension was loaded into Chromium microfluidic chips with 3’ (v3) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ (v3) reagent kit (10X Genomics) according to the manufacturer’s recommendations. Sequencing was performed with Illumina (NovaSeq) according to the manufacturer’s recommendations (Illumina).
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Authors state:
We are currently unable to deposit the raw data due to privacy concerns, but will have the raw data available once we obtain permission from our institutions.
Please contact the submitter directly regarding access to raw data on a case-by-case basis.

first: Yong

last: Cao

last: Wang

first: Yiyun

last: Chen


title: Protection of TLR5 agonist, CBLB502, against cisplatin treated mouse liver and kidney

first: Changhui

last: Ge

email: chge502@163.com, chge88@sina.com

address: 27 Taiping Rd., Haidian Dist.

department: Department of Experimental Hematology and Biochemistry

institute: Beijing institute of Radiation Medicine

summary: TLR5 agonist CBLB502 has been reported playing protective effects again IR, Here we find CBLB502 might protect cis-platin induced liver and kidney damages.

overall_design: C57BL/6 mice were treated 20mg/kg cis-platin i.p., CBLB502 were pre-treated with 0.2mg/kg at 30min before aminstation of cis-platin, 72 h later, liver and kidney were collected and performed RNA sequencing analysys.

first: Pengzhen

last: Niu

first: hanjiang

last: Fu

first: Xiaofei

last: Zheng


title: Immune microenvironment and molecular mechanism of oral lichen planus [Spatial transcriptomics]

city: Chengdu

first: Hao

last: Xu

state: China

address: No.17 section3 renmin south road, chengdu

institute: Sichuan university

summary: Oral lichen planus (OLP) is a poorly understood chronic inflammatory mucocutaneous disease and is associated with many systemic diseases, which may lead to the erosion of oral mucosa and bring physical and psychological disorders to patients. However, the pathogenesis and immune microenvironment of OLP with different clinical subtypes are unclear. therefore, this study utilized single cell RNA-sequencing and spatial transcriptomics to explore the immune microenvironment and molecular mechanism of oral lichen planus with different clinical subtypes. Moreover, this study established a clinical cohort of OLP with 1-year follow-up and obtained the clinical information and bulk RNA-seq files to further confirm the above results.

overall_design: Comparative spatial heterogeneity analysis of spatial transcriptomics for non-erosive OLP (NEOLP) and erosive OLP (EOLP).

first: Qianhui

last: Shang

first: Maofeng

last: Qing

first: Qianming


title: Thinking out of the box to evaluate the performance of engineered SOX17 in pluripotency reprogramming (RNA-Seq)

overall_design: We analyzed the gene expression profiles of SOX2 and SOX17FNV rescued 2TS22C mouse ESC cells lines using the non-transduced 2TS22C cells as the control. Cells cultured in basic mouse serum/Lif ESC medium and 2i serum/Lif midium were both analyzed in this study.


title: Overexpression of Brassica napus COMT1 in Arabidopsis heightens UV-B-mediated resistance to Plutella xylostella herbivory

city: Newcastle Upon Tyne

first: Kirsty

middle: Jamie

last: McInnes

address: Kings road, newcastle university, newcastle upon tyne, NE1 7RU

country: United Kingdom

institute: Newcastle University

summary: UV-B radiation regulates numerous morphogenic, biochemical and physiological responses in plants, and can stimulate some responses typically associated with other abiotic and biotic stimuli, including invertebrate herbivory. Removal of UV-B from the growing environment of various plant species has been found to increase their susceptibility to consumption by invertebrate pests, however, to date, little research has been conducted to investigate the effects of UV-B on crop susceptibility to field pests. Here, we report findings from a multi-omic and genetic-based study investigating the mechanisms of UV-B-stimulated resistance of the crop, Brassica napus (oilseed rape), to herbivory from an economically important lepidopteran specialist of the Brassicaceae, Plutella xylostella (diamondback moth). The UV-B photoreceptor, UV RESISTANCE LOCUS 8 (UVR8), was not found to mediate resistance to this pest. RNA-Seq and untargeted metabolomics identified components of the sinapate/lignin biosynthetic pathway that were similarly regulated by UV-B and herbivory. Arabidopsis mutants in genes encoding two enzymes in the sinapate/lignin biosynthetic pathway, CAFFEATE O-METHYLTRANSFERASE 1 (COMT1) and ELICITOR-ACTIVATED GENE 3-2 (ELI3-2), retained UV-B-mediated resistance to P. xylostella herbivory. However, overexpression of B. napus COMT1 in Arabidopsis further reduced plant susceptibility to P. xylostella herbivory in a UV-B-dependent manner. These findings demonstrate that overexpression of a component of the sinapate/lignin biosynthetic pathway in a member of the Brassicaceae can enhance UV-B-stimulated resistance to herbivory from P. xylostella.

overall_design: The experiment was performed at the Glasgow Polyomics Facility (University of Glasgow) using true leaf tissue from 21-day old Brassica napus. Three biological replicates of each treatment were sequenced on a NextSeq™ 500 (Illumina) desktop machine. B. napus treatments and harvested time points were: +UV-B (treatment) or -UV-B (control) conditions, harvested after 4 hours; exogenous application of 4 mL 100µM MeJA (MeJA treatment) or  4mL distilled water (MeJA control); harvested after 4 hours; a 1 h-period of herbivory (herbivory treatment) or no herbivory (herbivory control), followed by 3 hours under -UV-B conditions.

middle: J

first: Justin

last: van der Hooft

first: Ashutosh

last: Sharma

first: Pawel

last: Herzyk

first: Penny

last: Hundleby

first: Henk-Jan

last: Schoonbeek

first: Anna

last: Amtmann

first: Christopher

last: Ridout

first: Gareth

middle: I

last: Jenkins


title: Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet.

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

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

overall_design: Refer to individual Series


title: Mycobacterial DNA binding protein 1 (MDP1) mediates gene regulation in Mycobacterium tuberculosis variant Bacillus Calmette-Guerin

city: Niigata

first: Shaban

middle: Amina

last: Kaboso

address: Asahimachi-Dori 1-757l, Chuo

department: Bacteriology

country: Japan

institute: Niigata University

summary:
To investigate the role of MDP1 in global transcription regulation, we established MDP1 conditional knockdown BCG using CRISPR/dCas9 system.
Transcriptome profiling was then performed using data obtained from RNA-seq of two BCG MDP1 mutants compared to the vector control at three growth time points.

sample_organism: Mycobacterium tuberculosis variant bovis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BCG Tokyo  and its MDP1 cKD derivatives (MDP1_#1 cKD and MDP1_#2 cKD ).

first: Amina

middle: K

last: Shaban

first: Geberemichal

last: Geberetsadik

first: Hakamata

last: Mariko

first: Erina

last: Inouchi

first: Yuriko

last: Ozeki

first: Yoshitaka

last: Tateishi

first: Akihito

last: Nishiyama

first: Yukiko

last: Nishiuchi

first: Takehiro

last: Yamaguchi

first: Hayato

last: Takihara

first: Shujiro

last: Okuda

first: Sohkichi

last: Matsumoto


title: Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet [RNA-seq]

summary: Fatty acid homeostasis is critical for normal cellular physiology and leads to severe diseases when deregulated. Here we report Nucleoside-Diphosphate Kinase 1 and 2 (NME1/2) as major cellular co-enzyme A (CoA) and acetyl-CoA binding proteins and negative regulators of de novo lipogenesis (DNL). Structural studies demonstrate that Nme1 recognizes CoA through its nucleotide moiety, which competes for binding with ADP/ATP. By using a Nme2 ko mouse model, we observe that NME2 is required for the gene transcriptional response to a high fat diet (HFD) in liver cells, leading to a repression of lipogenesis and the activation of a protective gene response. Nme2 ko mice submitted to a HFD challenge are unable to repress key lipogenic genes, resulting in an excessive triglyceride synthesis and liver steatosis. Mechanistically, the NME2-dependent down-regulation of DNL in response to HFD changes the balance for the use of acetyl-CoA between the competing paths of acetylation and DNL, thereby increasing TSS-targeted histone acetylation and gene activation. A structure-guided generation of a NME1 mutant, with intact NDK activity, but unable to bind CoA, directly demonstrates the functional impact of acetyl-CoA/CoA binding by NME1/2 in repressing DNL. Taken together, these findings highlight a yet unknow protective liver response to HFD, regulated by multi-ligand binding proteins which act as direct sensors for the cellular levels of NDP/NTP and CoA/acetyl-CoA.

overall_design: Transcriptomic analysis was performed in mouse liver samples obtained from 4 conditions, corresponding to two genotypes, Nme2 WT (nme2wt) and KO (nme2ko), and two experimental diets, normal diet (normal) and high fat diet (hghfat). For each condition, RNAseq was performed in 4 replicates corresponding to 4 individual mice.

first: Florent

last: Chuffart

first: Domenico

last: Iuso

first: Faycal

last: Boussouar

last: Barral

first: Lisa

last: Bargier

first: Denis

last: Puthier

first: Saadi

last: Khochbin


title: Gut bacteria induce IgA expression in pituitary hormone-secreting cells during aging

status: Public on Jul 31 2023

first: Yehua

last: Li

address: shengmingkexueyuanlu7hao, changping

institute: NIBS

summary: Using the single-cell sequencing technology, the authors aim to make a construction of a single-cell cell atlas of young and old pituitary cells. Moreover, the sorted Ai6+ cells from pituitary of Igha-Cre; Ai6 were also analyzed by single-cell sequencing.

overall_design: The sorted live young and old mouse pituitary cells, as well as sorted Igha-Cre; Ai6+ pituitary cells were captured and analyzed using the 10× Chromium platform.

first: Jiawen

last: Wang

first: Rui

first: Ying

last: Chang

first: Xioadong


title: Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet [ChIP-seq]

first: Sophie

last: Rousseaux

overall_design: ChIPseq analysis was performed in mouse liver samples obtained from 4 conditions, corresponding to two genotypes, Nme2 WT (nme2wt) and KO (nme2ko), and two experimental diets, normal diet (normal) and high fat diet (hghfat). For each condition, chromatin immunoprecipitation was performed twice in the respective livers of two independent mice using anti-H3K9ac antibody of MNase digested chromatin and both the immune-precipitated (chip) and input (inpt) materials were sequenced.


title: XCR1 expression distinguishes human conventional dendritic cells type 1 with full effector functions from their immediate precursors

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

institute: Biozentrum

summary: Dendritic cells (DCs) are major regulators of innate and adaptive immune responses. DCs can be classified into plasmacytoid DCs and conventional DCs (cDCs) type 1 and 2. Murine and human cDC1 share the mRNA expression of XCR1. Murine studies indicated a specific role of the XCR1-XCL1 axis in the induction of immune responses. Here, we describe that human cDC1 can be distinguished into XCR1- and XCR1+ cDC1 in lymphoid as well as non-lymphoid tissues. Steady state XCR1+ cDC1 display a pre-activated phenotype compared to XCR1- cDC1. Upon stimulation, XCR1+ cDC1, but not XCR1- cDC1, secreted high levels of inflammatory cytokines as well as chemokines. This was associated with enhanced activation of NK cells mediated by XCR1+ cDC1. Moreover, XCR1+ cDC1 excelled in inhibiting replication of Influenza A virus. Further, under DC differentiation conditions, XCR1- cDC1 developed into XCR1+ cDC1. After acquisition of XCR1 expression, XCR1- cDC1 secreted comparable level of inflammatory cytokines. Thus, XCR1 is a marker of terminally differentiated cDC1 that licenses the antiviral effector functions of human cDC1, while XCR1- cDC1 seem to represent a late immediate precursor of cDC1.

overall_design: 4 samples are analyzed, each sample of cDC1 steady state and R848 have one additional replicate (n=2)

first: Lukas

last: Heger

last: Hatscher

first: Christian

last: Lehmann

last: Amon

first: Diana

last: Dudziak


title: CDK4 promotes beta cell differentiation

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: Expanding beta cell mass is a critical goal in the fight against diabetes. CDK4, an extensively characterized cell cycle activator, is required to establish and maintain beta cell number. Beta cell failure in the IRS2-deletion mouse type 2 diabetes model is in part due to loss of CDK4 regulator Cyclin D2. We set out to determine whether replacement of endogenous CDK4 with the inhibitor-resistant mutant CDK4-R24C rescued the loss of beta cell mass in Irs2-deficient mice. Surprisingly, not only beta cell mass but also beta cell dedifferentiation was effectively rescued, despite no improvement in whole body insulin sensitivity. Ex vivo studies in primary islet cells revealed a novel mechanism in which CDK4 intervened downstream in the insulin signaling pathway to prevent FOXO1-mediated transcriptional repression of critical beta cell transcription factor Pdx1. FOXO1 inhibition was not related to E2F1 activity, to FOXO1 phosphorylation, or even to FOXO1 subcellular localization, but rather was related to deacetylation and reduced FOXO1 abundance. Taken together, these results demonstrate a novel differentiation-promoting activity of the classical cell cycle activator CDK4 and support the concept that beta cell mass can be expanded without compromising function.

overall_design: Pancreatic islets were isolated from littermate mice of genotypes IRS2+/+;CDK4 wt/wt ("WT"), IRS2-/-;CDK4 wt/wt ("KO"), or IRS2-/-;CDK4 R24C/R24C ("RRKO"), hand picked, and flash frozen for RNA isolation.

first: Alonso

last: Laura

first: Stamateris

last: Rachel

first: Redmond

last: David


title: Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics

city: Durham

first: Christopher

middle: Vincent

last: Nicchitta

state: NC

department: Department of Cell Biology

institute: Duke University School of Medicine

summary: Recent efforts towards the comprehensive identification of RNA-bound proteomes have revealed a large, surprisingly diverse family of candidate RNA-binding proteins (RBPs). Quantitative metrics for characterization and validation of protein-RNA interactions and their dynamic interactions have, however, proven to be analytically challenging and prone to error. Here we report a novel method termed LEAP-RBP for the selective, quantitative recovery of UV-crosslinked RNA-protein complexes. By virtue of its high specificity and yield, LEAP-RBP distinguishes RNA-bound and RNA-free protein levels and reveals common sources of experimental noise in RNA-centric RBP enrichment methods. We introduce new strategies for accurate RBP identification and signal-based metrics for quantifying protein-RNA complex enrichment, relative RNA occupancy, and method specificity. The utility of our approach is validated by comprehensive identification of RBPs whose association with mRNA is modulated in response to global mRNA translation state changes and through in-depth benchmark comparisons with current methodologies.

overall_design: The purpose of this experiment was to determine if the UV crosslinking protocol for capturing RNA binding protein - RNA interactions and the associated isolation procedure for enriching RNA binding protein-RNA complexes included RNA binding protein - small RNA interactions. This question is significant because different RNA-centric methods for capturing protein-RNA interactions are biased against protein-small RNA interactions. In this straightforward experiment, biological duplicate cultures of HeLa cells were subjected to UV irradiation and protein-RNA crosslinked complexes were isolated by organic solvent extraction and precipitation via a liquid emulsion assisted RNA binding protein precipitation protocol (LEAP-RBP). The small RNA content of the total HeLa cellular protein-small RNA adducts was then determined by small RNA sequencing, or sRNAseq.

first: Kristofich

last: JohnCarlo

first: Nicchitta

last: Christopher V.


title: Amyloid precursor protein (APP) regulates gliogenesis and 2 neurogenesis of human neural stem cells by several signaling 3 pathways

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

country: Spain

institute: Institute of Health Carlos III

summary: we have evaluated the effects of APP overexpression in hNSCs at a global 16 level by a transcriptomic analysis using the massive RNA sequencing (RNA-seq) technology. Spe-17 cifically, we have focused on differentially expressed genes that are related to neuronal and glial 18 differentiation processes, as well as on groups of differentially expressed genes associated with dif-19 ferent signaling pathways, in order to find a possible interaction between them and APP

overall_design: In this study, hNS1 cells were cultured adherently on plates pre-treated with poly-L-329 lysine (10μg/ml, Sigma) and proliferated on a chemically defined human stem cell (HSC) 330 medium supplemented with fibroblast growth factor (FGF2) (20ng/ml, Peprotech) and ep-331 idermal growth factor (EGF) (20ng/ml, Peprotech). Proliferating hNS1 cells at 70-80% con-332 fluence were dissociated with trypsin (0.25%, Gibco), centrifuged (4 minutes at 900 rpm) 333 and nucleofected (Nucleofector Amaxa 2B, Lonza) according to manufacturer’s instruc-334 tion. Briefly, for the APP overexpression group, hNS1 cells were pre-mixed with 4μg of 335 pcDNA3-APP695 plasmid (contains the human gene of APP695 isoform and was kindly 336 provided by Dr. Daniel Lu, UCLA) in 100μl of nucleofection solution (Lonza).

first: Isabel

last: Liste

first: Raquel

last: Coronel


title: Durable Alterations of Hematopoiesis and Chromatin post-COVID-19 [bulkRNA-Seq]

first: Jin-Gyu

last: Cheong

summary: Acute SARS-CoV-2 infection is often highly inflammatory and protracted. Recent advances have established that inflammation can trigger innate immune memory and a persistent influence on hematopoietic development, through epigenetic mechanisms. However, these phenotypes and their molecular and cellular features are poorly described in humans. Here we reveal epigenomic alterations in innate immune and hematopoietic stem and progenitor cells (HSPC) post-COVID-19, with distinct molecular programs across disease severities. Enabled by novel approaches to study hematopoiesis from peripheral blood, we find persisting HSPC epigenetic programs conveyed, for months to a year, to short-lived progeny monocytes. These epigenetic changes are associated with increased myeloid cell differentiation and inflammatory and antiviral programs. We provide insights into post-infectious HSPC and innate immune cell epigenetic alterations that are broadly relevant.

overall_design: To discover changes in chromatin post-SARS-CoV-2 infection, RNA-seq was performed on CD34+ HSPCs and CD14+ monocytes sorted from PBMC of healthy, non-COVID-19 post-ICU pateitns, mild convalescent, and severe convalescent COVID-19 patients.

first: Arjun

last: Ravishankar

first: Siddhartha

last: Sharma

last: Parkhurst

first: Steven

middle: Z

last: Josefowicz

first: Duygu

last: Ucar


title: Altered thymic NKT1 and NKT2 differentiation in murine haploidentical bone marrow transplantation with chronic GvHD

first: Yujia

last: Wang

state: Beijing

address: 38 Xueyuan Road, Haidian District

department: Department of Immunology

institute: Peking university school of basic medical sciences

summary: To investigate whether intermediate iNKT precursor cells were affected in GvHD mice along the differentiation journey toward mature effector cells, we performed scRNA-seq on thymic iNKT precursors from BMT mice with and without cGvHD and non-BMT mice. We identified Multiple early and late NKT1 precursor clusters and further explored the development of NKT1 under physiological as well as transplantation condition.

overall_design: We performed scRNA-seq on thymic TCRβ+CD1d-tet+CD24-NK1.1-  iNKT precursors from BMT mice with and without cGvHD and non-BMT mice. We identified Multiple early and late NKT1 precursor clusters and further explored the development of NKT1 under physiological as well as transplantation condition.

first: Weijia

last: Zhao

first: Xinwei

last: Zhang

first: Jie

last: Hao

first: Kunshan

first: Xiaojun

last: Huang

first: Yingjun

last: Chang

first: Hounan

last: Wu

first: Rong

last: Jin

first: Qing

last: Ge


title: Transcriptional regulation by the NSL complex enables diversification of IFT functions in ciliated versus non-ciliated cells.

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics


title: Transcriptional regulation by the NSL complex enables diversification of IFT functions in ciliated versus non-ciliated cells [ChIP-Seq 2]

summary: Members of the NSL histone acetyltransferase complex are involved in multi-organ developmental syndromes. While the NSL complex is known for its importance in early development, its role in fully differentiated cells remains enigmatic. Using a kidney-specific model, we discovered that deletion of NSL complex members KANSL2 or KANSL3 in post-mitotic podocytes led to catastrophic kidney dysfunction. A systematic comparison of two primary differentiated cell types revealed that the NSL complex is a master regulator of intraciliary transport genes in both dividing and non-dividing cells. NSL complex ablation led to loss of cilia and impaired sonic hedgehog pathway in ciliated fibroblasts. By contrast, non-ciliated podocytes responded with altered microtubule dynamics and obliterated podocyte functions. Finally, overexpression of wild type but not a double zinc-finger (ZF-ZF)-domain mutant of KANSL2 rescued the transcriptional defects, revealing a critical function of this domain in NSL complex assembly and function. Thus, the NSL complex targets exhibit bifurcation of functions to enable diversity of specialized outcomes in differentiated cells.

overall_design: Histone modification Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of multiple histone marks in MEFs in the indicated genotype : WT (K2-iWT-Vector), KO (K2-iKO-Vector) and KO complimented with WT-KANSL2 (K2-iKO-WT).H4K5ac and H4K12ac were tested. H3 was used for normalization.

first: Tsz

middle: H

last: Tsang


title: Transcriptional regulation by the NSL complex enables diversification of IFT functions in ciliated versus non-ciliated cells [ChIP-seq]

overall_design: Histone modification Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of multiple histone marks in WT (nCre) and KO (KANSL2-pKO) podocytes, including H3K4Me3, H3K9ac, H3K27ac, H4K5ac, H4K12ac and H4K16ac, H3 was used for normalization. MOF and KANSL3 ChIP-seq in WT (nCre) podocytes, H3 was used for normalization.

first: Meike

last: Wiese


title: Effect of Pak4 ablation on transcriptome in liver of fasted mice

city: Jeonju-si

first: Byung-Hyun

last: Park

address: 567 Baekje-daero, Deokjin-gu

country: South Korea

institute: Jeonbuk National University Medical School

summary: Hepatic ketogenesis is crucial for energy homeostasis in a fast state, whereas defective ketogenesis is associated with various diseases. We explored the role of PAK4, an oncoprotein, in ketogenesis. To investigate the molecular basis, we carried out RNA-sequencing analysis using littermate WT and hepatocyte-specific Pak4 KO mice in fasted conditions.

overall_design: Examination of RNA profile in liver of WT and hepatocyte-specific Pak4 KO mice in 24 h fasted condition.

first: Min

last: Shi

first: Chang

last: Han

first: Eun

last: Bae


title: Day-night fluctuations in choroid plexus transcriptomics and CSF metabolomics

city: Copenhagen

first: Søren

middle: Norge

last: Andreassen

state: Region Hovedstaden

address: Blegdamsvej 3

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

summary: Male Sprague-Dawley rats, kept in light-controlled 12:12 conditions, presented with diurnally modulated CSF metabolite composition. This change was accompanied with differential expression of 2778 genes within the choroid plexus, with several plasma membrane transporters and CLOCK-associated genes diurnally modulated.

overall_design: Differential expression analysis of male Sprague-Dawley rats 8 hours after light on (ZT8) and 8 hours after light off (ZT20)

first: Beatriche

last: Edelbo

first: Annette

middle: B

last: Steffensen

first: Nanna

last: MacAulay


title: Transcriptional regulation by the NSL complex enables diversification of IFT functions in ciliated versus non-ciliated cells [RNA-seq]

city: Freiburg

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT (nCre) and KO (KANSL2-pKO, KANSL3-pKO ) podocytes. Comparative gene expression profiling analysis of RNA-seq data for WT (KANSL2-iWT, KANSL3-iWT) and KO (KANSL2-iKO, KANSL3-iKO) MEFs .


title: WT naïve vs. M. avium infected scRNA-seq

status: Public on Jul 30 2023

city: Houston

first: Bailee

last: Kain

address: 1102 Bates Avenue

institute: Baylor College of Medicine

summary:
purpose: Chronic inflammation induced by Mycobacterium avium infection (timepoint= 1 month) results in transcriptomic changes within the HSC population subset  upon bulk RNA-seq, particularly in pathways involved in the immune response, interferon gamma signaling (Th1 immune response) pathway, stat signaling, and antigen processing and presentation. We have also shown that chronic inflammation results in a myeloid differentiation bias of HSPCs. We hypothesize that these transcriptomic changes induced by chronic inflammation may be specific to a certain subset of HSPCs and could be passed on to specific terminally differentiated subsets. To investigate this hypothesis, we performed scRNA-seq using the 10x genomics platform to test the transcriptomic differences induced upon infection in HSC, progenitor, myeloid, and lymphoid cell populations along with heterogeneity observed within the HSC population.
methods:  CD45.2 mice were infected with 2 x 10^6 CFU M. avium for one month prior to bone marrow harvesting. One month post infection, experimental mice were euthanized and infection was confirmed by measuring splenic weight and size. WBM from the hips, tibias, and femurs of each mouse was extracted through crushing with a mortar and pestle. The suspension was then RBC lysed and CD117 (c-kit)+ and cKit- cells were separated using a manual magnetic separation system (Miltenyi). Experimental samples were stained with desired antibodies (listed in key resources table) and sorted using a BD FACS Aria cell sorter. The following cell types were isolated according to the following phenotypic definitions (please see file phenotypic_definitions.txt).
The cellular purity and count of each sample was confirmed prior to pooling for submission to the BCM Single Cell Core. Depending on the rarity of the isolated population, 20,000-50,000 sorted cells were combined to a concentration of ~7200 cells/uL. Samples were loaded into the Chromium controller system and generated 3’ 10x scRNAseq barcoded libraries for each sample. Prior to sequencing, quality control of the libraries was completed using a Bioanalyzer (Agilent, Santa Clara, CA) and Nanodrop system. Samples were sequenced on a NovaSeq at a sequencing depth of 300M reads at the BCM Genomic and RNA Profiling (GARP) core. After sequencing, fastq files for each sample were generated (R1, R2, and I1 files) to demultiplex the data using the CellRanger pipeline
results: scRNA-seq studies revealed that training led to a bimodal distribution of gene expression, with a subset showing activation of immunity-related genes. This gene signature was propagated to innate immune cells but was not conserved in B cells, indicating specific patterns of gene signature inheritance. M. avium training also led to the emergence of an “activated” HSC subpopulation, indicating subsets of HSCs are more responsive to training
conclusions: Transcriptomic signatures induced by M. avium exposure, particularly in IFNg response genes, are heterogeneous and are propagated in a myeloid biased manner

overall_design: Single cell comparison of seven different HSC (LT-HSCs, MPP3, GMP, CD41+ HSCs, Inflammatory Macrophages, Neutrophils, B cells) or terminally differentiated immune cell transcriptomes

first: Pamela

last: Luna

first: Chad

last: Shaw

first: Brandon

last: Tran

first: Katherine

last: King


title: One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

institute: Prinses maxima centrum

summary: Optimization of CRISPR/Cas9-mediated genome engineering has resulted in base editors that hold promise for mutation repair and disease modeling. Here, we demonstrate the application of base editors for the generation of complex tumor models in human ASC-derived organoids. First we show Efficacy of cytosine and adenine base editors in modelingCTNNB1hot-spot mutations in hepatocyte organoids. Next, we use C>T base editors to insert nonsense mutations inPTENin endometrial organoids and demonstrate tumorigenicity even in the heterozygous state. Moreover, drug screening assays on organoids harboring eitherPTENorPTENandPIK3CAmutations reveal the mechanism underlying the initial stages of endometrial tumorigenesis. To further increase the scope of base editing we combine SpCas9 and SaCas9 for simultaneous C>T and A>G editing at individual target sites. Finally, we show that base editor multiplexing allow modeling of colorectal tumorigenesis in a single step by simultaneously transfecting sgRNAs targeting five cancer genes.

overall_design: Different base editied ASC-derived organoids were compared to assess WNT-dependency by RNA-sequencing.

first: Maarten

last: Geurts

first: Shashank

last: Gandhi

first: Matteo

last: Boretto

first: Ninouk

last: Akkerman

first: Lucca

last: Derks

first: Martina

last: Celotti

first: Sarina

last: Harshuk-Shabso

first: Flavia

last: Peci

first: Harry

last: Begthel

first: Delilah

last: Hendriks

first: Paul

last: Schürmann

first: Amanda

last: Andersson-Rolf

first: Susana

last: Chuva de Sausa Lopes

first: Johan

last: van Es

first: Ruben

last: van Boxtel

first: Hans

last: Clevers


title: Testing data

city: Shanghai

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

summary: Microglia are important immune cells in the central nervous system (CNS). Dysfunctions of gene-deficient microglia contribute to the development and progression of multiple CNS diseases. Microglia replacement by nonself cells has been proposed to treat microglia associated disorders. However, most of attempts are failed due to low replacement efficiencies, such as with the traditional bone marrow transplantation approach. In this study, we develop three efficient strategies for microglia replacement: microglia replacement by bone marrow transplantation (mrBMT), microglia replacement by peripheral blood (mrPB) and microglia replacement by microglia transplantation (mrMT). mrBMT and mrPB allow microglia-like cells to efficiently replace resident microglia in the whole CNS. On the other hand, mrMT achieves microglia replacement in brain regions of interest. In summary, the present study offers effective tactics for microglia replacement with diverse application scenarios, which potentially opens up a window on treating microglia-associated CNS disorders.

overall_design: Single-cell RNA-seq for normal microglia and microglia (or microglia-like cells) from mrMT, mrBMT and mrPB. Cells were collected 3 months after transplantation.

first: Yanxia

last: Rao


title: SSN-seq: Multiplexed single-cell transcriptomic profiling via genetic barcoding with shielded small nucleotides

first: Pawel

last: Mazur

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

summary: To facilitate scalable longitudinal profiling of single cells we developed a universal permanent genetic cell barcoding technology based on the expression of shielded small nucleotides coupled with single-cell RNA-seq (SSN-seq). SSN barcodes are highly expressed and contain direct-capture sequences to enable recovery of distinct barcodes directly in each single-cell transcriptome allowing cell identity history to be recorded over time, in parallel with cell identity. SSN-seq is compatible with both 3’ and 5’ single-cell profiling and is readily adaptable to numerous cell types including human primary T cells and CAR T cells making it a promising tool for rapidly improving adoptive cell therapies and expanding their functionality. We applied SSN-seq to track the dynamics of CAR T cell states at the time of infusion and upon isolation from in vivo tumor rechallenge model. Our study identified that a novel combination of cytokines and small molecule inhibitors used for CAR T cells manufactured ex vivo, promotes the expansion of persistent CD4+ memory T cell populations in vivo. Together, these results demonstrate the utility of our method for multiplexed perturbation experiments that reveal the dynamics of cell states over time, with a high degree of confidence.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: scRNA-seq of SSN-barcoded cells in vitro and in vivo

first: Xiaoyin

last: Lu


title: Evaluation of global gene expression changes in the larval intestines of PNGase-like (Pngl) mutant Drosophila

city: Heidelberg

first: Benjamin

middle: Andrew

last: Story

address: Meyerhofstrasse 1

department: Genomics

institute: European Molecular Biology Laboratory (EMBL)

summary: Mutations in Drosophila Pngl lead to structural and functional abnormalities in the larval intestine. Here we report using RNA-sequencing of Drosophila larval intestines to determine the effects of loss of Pngl on the transcriptome in this tissue.

overall_design: Third instar Drosophila larvae with the following four different genotypes were synchronized at 96 hours after egg laying: 1. yellow white (y w control), 2. y w; Pngl[ex14]/CyO (Pngl heterozygous), 3. y w; Pngl[ex14]/Pngl[ex14] (Pngl homozygous), and 4. y w; Pngl[ex14]/Pngl[ex14]; PBac{Pngl[wt]Ch322-3O13}VK27 (Pngl homozygous rescued by one copy of a Pngl genomic transgene).


title: The Trim33 ubiquitin ligase limits E2f4-dependent DNA replication [Cut&Run II]

status: Public on Jul 28 2023

city: Tübingen

first: Nikita

last: Popov

address: Otfried-Müller-Str 14

department: Clinical Tumor Biology

institute: University Hospital Tübingen

summary: Deregulation of RNA polymerase II (RNAPII) by oncoproteins, such as transcription factor Myc, interferes with DNA replication and is a major source of DNA damage and genomic instability. Ubiquitination is a key pathway controlling RNAPII activity via modification of RNAPII subunits or associated regulatory proteins. We uncover a mechanism for genome maintenance by ubiquitin ligase Trim33 and transcription factor E2f4. We show that Trim33 promotes E2f4 protein turnover, restricting interactions of E2f4 with chromatin and with the Recql DNA helicase. Replicative stress blunts Trim33-dependent regulation, which stimulates Recql recruitment to chromatin and facilitates recovery of DNA synthesis. Deletion of Trim33 triggers chronic recruitment of Recql and accelerates DNA replication under stress, accompanied by compromised DDR signaling and DNA repair. Depletion of Trim33 in Myc-overexpressing cells leads to accumulation of replication-associated DNA damage and delays Myc-driven tumorigenesis. We propose that the Trim33-E2f4-Recql axis provides a mechanism to control DNA replication at transcriptionally active chromatin to maintain genome integrity.

overall_design: Cut&Run assay in p19Nras Trim33-KO cells, expressing HA-tagged E2f4-FL, E2f4-deltaC or E2f4-deltaDB

first: Vanessa

last: Rousseau


title: Metabolic Programs of T Cell Tissue Residency Empower Tumor Immunity [Human scRNA-seq]

city: La Jolla

first: Miguel

last: Reina-Campos

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Tissue-resident memory CD8 T cells (TRM) offer fast, robust, and long-term protection at sites of re-infection1. Tumor-infiltrating lymphocytes (TIL) with characteristics of TRM maintain enhanced effector functions, predict responses to immunotherapy, and accompany better prognoses2,3. Thus, an improved understanding of the metabolic strategies that enable tissue residency could inform new approaches to empower T cell responses in tissues and solid tumors. To systematically define the basis for the metabolic reprogramming supporting TRM differentiation, survival, and function, we leveraged in vivo functional genomics, untargeted metabolomics, and transcriptomics of virus-specific memory CD8 T cell populations. We found that memory CD8 T cells deployed a range of adaptations to tissue residency, including a marked reliance on non-steroidal products of the mevalonate/cholesterol pathway, such as Coenzyme Q (CoQ), driven by increased activity of the transcription factor Srebp2. This metabolic adaptation was most pronounced in the small intestine (SI), where TRM interface with dietary cholesterol and maintain a heightened state of activation4, and was shared by functional TIL in diverse tumor types in mice and humans. Enforcing CoQ synthesis through Fdft1 deletion or Pdss2 overexpression promoted mitochondrial respiration, memory formation upon viral infection, and enhanced antitumor immunity. In sum, through a systematic exploration of TRM metabolism, we reveal how these programs can be leveraged to empower CD8 T cell memory formation in the context of acute infections and enhance antitumor immunity.

overall_design: Single-cell RNA-seq of immune cell from 5 human donors, profiled in the same human study contained in GSE125527.

first: Ananda

middle: W

last: Goldrath

first: John

middle: T

last: Chang

first: Brigi

middle: S

last: Boland


title: The Trim33 ubiquitin ligase limits E2f4-dependent DNA replication [RNA-seq]

overall_design: Gene expression profiling of Trim33-WT and Trim33KO cells was perfromed using RNA-seq


title: The Trim33 ubiquitin ligase limits E2f4-dependent DNA replication [DSB]

overall_design: DSB-capture in Trim33-WT and Trim33-KO cells before and after exposure to hydroxyurea


title: The Trim33 ubiquitin ligase limits E2f4-dependent DNA replication

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

overall_design: Refer to individual Series


title: Transcriptomic Analyses of Ovarian Clear-Cell Carcinoma with Concurrent Endometriosis

status: Public on Jul 29 2023

city: Indianapolis

first: Shannon

middle: M.

last: Hawkins

state: IN

address: 550 N University Blvd UH2440

institute: Indiana University School of Medicine

summary: Endometriosis, a benign inflammatory disease whereby endometrial-like tissue grows outside the uterus, is a risk factor for endometriosis-associated ovarian cancers. In particular, ovarian endometriomas, cystic lesions of deeply invasive endometriosis, are considered the precursor lesion for ovarian clear-cell carcinoma (OCCC). To explore the transcriptomic landscape, OCCC from women with pathology-proven concurrent endometriosis (n = 4) were compared to benign endometriomas (n = 4) by bulk RNA and small-RNA sequencing.

overall_design: RNA-seq was performed on 8 primary tissue samples (OCCC from women with pathology-proven concurrent endometriosis (n = 4) were compared to benign endometriomas (n = 4)). RNA samples were sequenced on Illumina NextSeq 500 (Illumina, San Diego, CA). The resulting reads were mapped to the reference genome (Homo sapiens, ensemble, GRCh38) using MiRDeep2. Differential expression analysis for bulk RNA and miRNA was performed using the DESeq2 package (version 1.36.0) in R/Bioconductor (R version 4.2.0)

first: Kaitlyn

middle: E

last: Collins

first: Xiyin

last: Wang

first: Yuliya

last: Klymenko

first: Noah

last: Davis

first: Maria

middle: C

last: Martinez

first: Chi

last: Zhang

first: Kaman

last: So

first: Aaron

last: Buechlein

first: Douglas

last: Rusch

first: Chad

last: Creighton

middle: M


title: IL-12 sensing in neurons induces neuroprotective CNS tissue adaptation and attenuates neuroinflammation in mice

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary:
Interleukin-12 (IL-12) is a potent driver of type 1 immunity. Paradoxically, in
autoimmune conditions, including of the CNS, IL-12 reduces inflammation.
The underlying mechanism behind these opposing properties and the
involved cellular players remain elusive. Here, we map IL-12 receptor (IL-
12R) expression to NK and T cells as well as neurons and
oligodendrocytes.
Conditionally ablating the IL-12R across these cell types in adult mice and
assessing their susceptibility to experimental autoimmune encephalomyelitis
revealed that the neuroprotective role of IL-12 is mediated by
neuroectoderm-derived cells, specifically neurons, and not immune cells.
In human brain tissue from donors with multiple sclerosis, we observe an
IL-12R distribution comparable to mice, suggesting similar mechanisms in
mice and humans. Combining flow cytometry, bulk and single-nucleus RNA
sequencing, we reveal an IL-12-induced neuroprotective tissue adaption
preventing early neurodegeneration and sustaining trophic factor release
during neuroinflammation, thereby maintaining CNS integrity in mice.

overall_design: Expression profiling of primary murine neurons stimulated with recombinant IL-12 by high throughput sequencing. Primary neuronal cultures were incubated with IL-12 (30 ng/ml and 100 ng/ml) for 18 hours and subjected to bulk RNA-seq (n=5 replicates per group).

first: Myrto

last: Andreadou

first: Florian

last: Ingelfinger

first: Donatella

last: De Feo

first: Teresa

last: Cramer

first: Selma

last: Tuzlak

first: Ekaterina

last: Friebel

first: Bettina

last: Schreiner

first: Pascale

last: Eede

first: Shirin

last: Schneeberger

last: Geesdorf

first: Frederike

last: Ridder

first: Christina

middle: A

last: Welsh

first: Laura

last: Power

first: Daniel

last: Kirschenbaum

first: Shiva

last: Tyagarajan

first: Melanie

last: Greter

first: Frank

middle: L

last: Heppner

first: Sarah

last: Mundt

first: Burkhard

last: Becher


first: Genome

last: Informatics

overall_design: We performed single-nucleus RNA sequencing (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 protocol, 10X Genomics) of FANS-isolated Hoechst+ nuclei from the cerebellum, brainstem and cervical spinal cord of NestinCre/+Il12rb2fl/fl mice and their Il12rb2fl/fl littermates at steady-state and onset of clinical Experimental Autoimmune Encephalomyelitis (EAE) symptoms (10 days post-immunization). We performed three independent sequencing experiments and successfully sequenced 11 samples.

first: Myrto

last: Andreadou

first: Florian

last: Ingelfinger

last: De Feo

first: Maria

middle: K


title: Effect of Curcuphenols and cannaniboids on H3K27Ac marks in cell lines

city: Vancouver

first: Wilfred

last: Jefferies

state: BC

address: 2260 Oak st

department: Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

summary: Turmeric, is both a culinary spice but also used it traditional medicines and dietary supplements for a growing list of disorder including arthritis, digestive disorders  respiratory infections, allergies, liver disease, depression. The activities of turmeric are commonly attributed to  curcuminoids. To understand this,  In this study we compare the alters epigenetic H3K27Ac marks caused by curcupheols and cannabinoids in tissue culture cell lines.

overall_design: H3K27ac IP vs input in A9 cells treated with DMSO, Curcuphenol, or IFN gamma.

first: Jefferies

last: Wilfred

first: Lack

last: Nathan

first: Morova

last: Tunc


title: Sexual Dimorphic Gene Expression Profile of Perirenal Adipose Tissue in Ovine Fetuses with Growth Restriction.

status: Public on Jul 27 2023

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

institute: University of Arizona

summary: Worldwide, fetal growth restriction (FGR) affects 7 to 10% of pregnancies, or roughly 20.5 million infants, each year. FGR not only increases neonatal mortality and morbidity but also the risk of obesity in later life. Currently, the molecular mechanisms by which FGR "programs" an obese phenotype are not well understood. Studies demonstrate that FGR females are more prone to obesity compared to males; however, the molecular mechanisms that lead to the sexually dimorphic programming of FGR are not known. Thus, we hypothesized that FGR leads to the sexually dimorphic programming of preadipocytes and reduces their ability to differentiate into mature adipocytes. To test the hypothesis, we utilized a maternal hyperthermia-induced placental insufficiency to restrict fetal growth in sheep. We collected perirenal adipose tissue from male and female near-term FGR and normal-weight fetal lambs (N=4 in each group, 16 total), examined the preadipocytes' differentiation potential, and identified differential mRNA transcript expression in perirenal adipose tissue. Male FGR fetuses have lower cellular density compared to control male fetuses. However, no difference was observed in female FGR fetuses compared to control female fetuses. In addition, the ability of preadipocytes to differentiate into mature adipocytes with fat accumulation was impaired in male FGR fetuses, but this was not observed in female FGR fetuses. Finally, we examined the genes and pathways involved in the sexually dimorphic programming of obesity by FGR. On enrichment of differentially expressed genes in males compared to females, the Thermogenesis KEGG Pathway was downregulated, and the Metabolic and Steroid Biosynthesis KEGG pathways were upregulated. On enrichment of differentially expressed genes in male FGR compared to male control, the Steroid Biosynthesis KEGG Pathway was downregulated, and the PPAR Signaling KEGG pathway was upregulated. No pathways were altered in females in response to growth restriction in perirenal adipose tissue. Thus, the present study demonstrates a sexually dimorphic program in response to growth restriction in sheep fetal perirenal adipose tissue.

overall_design: Comparative gene expression analysis of perirenal adipose tissues from four groups - control male, control female, growth restricted male, and growth restricted female.


title: circRNAs and papillary thyroid cancer

city: Ningbo

first: Xianjiang

last: Wu

state: None Selected

address: No.41 Xibei Street

institute: Ningbo No.2 Hospital

summary: The dysregulation of circular RNAs (circRNAs) has been implicated in the development and progression of papillary thyroid cancer (PTC). In this study, we analyzed the dysregulated circRNA profile using PTC tissues and matched adjacent normal tissues by RNA-seq.

overall_design: To investigate the involvement of circRNAs in the progression of PTC, we conducted RNA-seq analyses on total RNA extracted from 4 paired PTC and adjacent normal thyroid tissues

first: Lei

last: Dai


title: The transcriptome of platelets from healthy donors treated with SARS-CoV-2 envelope (E) protein

first: Tingting

last: Liu

state: Shanghai

address: No. 197 Ruijin Second Road

institute: Shanghai Jiao Tong University

summary: The mRNA sequencing of platelets from healthy donors treated with SARS-CoV-2 E protein or phosphate buffered saline (PBS) was performed in this study exhibiting the distinct mRNA protfile of the two groups.

overall_design: The mRNA sequencing of platelets from healthy donors treated with SARS-CoV-2 E protein (n=3) or PBS (n=3) performed in this study.

first: Chengde

last: Yang

first: Zihan

last: Tang


title: Xrn1-sensitive lncRNAs are insensitive to Dbp2 nuclear depletion

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

institute: Institut Curie

summary: To investigate whether the action of Dbp2 on Xrn1-sensitive lncRNAs depends on a nuclear or cytoplasmic localization, we used the anchor-away approach to deplete a Dbp2-FRB-GFP fusion from the nucleus upon rapamycin treatment.

overall_design: Strand-specific total RNA-seq in parental (PS) and Dbp2-FRB-GFP cells, treated or not with rapamycin (R). There are 2 biological replicates per condition.

last: WERY

first: Ugo

last: SZACHNOWSKI

first: Sara

last: ANDJUS

first: Alvaro

last: DE ANDRES-PABLO

first: Antonin

last: MORILLON


title: MSL2 cut and run profiles in S2 cell lines

city: Munich

first: Nikolas

last: Eggers

address: Grosshaderner Strasse 9

department: Molecular Biology

institute: LMU Munich

summary: MSL2, the DNA-binding subunit of the Drosophila dosage compensation complex, cooperates with the ubiquitous protein CLAMP to bind MSL recognition elements (MREs) on the X chromosome. We explore the nature of the cooperative binding to these GA-rich, composite sequence elements in reconstituted naïve embryonic chromatin.   We found that the cooperativity requires physical interaction between both proteins. Remarkably, disruption of this interaction does not lead to indirect, nucleosome-mediated cooperativity as expected, but to competition. The protein interaction apparently not only increases the affinity for composite binding sites, but also locks both proteins in a defined dimeric state that prevents competition.  High Affinity Sites of MSL2 on the X chromosome contain variable numbers of MREs. We find that the cooperation between MSL2/CLAMP is not influenced by MRE clustering or arrangement, but happens largely at the level of individual MREs.  The sites where MSL2/CLAMP bind strongly in vitro locate to all chromosomes and show little overlap to an expanded set of X-chromosomal MSL2 in vivo binding sites generated by CUT&RUN. Apparently, the intrinsic MSL2/CLAMP cooperativity is limited to a small selection of potential sites in vivo. This restriction must be due to components missing in our reconstitution, such as roX2 lncRNA.

overall_design: Cut and Run profiles of MSL2 in S2 cell lines

first: Fotios

last: Gkountromichos


title: The Trim33 ubiquitin ligase limits E2f4-dependent DNA replication [ChIP-seq]

first: Nikita

last: Popov

overall_design: Chromatin immunoprecipitation with anti-E2f4 antibody from p19KO/Nras-Ctrl and p19KO/Nras-Trim33KO cells.

first: Vanessa

last: Rousseau


title: The Trim33 ubiquitin ligase limits E2f4-dependent DNA replication [Cut&Run]

overall_design: Cut&Run assay in Trim33-WT and Trim33-KO cells, expressing HA-tagged Recql before and after exposure to hydrohyurea (HU)


title: Metabolic Programs of T Cell Tissue Residency Empower Tumor Immunity [RNA-seq II]

first: Miguel

last: Reina-Campos

overall_design: Mouse previously infected (> 30 days) with LCMV and transferred with P14 CD8 T cells were fed a low or high cholesterol diet for 7 days. 3 replicates per condition. Each replicate contains 1000 cells re-sorted from a first sort of 5000 cells pooled from at least 2 different mice. After preparation of single-cell suspensions, 5 x 103 iv- P14 CD8 T cells were sorted from the IEL, into PBS + 5% BSA + 2% FBS + 0.5 M EDTA. 1 x 103 cells were then resorted into 5 ul of 1x TCL lysis buffer + 1% 2-mercaptoethanol. Library preparation for ULI RNA-seq was performed as described online at Immgen (“ImmGenULI_RNAseq_methods.pdf”).

first: Ananda

last: Goldrath


title: Effects of Dexamethasone in COVID-19 patients

status: Public on Jul 26 2023

city: Nijmegen

first: Nick

last: Keur

address: Geert Grooteplein Zuid 10

department: Internal medicine

institute: Radboudumc

summary: Dexamethasone improves the survival of COVID-19 patients in need of supplemental oxygen therapy. Hospitalized COVID-19 patients eligible for dexamethasone therapy were recruited from the general care ward  in several centers in Greece and the Netherlands and whole blood transcriptomic analysis was performed before and after starting dexamethasone treatment. Peripheral blood mononuclear cells (PBMCs) were isolated from healthy individuals and COVID-19 patients and stimulated with inactivated SARS-CoV-2 ex vivo  in the presence or absence of dexamethasone and their transcriptome was assessed.

overall_design: 114 samples

first: N

first: J

middle: J

last: Engel

first: C

middle: I

last: van der Made

first: A

last: Ziogas

first: V

last: Kumar


title: Flt3L therapy induces a Treg‐promoting cDC1 state in triple‐negative breast cancer

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Conventional dendritic cells (cDCs) are at the forefront of activating the immune system to mount an anti‐tumor immune response. Flt3L is a cytokine required for DC development that can increase DC abundance in the tumor when administered therapeutically. However, the impact of Flt3L on the phenotype of distinct cDC subsets in the tumor microenvironment is still largely undetermined. Here, using multi‐omic single‐cell analysis, we show that Flt3L therapy increases all cDC subsets in orthotopic E0771 triple‐negative breast cancer, but this did not result in a reduction of tumor growth. Interestingly, a CD81+migcDC1 population, likely developing from cDC1, was induced upon Flt3L treatment. This subset is characterized by the expression of both canonical cDC1 markers as well as migratory cDC activation and regulatory markers and displayed a higher Treg‐inducing potential compared to other migcDCs. To shift the cDC phenotype towards a T‐cell stimulatory phenotype, CD40 agonist therapy was administered in combination with Flt3L. However, while αCD40 reduced tumor growth, Flt3L failed to improve the therapeutic response to αCD40 therapy. Interestingly, Flt3L+αCD40 combination therapy increased the abundance of Treg promoting CD81+migcDC1. Nonetheless, while Treg‐depletion and αCD40 therapy were synergistic, the addition of Flt3L to this combination did not result in any added benefit. Overall, these results indicate that merely increasing cDCs in the tumor by Flt3L treatment cannot improve anti‐tumor responses and therefore might not be beneficial for the treatment of triple‐negative breast cancer, though could still be of use to increase cDC numbers for autologous DC‐therapy.

overall_design: Tumor‐bearing mice were treated at day 12 after E0771 inoculation and treated for 9 consecutive days with vehicle or Flt3L. Similarly sized tumors, collected at day 21 after tumor inoculation, were pooled from three mice/condition. Living CD45+ cells were sorted using FACS (Fluorescence-activated cell sorting) and subsequently analyzed using CITE-seq.

first: Emile

last: Clappaert

first: Jan

last: Brughmans

first: Ayla

last: Debraekeleer

first: Pauline

last: Bardet

first: Yvon

last: Elkrim

first: Dagmar

last: Lacroix

first: Maida

last: Živalj

first: Ahmed

last: Hamouda

first: Jo

last: Van Ginderachter

first: Sofie

last: Deschoemaeker

first: Damya

last: Laoui


title: Transcription factor cooperation and competition

first: Nikolas

last: Eggers

summary: Transcription factors have to distinguish proper targets from a large pool of potential binding sites. Here we explore how MSL2 and CLAMP cooperate to bind their specific targets. Using an in vitro chromatin reconstitution system and by mutating the interaction domain of CLAMP we show how direct and indirect cooperation of TF binding influence binding specificity.

overall_design: ChiP-seq profiles of MSL2 CLAMP and CLAMP mutant in vitro reconstituted chromatin


title: The RNA helicases Dbp2 and Mtr4 regulate the expression of Xrn1-sensitive long non-coding RNAs in yeast

first: Maxime

last: Wery


title: Single-cell RNA sequencing of human non-hematopoietic bone marrow cells reveals a unique set of inter-species conserved biomarkers for native mesenchymal stromal cells

city: Muenster

first: Marcos

last: Araúzo-Bravo

address: Rontgenstr. 20

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary: Native bone marrow mesenchymal stem/stromal cells (BM-MSCs) participate in generating and shaping the skeleton and bone marrow throughout the lifespan. Moreover, BM-MSCs regulate hematopoiesis by contributing to the hematopoietic stem cell niche in providing critical cytokines, chemokines and extracellular matrix components. However, BM-MSCs per se contain a heterogeneous cell population that remains ill-defined. Although studies on the taxonomy of native BM-MSCs in mice have just started to emerge, the taxonomy of native human BM-MSCs remains unelucidated. By using single-cell RNA sequencing (scRNA-seq), we aimed to define a proper taxonomy for native human BM non-hematopoietic subsets including endothelial cells (ECs) and mural cells (MCs) but with a focal point on MSCs. To this end, transcriptomic scRNA-seq data were generated from 5 distinct BM donors and were analyzed together with other transcriptomic data and with bioinformatics analyses at different levels to identify, characterize and classify distinct native subsets with relevant biomarkers. We could ascribe novel specific biomarkers to ECs, MCs and MSCs. Unlike ECs and MCs, MSCs exhibited an adipogenic transcriptomic pattern while co-expressing genes related to hematopoiesis support and multilineage commitment potential. Furthermore, by a comparative analysis of scRNA-seq of BM cells from humans and mice, we identified core genes conserved in both species. Notably, we identified MARCKS, CXCL12, PDGFRA, and LEPR together with adipogenic factors as archetypal biomarkers to reveal native MSCs within BM. In addition, our data suggest some complex gene nodes regulating critical biological functions of native BM-MSCs together with a preferential commitment toward an adipocyte lineage. Overall, our taxonomy for native BM non-hematopoietic compartment provides an explicit depiction of gene expression in human ECs, MCs and MSCs at single-cell resolution. This analysis helps enhance our understanding of the phenotype and the complexity of biological functions of native human BM-MSCs.

overall_design: Single cell RNA-seq analysis of human bone marrow (BM) cells of 5 donors. The data for each donor is split in 3 fastq files. Single cell RNA-seq analysis of human bone marrow (BM) cells of 5 donors. The data for each donor is split in 3 fastq files. Single cell RNA-seq analysis of human bone marrow (BM) cells of 5 donors. The data for each donor is split in 3 fastq files. Single cell RNA-seq analysis of human bone marrow (BM) cells of 5 donors. The data for each donor is split in 3 fastq files. Single cell RNA-seq analysis of human bone marrow (BM) cells of 5 donors. The data for each donor is split in 3 fastq files. Single cell RNA-seq analysis of human bone marrow (BM) cells of 5 donors. The data for each donor is split in 3 fastq files.

first: M

middle: F

last: Loïc

first: Nicolas

last: Espagnolle

first: Daniela

last: Gerovska

first: David

last: Bernard

first: Camille

last: Laurent

first: Pierre

last: Layrolle

first: Julien

last: De Lima

last: Reina

first: Louis

last: Casteilla

first: Naji

last: Abderrahim

first: Jean-Christophe

last: Pagès

first: Frédéric

last: Deschaseaux


title: Xrn1-sensitive lncRNAs accumulate upon inactivation of Dbp2 and Mtr4

summary: To investigate the role of the helicases Dbp2 and Mtr4 in the decay of Xrn1-sensitive lncRNAs, we performed RNA-Seq in yeast cells lacking Dbp2 or depleted for Mtr4.

overall_design:
Strand-specific total RNA-seq in WT, xrn1-delta and dbp2-delta cells, as well as WT and tetOFF-MTR4 cells treated for 6 hours with doxycyclin (Dox).
There 2 biological replicates per condition.

last: WERY

first: Ugo

last: SZACHNOWSKI

first: Sara

last: ANDJUS

first: Alvaro

last: DE ANDRES-PABLO

first: Antonin

last: MORILLON


title: Xrn1-sensitive lncRNAs are globally insensitive to the cytoplasmic helicases Ecm32, Ski2, Slh1, Dbp1 and Dhh1

first: Maxime

last: Wery

summary: To investigate the role of cytoplasmic helicases in the decay of Xrn1-sensitive lncRNAs, we performed RNA-Seq in WT, ecm32-delta, ski2-delta, slh1-delta, dbp1-delta and dhh1-delta yeast cells.

overall_design: Strand-specific total RNA-seq in WT, ecm32-delta, ski2-delta, slh1-delta, dbp1-delta and dhh1-delta yeast cells (2 biological replicates per condition).


title: Spinal Cord Injury regulates circular mRNA expression in axons

status: Public on Jul 25 2023

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Injured axons in the CNS do not spontaneously regenerate leading to paralysis. Neurons can transport RNA and ribosomes to the site of injury where de novo translation has been known to occur, facilitating repair. Yet the tools available for studying axonal specific RNA are limited. We came up with a simple modification using Cold Active Proteases that enabled us to enrich for axonal RNA from rats with spinal cord injury (SCI) compared to non-injured. Our enriched axonal prep was then analyzed by bulk RNA-seq, where we looked at total RNA and we found differentially expressed genes (DEGs). Analyzing our bulk RNA-seq by Gene Ontology, we found the second most significant pathway for all DEGs was for axonogenesis, with markedly low glial cell contamination. From our DEGs we detected Rims2, which is reported to be predominately a circular RNA (circRNA) in the rodent CNS. Upon further annotation, we found over 200 putative circRNAs. circRNAs are abundant and well conserved in the brain, they are thought to be transcriptional regulators by functioning as microRNA (miR) sponges or binding to RNA-binding proteins (RBPs). By computational analysis using Circular RNA Interactome, we are able to predict which miRs or RBPs could bind to circRims2.

overall_design: Our approach was to utilize the latest in detection of novel RNAs from spinal cord tissue that we enriched for axons, with advanced computational techniques, to determine novel Differential Expressed Genes (DEGs) expressed. Using spinal cords from rats with spinal cord contusions or controls with no injury, we utilized Cold Active Proteases to separate out the Acellular Fraction from the pelleted cells. We performed bulk-seq analysis on the Acellular Fraction and determined that it was enriched for known Axonal RNA, with limited glial cell contamination and detected novel DEGs. We used computational programs such as Gene Ontology and found axonogenesis to be a highly significant pathway for all DEGs. We confirmed for expression of some of the novel DEGs detected by RNA-scope in primary cortical cultures and adult rat spinal cord. Upon further annotation we detected novel circRNAs in our enriched axonal RNA. Using Ribonuclease R which digests linear RNA, but not circRNA, we validated that we could indeed detect circRNA by both RNA-scope of the spinal cord and RT-qPCR.

first: Mustafa

last: Siddiq

first: Carlos

last: Toro

first: Nicholas

middle: P

last: Johnson

first: Yuguang

last: Xiong

first: Wilfredo

last: Mellado

first: Rosa

last: Tolentino

first: Kaitlin

first: Gomathi

last: Jayaraman

first: Zaara

last: Suhail

first: Lauren

last: Harlow

first: Kristin

middle: G

last: Beaumont

first: Robert

last: Sebra

first: Dianna

last: Willis

first: Christopher

last: Cardozo

first: Ravi

last: Iyengar


title: scRNA-seq of brain cells from control and 3xDR mouse brains

first: Bo

last: Peng

address: 138 Yixueyuan Road

institute: Fudan University

summary: As important immune cells, microglia undergo a series of alterations during aging that increase the susceptibility to brain dysfunctions. However, the longitudinal characteristics of microglia remain elusive. In this study, we mapped the transcriptional and epigenetic profiles of microglia from 3- to 24-month-old mice. We observed unexpected sex differences and identified age-dependent microglia (ADEM) genes during the aging process. We then compared the characteristics of aging and reactivity in female microglia at the single-cell resolution and epigenetic level. To dissect the functions of aged microglia excluding the influence from other aged brain cells, we established an accelerated microglial turnover model without directly affecting other brain cells. By this model, we achieved aged microglia in non-aged brains and confirmed that aged microglia per se contribute to cognitive decline. Collectively, our work provides a comprehensive resource for decoding the aging process of microglia, shedding light on how microglia maintain brain functions.

overall_design: Colony-stimulating factor 1 receptor (CSF1R) inhibition by PLX5622 for 14 days results in the ablation of 99% of microglia in the brain without directly affecting other cells. Once this inhibition is removed, residual microglia (100% - 99% = 1%) rapidly proliferate, repopulate the whole brain and recover to a normal density (100%) within 2 weeks. Each microglial cell proliferates approximately log2(100%/1%) = 6.64 times during 1-round depletion-repopulation (1xDR). Thus, after 3xDR, each microglial cell has proliferated approximately 6.64 × 3 ≈ 20 times, close to the Hayflick limit (for some cells, the Hayflick Limits is 10~15 population doublings). Whole brain cells from control and 3-round microglia depletion-repopulation (3xDR) mice were collected for sequencing.

first: Yanxia

last: Rao

first: Xiaoyu

last: Li