title: Single-cell RNA sequencing reveals the molecular features of peripheral blood immune cells in children, adults and centenarians

city: Chongqing

first: Qilin

last: Chen

address: No. 1 Yixueyuan Road, Yuzhong District, Chongqing

institute: Chongqing Medical University

summary: The molecular and functional characteristics of peripheral blood immune cells in childhood may contribute to the specialized immune system in children. At present, few researches have compared immune cells in childhood with other age groups, and there is a lack of understanding of immune cells in childhood from the whole lifespan. To display the molecular characteristics of peripheral blood immune cells in childhood at the single-cell level, we performed a comparative study by constructing a peripheral blood mononuclear cell (PBMC) atlas of multiple age groups, including children, young adults, middle-aged adults, aged adults and supercentenarians. The atlas revealed that monocytes in childhood were markedly different from those in other periods. B cells in childhood had a greater ability to respond to viruses and to activate mast cells. Remarkably, we identified a new subtype of CD8+ cytotoxic T cells expressing both naïve and cytotoxicity genes specifically in childhood. The marker genes of this subtypes were used as marker proteins for flow cytometry analysis, and the results confirmed the findings of the scRNA-seq. Moreover, there was more frequent crosstalk between PBMCs in childhood than in other periods, which may be one of the characteristics of the immune system in childhood. Finally, the differences in the expression of susceptibility genes in the PBMCs of different age groups may indicate differences in the disease spectrum of different age groups. In conclusion, this research systematically described the molecular characteristics of peripheral blood immune cells in childhood from multiple levels, and provided new evidence to elucidate the special immune environment of childhood.

overall_design:
PBMCs from healthy children controls were subjected to scRNA-seq with 10x Genomics.

>>>Raw data are not available due to patient privacy concerns<<<

first: Jinjie

last: Zhong

first: Qiu

last: Li


title: Comparative analysis of miRNA profile in sheep serum and serum-derived extracellular vesicles before and after single stage Fontan surgery

status: Public on Dec 30 2022

city: Atlanta

first: Michael

middle: E.

last: Davis

address: 2015 Uppergate Dr NE

country: USA

institute: Emory University

type: Non-coding RNA profiling by high throughput sequencing

summary: There are no curative treatment options for patients with single ventricle disease. Rather, the standard of care includes a series of palliative procedures that culminate in the Fontan operation, which, while life-saving, nevertheless reduces longevity and quality of life. The cause of late term death in these patients is typically ascribed to insidious end organ sequelae associated with the Fontan circulation. The etiology underlying these pathological processes remains unknown, but is thought to be diverse and multifactorial, arising from progressive deterioration of end-organ function due to the non-physiologic Fontan hemodynamics and its consequences on tissue perfusion and remodeling.Our overall goal is to evaluate the impact of Fontan physiology on cardiopulmonary remodeling over long periods in an ovine Fontan survival model.

overall_design: Adolescent sheep with otherwise normal biventricular cardiac anatomy underwent a single-stage Fontan. Examination of miRNA content in serum and serum-EV with and without Fontan surgery is included in this study.  Our overall future experimental approach is to pair serial evaluation of the cardiovascular function by MRI, echo and catheterization with RNAseq, immuno-histology, and biomechanical assessments at prescribed endpoints to examine adverse remodeling in response to Fontan-induced hemodynamics.

first: Hyun-Ji

last: Park

first: John

last: Kelly

middle: E

first: Christopher

middle: K

last: Breuer

first: Toshi

last: Shinoka

first: Sergio

last: Carillo


title: mRNA translation efficiency analysis in liver at 0 h and 24 h after 70% partial hepatectomy

city: Shanghai

first: Yanhao

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: In order to detect changes in liver tissue protein translation efficiency during liver regeneration, we performed sucrose density gradient centrifugation to separate translated (associated with polysome fraction), and non-translated (associated with sub-polysome fraction) transcripts in extracts from mouse livers 0 h and 24 h post-surgery. We found that compared to liver tissues before surgery, extracts from tissues 24 h post-surgery had significantly fewer transcripts associated with polysomes, suggesting a reduction in protein synthesis activity.

overall_design: Liver polysome and sub-polysome RNA profiles of  mice at 0 h and 24 h after partial hepatectomy were generated by deep sequencing. Three samples from each group were included for sequencing.

first: Qiurong

last: Ding

first: Lanlan

first: Yuchen

last: Wang

first: Xiaojian

last: Liu


title: Polycomb  complexes in skin epithelium development

status: Public on Dec 31 2022

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: H3K27ac ChIP-seq Analysis in WT and MIER1 Depletion Liver Tissues at 0 h and 24 h after 70% Partial Hepatectomy

summary: To explore how Mier1 influence the genome H3K27ac levels during liver regeneration, we performed H3K27ac chromatin immunoprecipitation followed by sequencing in control and liver-specific Mier1 ko liver tissues at 0 h and 24 h after 70% partial hepatectomy (PHx). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals.Then we performed 70% partial hepatectomy, 3 weeks after AAV injection. Consistent with the increased expression of cell cycle genes during liver regeneration, we observed increased signals of H3K27ac at 24 h after hepatectomy, especially near some cell cycle genes, after MIER1 depletion in liver tissue.

overall_design: Examination of H3K27ac modifications in liver of control and liver-specific Mier1 KO mice at 0 h and 24 h after 70% partial hepatectomy. Chromatin was prepared from 3 biological replicates of animals in each group.


title: MIER1-FLAG ChIP-seq Analysis in Liver at 0 h and 24 h after 70% Partial Hepatectomy

summary: To explore how Mier1 influence liver regeneration, we performed chromatin immunoprecipitation followed by sequencing in liver tissues at 0 h and 24 h after 70% partial hepatectomy (PHx). Due to a lack of available MIER1 antibody for ChIP-seq analysis, exogenous liver expression of MIER1-FLAG under TBG promoter was executed using AAV vectors, and ChIP-seq was conducted using FLAG antibody. Liver tissues from animals receiving empty vectors were also collected for ChIP-seq with FLAG antibody as negative control to remove possible non-specific binding signals from FLAG antibody. We observed in total 9310 sites bound by MIER1 in total, with a majority of these binding sites around the transcription start sites or present in introns or exons. Further analysis combining the results from RNA-seq revealed a significant set of genes involved in cell cycle, DNA replication and chromosome organization, that were bound by MIER1 and upregulated after MIER1 loss in liver tissues 24 hours after surgery, indicating a direct functional regulation of these genes via MIER1.

overall_design: For the ChIP-seq analysis, chromatin was prepared from 3 biological replicates of animals in each group. Exogenous liver expression of a MIER1-FLAG under a liver-specific TBG promoter was executed using AAV vectors (AAV-MIER1-FLAG) and ChIP-seq was conducted using FLAG antibody. Liver tissues infected with AAV-LUCIFERASE viruses were used as control. Liver tissues were collected for analysis at 0 h and 24 h after 70% partial hepatectomy.


title: Rhythmic transcription drives mRNA level oscillations during C. elegans development [RNA-Seq]

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

summary: Thousands of transcripts accumulate in an oscillatory manner during C. elegans larval development. Here, we performed total RNA sequencing to confirm and quantify transcript levels oscillations on samples that we used in parallel to  probe rhythmic RNA polymerase II recruitment to these genes as a mechanism to generate RNA level oscillations (see parallel submission of ChIP-seq data)

overall_design: Synchronized L1-stage wild-type (N2) worms were plated on food, grown at 25°C and collected hourly from 22 hours until 33 hours developmental time.  Total RNA sequencing was performed on extracted RNA.

first: Milou

last: Meeuse


title: Immunologic predictors for clinical responses during immune checkpoint blockade in patients with myelodysplastic syndromes

status: Public on Dec 29 2022

city: Houston

first: Jin

middle: S

last: Im

state: Texas

address: 1515 Holcombe Blvd, Unit 900

institute: The University of Texas M.D. Anderson Cancer Center

summary: We investigated the immune-related gene expression signature in the tumor immune-microenvironment associated with response or resistance during immunotherapy, by performing targeted gene expression profiling and gene set enrichment analysis  using a custom NanoString panel composed of 579 immune-related genes

overall_design: Peripheral blood from 55 MDS patients were assessed for immune-related gene expression profiling pre and after the first treatment


title: Polycomb repressive complex 1 and 2 (PRC1 and PRC2) role in controling skin pigmentation


title: Rhythmic transcription drives mRNA level oscillations during C. elegans development [ChIP-Seq]

summary: Thousands of transcripts accumulate in an oscillatory manner during C. elegans larval development. Here, we confirmed these oscillations to result from rhythmic RNA polymerase II (RNAPII) binding to these oscillating genes by performing RNAPII ChIP-seq and total RNA-seq on the same samples (see related submission)

overall_design: Synchronized L1-stage wild-type (N2) worms were plated on food, grown at 25°C and collected hourly from 22 hours until 33 hours developmental time. RNA polymerase II ChIP was performed mouse anti-RNA polymerase II CTD antibody (8WG16, Abcam)


title: Epigenetic signals that direct cell type specific interferon beta response in mouse cells

city: Heidelberg

first: Markus

last: Muckenhuber

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

summary: The antiviral response induced by type I interferon (IFN) via the JAK-STAT signaling cascade results in the activation of a set of IFN-stimulated genes (ISGs). This response varies between different cell types of the organism. However, the linkage between the underlying epigenetic features and innate immune response is not well understood. We mapped ISGs and STAT1 and STAT2 binding sites in mouse embryonic stem cells and differentiated cells before and after treatment with IFNβ together with histone acetylation (ac) and mono- and tri-methylation (me1, me3) marks at histone H3 lysine residues for H3K4me1, H3K4me3, H3K9ac, H3K27ac, H3K9me3 and H3K27me3. Many ISGs were cell type specific and displayed distinct STAT1/2 binding patterns at promoters. Furthermore, binding to putative enhancers at intergenic and intronic site was driving ISGs as inferred from a co-regulation analysis of open chromatin sites in single cells. Activator binding was dependent on the chromatin context and positively correlated with pre-existing H3K4me1 enrichment and open chromatin states while the presence of H3K27me3 had the opposite effect. Chromatin features present before stimulation direct the cell type specific response to type I IFNs. Thus, epigenetic signals represent an additional regulatory layer that is responsible for the tissue dependent activity of this signaling pathway. The mechanistic insight gained in our study could be exploited for modulating innate immune response during virus infection or cancer immunotherapy.

overall_design:
RNA-seq, ChIP-seq, ATAC-seq, scRNA-seq and scATAC-seq of mouse embryonic stem cells compared to mouse embryonic fibroblasts and differentiated neuronal progenitor cells upon interferon beta treatment

Please note that processed data files generated from multiple samples are linked as Series supplementary files, along with 'readme.txt' describing the data.

first: Isabelle

last: Seufert

first: Karsten

last: Rippe


title: Epigenetic profiling of microglia-specific gene transcription and chromatin accessibility in mouse forebrain after chronic mild stress

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

summary: Multiple studies have suggested that stress induces neuroinflammation and contributes to emotion-related behavioral deficits. To study epigenetic changes in microglia after chronic stress, we purified microglia from mouse brain after exposure to chronic unexpected mild stress (CUMS), and then performed RNA-seq and ATAC-seq to study microglia-specific alterations of transcriptome and chromatin accessibility in response to chronic stress.

overall_design: Microglia-specific ATAC-seq and RNA-seq in stress and control mice, 3 animals per group.

first: Yuan

last: Zhang


title: Analysis of Control and Liver-specific Mier1 KO Liver Transcriptomes after 70% Partial Hepatectomy

last: Chen

summary: To explore how Mier1 affiects liver regeneration, we specifically knocked out Mier1 in mouse liver through adeno-associated virus (AAV). The mice we used were knocked in a Cre-induced Cas9 expression cassette. Through tail vein injection, we delivered the AAV expressing Cre-recombinase under TBG promoter, and sgRNA targeting Mier1 (AAV-Mier1 sgRNA), into the adult Cas9 knockin mice to knock out the Mier1 gene in liver. AAV vectors with no sgRNA inserted (AAV-Cre) were used in control animals. To assess the role of MIER1 in liver regeneration, we performed 70% partial hepatectomy, 3 weeks after AAV injection. We then performed RNA sequencing analysis on liver tissues collected from control and Mier1 ko groups at 0 h, 24 h, 36 h, 48 h and 72 h after partial hepatectomy. Interestingly, although MIER1 depletion did not cause a significant difference in expression of cell cycle genes before surgery, the increase of cell cycle gene expression during liver regeneration was significantly enhanced after MIER1 loss. Further analysis showed that after partial hepatectomy, MIER1 loss caused significant upregulation of genes enriched in cell proliferation relevant pathways.

overall_design: Liver RNA profiles of WT and liver-specific Mier1 KO mice at different time points after partial hepatectomy were generated by deep sequencing. Each sample contained pooled RNA from three biological replicas that were mixed with an equal mass of RNA. Two samples from each group were included for sequencing.


title: Sea anemone mesentery muscle profiling [bulk RNA-seq]

city: Vienna

first: Alison

middle: G

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

summary: Isolated mesenteries from MHC::mCherry Adults were used to generate FACS-sorted RNA sequencing libraries in order to characterize gene use in Cnidarian smooth muscle. Transgenic mCherry expressing cells are compared to the non-expressing cells of the surrounding tissues, and up-regulated genes within the muscle cell population can be identified as important muscle-related gene products.

overall_design: Adult mesenteries from eight Nematostella vectensis  MHC::mCherry transgenic lines were isolated and dissociated into single cell suspensions, performed in duplicate. These were FACS-sorted into mCherry+ and mCherry- populations,  used to generate four RNA sequencing libraries

first: Ulrich

last: Technau

first: Stefan

last: Jahnel


title: Urinary exosomal miRNA-663a shows variable expression in diabetic kidney disease patients with or without proteinuria

city: chandigarh

first: sanjeev

last: puri

department: uiet, biotechnology branch

country: India

institute: panjab university

summary: HK-2 cells were cultured in low and high  glucose conditions for 96 hours in serum free conditions. Exosomes were isolated from the supernatant of these cells. miRCURY LNATM Universal RT microRNA PCR Human panel I+II (Exiqon) were used to study the differential expression from three different high glucose treated exosomes (HE1, HE2, HE3) than to low glucose treated exosomes (LE1, LE2, LE3).

overall_design: qPCR miRNA expression profiling from three different exosomal samples. Each  sample was isolated  from low and high glucose treated HK-2 cells

first: Nisha

last: Sinha

first: Veena

last: Puri

first: Vivek

last: Kumar

first: Ritambhra

last: Nada

first: Ashu

last: Rastogi

first: Vivekanand

last: Jha

first: Sanjeev


title: Cytomegalovirus Vaccine-induced Unconventional T cell Priming and Protection against SIV Replication is Conserved Between Primate Species

status: Public on Dec 21 2022

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: Bulk RNA Sequencing of Mauritian cynomolgus macaque (MCM) whole blood pre- and post-vaccination with CyCMV/SIV

overall_design: MCMs were sampled at Day 0 (pre-vaccination), Days 3, 7, & 14 post-prime vaccination, just prior to boost vaccination (BD0), and Days 3, 7, & 14 post-boost vaccination

first: Daniel

last: Newhouse

first: Leanne

last: Whitmore

first: Elise

last: Smith

first: Jonah

last: Sacha

last: Gale Jr


title: RNA-seq data for: Anti-retroviral treatment with zidovudine alters pyrimidine metabolism, reduces translation, and extends healthy longevity via ATF-4

city: Amsterdam

first: Georges

last: Janssens

address: Meibergdreef 9

department: Laboratory Genetic Metabolic Diseases

country: Netherlands

institute: Amsterdam UMC

summary: The human population is aging, and the need for interventions to slow progression of age-related diseases (geroprotective interventions) is growing. Repurposing compounds already used clinically, usually at modified doses, allows for rapid implementation of geroprotective pharmaceuticals. Here we find the anti-retroviral nucleoside reverse transcriptase inhibitor (NRTI) zidovudine robustly extends lifespan and healthspan in C. elegans, independent of electron transport chain impairment or ROS accumulation. Rather, zidovudine treatment modifies pyrimidine metabolism and transcripts related to proteostasis. Testing regulators of mitochondrial stress and proteostasis shows that lifespan extension is dependent on activating transcription factor 4 (ATF-4). ATF-4 regulates longevity induced by mitochondrial stress, and specifically communication between mitochondrial and cytosolic translation. Translation is reduced in zidovudine-treated worms, also dependent on ATF-4. Finally, we show ATF-4-dependent lifespan extension induced by didanosine, another NRTI. Altogether, our work elucidates the geroprotective effects of NRTIs such as zidovudine in vivo, via reduction of translation and ATF-4.

overall_design: 4 samples each of C. elegans treated for 24 hours from larval stage 4 to day 1 of adulthood with 50 μM zidovudine or DMSO controls

first: Rebecca

middle: L

last: McIntyre


title: Gene expression analysis of control and Dnd1-cKO germ cells at E12.5 and E13.5.

status: Public on Dec 28 2022

city: Yokohama

first: Atsuki

last: Imai

state: Japan

country: Japan

institute: Yokohama National University

summary: The present investigation was to identify transcriptomic changes of control and Dnd1-cKO PGCs at E12.5 and E13.5 by microarray comparison. We identified 1470 upregulated and 924 downregulated genes in Dnd1-cKO PGCs.

overall_design: There were gene expression data of Nanog-EGFP positive PGCs from testes of control and Dnd1-cKO embryos at E12.5 and E13.5. Each contains three replicates of transcriptome data.

first: Yuki

last: Niimi

first: Atsushi

last: Suzuki


title: Global transcriptome analysis of long RNA molecules expressed in human keratinocyte cell line HaCaT pre-treated with TGF-β1 in response to silymarin, a natural plant extract involved in skin tissue regeneration

city: Orléans

first: Patrick

last: Baril

address: Rue Charles Sadron

country: France

institute: Centre de Biophysique Moléculaire, CNRS-UPR4301

summary: The goal of this study is to find out the exact mechanisms of action of silymarin (SM), a complex mixture of flavonolignans structures isolated from milk thistle (Silybum marianum), on the biological behavior (phenotype) of human HaCaT keratinocytes.

overall_design: To place the HaCaT cells in a context of a tissue re-epithelization process, we treated these cells for 24 hours with the Transforming Growth Factor β1 (TGF-β1, 10 ng/ml) in presence or absence of silymarin (SM, 31.25 µg/ml). Total RNA (longer than 200 nucleotides) were isolated, polyA RNA were enriched and sequenced from 3 biological replicate samples of TGF-β1-treated HaCaT cells (TGF) and 3 biological replicate samples of TGF-β1 plus SM-treated HaCaT cells (TGF.SM31).

first: Elodie

last: Henriet


title: An RNAi therapeutic targeting hepatic DGAT2 in a genetically obese mouse model of nonalcoholic steatohepatitis

city: Worcester

last: Czech

state: Massachusetts

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary:
Nonalcoholic steatohepatitis (NASH) is a severe liver disorder characterized by triglyceride accumulation, severe inflammation, and fibrosis. With the recent increase in prevalence, NASH is now the leading cause of liver transplantation, with no approved therapeutics available. Despite years of research, the exact molecular mechanism of NASH progression is not well understood, but fat accumulation is believed to be the primary driver of the disease. Therefore, diacylglycerol O-acyltransferase 2 (DGAT2), a key enzyme in triglyceride synthesis, has been explored as a NASH target. RNAi-based therapeutics is revolutionizing the treatment of liver diseases, with recent chemical advances supporting long term gene silencing with single subcutaneous administration. Here we identified a hyper-functional, fully chemically stabilized Gal-Nac conjugated siRNA targeting DGAT2 (Dgat2-1473) that upon injection elicits up to three months of DGAT2 silencing (>80-90%, p<0.0001) in wild-type and NSG-PiZ “humanized” mice.
Using an obesity-driven mouse model of NASH (ob/ob-GAN), Dgat2-1473 administration prevents and reverses triglyceride accumulation (> 50%, p:0.0008), resulting in significant improvement of the fatty liver phenotype. However, surprisingly, the reduction in liver fat didn’t translate into a similar impact on inflammation and fibrosis. Thus, while Dgat2-1473 is a practical, long-lasting silencing agent for potential therapeutic attenuation of liver steatosis, combinatorial targeting of a second pathway may be necessary for therapeutic efficacy against NASH.

overall_design: Liver samples from 4 mice for control (NTC) , 4 mice samples for treatment group (Dgat2-1473)

first: Batuhan

last: Yenilmez

first: Lawrence

last: Lifshitz

first: Anastasia

last: Khvorova


title: Tracking chromatin state changes using nanoscale protoproximity labeling (RNA-Seq)

status: Public on Dec 24 2022

city: Jupiter

first: Ciaran

last: Seath

state: Florida

address: 120 Scripps Way

institute: UF-Scripps

summary: Effect of JQ-1, Pinometostat, or histone mutation H2A E92K on global gene expression in HEK293T cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HEK293T cells transfected with H2A or H2A(E92K) and treated with either DMSO, JQ1 or Pinometostat

middle: P


title: Genome wide transcriptomic analysis reveals the mechanism underlying Stylosanthes roots in response to phosphorus deficiency

city: Haikou

first: Zhijian

last: Chen

email: jchen@scau.edu.cn, zjchen@catas.cn

address: Xueyuanlu 4

institute: Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences

summary: Phosphorus (P) is an important macronutrient for plant growth that participates in a series of biological processes. Thus, P deficiency is considered as one of the major constraints limiting crop growth and yield. Although stylo (Stylosanthes) is a dominate tropical legume that displays adaptation to low phosphate (Pi) availability in acid soils, its adaptive mechanisms remain largely unknown. In this study, variation in low P stress tolerance was investigated using two stylo cultivars in hydroponics, which revealed that the stylo RY2 cultivar exhibited higher adaptability to Pi starvation than the RY5 cultivar, as reflected by less reduction in dry weight under P deficient condition, and accompanied by higher P concentrations in shoot and root. Furthermore, better root growth performance and higher APase activity were found in leaves and roots of stylo RY2 cultivar compared to RY5. RNA‐seq analysis revealed 8,348 genes that exhibited differentially expressed under P deficient and sufficient conditions in RY2 roots, with many Pi starvation up-regulated genes associated with P metabolic process, protein modification process, transport and other metabolic processes. A group of differentially expressed genes (DEGs) involved in Pi uptake and homeostasis were identified, such as genes encoding Pi transporter (PT), purple acid phosphatase (PAP), multidrug and toxin extrusion (MATE) and aluminum-activated malate transporter (ALMT). Furthermore, a variety of genes related to transcription factors (TFs) and regulators involved in Pi signaling, including genes belonging to the PHOSPHATE STARVATION RESPONSE 1-like (PHR1), WRKY family, the SYG1/PHO81/XPR1 (SPX) domain, bHLH and ARP family, were also regulated by P deficiency in stylo roots. Taken together, this study suggests a complex adaptive response of stylo to P deficiency, contributing to maintain Pi homeostasis.

overall_design: Two stylo (Stylosanthes guianensis) cultivars Reyan 2 (RY2) and RY5, were used. Seeds of stylo were germinated for 3 d, and stylo seedlings were then transferred to a modified Hoagland nutrient solution (pH 5.8) for 14 d. After that, seedlings were separately transplanted into nutrient solution (pH 5.8) supplied with 0 and 250 µM KH2PO4. After 21 d of P treatments, roots were harvested for RNA-seq analysis.

first: Jianling

last: Song

first: Pandao

last: Liu


title: The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing

status: Public on Dec 23 2022

city: Erlangen

first: Benedikt

last: Kost

state: Bavaria

address: Staudtstraße 5

department: Biology

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

overall_design: Refer to individual Series


title: The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing [ChIP-Seq]

summary: Guanylate Binding Proteins (GBPs) are prominent regulators of immunity unknown to be required for nuclear envelope formation and function. The Arabidopsis GBP orthologue AtGBPL3 was identified as a novel component of the plant lamina, with essential functions in mitotic nuclear envelope reformation. AtGBPL3 is preferentially expressed in mitotically active root tips and accumulates at the nuclear envelope. Furthermore, fluorescent lifetime imaging experiments in the presence or absence of the chromatin-labelling dye Sytox-Orange suggested that GBPL3 might be able to interact with chromatin. Chromatin-immunoprecipitation followed by sequencing (ChIP-Seq) revealed only few GBPL3-associated chromatin domains, which were concentrated particularly within or near centromeric regions.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for guanylate-binding protein-like 3 (AtGBPL3) from Arabidopsis thaliana

first: Theresa

middle: M

last: Reimann

first: Christina

last: Müdsam


title: The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing [RNA-seq]

summary: Guanylate Binding Proteins (GBPs) are prominent regulators of immunity unknown to be required for nuclear envelope formation and function. The Arabidopsis GBP orthologue AtGBPL3 was identified as a novel component of the plant lamina, with essential functions in mitotic nuclear envelope reformation. AtGBPL3 is preferentially expressed in mitotically active root tips, accumulates at the nuclear envelope and interacts with further components of the nuclear lamina. To investigate effects of defective lamina components on gene expression, we analysed the transcriptomes of 4 day old wild-type, gbpl3-5, crwn4-1, crwn1-1crwn4-1, as well as gbpl3-5 mutants expressing GBPL3-GFP or the GTPase-dead GBPL3(K83A)-GFP under control of the AtGBPL3-promoter.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Arabidopsis thaliana (Col-0 and different mutants defective for putative components of the plant nuclear lamina (gbpl3-5, crwn4-1, crwn1-1crwn4-1), or transgenic lines (expressing either pAtGBPL3::GBPL3genomic-GFP or pAtGBPL3::GBPL3(K83A)genomic-GFP in the gbpl3-5 background)


title: The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain [ChIP-seq]

status: Public on Dec 20 2022

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

summary: The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrate that a winged helix (WH) domain at the very N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A with unmethylated CpG islands (CGIs) genome-wide. Mutation of the essential amino acids for DNA binding completely abrogates the enrichment of KAT6A at CGIs. In contrast, deletion of a second WH domain or the histone tail binding PHD fingers only subtly influences the binding of KAT6A to CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases.

overall_design: ChIP-Seq of wildtype and mutated Flag-tagged KAT6A in HEK293 cells, upon overexpression. ChIP-Seq of H3K9ac in the same cells.

first: Lisa

last: Weber

first: Bastian

last: Stielow

first: Andrea

last: Nist


title: Transcriptomic analysis of mouse embryonic stem cells and differentiated cells upon OGT inhibition

city: Wuhan

first: Xiang

last: Li

address: Youyi Road

institute: Hubei University

summary: To ask whether perturbations on global O-GlcNAc levels could alter embryonic stem cell identity and differentiation processes, we explored the gene expression of mouse embryonic stem cells (mESCs) and retinoic acid (RA)-inducted differentiated cells with or without OGT inhibition by per-acetylated 2-acetamido-2-deoxy-5-thio-D-glucopyranose (Ac45SGlcNAc, 5S).

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of mESCs and retinoic acid (RA)-inducted differentiated cells with or without OGT inhibition by Ac45SGlcNAc. For OGT inhibition,  mESCs were treated with 25 μM Ac45SGlcNAc for 48 h. For inducing mESC differentiation, the cells pre-treated with DMSO or Ac45SGlcNAc were then incubated with 1 μM RA for 48 h. N_NC: normal mouse embryonic stem cells, N_5S: 5S treated mouse embryonic stem cells, DIF_NC: normal differentiated cells, DIF_5S: 5S treated differentiated cells.

first: Yi

last: Hao

first: Xing


title: Clonal hematopoiesis is driven by aberrant activation of TCL1A [CITE-seq]

city: Palo Alto

first: Jayakrishnan (Jk)

last: Gopakumar

state: CA

address: 240 Pasteur Dr Rm 4600

institute: Stanford

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the different cell populations present after in vitro culture of HSPCs with or without TCL1A overexpression.

overall_design: Lin- CD34+ CD38- CD45RA- GFP+ were cultured in HSPC expansion media for 7 days before CITE-Seq scRNAseq was performed.

first: Joshua

last: Weinstock

first: Jk

first: Alex

last: Bick

first: Siddhartha

last: Jaiswal


title: β-Catenin signaling in alveolar macrophages enhances lung metastasis through a TNF-dependent mechanism

status: Public on Dec 19 2022

city: Buffalo

first: Elliot

middle: David

last: Kramer

state: New York

address: 665 Elm St

department: Immunology

institute: Roswell Park Comprehensive Cancer Center

summary: The main cause of malignancy-related mortality is metastasis. While metastatic progression is driven by diverse tumor-intrinsic mechanisms, there is a growing appreciation for the contribution of tumor-extrinsic elements of the tumor microenvironment (TME), especially macrophages. Recruited macrophages infiltrating the TME are correlated with worse outcomes, because they are rendered pro-tumorigenic through defined tumor-driven transcription factor-mediated programs. However, the pathways that govern the dysregulation of tissue-resident macrophages (TRMs) are less well understood.  Alveolar macrophages (AMs) are a TRM population with critical roles in both tissue homeostasis and metastasis. Wnt/β-catenin signaling is a hallmark of cancer and has been identified as a pathologic regulator of AMs in infection. We tested the hypothesis that β-catenin expression in AMs enhances metastasis in solid tumor models. Using a novel genetic β-catenin gain-of-function approach, we demonstrated that 1) enhanced β-catenin in AMs heightened lung metastasis; 2) β-catenin activity in AMs drove a dysregulated inflammatory program strongly associated with Tnf expression; and 3) localized TNF blockade abrogated this metastatic outcome. Lastly, CTNNB1 and TNF expression were positively correlated in AMs of lung cancer patients. Overall, our findings revealed a novel Wnt/β-catenin–TNF-α pro-metastatic axis in AMs with potential therapeutic implications against tumors refractory to TNF-α induced necrosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from alveolar macrophages isolated from the lungs of Lyz2Cre+/+YFP+/- (YFPCtr) and Lyz2Cre+/+Ctnnb1exon3del/wtYFP+/- (Triple) mice.

middle: D

first: Stephanie

last: Tzetzo

first: Sean

middle: H

last: Colligan

first: Mary

last: Hensen

first: Craig

last: Brackett

first: Björn

last: Clausen

first: Makoto

last: Taketo

first: Scott

middle: I

last: Abrams


title: The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain [RNA-seq]

first: Robert

last: Liefke

overall_design: RNA-Seq of Control and KAT6A knockout mouse ES cells (2 replicates).

first: Lisa

last: Weber

first: Bastian

first: Andrea


title: Spatially resolved transcriptomics reveals innervation-responsive functional cluster in skeletal muscle.

city: Paris

first: Lorenzo

last: Giordani

address: 105 bld de l'hôpital

department: Centre de Recherche en Myologie - UMRS974 Sorbonne Université

institute: INSERM

summary: Striated muscle is a highly organized structure composed by well-defined anatomical domains with integrated but distinct assignments. Indeed, the lack of a direct correlation between tissue architecture and gene expression has thus far limited our understanding of how each unit responds to physio-pathologic contexts.  Here, we show how the combined use of spatially resolved transcriptomics and immunofluorescence can bridge this gap by enabling the unbiased identification of such domains and the characterization of their response to external perturbations. Using a spatiotemporal analysis, we followed the changes in the transcriptomics profile of specific domains in muscle in a model of denervation. Furthermore, our approach allowed us to identify the spatial distribution and nerve dependence of atrophic signalling pathway and polyamine metabolism to glycolytic fibres. Indeed, we demonstrate a pronounced alteration of polyamine homeostasis upon denervation.

overall_design: Spatial Transcriptomics analysis of wildtype murine Tibialis Anterior and Extensor digitorum longus prior and after Nerve Crush  (3 days  and 30 days )

last: Giodani

first: Chiara

last: D'Ercole

first: Luca

last: Madaro


title: Grapevine response to a Dittrichia viscosa extract and a Bacillus velezensis strain

status: Public on Dec 18 2022

city: La Creueta

first: Mélina

last: Ramos

state: Girona

address: Edifici Jaume Casademont. Porta E, Carrer Pic de Peguera, 15, 4t,

country: Spain

institute: University of Girona

summary: The present study aims to evaluate the response of the three Mediterranean local grapevines ‘Garnacha Blanca’, ‘Garnacha Tinta’, and ‘Macabeo’ to treatments with biocontrol products (BPs), a botanical extract (Akivi, Dittrichia viscosa extract) and a beneficial microorganism (Bacillus UdG, Bacillus velezensis). A combination of transcriptomics and metabolomics approaches were chosen in order to study grapevine gene expression and to identify gene marker candidates, as well as, to determine grapevine metabolites differentially concentrated in response to BPs treatments. Grapevine plants were cultivated in greenhouse controlled conditions and submitted to the treatments, and thereafter, leaves were sampled 24h after treatment to conduct gene expression study by RNA-sequencing for ‘Garnacha Blanca’ leaves extract and by RT-qPCR for the three cultivars. Differentially expressed genes (DEGs) were investigated for both treatments and highly influenced DEGs were selected to be tested in the three cultivars as treatment gene markers. In addition, extraction of leaf components was performed to quantify metabolites such as phytohormones, organic acids, and phenols. Considering all the upregulated and downregulated genes and enhanced metabolites concentrations, the treatments had an effect on jasmonic acid, ethylene, and phenylpropanoids defense pathways. In addition, several DEG markers were identified presenting a stable overexpression after the treatments in the three grapevine cultivars.  These gene markers could be used to monitor the activity of the products in field treatments in future research. Further research will be necessary to confirm these first results under field conditions.

overall_design: The transcriptome of Vitis vinifera cv Garnacha Blanca plants treated by spray applications of a plant extract (Akivi, A) or a microbial (Bacillus UdG fresh culture or lyophilized, respectively B or BL) biocontrol products were compared to non-treated ones 24h post-treatment. Four biological replicates were used. Each biological replicate consisted of 10 grapevine leaves (2 leaves x 5 plants).

first: Núria

last: Daranas

first: Mercè

last: Llugany

first: Roser

last: Tolrà

first: Emilio

last: Montesinos

first: Esther

last: Badosa


title: The dogs of Chernobyl: demographic insights into populations inhabiting the nuclear exclusion zone

status: Public on Dec 14 2022

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

summary: The 1986 Chernobyl nuclear disaster initiated a series of catastrophic events resulting in long-term and widespread environmental contamination. We characterize the genetic structure of 302 dogs representing three free-roaming dog populations living within the power plant itself, or 15-45 km from the disaster site. Genome-wide profiles from Chernobyl, purebred, and free-breeding dogs world-wide reveal that the individuals from the power plant and Chernobyl City are genetically distinct, with the former displaying increased intrapopulation genetic similarity and differentiation. Analysis of shared ancestral genome segments highlights differences in the extent and timing of western breed introgression. Kinship analysis reveals 15 families, with the largest spanning all collection sites within the radioactive exclusion zone, reflecting migration of dogs between the power plant and Chernobyl City. This study presents the first characterization of a domestic species in Chernobyl, establishing their relevance for genetic studies into the effects of exposure to long-term, low-dose ionizing radiation.

overall_design: free-breeding dogs sampled from various locations near the Chernobyl Nuclear Power Plant

first: G

middle: J

last: Spatola

first: R

last: Buckley

first: M

last: Dillon

first: E

middle: V

last: Dutrow

first: J

middle: A

last: Betz

last: Pilot

first: H

last: Parker

first: W

last: Bogdanowicz

last: Thomas

first: I

last: Chyzhevskyi

last: Milinevsky

first: N

last: Kleiman

last: Breen

last: Ostrander

first: T

last: Mousseau


title: Intratumoral CD8+ T cells with a tissue-resident phenotype mediate local immunity and immune checkpoint responses in breast cancer

city: Melbourne

first: Franco

last: Caramia

state: Victoria

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: CD8+ tumor-infiltrating lymphocytes with a tissue-resident memory T (TRM) cell phenotype are associated with favorable prognosis in patients with triple negative breast cancer (TNBC). However, the relative contribution of CD8+ TRM cells to anti-tumor immunity and immune checkpoint blockade efficacy in breast cancer remains unknown. Here, we show that intratumoral CD8+ T cells in murine mammary tumors transcriptionally resemble those from triple-negative breast cancer patients. Phenotypic and transcriptional studies established two intratumoral sub-populations: one more enriched in markers of terminal exhaustion (TEX-like) and the other with a bona-fide resident phenotype (TRM-like). Treatment with anti-PD-1 and anti-CTLA-4 therapy resulted in a expansion of these intratumoral populations, with the TRM-like subset displaying significantly enhanced cytotoxic capacity. Importantly, we demonstrate that it is the TRM-like CD8+ T cells can provide local immune protection against mammary tumor re-challenge and that a gene signature from remaining TRM-like CD8+ T cells extracted from tumor-free tissue was significantly associated with improved outcomes in human TNBC patients treated with checkpoint inhibition. Overall, our data suggest that CD8+ T cells with a tissue resident phenotype play a critical role in response to local immunosurveillance and responses to immune checkpoint blockade in breast cancer

overall_design: FACS purified CD8+ T cell subsets were processed for RNA using the RNeasy mini kit (Qiagen) as per the manufacturer's instructions. RNA TapeStation (Agilent, USA) analysis was performed as per the manufacturer's instructions to assess the quantity and quality of RNA material isolated from TNBC tumors. 10ng total RNA was used for library preparation according to manufacturer’s instructions (QuantSeq 3' mRNA-Seq FWD, Lexogen). Indexed libraries were pooled and sequenced on a NextSeq500 (Illumina). The library was then amplified with 3’ PCR primers containing sample indices and the Illumina clustering guides. Five to ten million single-end 75 bp reads were generated as an output.

first: Balaji

last: Virassamy

first: Peter

last: Savas


title: H3K79me3 ChIP-Seq at FRB-Pyk1 and WT strains under addition of DMSO treatment

status: Public on Dec 10 2022

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

institute: Hubei university

summary: The glycolytic enzyme, pyruvate kinase Pyk1 maintains telomere heterochromatin by phosphorylating histone H3T11 (H3pT11), which promotes SIR (silent information regulator) complex binding at telomeres and prevents autophagy-mediated Sir2 degradation. However, the exact action mechanism of H3pT11 is poorly understood. Here, we identify Dot1-catalyzed H3K79 tri-methylation (H3K79me3) as the downstream effector of H3pT11 and uncover how this histone crosstalk regulates autophagy and telomere silencing. Mechanistically, Pyk1-catalyzed H3pT11 directly reduces the binding of Dot1 to chromatin and inhibits Dot1-catalyzed H3K79me3, which leads to transcriptional repression of autophagy genes and reduced autophagy. Despite the antagonism between H3pT11 and H3K79me3, they synergically promote the binding of SIR complex at telomeres to maintain telomere silencing. Furthermore, we identify Reb1 as a telomere-associated factor that recruits Pyk1-containing SESAME (Serine-responsive SAM-containing Metabolic Enzyme) complex to telomere regions to phosphorylate H3T11 and prevent the invasion of H3K79me3 from euchromatin into heterochromatin to maintain telomere silencing. Together, these results uncover a novel histone crosstalk and provide insights into dynamic regulation of silent heterochromatin and autophagy in response to cell metabolism.

overall_design: ChIP-Seq examination of H3K79me3.

first: He

last: Fei


title: Single-Cell Epitope-Transcriptomics Reveal Lung Stromal and Immune Cell Response Kinetics to Nanoparticle-delivered RIG-I and TLR4 Agonists

status: Public on Dec 12 2022

city: Atlanta

first: Krishnendu

last: Roy

state: GA

address: 950 Atlantic Dr NW

department: The Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory

institute: Georgia Institute of Technology

summary: Lung-resident and circulatory lymphoid, myeloid, and stromal cells, expressing various pattern recognition receptors (PRRs), detect pathogen and danger-associated molecular patterns (PAMPs/DAMPs), and defend against respiratory pathogens and injuries. Here, we report the early responses of murine lungs to nanoparticle-delivered PAMPs, specifically the RIG-I agonist poly-U/UC (PUUC), with or without the TLR4 agonist monophosphoryl lipid A (MPLA). Using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), we characterized the responses at 4 and 24 hours after intranasal administration. Within 4 hours, ribosome-associated transcripts decreased in both stromal and immune cells, followed by widespread interferon-stimulated gene (ISG) expression. Using RNA velocity, we show that lung-neutrophils dynamically regulate the synthesis of cytokines like CXCL-10, IL-1α, and IL-1β. Co-delivery of MPLA and PUUC increased chemokine synthesis and upregulated antimicrobial binding proteins targeting iron, manganese, and zinc in many cell types, including fibroblasts, endothelial cells, and epithelial cells. Overall, our results elucidate the early PAMP-induced cellular responses in the lung and demonstrate that stimulation of the RIG-I pathway, with or without TLR4 agonists, induces a ubiquitous microbial defense state in lung stromal and immune cells. Nanoparticle-delivered combination PAMPs may have applications in intranasal antiviral and antimicrobial therapies and prophylaxis.

overall_design: We performed CITE-Seq using BioLegend TotalSeqTM-A antibodies to generate antibody-derived tags (ADTs) and the 10x Genomics Chromium v3.1 kit to generate single-cell transcripts of murine lungs treated with PUUC or MPLA + PUUC nanoparticles at 4 and 24 h (n = 3). Control group of naive lungs were included. PUUC (poly-U/UC) is a RIG-I agonist. MPLA (mono-phosphoryl lipid A) is a TLR4 agonist.

first: Keenum

last: Mark Coleman

first: Chatterjee

last: Paramita

first: Atalis

last: Alexandra

first: Pandey

last: Bhawana

first: Jimenez

last: Angela

first: Roy

last: Krishnendu


title: H3T11p ChIP-Seq and H3K79me3 ChIP-Seq at FRB-Pyk1 and WT strains under addition of DMSO treatment


title: H3T11p ChIP-Seq at FRB-Pyk1 and WT strains under addition of DMSO treatment

overall_design: ChIP-Seq examination of H3pT11.


title: Transcriptome Analysis Reveals Association of Carotenoid Metabolism Pathway with Fruit Color in Melon

status: Public on Dec 06 2022

city: shanghai

first: shi

last: yao

address: jinqi road

department: Horticultural Research Institute

institute: Shanghai Academy of Agricultural Sciences

summary: To analyze the molecular mechanism underlying flesh color formation in different color melon.

overall_design: RNA-sequencing were performed to identify differentially expressed genes (DEGs) between the two inbred lines at different stages.

first: Qiannan

last: Diao

first: Yongping

last: Zhang


title: Metabolic behavior for a mutant Oenococcus oeni strain with high resistance to ethanol to survive under oenological multi-stress conditions.

status: Public on Nov 30 2022

city: Talca

first: Angela

last: Contreras

state: Talca

address: Av San Miguel 3605

country: Chile

institute: Universidad Católica del Maule

summary: Malolactic fermentation (MLF) positively influences the quality of the wine, and it occurs as a result of a lactic acid bacteria’s metabolism, mainly of the Oenococcus oeni species. However, delays and halting of MLF are frequent problems in the wine industry. This is mainly because O. oeni’s development is inhibited by different kinds of stress.    Even though the sequencing of the genome of the PSU-1 strain of O. oeni, as well as other strains, has made it possible to identify genes involved in the resistance to some types of stress, all of the factors that could be involved are still unknown.   With the aim of contributing to this knowledge, the random mutagenesis technique was used in this study as a strategy for genetic improvement of strains of the O. oeni species. The technique proved to be capable of generating a different and improved strain when compared to the PSU1 strain (the parent from which it descends). Then, we evaluated the metabolic behavior of both strains in three different wines. We used synthetic MaxOeno wine (pH 3.5; 15% v/v ethanol), red wine (Cabernet Sauvignon) and white wine (Chardonnay). Furthermore, we compared the transcriptome of both strains, grown in MaxOeno synthetic wine.   The specific growth rate of the E1 strain was on average 39% higher in comparison to the PSU1 strain. Interestingly, E1 strain showed an overexpression of the OEOE_1794 gene, which encodes a UspA-like protein, which has been described as promoting growth.   We observed that the E1 strain was able to convert, on average, 34% more malic acid into lactate than the PSU1 strain, regardless of the wine being used. On the other hand, the E1 strain showed a flux rate of fructose-6-phosphate production that was 86% higher than the mannitol production rate, and the internal flux rates increase in the direction of pyruvate production. This coincides with the higher number of OEOE_1708 gene transcripts observed in the E1 strain grown in MaxOeno. This gene encodes for an enzyme fructokinase (EC 2.7.1.4) involved in the transformation of fructose to fructose-6-phosphate. It is necessary to continue studying these genes in order to verify their biological function in O. oeni and their impact on MLF.

overall_design: The selected mutant strain (E1) and its parent strain (E1) were evaluated using synthetic wine called MaxOeno, with 15% v/v ethanol, which was previously developed by our group (Contreras et al., 2018). Both strains were inoculated into 100 ml flasks containing 75 ml of MaxOene at pH 3.5. The medium was inoculated at an optical density of 0.2 (at 600 nm) and the cultures were incubated at 25 °C, without shaking. Samples were taken in the middle of the exponential phase, and RNA was immediately extracted.

first: Ángela

first: Gabriela

last: Diaz

first: Sebastian

last: Mendoza

first: Mauricio

last: Canto

first: Eduardo

last: Agosin


title: Longitudinal Rectal tissue DNA methylation Profiling Identifies Cell-specific Signatures for Disease severity and Outcome in Ulcerative Colitis

status: Public on Dec 01 2022

first: Suresh

last: Venkateswaran

state: Georgia

address: 1760 Haygood Drive, HSRB, Room No: E-250

department: Pediatrics

institute: Emory University

type: Methylation profiling by genome tiling array

summary: Ulcerative colitis is heritable disorder with variable clinical outcome but to date only less than 10% of the disease susceptibility and the disease outcome is explained by IBD (inflammatory bowel disease) associated genetic loci. This missing heritability lay fertile grounds for investigating epigenetics as possible explanation. The aims of the study were to investigate genome-wide DNA methylation of the rectal tissue in an inception cohort of UC at two time points, once at baseline (treatment naïve) and at follow-up to explore how longitudinal DNA methylation influences the disease onset, disease progression and outcome. For this purpose, we profiled DNA methylation within rectal mucosal biopsies of pediatric UC (n=211) and non-IBD control patients (n=85) to perform epigenome-wide association studies (EWAS) of specific cell types (i.e epithelial, immune, and fibroblast), to identify UC specific differences.  We have also performed longitudinal analysis on follow-up samples (n =73), and also additional comparisons were made between patients eventually undergoing colectomy versus those who did not.

overall_design: DNA methylation was assessed in rectal biopsy from pediatric non-IBD controls and patients with Ulcerative colitis at two time points - at diagnosis and follow-up. Rectal biopsy DNA was extracted, bisulfite converted and genome-wide DNA methylation was interrogated using the HumanMethylationEPIC BeadChip (Illumina).

first: Hari

last: Somineni

first: Jason

last: Matthews

first: Varun

last: Kilaru

first: Jeffrey

last: Hyams

first: Lee

last: Denson

first: David

last: Cutler

first: Alicia

last: Smith

first: Karen

middle: N

last: Conneely

first: Subra

last: Kugathasan


title: Chronic CD27-CD70 costimulation promotes type 1-specific polarization of effector Tregs

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Most T lymphocytes, including regulatory T cells, express the CD27 costimulatory receptor in  steady state conditions. There is evidence that CD27 engagement on conventional T  lymphocytes favors the development of Th1 and cytotoxic responses in mice and humans, but  the impact on the regulatory lineage is unknown. In this report, we examined the effect of  constitutive CD27 engagement on both regulatory and conventional CD4+ T cells in vivo, in the  absence of intentional antigenic stimulation. Our data show that both T cell subsets convert into  type 1 effectors, characterized by cell activation, cytokine production, response to IFN-and  CXCR3-dependent migration to inflammatory sites. Our data highlight the role of the  transcription factor Eomes in this process. We conclude that CD27 may regulate the  development of Th1 immunity in peripheral tissues as well as the subsequent switch of the  effector response into long-term memory.

overall_design: We examined the effect of constitutive CD27 engagement on both regulatory and conventional CD4+ T cells in vivo, in the  absence of intentional antigenic stimulation.

first: Natalia

last: Bowakim-Anta

first: Valérie

last: Acolty

last: Azouz

first: Hideo

last: Yagita

first: Oberdan

last: Leo

first: Stanislas

last: Goriely

first: Guillaume

last: Oldenhove

first: Muriel

last: Moser


title: Comparison of the effects of HIIT and  exo-miRNAs upon obesity-associated metabolic dysfunction in HFD mice.

status: Public on Nov 29 2022

city: Barcelona

first: Carlos

last: Castaño

address: Rossello 153

institute: CIBER

summary:
We treated obese mice being fed a high-fat diet with exosomes transfected with a combination of inhibitors of obesity-associated miR-122 and miR-192 and a mimic of exercise-associated miR-133b.
We used microarrays to detail the global changes of gene expression induced by the exosomal treatment in liver, adipose and muscle tissues in comparison with HIIT.

overall_design: C57BL6/J male mice were rendered obese and glucose intolerant after being fed high-fat diet for 10 weeks. These mice were then randomly separated into three groups. One group was injected with transfected exosomes for 4 weeks (EXO). Another group underwent exercise training in parallel (HIIT), whereas a third group was left untreated (HFD). We also used a group of lean mice as controls (CT).

first: Marcelina

last: Parrizas


title: DNA methylation profiling upon treatment with NTX-301 or decitabine in AML cells

city: Daejeon

first: Byungho

last: Lim

address: 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea

country: South Korea

institute: KRICT

summary:
A novel hypomethylating agent NTX-301 is a promising therapeutic agent for AML patients.
To examine its mechanisms of action, we produced methylome data upon treatment with NTX-301 or decitabine (DAC) in MV4-11 cell line.

overall_design: Leukimia cells (MV4-11 and HL-60) were cultured using the RPMI1640 medium. Cells were plated on 10cm dishes at the day before drug treatment, and DMSO, NTX-301 (60nM), and DAC (60nM) were treated during 48h. After extracting genomic DNA and assessing DNA QC,


title: Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma

city: Rehovot

first: Itay

last: Tirosh

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

summary: Head and neck squamous cell carcinoma (HNSCC) includes a large subset of cancers that are driven by the human papilloma virus (HPV) and occur primarily in the oropharynx. Here, we use 10x single cell RNA-seq to profile 70,970 cells from 11 HPV-positive and 5 HPV-negative oropharyngeal tumors in order to uncover diversity in chromosomal aberrations, cellular states and viral gene expression between and within tumors.

overall_design: 16 tumors from treatment-naïve patients were dissociated after surgery and profiled by 10X. For three of the tumors, samples of normal tissue from the tumor margin were additionally profiled separately, and for one sample, a metastatic lymph node was separately profiled. Four samples had were FACS-sorted into CD45+ and CD45- fractions that were profiled separately. Of these, two were profiled using 10x 5'-sequencing. All other samples were profiled using 3' sequencing.

first: Michael

last: Mints


title: Oct1 cooperates with Smad transcription factors to promote mesodermal lineage specification [HiChIP]

status: Public on Nov 26 2022

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

institute: University of Utah

summary: The pathways used by cells to transition between pluripotent and tissue-specific states are incompletely understood. Here we show that the widely-expressed transcription factor Oct1/Pou2f1 activates silent, developmental lineage-appropriate genes to “canalize” developmental progression. Using Oct1 inducible knockout embryonic stem cells, we show that that Oct1 deficiency impairs mesodermal and terminal muscle differentiation in a manner that can be rescued by Oct1 retroviral expression. We show that mesoderm-specific genes are not correctly induced early in the differentiation timecourse. Oct1-deficient cells lose temporal coherence in the induction of lineage-specific genes and show inappropriate developmental lineage branching, resulting in poorly differentiated cells states retaining epithelial characteristics. In embryonic stem cells, Oct1 co-binds with Oct4 to genes critical for mesoderm induction, and continues to bind these genes during differentiation. Oct1 binding events are enriched at the termini of chromatin loops, including loops gained with differentiation. The Utx/Kdm6a histone lysine demethylase also binds to many of these genes, and using a prototypic Pax3 gene we show that Oct1 recruits Utx to remove inhibitory H3K27me3 marks and activate expression. The specificity of the ubiquitous Oct1 protein for mesodermal genes can be explained by cooperative interactions with lineage-driving Smad transcription factors, as we show that Smad and Oct binding sites frequently coexist mesoderm-specific genes, and that Oct1 and Smad3 act cooperatively at the Myog enhancer. Overall, these results identify Oct1 as a key mediator of the induction of mesoderm lineage-specific genes.

overall_design: Parental ESCs are differentatiated toward mesodermal and neuro-ectodermal linegaes (RA) and profiled using Hi-ChIP.

first: Hosiana

last: Abewe

first: Jason

last: Gertz

first: Jelena

last: Perovanovic


title: Oct1 cooperates with Smad transcription factors to promote mesodermal lineage specification [BulkRNAseq7221]

summary: The pathways used by cells to transition from undifferentiated, pluripotent gene expression programs into cell type-specific gene expression programs are incompletely understood. Here we show that the transcription factor Oct1/Pou2f1 recruits histone lysine demethylase complexes to allow for correct induction of silent, developmental lineage-specific genes and “canalize” developmental progression. Using mesodermal differentiation of inducible-conditional Oct1 knockout embryonic stem cells and single-cell gene expression profiling, we show that the potential to progress efficiently through mesodermal development is impaired in the Oct1 deficient condition. Oct1 deficient cells fail to form late presomitic mesoderm and early somite stage populations, and show “leaky” developmental trajectories with inappropriate lineage branching and accumulation of poorly differentiated cells that retain gene expression and metabolic hallmarks of pluripotency. Oct1 directly binds and regulates genes critical for developmental regulation, including genes encoding mesoderm-specific master regulators and components of chromatin regulatory complexes. Cells lacking Oct1 fail to positively resolve gene bivalency and activate gene expression by removing inhibitory H3K27me3 chromatin marks at mesoderm-specific genes. The Oct1 protein interacts with and recruits UTX to lineage-specific bivalent/poised targets, explaining the failure of Oct1 deficient cells to remove H3K27me3. Ectopic Oct1 expression improves the ability of cells to differentiate accurately under mesoderm lineage-inducing conditions.

overall_design: Parental and cKO ESCs are differentatiated using mesodem inducing differentatiation protocol and profiled using bulk RNAseq. Briefly, depleated ESCs were plated on 0.01% gelatin and differentited as previoulsy described in Chal et al. 2015.


title: Oct1 cooperates with Smad transcription factors to promote mesodermal lineage specification [ChIPSeq7221]

overall_design: Embryonic stem cells are differentatiated toward mesodermal lineage and profiled  using ChIPseq. For mesodermal differentiation, depleated ESCs were plated on 0.1% gelatin and diffrentiated as described in Chal et al., 2015.Briefly, cells were differentiated in N2B27medium supplemented with Bmp4 for 2 days, and then switched to DMEM based medium supplemented with Rspo3 and LDN-193189 for 4 days..


title: Oct1 cooperates with Smad transcription factors to promote mesodermal lineage specification [single-cell RNA-seq]

overall_design: Parental and cKO ESCs are differentatiate toward mesodermal lineages and profiled using scRNAseq. Depleated ESCs were plated on 0.1% gelatin and diffrentiated as described in Chal et al., 2015.Briefly, cells were differentiated in N2B27medium supplemented with Bmp4 for 2 days, and then switched to DMEM based medium supplemented with Rspo3 and LDN-193189 for 4 days.


title: Oct1 cooperates with Smad transcription factors to promote mesodermal lineage specification [ChIP-seq]

overall_design: Parental and cKO ESCs are differentatiate toward mesodermal and neuro-ectodermal linegaes (RA) and profiled  using ChIPseq. For mesodermal differentiation, depleated ESCs were plated on 0.1% gelatin and diffrentiated as described in Chal et al., 2015.Briefly, cells were differentiated in N2B27medium supplemented with Bmp4 for 2 days, and then switched to DMEM based medium supplemented with Rspo3 and LDN-193189 for 4 days.. For RA differentiation,  depleated ESCs were plated on 0.01% gelatin and differentited using DMEM supplemented with 1.5ug/ml final retionoic acid, NEAA, L-glutamine, Pen/Strep.


title: Oct1 cooperates with Smad transcription factors to promote mesodermal lineage specification [bulk RNA-seq]

overall_design: Parental and cKO ESCs are differentatiated using RA differentatiation protocol and profiled using bulk RNAseq. Briefly, depleated ESCs were plated on 0.01% gelatin and differentited using DMEM supplemented with 1.5ug/ml final retionoic acid, NEAA, L-glutamine, Pen/Strep.


title: Bakuchiol and ethyl (linoleate/oleate) synergistically modulate endocannabinoid tone in keratinocytes and repress inflammatory pathway mRNAs

status: Public on Nov 23 2022

city: Dallas

first: William

middle: R

last: Swindell

state: TX

address: 6201 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern Medical Center

summary: The endocannabinoid (eCB) system plays an active role in epidermal homeostasis. Phytocannabinoids such as CBD modulate this system but also act through eCB-independent mechanisms. This study evaluated effects of CBD, bakuchiol (BAK) and ethyl (linoleate/oleate) (ELN) in keratinocytes (KCs) and reconstituted human epidermis (RHE). Molecular docking simulations showed that each compound binds the active site of the eCB carrier fatty-acid-binding protein 5 (FABP5). However, BAK and ethyl linoleate bound this site with highest affinity when combined 1:1 (w/w) and in vitro assays showed that BAK+ELN most effectively inhibited FABP5 and fatty acid amide hydrolase (FAAH). In TNF-stimulated KCs, BAK+ELN reversed TNF-induced expression shifts and uniquely down-regulated type I interferon genes and PTGS2 (COX-2). BAK+ELN also repressed expression of genes linked to KC differentiation but up-regulated those associated with proliferation. Finally, BAK+ELN inhibited cortisol secretion in RHE skin (not observed with CBD). These results support a model in which BAK and ELN synergistically interact to inhibit eCB degradation, favoring eCB mobilization and inhibition of downstream inflammatory mediators (e.g., TNF, COX-2, type I interferon). Topical combination of these ingredients may thus enhance cutaneous eCB tone or potentiate other modulators, suggesting new ways to modulate the eCB system for innovative skincare product development.

overall_design: We generated 12 samples with treatments corresponding to non-treated control KCs (CTL, n = 2), TNF-treated KCs (TNF, n = 2), KCs treated with TNF and CBD (TNF+CBD, n = 2), KCs treated with TNF and bakuchiol (TNF+BAK, n = 2), KCs treated with TNF and ethyl (linoleate/oleate) (TNF+ELN, n = 2), and KCs treated with TNF and 1:1 (w/w) combination of bakuchiol and ethyl (linoleate/oleate) (BAK+ELN, n = 2).

first: Krzysztof

last: Bojanowski

first: Ratan

last: Chaudhuri


title: Oct1 cooperates with Smad transcription factors to promote mesodermal lineage specification

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

overall_design: Refer to individual Series


title: Latent Membrane Protein 1 and macrophage-derived TNFα synergistically activate and mobilize invadopodia to drive invasion of nasopharyngeal carcinoma

status: Public on Nov 22 2022

city: Hong Kong

first: Wingchung

last: Tang

state: Hong Kong

address: Rm321, 3/F, Cancer Center, Prince of Wales Hospital, Sha Tin

country: Hong Kong

institute: CUHK ACP

summary:
To investigate the effect of TNFα and EBV on invadopodia formation, we treated the EBV-positive and -negative NPC43 cells seeded on gelatin with or without TNFα
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different groups

overall_design: Comparative gene expression profiling analysis of RNA-seq data for -positive and -negative NPC43 EBV and the TNFα-treated counterpart


title: Transcriptome, Biochemical and Phenotypic Analysis of the Effects of a Precision Engineered Biostimulant for Inducing Salinity Stress Tolerance in Tomato

status: Public on Nov 16 2022

city: Tralee

first: Oscar

last: Goñi

address: South Campus Kerry

country: Ireland

institute: Munster Technological University

summary: Salinity stress is a major problem affecting plant growth and crop productivity. While plant biostimulants have been reported to be an effective solution to tackle salinity stress in different crops, the key genes and metabolic pathways involved in these tolerance processes remain unclear. This study focused on integrating phenotypic, physiological, biochemical and transcriptome data obtained from different tissues of Solanum lycopersicum L. plants (cv. Micro-Tom) subjected to a saline irrigation water program for 61 days (EC: 5.8 dS/m) and treated with a combination of protein hydrolysate and Ascophyllum nodosum-derived biostimulant, namely PSI-475. The biostimulant application was associated with the maintenance of higher K+/Na+ ratios in both young leaf and root tissue and the overexpression of transporter genes related to ion homeostasis (e.g., NHX4, HKT1;2). A more efficient osmotic adjustment was characterized by a significant increase in relative water content (RWC), which most likely was associated with osmolyte accumulation and upregulation of genes related to aquaporins (e.g., PIP2.1, TIP2.1). A higher content of photosynthetic pigments (+19.8% to +27.5%), increased expression of genes involved in photosynthetic efficiency and chlorophyll biosynthesis (e.g., LHC, PORC) and enhanced primary carbon and nitrogen metabolic mechanisms were observed, leading to a higher fruit yield and fruit number (47.5% and 32.5%, respectively). Overall, it can be concluded that the precision engineered PSI-475 biostimulant can provide long-term protective effects on salinity stressed tomato plants through a well-defined mode of action in different plant tissues.

overall_design: The main goal of the experiment is to compare the transcriptomes between treated (PSI-475) and control (Untreated) groups of two different tomato plant tissues (Leaf and Root)

first: Elomofe

last: Ikuyinminu

first: Shane

last: O’Connell

first: Łukasz

last: Łangowski


title: Neddylation is required for perinatal cardiac development through stimulation of metabolic maturation

status: Public on Nov 19 2022

city: Augusta

first: Jianqiu

last: Zou

address: 1460 Laney Walker Blvd

department: VBC

country: USA

institute: Augusta University

summary: The heart undergoes significant structural, metabolic, gene expression and functional alterations during the perinatal to postnatal transition. While recent studies have identified multiple epigenetic and transcriptional regulators of cardiac maturation, post-transcriptional mechanisms regulating this process remain poorly understood. Neddylation is a post-translational modification that conjugates a small ubiquitin-like protein, NEDD8, to protein substrates via an E1-E2-E3 enzymatic cascade. The goal of this study was to define the role of neddylation in perinatal cardiac development and cardiac maturation. Neddylation was inhibited in adult mouse hearts by cardiac-specific deletion of NAE1 gene, a regulatory subunit of NEDD8 E1 enzyme, or in neonatal cardiomyocytes (CMs) with a pharmacological neddylation inhibitor, MLN4924. The impact on cardiac transcriptome, metabolism, maturation and function was assessed. Mosaic deletion of NAE1 in ~40% neonatal CMs disrupted aspects of maturation, including transverse-tubule formation, cellular hypertrophy and fetal/adult isoform switching, whereas deletion of NAE1 in over 80% CMs led to rapid development of cardiomyopathy and heart failure. Transcriptome analysis demonstrated an association of metabolic derangement with immature cardiomyocyte signature. Biochemical, ultrastructural and metabolomics analyses confirmed downregulation of fatty acid and oxidative phosphorylation genes, deficits in fatty acid utilization, mitochondrial dysfunction, and significantly altered metabolic profiles in NAE1-deficient hearts or MLN4924-treated neonatal CMs. Mechanistically, we found that HIF1α, a transcription factor known to promote glycolysis and suppress oxidative metabolism, is a putative NEDD8 target. Inhibition of neddylation resulted in HIF1α accumulation and activation, which contributed to diminished fatty acid utilization. Taken together, we conclude that neddylation plays a crucial role in CM maturation and postnatal cardiac development through sustaining the glycolytic to oxidative metabolic switch in perinatal hearts.

overall_design: We analyzed the transcriptomes of αMHCCre-driven neonatal NAE1 knockout hearts (NAE1CKO) with RNA-seq of 4 knockout ventricles versus 4 wildtypes collected at the age of P1.

first: Wenjuan

last: Wang

first: Juan

last: Ayala

first: Jie

last: Li

first: Huabo

last: Su


title: Functional T cells are capable of supernumerary cell division and longevity [RNA-seq]

status: Public on Nov 17 2022

city: Minneapolis

first: David

last: Masopust

state: MN

address: 2101 6th St SE

institute: University of Minnesota

summary: Differentiated somatic mammalian cells putatively exhibit species-specific division limits that impede cancer but may constrain lifespans. To provide immunity, transiently stimulated CD8 T cells undergo unusually rapid bursts of numerous cell divisions, then form quiescent long-lived memory cells that remain poised to reproliferate in response to subsequent immunological challenges. Here, we addressed whether T cells are intrinsically constrained by chronological or cell division limits. We activated mouse T cells in vivo using acute heterologous-prime-boost-boost vaccinations, transferred expanded cells to new mice, and then repeated that process iteratively. Over a period of 10 years (greatly exceeding the mouse lifespan) and 51 successive immunizations, T cells remained competent to respond to vaccination. Cells did require sufficient rest between stimulation events. Despite demonstrating the potential to expand the starting population at least 10^40-fold, cells did not show loss of proliferation control and results were not due to contamination with young cells. Persistent stimulation by chronic infections or cancer can result in a well-described transcriptional program that results in T cell proliferative senescence, functional exhaustion, and death. We found that while iterative acute stimulations also induced sustained expression and epigenetic remodeling of common exhaustion markers, including PD-1 and Tox, these cells retained the capacity to proliferate, execute antimicrobial functions, and form quiescent memory cells. These observations provide a model to better understand memory cell differentiation, exhaustion, and aging, and show that functionally competent T cells can retain the potential for extraordinary population expansion and longevity well beyond their organismal lifespan.

overall_design:
mRNA profiles of sorted N-specific memory T cells upon 1,3,6,9,18,27,30,39, and 45 immunizations

27-ary, 30ary, 39-ary, and 45-ary samples are from a single cohort. Senary and 18-ary samples are from a trailing cohort, and nonary samples are from a different trailing cohort. Cohort details are listed with individual samples.

first: Andrew

last: Soerens

first: Marco

last: Kuenzli


title: Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci [scRNA-seq]

status: Public on Nov 21 2022

city: Wuhan

first: Junpeng

last: Zhan

address: 1 Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

summary: The anther-enriched phased, small interfering RNAs (phasiRNAs) play vital roles in regulating male fertility in grass species. The long non-coding precursors of phasiRNAs are products of RNA polymerase II and are likely regulated by transcription factors (TFs). A few putative transcriptional regulators of the 21- or 24-nucleotide phasiRNA loci (i.e., 21- or 24-PHAS loci) have been identified in maize (Zea mays), but whether any of the individual TFs or TF combinations are sufficient to activate the PHAS loci is unclear. Here, we identified the temporal gene coexpression networks (modules) associated with maize anther development, including two modules highly enriched for the 21- or 24-PHAS loci. Comparisons of these coexpression modules and gene sets dysregulated in several reported male sterile TF mutants revealed new insights into the timing of activities of the TFs, including antagonistic roles for OUTER CELL LAYER 4 and Male sterile 32. Trans-activation assays of individual TFs using bulk-protoplast RNA sequencing (RNA-seq) showed that two of the TFs coexpressed with 21-PHAS loci could activate several 21-nt phasiRNA pathway genes, but none was sufficient to activate 21-PHAS loci. Screens for combinatorial activities of these TFs and, separately, the recently reported putative transcriptional regulators of 24-PHAS loci using single-cell (protoplast) RNA-seq, did not detect reproducible activation of 21-PHAS or 24-PHAS loci. Collectively, our results suggest that the endogenous transcriptional machineries and/or chromatin states in the anthers are necessary to activate reproductive PHAS loci. Nonetheless, the single-cell RNA-seq approach shows potential for future studies of combinatorial activities of TFs.

overall_design: Single-cell ene expression profiling of maize leaf protoplasts ectopically expressing putative transcriptional regulators of anther-enriched eproductive phasiRNAs

first: Lily

last: O'Connor

first: D

middle: B

last: Marchant

first: Chong

last: Teng

first: Virginia

last: Walbot

first: Blake

middle: C

last: Meyers


title: Loss of p53 enhances the tumor-initiating potential and drug resistance of clonogenic multiple myeloma cells

status: Public on Nov 15 2022

city: Austin

first: Yu-Tai

last: Chang

state: Texas

address: 1601 Trinity St Bldg B

department: Livestrong Cancer Institutes

institute: UT Austin Dell Medical School

summary: To understand the molecular and cellular impact of p53 loss on gene expression profile of multiple myeloma cells, we generated isogenic pairs of TP53 wild-type and knockout cells by CRISPR/Cas9. We then performed RNAseq analysis using data obtained from RNA-seq of three p53-KO clones and one scrambled control cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MM.1S CRISPR p53-KO cells (A7, B6, B16 clones) and its non-targeted scrambled control (Scr) cells.

first: William

last: Matsui

first: Jeanne

last: Kowalski-Muegge


title: Porcine oocytes matured in a chemically defined medium are transcriptionally active

status: Public on Nov 11 2022

city: Liběchov

first: Matej

last: Murín

state: Central Bohemia

address: Rumburská, 89

department: Laboratory of Developmental Biology

country: Czech Republic

institute: Institute of Animal Physiology and Genetics CAS

summary: The statement that fully-grown porcine oocytes are transcriptionally quiescent is not as strong as before. Currently, we know that there is a difference in the transcription profile of germinal vesicle (GV) and metaphase II (MII) oocytes. The goal of our study was to compare the transcription profile of GV, germinal vesicle breakdown (GVBD), metaphase I (MI), and metaphase (MII) oocytes cultivated in a chemically defined, FLI medium. Oocytes were sequenced and subsequently validated using quantitative reverse transcription polymerase chain reaction (RT-qPCR).

overall_design: Total RNA was isolated from denuded porcine oocytes from 4 experimental groups. RNA libraries were prepared and sequenced using RNAseq.

last: Murin

first: Lucie

last: Nemcova

first: Alexandra

last: Bartkova

first: Ahmed

last: Gad

first: Andrea

last: Lucas-Hahn

first: Frantisek

last: Strejcek

first: Radek

last: Prochazka

first: Jozef

last: Laurincik


title: Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament

status: Public on Nov 20 2022

city: Lexington

first: Oliver

last: Vöcking

state: KY

address: 675 Rose Street

institute: University of Kentucky

summary: Anterior segment dysgenesis (ASD), resulting in vision impairment, stems from maldevelopment of anterior segment (AS) tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells (POM).  POM cells specify into anterior segment mesenchyme (ASM) cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS

overall_design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development, Tg[foxc1b:GFP], we isolated GFP+ ASM cells at several developmental timepoints (48-144hpf) and performed single cell RNA sequencing

first: Jakub

last: Famulski


title: The microbiota influences lateral root formation through ethylene response activation

status: Public on Oct 31 2022

city: Loughborough

first: Gabriel

last: Castrillo

address: Nr Loughborough

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

summary: To identify the mechanism of how the microbiota induces lateral root development independently of auxin signalling, we performed a transcriptional analysis using roots of wild type plants and lateral root mutants arf7 arf19, nph4-1, lbd16-1, and gnom184, in mono-association with a selection of 16 bacteria able to restore the lateral root formation in the mutants used.

overall_design: Comparative gene expression profiling analysis and hierarchical gene filtering of RNA-seq data for roots of wild type plants and lateral root mutans grown axenically and those exposed to each individual bacterium. We used three independent biological replicas per treatment and we repeated this experiment twice.

first: Isai

last: Salas-Gonzalez


title: Highly efficient generation of blastocyst-like structures from mouse totipotent blastomere-like cells

status: Public on Nov 08 2022

city: Guangzhou

first: xuzhao

last: zhai

address: Kaiyuan avenue

institute: Guangzhou Laboratory

summary: Mammalian embryogenesis begins with a totipotent zygote. Early embryogenesis can be recapitulated by aggregated extended pluripotent stem cells (EPSCs) in a 3D culture system. However, the efficiency of generating blastoids is low and whether other reported totipotent stem cells retained a similar capacity remains unknown. Here we show that spliceosomal repressed totipotent blastomere-like cells (TBLCs) form blastocyst-like structures when aggregated in 3D microwells with around 80% efficiency. TBLC-blastoids resemble blastocysts in morphology and cell-lineage allocation, show similar transcriptional profile with natural blastocysts and contain more TE cells and fewer undefined intermediate cells compared to blastoids from EPSCs. Moreover, TBLC-blastoids can develop beyond the implantation stage in vitro and induce decidualization after transferred into uterus. In summary, we supply an alternative cell type to generate ameliorated blastoids highly efficiently for studying early mouse embryogenesis.

overall_design: RNA-seq were performed on mESCS and mCMG-TBLCs with mCMG  ESCs in ES medium plus 2.5 nM PlaB on feeders for over 6 passages; scRNA-seq were performed on TBLC-blastoids.

first: P

last: Zhang

first: X

last: Zhai

first: B

last: Huang

first: M


title: Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates [scATAC-Seq 2]

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: Longitudinal scATAC-seq  from LCMV-specific P14 CD8 T cells in LCMV-Armstrong and LCMV-Clone 13 infection

overall_design: LCMV-specific P14 cells were sorted from mice infected with LCMV-Arm or LCMV-Cl13 on days 8, 15, or 30 post infection. An additional group of mice was treated with anti-PDL1 every three days starting at day 16; cells were sorted at day 30. scATAC-seq  libraries were prepared using 10x Genomics kits.

first: Josephine

last: Giles

last: Wherry


title: IRX5 promotes DNA damage repair and activation of hair follicle stem cells

status: Public on Nov 01 2022

city: Irvine

first: Jefferson

middle: K

last: Chen

address: UC Irvine

institute: UC Irvine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: The EMT transcription factor ZEB1 governs a fitness-promoting but vulnerable DNA replication stress response - Gene expression profile at single cell level of routinely cultured MDA-MB-231 cells (Sort-Seq)

status: Public on Nov 07 2022

city: Erlangen

first: Harald

last: Schuhwerk

address: Glückstrasse 6

country: Germany

summary: Cancer cell lines in routine culture are considered as a fairly homogeneous population, but heterogeneity  can readily be observed by imunofluorescene microscopy and other single-cell techniques. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of MDA-MB-231 cells in routine culture.

overall_design: Routinely cultured MDA-MB-231 cells, plated randomly as single cells into commercially available 384-well capture plates (Sort-Seq Platform, Single Cell Discoveries, Utrecht, NL) by FACS. Empty wells were included as controls.


title: Rapid changes in transcriptomic profile and mitochondrial function in human soleus muscle after three-day dry immersion

status: Public on Nov 02 2022

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

summary: We aimed to explore the effect of the 3-day dry immersion - a model of physical unloading - on mitochondrial function, transcriptomic and proteomic profiles in a slow-twitch m. soleus of six healthy females. We registered that a marked reduction (25-34%) in the ADP-stimulated respiration in permeabilized muscle fibers was not accompanied by a decrease in the content of mitochondrial enzymes (mass spectrometry-based quantitative proteomics), hence it is related to the disruption in regulation of respiration. We detected a widespread change in the transcriptomic profile (RNA-seq) upon dry immersion. Down-regulated mRNAs were strongly associated with mitochondrial function, as well as with lipid metabolism, glycolysis, insulin signaling, and various transporters. Despite the substantial transcriptomic response, we found no effect on the content of highly abundant proteins (sarcomeric, mitochondrial, chaperon and extracellular matrix-related, etc.) that may be explained by long half-life of these proteins. We suggest that during short-term disuse the content of some regulatory (and usually low abundant) proteins such as cytokines, receptors, transporters, transcription regulators is largely determined by its mRNA concentration. These mRNAs revealed in our work may serve as putative targets for the future studies aimed at developing the approaches for the prevention of muscle deconditioning-induced by disuse.

overall_design: Six healthy females (25-39 years old [range]; median height 1.64 m and interquartile range [1.62-1.70] m; body mass 64.9 [60.8-67.9] kg; BMI 22.39 [20.19-24.59] kg/m2) were exposed to 3 days of “dry” immersion. Samples from the soleus muscle were taken prior to and after “dry” immersion from the left leg using a modified Bergström biopsy needle with manual suction under local anesthesia (2 ml 2% lidocaine). Both biopsies were taken on the 10-th day of the menstrual cycle. Strand-specific libraries were prepared and sequenced (75 nucleotides, single end) by NextSeq 550 (Illumina, USA).

first: Daniil

last: Popov

last: Makhnovskii


title: Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates


title: Maximal interferon induction in the absence of influenza NS1 is infrequent owing to requirements for replication and export

status: Public on Oct 27 2022

city: San Diego

first: Alistair

middle: Brian

last: Russell

state: CA

address: 9500 Gilman Dr,

department: Biological Sciences

institute: University of California, San Diego

summary: Influenza A virus exhibits high rates of replicative failure due to a variety of genetic defects. As such, most viral particles cannot complete the life cycle. However, despite this failure, this virus is incredibly successful in the suppression of innate immune detection and the production of interferons, succeeding at remaining undetected in >99% of cells in tissue-culture models of infection. As the same variation that leads to replication failure can, by chance, inactivate the major innate immune antagonist in influenza A virus, NS1, what features prevent these events from triggering massive amounts of interferon production? By studying how genetic and phenotypic variation in a viral population lacking NS1 correlates with interferon production, we have built a model of the "worst-case" failure from an improved understanding of the steps at which NS1 acts in the viral lifecycle to prevent triggering of an innate immune response. In doing so, we find that NS1 prevents the detection of de novo innate immune ligands, and protects against both defective viral genomes, bearing large deletions, and viral products exported from the nucleus. Taken together, the highest level of stimulation we observe ( 97% of infected cells), requires a high level of replication in the presence of defective viral genomes with NS1 and NS1 alone from the NS segment bearing an inactivating mutation. This is incredibly unlikely to occur within the standard variation found within a viral population, and would generally require direct, artificial, intervention to achieve at an appreciable rate. Thus from our study, we procure at least a partial explanation for the seeming contradiction between high rates of replicative failure and the rarity of the interferon response to influenza infection.

sample_organism:
Homo sapiens
Canis lupus familiaris
Influenza A virus (A/WSN/1933(H1N1))

overall_design: A549 cells infected with either wild-type, or NS1stop, influenza A virus were processed, mixed with canine cells, fixed with methanol, and analyzed by scRNAseq. Additionally, viral populations bearing a large number of defective particles were used to infect interferon lambda reporter A549 cells, sorted on interferon production, and vRNA was sequenced to look for variation that co-enriches with interferon induction


title: Effect of FSCN1 gene inactivation in the H295R cell line

status: Public on Oct 25 2022

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

institute: IPMC

summary:
The actin-bundling protein fascin (FSCN1) is overexpressed in aggressive adrenocortical carcinoma (ACC) and represents a reliable prognostic indicator. We investigated the effects of FSCN1 inactivation by CRISPR/Cas9 in ACC H295R cells on global gene expression profiles in those cells.
We  performed gene expression profiling analysis using data obtained from RNA-seq of 2 different H295R control clones and 2 different FSCN1 KO clones (2 biological replicates for each  clone).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and FSCN1 KO H295R clones.

last: Lalli


title: Base Editing Correction of a Hypertrophic Cardiomyopathy-Causing MYH7 Mutation in Human Cardiomyocytes and Humanized Mice

city: Dallas

first: Andreas

last: Chai

address: 6000 Harry Hines Blvd.

department: Molecular Biology

summary: The most common form of genetic heart disease is hypertrophic cardiomyopathy (HCM), which is caused by mutations in cardiac sarcomeric genes and leads to abnormal heart muscle thickening. Complications of HCM include heart failure, arrhythmia, and sudden cardiac death. The dominant-negative c.1208 G>A (p.R403Q) mutation in b-myosin (MYH7) is a common and well-studied mutation that leads to increased cardiac contractility and HCM onset. Here we identify an adenine base editor (ABE) and single-guide RNA system that can efficiently correct this human pathogenic mutation with minimal off-target and bystander editing. We show that delivery of base editing components rescues pathological manifestations of HCM in iPSC-cardiomyocytes derived from HCM patients and in a humanized mouse model of HCM. Our findings demonstrate the use of base editing to treat inherited cardiac diseases and prompt the further development of ABE-based therapies to correct a variety of monogenic mutations causing cardiac disease.

overall_design: The objective of this study was to determine whether base editing correction of a pathogenic HCM-causing mutation could prevent the onset of HCM pathological features in human cardiomyocytes and a humanized mouse model. In a humanized mouse model containing the mutation Myh6 R403Q, a dual AAV9 system was used to deliver the base editing components to cardiomyocytes and changes in heart function, dimensions, and transcriptomics were measured. CM nuclei were collected from WT, HCM mice, and ABE-treated HCM mice and transcriptomes were profiled by RNA-seq

first: Kenian

first: Eric

last: Olson


title: RNA-seq of injured mouse hearts depleted for myofibroblast Yap and Wwtr1

status: Public on Oct 29 2022

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

summary: A myofibroblast specific tamoxifen inducible Cre was used to assess the role of Yap and Wwtr1 in the mouse heart after myocardial infarction

overall_design: We implemented a Cre-lox system whereby inducible Cre expressed under the myofibroblast specific Periostin promoter is crossed with Yap and Wwtr1 floxed animals, facilitating inducible depletion of Yap (both alleles) and Wwtr1 (one allele). Mice were siblings with floxed Yap/Wwtr1 alleles and either a copy of MerCreMer under the endogenous periostin promote or wildtype Periostin. Permenant ligation of the left anterior descending artery was used to produce a surgical myocardial infarction. Mice were administered tamoxifen citrate diet ad libitum immediately after surgery to promote excession of myofibroblast yap and left ventricles were collected 4 days post injury.

last: Patterson

first: C

last: CO'Meara


title: A skeletal-muscle senescence blueprint defines an aged-like inflamed niche that inhibits regeneration over lifetime [scRNA-seq]

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

institute: UPF

summary: A new sorting protocol was used to identify and isolate different senescent cell types from damaged muscles of young and geriatric mice. Analysis revealed conservation of two universal senescence hallmarks (inflammation and fibrosis) across cell type, regeneration time, and aging, while cell identity traits were preserved. Senescent cells create an “aged-like” inflamed niche, mirroring inflammation-associated with aging (inflammaging), that arrests stem cell proliferation and regeneration.

overall_design: Muscles were mechanically disaggregated and incubated in Dulbecco's Modified Eagle's medium (DMEM) containing liberase (Roche) and dispase at 37°C with agitation for 1-2 hours. When required, SPiDER-b-gal reagent (Dojindo) was added during the second hour. The supernatant was then filtered and cells were incubated in lysis buffer (BD Pharm Lyse) for 10 min on ice, resuspended in PBS with 2.5% fetal bovine serum (FBS), and counted. BV711-conjugated anti- CD45 (BD), APC-Cy7-conjugated anti F4/80 (Biolegend), PE- conjugated anti-a7-integrin (Ablab), APC-conjugated anti-CD31 (eBioscience) and PE-Cy7-conjugated anti-Sca-1 (Biolegend) antibodies were used to isolate MCs (CD45+ and F4/80+), SCs (a7-integrin+, CD45+, F4/80+ and CD31+) and FAPs (Sca-1+, MCs CD45+, F4/80+, a7-integrin+ and CD31+). PE-Cy7-conjugated anti-CD45 antibody (Biolegend) was used to isolate CD45 positive and negative populations. SPiDER-b-gal (SPiDER) was employed to isolate senescent cells (SPiDER+) from non-senescent cells (SPiDER–) of each cell type. Isolated cells were subjected to single-cell RNA sequencing. 1 and 2 are biological replicates.

first: Victoria

last: Moiseeva

first: Lai

last: Yiwei

first: Juan

last: An

first: Andrés

last: Cisneros

first: Oleg

last: Deryagin

first: Giacomo

last: Volpe

first: Miguel

last: Esteban

first: Pura

last: Munoz-Canoves