title: TGF-β uncouples glycolysis and inflammation in macrophages and controls the survival during sepsis [LPS]

city: Bethesda

first: Thierry

last: Gauthier

state: MD

address: 30 convent drive (NIH)

institute: NIH/NIDCR

summary: The mechanisms by which macrophage metabolism is regulated and the effects of metabolism on diseases remain largely unknown. We show here that TGF-β regulates the glycolysis of macrophages independently of inflammatory cytokine production, and thus affects the survival in experimental sepsis. Specifically, TGF-β increased expression and activity of phosphofructokinase-1 liver type (PFKL) in macrophages and thus promoted their glycolysis during cell activation, yet paradoxically suppressed the production of proinflammatory cytokines in the same macrophages. The upregulation of glycolysis was mediated by a mTOR-c-MYC dependent pathway, whereas the inhibition of cytokines was ascribed to the activation of SMAD3 and a downregulated activation of the pro-inflammatory transcription factors AP-1, NFkB and STAT1. Importantly, in an LPS-induced sepsis model, TGF-β enhancement of macrophage glycolysis led to a decreased survival in mice, which was associated with increased blood coagulation. Analysis of cohorts of patients with sepsis and covid-19 revealed that the expression of PFKL, TGF-b receptors TGFBRI and coagulation factor F13A1 in myeloid cells positively correlated with the progression of the disease. Thus, TGF-β is emerging as a critical cytokine regulating macrophage metabolism and could serve as a therapeutic target in patients with sepsis.

overall_design: Peritoneal elicited macrophages treated in vitro with LPS for 6h or TGF for 24h followed by LPS for 6h

first: Chen

last: Yao

first: Tyrone

last: Dowdy

first: Wenwen

last: Jin

first: Yun-Ji

last: Lim

first: Liliana

last: Patiño

last: Liu

first: Shannon

middle: I

last: Ohlemacher

first: Andrew

last: Bynum

first: Rida

last: Kazmi

first: Carole

last: Bewley

first: Mladen

last: Mitrovic

first: Daniel

last: Martin

first: Robert

last: Morell

first: Mioara

last: Larion

first: Roxane

last: Tussiwand

first: John

last: O'Shea

first: WanJun

last: Chen


title: Gene regulatory networks underlying human microglia maturation

status: Public on Aug 14 2023

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

country: USA

institute: University of California, San Diego

type: Expression profiling by high throughput sequencing

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: TGF-β uncouples glycolysis and inflammation in macrophages and controls the survival during sepsis [STIM]

first: Thierry

last: Gauthier

overall_design: Peritoneal elicited macrophages treated in vitro with TGFB, IL4, IL10 or LPS for 24 h

first: Chen

last: Yao

last: Dowdy

middle: C

middle: A

middle: J


title: TGF-β uncouples glycolysis and inflammation in macrophages and controls the survival during sepsis


title: TGF-β uncouples glycolysis and inflammation in macrophages and controls the survival during sepsis [ATAC-Seq]

overall_design: Peritoneal elicited macrophages treated in vitro with or without TGFB for 24h followed by LPS for 24h

first: Tyrone

first: Wenwen

last: Jin

last: Lim

last: Patiño


title: Single-cell transcriptomics reveals prominent expression of IL-14, IL-18 and IL-32 in psoriasis

city: Leipzig

first: Maria

last: Schmidt

address: Härtelstr. 16-18

country: Germany

institute: IZBI

summary: Several different immune-activated cell types with particular cytokine patterns are identified such as keratinocytes, T helper cells, cytotoxic T cells, dendritic cells, macrophages, fibroblasts, and endothelial cells. The expression of well-known pathogenic factors such as TNF-α, IL-8 (CXCL8), L-23 and IL-17 is confirmed in different inflammatory cells. Furthermore, IL-14 (TXLNA; alpha-taxilin), IL-18 and IL-32 are identified as less well-known, and putative new pathogenic factors. Prominent expression of IL-18 is found in keratinocytes, macrophages and Langerhans cells, prominent IL-32 is found in T helper and regulatory T cells, IL-14 is mainly expressed by keratinocytes, fibroblasts and macrophages. Validation of gene expression is performed by ISH of human skin samples. In a murine model of psoriasis, IL-14 and IL-18 are significantly higher expressed in psoriasis-like skin lesions than in normal skin. In an analysis of serum samples from psoriasis patients, IL-18 shows higher expression in psoriasis patients compared to controls, and serum levels in psoriasis responded to treatment with IL-17 inhibitors.

overall_design: Human skin biopsies of lesional skin from patients suffering from plaque-type psoriasis were isolated using the Whole Skin Dissociation Kit (Miltenyi, Gladbach, Germany) and analyzed using 10x Genomics RNAseq.

first: Bennet

last: Frost

first: Benjamin

last: Klein

first: Henry

last: Loeffler-Wirth

first: Knuth

last: Krohn

first: Timo

last: Reidenbach

first: Hans

last: Binder

first: Antonia

last: Stubenvoll

first: Jan

last: Simon

first: Anja

last: Saalbach

first: Manfred

last: Kunz


title: Brain transcriptome of mice infected with T. gondii parasites

city: Pittsburgh

first: Jon

middle: P

last: Boyle

state: PA

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

summary: Mice were infected with up to 250,000 tachyzoites of T. gondii VEG strain parasites genetically engineered to be deficient in either the ROCY1 gene (TGVEG_311100) or the BFD1 gene (TGVEG_200385).  Mice were infected intraperitoneally and monitored using in vivo bioluminescence imaging. Mice were sacrificed at either 4 weeks or 9 weeks post infection as indicated, and RNA was isolated from their brains and transcript abundance was determined using RNAseq.

sample_organism:
Toxoplasma gondii
Mus musculus

platform_organism:
Toxoplasma gondii
Mus musculus

overall_design: 4-6 biological replicates for the 4 week samples and only 1-2 replicates for the 9 weeks samples.

first: Sarah

middle: S

last: Borrelli

first: Leah

middle: F

last: Cabo


title: In vitro analysis of pH responsiveness of T. gondii and H. hammondi sporozoites, and of T. gondii tachyzoites lacking either the BFD1 or the ROCY1 gene.

summary: There are two experiments included in this particular GEO accession: For the first, freshly excysted sporozoites of T. gondii VEG or H. hammondi Amer1 were put into culture for 2 days, and then either allowed to continue growth in control (pH 7.2, 5% C02, 10% FCS) or high pH, bradyzoite-inducing (pH 8.2, low C02, 1% FCS) conditions for 3 days and then harvested for RNAseq analysis. In the second, T. gondii strain VEG was genetically manipulated to ablate either the ROCY1 gene (TGVEG_311100) or the BFD1 gene (TGME49_200385) and then compared to Wild Type VEG in a bradyzoite induction assay. Specifically, each parasite line was grown for 2 days in control conditions (same as above) or bradyzoite induction conditions (same as above) and then harvested for RNAseq.  Data were mapped to the parasite genomes transcript abundance was normalized and calculated using DESeq2.

sample_organism:
Toxoplasma gondii
Hammondia hammondi

platform_organism:
Toxoplasma gondii
Hammondia hammondi

overall_design: For the first experiment each condition has three biological replicates, where each biological replicate was a distinct well of a 24 well plate.  For the second experiment each condition has between 2 and 3 biological replicates, where each biological replicate is a separate well of a 24 well plate.


title: Cell type-specific role of CBX2-cPRC1 at the onset of spermatogonial differentiation [RNA-seq]

city: Ithaca

first: Jongmin

last: Kim

state: NY

address: 930 Campus Road

department: Biomedical Sciences

institute: Cornell University

summary: Polycomb group (PcG) proteins maintain the repressed state of lineage-inappropriate genes and are therefore essential for embryonic development and adult tissue homeostasis. One critical function of PcG complexes is modulating chromatin structure. Canonical Polycomb repressive complex 1 (cPRC1), particularly its component CBX2, can compact chromatin and phase separate in vitro. These activities are hypothesized to be critical for forming a repressed physical environment in cells. While much has been learned by studying these PcG activities in cell culture models, it is largely unexplored how cPRC1 regulates adult stem cells and their subsequent differentiation during tissue homeostasis in living animals. Here we show that CBX2 is upregulated as spermatogonial stem cells differentiate and is required in the differentiating spermatogonia of the male germ line. CBX2 forms condensates, similar to previously described Polycomb-bodies, that co-localize with target genes that are repressed in differentiating spermatogonia. Single cell analyses of mosaic Cbx2 mutant testes show CBX2 is specifically required to produce differentiating, A1 spermatogonia. Furthermore, the domain of CBX2 responsible for compaction and phase separation is needed for the long-term maintenance of male germ cells in the animal. These results emphasize that the regulation of chromatin structure by CBX2 at a specific stage of spermatogenesis is critical for the continued production of sperm and, ultimately, the transmission of genetic material to the next generation.

overall_design: Goal#1) Identify changes in gene expression by inducible Cbx2 deletion by Tamoxifen injections. FACS-sorted c-KIT(+) spermatogonia were profiled by RNA-seq. Goal#2) Identify changes in gene expression by KR-to-A mutations in the CaPS domain of Cbx2. FACS-sorted c-KIT(+) spermatogonia were profiled by RNA-seq.

first: Robert

last: Kingston


title: KaryoCreate: a CRISPR-based technology to study chromosome-specific aneuploidy by targeting human centromeres

city: New York

first: Joseph

middle: Charles

last: Mays

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU School of Medicine

summary: Aneuploidy, the presence of chromosome gains or losses, is a hallmark of cancer and congenital syndromes. Here, we describe KaryoCreate (Karyotype CRISPR Engineered Aneuploidy Technology), a system that enables generation of chromosome-specific aneuploidies by co-expression of a sgRNA targeting chromosome-specific CENPA-binding ɑ-satellite repeats together with dCas9 fused to a mutant form of KNL1. We designed unique and highly specific sgRNAs for 19 out of 24 chromosomes. Expression of these sgRNAs with KNL1Mut-dCas9 leads to missegregation and induction of gains or losses of the targeted chromosome in cellular progeny with an average efficiency of 8% and 12% for gains and losses, respectively (up to 20%), tested and validated across 9 chromosomes. Using KaryoCreate in colon epithelial cells, we show that chromosome 18q loss, a frequent occurrence in gastrointestinal cancers, promotes resistance to TGFβ, likely due to synergistic hemizygous deletion of multiple genes. Altogether, we describe a novel technology to create and study chromosome missegregation and aneuploidy in the context of cancer and beyond.

overall_design: KaryoCreate was used to generate an hCEC clone with (clone 14) and without (clone 13) chromosome 18q loss. Bulk RNA- sequencing was performed on these two clones (2 biological replciates each). Differential expression analysis using DESeq2 and gene set enrichment analysis (GSEA) were then performed.

first: Nazario

last: Bosco

first: Aleah

last: Goldberg

first: Xin

last: Zhao

first: Pan

last: Cheng

first: Adam

last: Johnson

first: Joy

last: Bianchi

first: Cecilia

last: Toscani

first: Elena

last: Di Tommaso

first: Lizabeth

last: Katsnelson

first: Dania

last: Annuar

first: Sally

last: Mei

first: Roni

middle: E

last: Faitelson

first: Ilan

middle: Y

last: Pesselev

first: Kareem

last: Mohamed

first: Angela

last: Mermerian

first: Elaine

middle: M

last: Camacho-Hernandez

first: Courtney

last: Gionco

first: Julie

last: Manikas

first: Yi-Shuan

last: Tseng

first: Zhengxi

last: Sun

first: Somayeh

last: Fani

last: Keegan

first: Scott

last: Lippman

first: David

last: Fenyö

first: Simona

last: Giunta

first: Stefano

last: Santaguida

first: Teresa

last: Davoli


title: KaryoCreate

first: Joseph

last: Mays


title: Comprehensive Landscape of Resistance Mechanisms for Neoadjuvant Therapy in Esophageal Squamous Cell Carcinoma by single-cell Transcriptomics

city: Ningbo

first: Yanguo

last: Li

state: zhejaing

address: fenghua road 818

department: IDDT

country: China

institute: Ningbo university

summary: Neoadjuvant therapy has been shown to improve survival for locally advanced esophageal squamous cell carcinoma (ESCC). However, some cases may acquire therapy resistance and the mechanism is still unclear. Here, we applied single-cell RNA sequencing on 7 ESCC patients with neoadjuvant therapy and 2 ESCC patients underwent general surgery alone to delineate the tumor heterogeneity, tumor microenvironment (TME) and potential hallmarks of therapy resistance. In total, 13 tumor cell lineages and its corresponding lineage-specific gene signatures, pathway activities, and transcription factors were identified, representing different mechanisms and hallmarks of neoadjuvant therapy resistance, such as oxidative stress response, hypoxia, DNA repair, ECM and EMT. Typically, tumor cell lineage Ep-C2 with signatures of oxidative stress response showed the strongest resistance to neoadjuvant therapy, particularly under chemoradiotherapy and immunotherapy combination. Excepting for the resistance mechanisms associated with tumor cell lineages, we also investigated three TME characteristics response to neoadjuvant therapy resistance, including the infiltration of cytotoxic-insufficient GZMK+ effector memory T cells, angiogenesis-promoting effect of myeloid lineages and the cell-cell communication of tumor-associated fibroblasts. These hallmarks of neoadjuvant therapy will help us to understand the therapy resistance in ESCC and provide important clues to identify potential targets to improve therapy sensitivity.

overall_design: We applied single-cell RNA sequencing on 7 ESCC patients with neoadjuvant therapy and 2 ESCC patients underwent general surgery alone

first: Yushang

last: Yang

first: Haopeng

last: Yu

first: Jiahan

last: Cheng

first: Longqi

last: Chen

first: Xiaoxi

last: Zeng

first: Shunmin

last: He

first: Qi

last: Liao

first: Yi

last: Zhao

first: Yong

last: Yuan


title: KaryoCreate: a new CRISPR-based technology to generate chromosome-specific aneuploidy by targeting human centromeres

summary: Aneuploidy, the presence of chromosome gains or losses, is a hallmark of cancer and congenital syndromes. Here, we describe KaryoCreate (Karyotype CRISPR Engineered Aneuploidy Technology), a system that enables generation of chromosome-specific aneuploidies by co-expression of a sgRNA targeting chromosome-specific CENPA-binding ɑ-satellite repeats together with dCas9 fused to a mutant form of KNL1. We designed unique and highly specific sgRNAs for 19 out of 24 chromosomes. Expression of these sgRNAs with KNL1Mut-dCas9 leads to missegregation and induction of gains or losses of the targeted chromosome in cellular progeny with an average efficiency of 8% and 12% for gains and losses, respectively (up to 20%), tested and validated across 9 chromosomes. Using KaryoCreate in colon epithelial cells, we show that chromosome 18q loss, a frequent occurrence in gastrointestinal cancers, promotes resistance to TGFβ, likely due to synergistic hemizygous deletion of multiple genes. Altogether, we describe a novel technology to create and study chromosome missegregation and aneuploidy in the context of cancer and beyond.

overall_design: KaryoCreate-treated cell cultures were harvested and analyzed using scRNAseq to infer induced copy number variation.

first: Nazario

last: Bosco

first: Aleah

last: Goldberg

first: Adam

last: Johnson

first: Xin

first: Pan

first: Joy

last: Bianchi

first: Cecilia

last: Toscani

first: Lizabeth

last: Katsnelson

first: Dania

last: Annuar

first: Sally

last: Mei

first: Roni

last: Faitelson

first: Ilan

last: Pesselev

first: Kareem

last: Mohamed

first: Angela

last: Mermerian

first: Elaine

last: Camacho-Hernandez

first: Courtney

last: Gionco

first: Julie

last: Manikas

first: Yi-Shuan

last: Tseng

first: Zhengxi

last: Sun

first: Somayeh

last: Fani

first: Sarah

last: Keegan


title: Fasting Mimic Diet Inhibits Tumor Progression by Targeting IgA+ Cells in Colorectal Cancer

city: Shanghai

first: Ziwen

last: Zhong

address: No. 180, Fenglin Road, Xuhui District

institute: Zhongshan Hospital Fudan University

summary: Globally, colorectal cancer (CRC) is the third most commonly diagnosed malignancy and the third leading cause of cancer death. Evidence based on epidemiological, animal, and human studies strongly support the influence of dietary factors on CRC risk. Numerous prospective clinical trials have shown that fasting mimicking diets (FMD) exerts a wide range of antitumor effects. FMD as an adjunct to cancer treatment can reinforce tumor immunity and, therefore, boost the efficacy of chemo- and immunotherapy.  Thus, it makes systematic analysis of key targets and molecular mechanisms of FMD in the immunomodulation important clinical significance in the prevention and treatment of CRC. In this study, we used single cell RNA sequencing (scRNA-seq) to analyze changes in tumor immune microenvironment of CRC after FMD treatment.

overall_design: Single-cell transcriptomes were assessed in FACS-sorted CD45+ immune cells, isolated from ad libitum or FMD group in AOM-DSS induced CRC model. Each sample was pooled with 4 mice.

first: Changhong

last: Miao


title: Identifying Biomarkers of Heterogeneity and Transplantation Efficacy in Retinal Pigment Epithelial Cells [Bulk RNA-seq]

city: Rensselaer

first: Farhad

last: Farjood

address: 1 Discovery Drive

institute: Neural Stem Cell Institute

summary: Transplantation of retinal pigment epithelial (RPE) cells holds great promise for patients with retinal degenerative diseases such as age-related macular degeneration. In-depth characterization of RPE cell product identity and critical quality attributes are needed to enhance efficacy and safety of replacement therapy strategies. Here we characterized an adult RPE stem cell-derived (RPESC-RPE) cell product using bulk and single cell RNA sequencing (sc-RNA-seq), assessing functional cell integration in vitro into a mature RPE monolayer and in vivo efficacy by vision rescue in the Royal College of Surgeons rats. scRNA-seq revealed several distinct subpopulations in the RPESC-RPE product, some with progenitor markers. We identified RPE clusters expressing genes associated with in vivo efficacy and increased cell integration capability. Gene expression analysis revealed a lncRNA (TREX) as a predictive marker of in vivo efficacy. TREX knockdown decreased cell integration while overexpression increased integration in vitro and improved vision rescue in the RCS rats.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cultured RPESC-RPE cells

first: Farjood

last: Farhad

first: Justine

middle: D

last: Manos

first: Yue

last: Wang

first: Anne

middle: L

last: Williams

first: Cuiping

last: Zhao

first: Susan

last: Borden

first: Nazia

last: Alam

first: Glen

last: Prusky

last: Temple

first: Jeffery

middle: H

last: Stern

first: Nathan

last: Boles


title: Identifying Biomarkers of Heterogeneity and Transplantation Efficacy in Retinal Pigment Epithelial Cells [scRNA-seq]

overall_design: RPE cells were isolated from donor eyes, cultured, passaged and frozen down at passage1. Passage 1 cells were thawed and cultured on Transwells for 2-8 weeks and analyzed using scRNAseq.

first: Sally

first: Jeffrey


title: Loss of CD4+ T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection

first: Behdad (Ben)

last: Afzali

address: 10 Center Drive, Building 10

department: NIDDK

institute: National Institutes of Health

summary: Arginase 1 (Arg1), the enzyme catalyzing the conversion of arginine to ornithine, is a hallmark of IL-10-producing immunoregulatory M2 macrophages. However, its expression in T cells is disputed. Here, we demonstrate that induction of Arg1 expression is a key feature of lung CD4+ T cells during mouse in vivo influenza infection. Conditional ablation of Arg1 in CD4+ T cells accelerated both virus-specific T helper 1 (Th1) effector responses and its resolution, resulting in efficient viral clearance and reduced lung pathology. Using unbiased transcriptomics and metabolomics, we found that Arg1-deficiency was distinct from Arg2-deficiency and caused altered glutamine metabolism. Rebalancing this perturbed glutamine flux normalized the cellular Th1 response. CD4+ T cells from rare ARG1-deficient patients or CRISPR-Cas9-mediated ARG1-deletion in healthy donor cells phenocopied the murine cellular phenotype. Collectively, CD4+ T cell-intrinsic Arg1 functions as an unexpected rheostat regulating the kinetics of the mammalian Th1 lifecycle with implications for Th1-associated tissue pathologies.

overall_design: RNA-seq data for CD4 T cells isolated from lungs and spleen of influnza infected WT mice and in vitro activated  WT, Arg1 KO and Arg2 KO CD4 T cells

first: Erin

last: West

first: Nicolas

last: Merle

first: Marcin

last: Kamiński

first: Gustavo

last: Palacios

first: Dhaneshwar

last: Kumar

first: Luopin

first: Jack

last: Bibby

first: Kirsten

last: Overdahl

first: Alan

middle: K

last: Jarmusch

first: Simon

last: Freeley

first: Duck-Yeon

last: Lee

first: J

middle: W

last: Thompson

first: Zu-Xi

last: Yu

first: Naomi

last: Taylor

first: Marc

last: Sitbon

first: Douglas

middle: R

last: Green

first: Andrea

last: Bohrer

first: Katrin

last: Mayer-Barber

first: Behdad

first: Majid

last: Kazemian

first: Sabine

last: Scholl-Buergi

first: Daniela

last: Karall

first: Martina

last: Huemer

first: Claudia

last: Kemper


title: Cell type-specific role of CBX2-cPRC1 at the onset of spermatogonial differentiation

first: Jongmin

last: Kim


title: Cell type-specific role of CBX2-cPRC1 at the onset of spermatogonial differentiation [scRNA-Seq]

overall_design: Goal#1) Obtain single cell gene expression profile of adult testes, Goal#2) Induce Cbx2 deletion by Tamoxifen injections, and profile changes in cell types and gene expression by single cell RNA-seq. In addition, make cell barcoded Cbx2 amplicons to determine cellular Cbx2 genotypes from Cbx2 transcript information.

first: Robert

last: Kingston


title: Cell type-specific role of CBX2-cPRC1 at the onset of spermatogonial differentiation [CUT&RUN]

overall_design: CUT&RUN-sequencing profiles of PRC1-associated factors in cKIT(+) differentiating spermtatogonia of mice. Goal#1) Identification of CBX2 target genes (WT_IgG, WT_CBX2-855, WT_HA-ab9110_NegCtrl, WT_HA-16B12_NegCtrl, WT_HA-C29F4_NegCtrl, HACBX2_HA-ab9110, HACBX2_HA-16B12, HACBX2_HA-C29F4); Goal#2) Identification of CBX2-associated PRC1 target genes (WT_RING1B_rep1, WT_RING1B_rep2, WT_BMI1_rep1, WT_BMI1_rep2, WT_PHC2_rep1, WT_PHC2_rep2, WT_H3K4me3_rep1, WT_H3K4me3_rep2, WT_H3K27me3_rep3), and Goal#3) Comparison of CBX2 and H3K27me3 profiles between WT and Cbx2[23KRA/23KRA] (WT_CBX2-856_rep1, WT_CBX2-856_rep2, WT_H3K27me3_rep1, WT_H3K27me3_rep2, CBX2KRA_CBX2-856_rep1, CBX2KRA_CBX2-856_rep2, CBX2KRA_H3K27me3_rep1, CBX2KRA_H3K27me3_rep2)


title: Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity [Exp 3]

city: Oxford

first: Lucy

last: Garner

address: Experimental Medicine, Level 5, John Radcliffe Hospital

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: MAIT cells are innate-like T cells that recognize microbial metabolites through a semi-invariant T cell receptor (TCR). Major questions remain regarding the extent of human MAIT cell functional and clonal diversity. To address these, we analyzed the single-cell transcriptome and TCR repertoire of blood and liver MAIT cells and developed functional RNA-sequencing (fRNA-seq), a method to integrate function and TCR clonotype at single-cell resolution. MAIT cell clonal diversity was comparable to conventional memory T cells, with private TCR repertoires shared across matched tissues. Baseline functional diversity was low and largely related to tissue site. MAIT cells showed stimulus-specific transcriptional responses in vitro, with cells positioned along gradients of activation. Clonal identity influenced resting and activated transcriptional profiles, but intriguingly was not associated with the capacity to produce IL-17. Overall, MAIT cells show phenotypic and functional diversity according to tissue localization, stimulation environment, and clonotype.

overall_design: Enriched CD8+ T cells (n = 3 donors) were left unstimulated, or stimulated with MR1/5-OP-RU + αCD28 or IL-12 + IL-18. After 20 hours, MAIT cells (CD3+CD8+CD26+CD161hiVα7.2+) were sorted for single-cell RNA-sequencing (scRNA-seq) and single-cell TCR-sequencing (scTCR-seq) using 10x Genomics technology.

first: Nicholas

last: Provine

first: Paul

last: Klenerman


title: Immunomodulatory-Photodynamic Nanostimulators for Invoking Pyroptosis to Augment Tumor Immunotherapy

status: Public on Aug 13 2023

city: guangzhou

first: yuhua

last: xiao

state: guangdong province

address: jinsui load

department: zhongshan Ophthalmic  center

institute: Sun Yat-sen University

summary: Acidic tumor microenvironment (TME)-evoked MRC nanoparticles (MRC NPs) co-delivering immune agonist RGX-104 and photosensitizer chlorine e6 (Ce6) are reported for pyroptosis-mediated immunotherapy. RGX-104 remodels TME by transcriptional activation of ApoE to regress myeloid-derived suppressor cells’ (MDSCs) activity, which neatly creates foreshadowing for intensifying pyroptosis. Considering Ce6-triggered photodynamic therapy (PDT) can strengthen oxidative stress and organelles destruction to increase immunogenicity, immunomodulatory-photodynamic MRC nanodrugs will implement an aforementioned two-pronged strategy to enhance gasdermin E (GSDME)-dependent pyroptosis. RNA-seq analysis of MRC at the cellular level is introduced to first elucidate the intimate relationship between RGX-104 acting on LXR/ApoE axis and pyroptosis, where RGX-104 provides the prerequisite for pyroptosis participating in antitumor therapy. Briefly, MRC with favorable biocompatibility tackles the obstacle of hydrophobic drugs delivery, and becomes a powerful pyroptosis inducer to reinforce immune efficacy. MRC-elicited pyroptosis in combination with anti-PD-1 blockade therapy boosts immune response in solid tumors, successfully arresting invasive metastasis and extending survival based on remarkable antitumor immunity. MRC may initiate a new window for immuno-photo pyroptosis stimulators augmenting pyroptosis-based immunotherapy. Owing to the transcriptome sequencing on 4T1 cells exposed to various treatment, pyroptosis mechanism of MRC was thoroughly analyzed via comparing the expression discrepancy among PBS, MRC, and MRC+L groups.

overall_design: Examination of differential expression genes (DEGs)  in three treatment groups (PBS, MRC and MRC+L groups)

first: Wei

last: Qiu

first: Wen

last: Su


title: NUP1 modulates proteasome based degradation of ABI5 in Nuclear Pore Complex region to regulate Arabidopsis seed germination

city: London

first: Yuhai

last: Cui

state: ON

address: 1391 Sandford St,

country: Canada

institute: Agriculture and AgriFood Canada

summary: NUCLEOPORIN 1 (NUP1), a member of the Nuclear Pore Complex (NPC), is located on the inner side of the nuclear membrane. It is highly expressed in seeds; however, its role in seeds including germination has not been explored yet. Here, we identified an ABA hypersensitive phenotype of nup1 during germination. ABA treatment drastically changes the expression pattern of thousands of genes in nup1, including the major transcription factors (TFs) involved in germination, ABI3, ABI4, and ABI5. Double mutant analysis of NUP1 and these ABA-related genes showed that mutations in ABI5 can rescue the phenotype of nup1, suggesting that NUP1 acts upstream of ABI5 to regulate seed germination. ABI5, a negative regulator of germination was previously reported to be predominantly expressed in nucleus. Our subnuclear localization study indicates ABI5 is mostly localized in nucleoplasm. It is abundant in dry seeds and rapidly degraded during germination, but the details of its degradation site is unclear. Here, we found that NUP1 is physically associated with ABI5 and the 19S regulatory particle (RP) of the 26S proteasome near NPC. Mutation in NUP1 delayed the ABI5 degradation through its post-translation retention in nucleolus after abiotic stress treatment. Taken together, we propose, NUP1 anchors the proteasome to NPC and modulates Arabidopsis seed germination through proteasome-mediated degradation of ABI5 in the vicinity of NPC in nucleoplasm.

overall_design: We measured the transcriptomic difference between 5-day-old Col-0 and nup1-1 with and without ABA treatment.

first: Raj

last: Thapa


title: Functional analysis of miR-375 in oral squamous cell carcinoma cells

city: Toon

first: Saika

last: Masato

state: Ehime

department: Department of Oral and Maxillofacial Surgery

country: Japan

institute: Ehime University Graduate School of Medicine

summary: We attempted to identify the miR-375-3p target genes using a microarray analysis to evaluate the function and transfection efficiency of miR-375-3p mimic.

overall_design: MicroRNA (miR)-375 was identified and function analyzed as lymph node metastasis (LNM)-related microRNAs in OSCC. By miRNA microarrays of early OSCC tissues (T1-2) in tumor part compared to adjacent normal part, miR-375 was a significant decrease in expression level with LNM cases. In thi study, we performed a functional analysis of miR-375 and search the target genes in OSCC cells.

first: Masato

last: Saika

first: Koh-ichi

last: Nakashiro


title: Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity [Exp 1]

overall_design: MAIT cells (CD3+MR1/5-OP-RU+) were sorted from matched human blood (n = 3) and liver (n = 4) for single-cell RNA-sequencing (scRNA-seq) and single-cell TCR-sequencing (scTCR-seq) using 10x Genomics technology.


title: Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity

overall_design: Refer to individual Series


title: The role of DNMT3A in AITL

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: To investigate the role of DNMT3A in AITL, single cell RNA-seq (scRNA-seq) is performed to analysis the lymph nodes generated from the control, RHOAG17V and RHOAG17V DNMT3AR882H AITL mice. The mitoQC maps shows the distributions of unique gene detected and mitochondrial genes detected in each single cell. After the quality control, a total of 23,805 cells (7576 of control, 7913 of RHOAG17V and 8316 of RHOAG17V DNMT3AR882H) are used for clustering and further analyzing

sample_organism:
Homo sapiens
Mus musculus

overall_design:
single-cell RNA-seq

This record includes re-analysis of all samples in GSE197188. Data processing description and re-analyzed data (GSE218137_AITL_patient.rds.gz) are available for download at the foot of this record.

first: Xiangyu

first: Jianan

last: Zheng

first: Zhongwang

last: Wang

first: Chong

last: Chen

first: Yu

last: Liu


title: B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function

city: Nanjing

first: chen

address: xianlin street num 163

institute: Nanjing University


title: Farnesol prevents aging-related muscle weakness in mice through enhanced farnesylation of Parkin-interacting substrate

status: Public on Aug 12 2023

city: Suwon

first: Ju-Hyeon

last: Bae

state: Gyeonggi-do

address: Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 2066

department: school of medicine

country: South Korea

institute: Sungkyunkwan University

summary: Peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α) is a master regulator of mitochondrial biogenesis. Reduced PGC-1α abundance is linked to skeletal muscle weakness in aging or pathological conditions; thus, elevating PGC-1α abundance might be a promising strategy to treat muscle aging. Here we performed high-throughput screening and identified a natural compound, farnesol, as a potent inducer of PGC-1α. Farnesol administration enhanced oxidative muscle capacity and muscle strength, leading to metabolic rejuvenation in aged mice. Moreover, farensol treatment accelerated the recovery of muscle injury associated with enhanced muscle stem cell function. The protein expression of Parkin-interacting substrate (PARIS/Zfp746), a transcriptional repressor of PGC-1α, was elevated in aged muscles, likely contributing to PGC-1α reduction. The beneficial effect of farnesol on aged muscle was mediated through enhanced PARIS farnesylation, thereby relieving PARIS-mediated PGC-1α suppression. Furthermore, short-term exercise increased PARIS farnesylation in the muscles of young and aged mice, whereas long-term exercise decreased PARIS farnesylation in the muscles of aged mice, leading to the elevation of PGC-1α. Collectively, the current study demonstrated that the PARIS-PGC-1α pathway is linked to muscle aging and that farnesol treatment can restore muscle functionality in aged mice through increased farnesylation of PARIS.

overall_design: To further investigate the effect of farnesol in aged muscles, RNA-sequencing analysis was performed on GAS muscles from vehicle (V)- or farnesol (F)-fed 26-month-old mice. Farnesol is orally administrated for 30 days. Then, we harvested gastrocnemius (GAS) muscles and performed RNA-sequencing using isolated total RNA.

first: Jong-Sun

last: Kang

first: Yun-Il

last: Lee

first: Yu-Seon

last: Kim


title: B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function [IL-10 KO-16s-DNA-sequence]

summary:
Background & Aims: Gut microbiota dysbiosis is associated with the pathogenesis of Crohn's disease (CD), but the underlying mechanisms by which colon bacteria contribute to the development of CD remain largely unclear. Here, we investigated whether colon bacteria, particularly Bacteroides acidifaciens (B. acidifaciens), promote CD pathogenesis through their small RNAs (sRNAs).
Methods: The composition of gut bacteria were analyzed in the fecal samples of IL-10 knockout (KO) mice and CD45RBhigh mice that spontaneously develop colitis via 16S amplification sequencing, and the expression pattern of B. acidifaciens in both experimental colitis mice and CD patients was confirmed by quantitative RT-PCR (qRT-PCR). The effects of B. acidifaciens and their total and small RNA contents on colitis development were evaluated in IL-10 KO mice. Furthermore, the expression profile of B. acidifaciens-derived sRNA (BA-sRNA) in IL-10 KO mice was established by RNA sequencing, and BA-sRNA-172 levels in experimental colitis mice and CD patients were determined. Lentivirus carrying BA-sRNA-172 and BA-sRNA-172-deficient B. acidifaciens were then constructed and used to investigate the role of BA-sRNA-172 in the development of colitis. The activities of BA-sRNA-172 in regulating mucin2 (MUC2) expression and gut mucosal barrier function was systematically studied by in situ hybridization, immunofluorescence staining, qRT-PCR, western blot, RNA pull-down and luciferase assays in vitro. Finally, the effects of anti-BA-sRNA-172 and anti-MUC2 shRNA on intestinal barrier function and colitis development were evaluated.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: stool bacteria profiles of wild type (WT) and IL-10 knockout (KO) mice

first: Chen

first: Yuqian

last: Zhang


title: B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function [RNA-Seq]

overall_design: mRNA profiles of Complexes of biotinylated BA-sRNA-172 and lysates of Mice CECs


title: B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function [CD45RB high-16s-DNA-sequence]

overall_design: stool bacteria profiles of C57BL/6 RAG KO (control) and CD45RB high mice


title: Transcriptome data of Foxp3-Cre, Ube2m&Ube2f-deficient Treg cells and Foxp3-Cre, Rbx1&Sag-deficient Treg cells from mice

city: Hangzhou

first: Di

last: Wu

state: Zhejiang

address: No. 268, Kaixuan Road

institute: Zhejiang University

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


title: B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function [IL-10 KO-sRNA-sequence]

overall_design: stool sRNA profiles of wild type (WT) and IL-10 knockout (KO) mice


title: Melatonin, as a downstream molecule of follicle-stimulating hormone, improves nutrient accumulation and mitochondrial function in mammalian oocytes.

city: Wuhan

first: changjiu

last: he

state: Hubei

address: 1 Shizishan street, Hongshan District

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

summary:
Background: Melatonin (MLT) supplementation has been shown to improve the quality of oocytes and embryos in vitro through its antioxidant mechanism. However, it is unclear whether endogenous MLT plays a role in oocyte quality control, casting doubt on the rationality of oral MLT in improving oocyte quality or fecundity.
Methods:we measured the effects of PMSG on MLT synthesis in follicles, evaluated the effects of MLT on oocyte growth and quality in mice and goat, used RNA-seq to explore the mechanism underlying MLT’s effects on oocyte growth and quality, and generated SNAT-knockout mice to assess the effects of endogenous MLT on oocyte growth and quality. Lastly, we investigated the feasibility of short-term MLT intake to improve the fertility of older mice.
Result: we revealed that the follicle-stimulating hormone induces the expression of intra-ovarian SNAT, resulting in increased levels of intra-ovarian MLT in mice. Administering MLT during the gonadotropin-dependent phase improved the oocyte size and quality in both mice and goat by enhancing nutrient accumulation and mitochondrial function. Deficiency of MLT in mice reduced oocyte size and weakened mitochondrial function. Furthermore, our findings demonstrate that short-term MLT intake during the gonadotropin phase improves the litter size of older mice.
Conclusion: This study reveals that endogenous MLT is involved in determining oocyte quality as a target molecule of follicle-stimulating hormone, shedding light on its potential utilization in improving oocyte quality or rejuvenating aged mammalian oocytes.

overall_design: Follicular mRNA  profiles of  gonadotropin-induced ovaries in mice.There are 8 samples represented two treatments, Control (n=4) and Melatonin (n=4).

first: Changjiu

last: He

first: Hao

first: Guoshi

first: Xiang

last: Li


title: HD2B and HD2C interact with Argonaute 4 to promote tolerance and heterochromatin stabilization during heat stress [BS-Seq]

first: Xiangsong

address: Bayi Road

institute: Wuhan university

type: Methylation profiling by high throughput sequencing

summary: In this study, we show that HD2B/C work with AGO4 to promote heat tolerance

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and hd2b/c plants under normal and heat-treated conditions,whole-genome bisulfite sequencing in WT and hd2b/c under both normal and heat conditions,high-throughput small RNA sequencing in WT and hd2b/c

first: Yingnan

last: Sun

first: Fangfang

last: Yang


title: Transcriptome data of Foxp3-Cre, Ube2m&Ube2f-deficient Treg cells from mice

summary: Neddylation is necessary for activation of Cullin-RING Ligases (CRLs) which degrade various immune regulatory proteins. Our recent study showed that while depletion of neddylation E2-E3 pair Ube2f-Sag in regulatory T cells (Treg cells) had no obvious phenotype, the same depletion of either Ube2m or Rbx1 caused inflammation disorders with different severity. Whether these E2s or E3s compensate each other in functional regulations of Treg cells is, however, previously unknown. In this report, we generated Foxp3Cre;Ube2mfl/fl;Ube2ffl/fl or Foxp3Cre;Rbx1fl/fl;Sagfl/fl double null mice by simultaneously deletion of both neddylation E2s or E3s in Treg cells, respectively. Remarkably, Ube2m&Ube2f double null mice developed much severe autoimmune phenotypes than Ube2m-null mice, indicating Ube2m significantly compensates Ube2f in Treg cells. The minor worsen autoimmune phenotypes seen at very early stage in Rbx1&Sag double null than Rbx1-null mice, is likely due to already severe phenotypes of the later, indicating a minor compensation of Rbx1 for Sag. The RNA profiling-based analyses revealed that up- and down-regulations of few signaling pathways in Treg cells are associated with the severity of autoimmune phenotypes. Finally, severer inflammation phenotypes seen in mice with double E3-null than with double E2-null Treg cells indicate a neddylation-independent mechanism of two E3s, also known to serve as the RING component of CRLs in regulation of Treg cell fitness.

overall_design: CD4+YFP+ Treg cells were sorted from the peripheral lymph nodes and spleens of indicated mice (8-12 weeks old). To generate enough materials, 2-3 mice were pooled for one sample. RNA was purified from the sorted cells with the miRNeasy Mini Kit (Qiagen, 21704). The RNAs were reverse transcribed, amplified, labeled (Affymetrix GeneChip pico kit, 703308) to achieve enough cDNAs. Then the cDNA samples were hybridized to Clariom S Arrays, mouse (902931). The Applied Biosystems Expression Console Software 1.4 was employed to analyze the microarray data sets.

first: Yi


title: Exploration of the synergistic mechanism of Gegen Qinlian Decoction on Wnt signaling pathway based on an integrated strategy of network pharmacology and transcriptomics

city: beijing

first: wenjuan

last: xu

address: Beijing University of Chinese Medicine, No.11 North 3rd Ring East Road, Chao-Yang District, Beijing

institute: Beijing University of Chinese Medicine

summary: Network pharmacology study indicated that Puerarin (PUE), wogonin (WOG), berberine (BER) and glycyrrhetinic acid (GLY) were the active components in GQD and performed synergistic effect on the targets of the Wnt signaling pathway. Pharmacologic research revealed that WOG, BER, GLY performed inhibited effect on SW480 cells and PUE only exhibited effective antitumor activity when combined with GLY. RNA-seq were used to discover synergistic mechanism of PUE-GLY and CTNNB1, CCND1, SMAD4 were identified as synergistic targets inhibited by PUE-GLY. Moreover, mechanism study explored PUE-GLY could affect the Wnt signaling pathway by up-regulated GSK3B and down-regulated CTNNB1 synergistically. Importantly, it showed that GLY could effectively increase the intracellular content of PUE based on HPLC/MS analysis, and this process was achieved by GLY through influencing the targets of membrane’s pathway, such as cell adhesion molecules, focal adhesion and tight junction. Our study revealed multi-target mechanism of GLY, down-regulated CTNNB1 as the material for efficacy and intervene membrane protein (CDH1, CADM1, ITGB2, ICAM1) as courier in the formulae. Moreover, the mechanism of synergistic antitumor action of Puerariae Lobatae Radix (Gegen-Monarch) and Glycyrrhiza Radix et Rhizoma (Gancao-Assistant) on Wnt signaling pathway was explored systematically.

overall_design: Examination of different expression of gene in SW480 cells.

first: Ling

last: Dong

first: Wenjuan

last: Xu

first: Yanping

first: Yiting

last: Gong


title: m6A modification of EBV transcripts

city: PHILADELPHIA

first: Fengchao

last: Lang

address: 3610 Hamilton Walk

institute: University of Pennsylvania

summary: We examined the viral epitranscriptome in EBV transformed lymphoblastoid cell lines (LcLs) and EBV-positive Burkitt's lymphoma, Akata cells, using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Biological replicates of ribo-RNA deleted mRNA of each cell type were prepared for MeRIP-seq followed by peak calling using the exome Peak package with settings for stringent peak calling on both strands of the genome.

overall_design: We examined the viral epitranscriptome in 2 different EBV positive cell lines during latency and lytic infection.

first: Erle

last: Robertson


title: Placental ischemia disrupts DNA methylation patterns of distal regulatory regions in rat

first: Xiaoguo

last: Zheng

address: 145 Guangyuan Road

institute: Shanghai Jiaotong University

summary:
We carry out whole-genome bisulfite sequencing (WGBS) of rat placental DNA to investigate epigenome-wide alterations in a reduced uterine perfusion pressure (RUPP) PE model.
The Hidden Markov Model (HMM) was applied to identify functional epigenetic structures including partially methylated domains (PMDs), low methylated regions (LMRs) and unmethylated regions (UMRs).

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Whole genome bisulfite sequencing (WGBS) of six placenta samples, including three reduced uterine perfusion pressure (RUPP) rat placenta samples and three control placenta samples

first: Xinzhi

last: Zhao

first: Yahan

last: Lian

first: Qian

last: Zhou


title: A module of microRNAs cooperatively regulating neurogenesis

status: Public on Aug 11 2023

city: Marseille

first: christophe

last: beclin

state: Bouches du Rhone

address: campus de Luminy, case 907

department: Aix-Marseille université

country: France

institute: CNRS

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are essential regulators of all developmental processes, including neurogenesis, when the production of large numbers of neurons from a limited number of neural stem cells depends on the precise control of determination, proliferation and differentiation. However, miRNA regulation of target mRNAs is highly promiscuous, a single miRNA can target many mRNAs and vice versa, raising the question of how specificity is achieved to elicit a precise regulatory response.   Here we introduce in vivo AGO-APP, a novel approach to purify Argonaute-bound miRNAs directly from living cells and tissues. Using this technology, we isolate actively inhibiting miRNAs from different neural cell populations in the larval Drosophila central nervous system. We identify a defined group of miRNAs that redundantly target all iconic genes known to control the transition from neuroblasts to neurons. In vivo functional studies demonstrate that knockdown of individual miRNAs among this group does not induce detectable cellular phenotypes. However, simultaneous knockdown of multiple miRNAs leads to precocious stem cell differentiation, demonstrating functional interdependence. Our study shows that miRNAs cooperate within a regulatory module to specify the targeted gene network.

overall_design: Using the UAS-Gal4 system we generated transgenic flies conditionnally expressing a T6B-YFP fusion protein either in neuroblast (nab driver) or in the entire neuronal lineage (elav driver) or in glial cells (repo driver). After induction at the L3 larvae stage, T6B bound micro-RNAs were pulled down using an anti-GFP antibody and sequenced. Micro-RNA sequencing was performed using the Illumina protocol modified by Kim et al. (2019).

first: Christophe

last: Beclin

first: Norbert

last: Eichner

first: Cedric

last: Maurange

first: Harold

last: Cremer

first: Gunter

last: Meister

first: Surbhi

last: Surbhi

first: Karine

last: Narbonne

first: Andrea

last: Erni


title: Novel Roles for the Transcriptional Repressor E4BP4 in Both Cardiac Physiology and Pathophysiology

city: Birmingham

first: Lamario

last: Williams

state: AL

address: 1825 University Boulevard, Room 121

department: Medicine

institute: University of Alabama at Birmingham

summary: Circadian clocks temporally orchestrate biological processes critical for cellular/organ function. For example, the cardiomyocyte circadian clock modulates cardiac metabolism, signaling, and electrophysiology over the course of the day, such that, disruption of the clock leads to age-onset cardiomyopathy (through unknown mechanisms). Here, we report that genetic disruption of the cardiomyocyte clock results in chronic induction of the transcriptional repressor E4BP4. Importantly, E4BP4 deletion prevents age-onset cardiomyopathy following clock disruption. These studies also indicate that E4BP4 regulates both cardiac metabolism (eg, fatty acid oxidation) and electrophysiology (eg, QT interval). Collectively, these studies reveal that E4BP4 is a novel regulator of both cardiac physiology and pathophysiology.

overall_design: Comparative gene expression profiling analysis of  RNA-seq data for biventricular heart tissue isolated from cardiomyoycte-specific E4BP4 knockout (CEK) and littermate control (CON) mice. Heart tissue samples were harvested at different times of the day denoted as zeitgeber time (ZT).

first: Sobuj

last: Mia

first: Ravi

last: Sonkar

first: Mary

last: Latimer

first: David

last: Rawnsley

first: Samir

last: Rana

first: Jin

last: He

first: Pieterjan

last: Dierickx

first: Teayoun

last: Kim

first: Min

last: Xie

first: Kirk

last: Habegger

first: Masato

last: Kubo

first: Lufang

first: Morten

last: Thomsen

first: Sumanth

last: Prabhu

first: Stuart

last: Frank

first: Paul

last: Brookes

first: Mitchell

last: Lazar

first: Abhinav

last: Diwan

first: Martin

last: Young


title: Proteomics coupled transcriptomics reveals Slc34a1 and Slc34a3 downregulation as potential features of nephrotoxin-induced acute kidney injury

city: Chongqing

first: Qihuan

last: Fu

state: Chongqing

address: 181 Hanyu Road, Shapingba District

department: Chongqing University Cancer Hospital

institute: Chongqing University

summary: Acute kidney injury (AKI) is a clinically common and severe disease with a significant economic burden worldwide. Although several studies have focused on the pathogenesis of AKI, much remains unknown about its complex molecular regulatory network and pathophysiological mechanisms. This study combines mass spectrometry and RNA sequencing technologies to investigate nephrotoxin-induced AKI mice's protein and RNA expression profiles. The results revealed that Slc34a1 and Slc34a3 were significantly down-regulated in nephrotoxin-induced AKI mice and may be potential diagnostic and therapeutic targets.

overall_design: Mice were randomly divided into three groups: control group, cisplatin , and LPS group .

first: Jiangbei

last: Yuan

first: Xiaoyang

last: Wang

first: Zhaojing

last: Zhu


title: Spatial Co-transcriptomics Reveals Discrete Stages of the Arbuscular Mycorrhizal Symbiosis I

city: Berkeley

first: Benjamin

last: Cole

address: 1 Cyclotron Road

department: Biosciences

institute: Lawrence Berkeley National Laboratory

summary: The symbiotic interaction of plants with arbuscular mycorrhizal fungi (AM fungi) is ancient and widespread. Plants provide AM fungi with carbon in exchange for nutrients and water, making this interaction a prime target for crop improvement. However, plant-fungal interactions are restricted to a small subset of root cells, precluding the application of most conventional functional genomic techniques to study the molecular bases of these interactions. Here we used single-nucleus and spatial RNA sequencing to explore both M. truncatula and R. irregularis transcriptomes in AM symbiosis at cellular and spatial resolution. Integrated spatially-registered single-cell maps of interacting cells revealed major infected and uninfected plant root cell types. We observed that cortical cells exhibit distinct transcriptome profiles during different stages of colonization by AM fungi, indicating dynamic interplay between both organisms during establishment of the cellular interface enabling successful symbiosis. Our study provides insight into a symbiotic relationship of major agricultural and environmental importance and demonstrates a paradigm combining single-cell and spatial transcriptomics for the analysis of complex organismal interactions.

overall_design:
Nuclei from R. irregularis - inoculated and non-inoculated M. truncatula root tissue were isolated by fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.
med.RDS - Seurat Object with all seven medicago root datasets generated for this study (4 inoculated, 3 not-inoculated)
med_AMF.RDS - Seurat Object with 28dpi (2) and 38dpi (1) R. irregularis inoculated root tissue datasets
med_metaData.csv - metadata for 'med' Seurat Object
med_AMF_metaData.csv - metadata for 'med_AMF' Seurat Object

first: Karen

last: Serrano

first: Margot

last: Bezrutczyk

first: Thai

last: Dao

first: Danielle

last: Goudeau

first: Ronan

last: O'Malley

first: Rex

last: Malmstrom

first: Axel

last: Visel

first: Henrik

middle: V

last: Scheller


title: PRDX1 Cys52Ser Variant Alleviates Nonalcoholic Steatohepatitis by Reducing Inflammation in Mice

city: TIANJIN

first: Yin

last: Wen

state: TIANJIN

address: Address:No.6 North Huanrui Rd, Beichen District, Tianjin, P.R China

department: NHC Key Laboratory of Hormones and Development

institute: Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University

summary:
Objective: Peroxiredoxin 1 (PRDX1) is a peroxidase and guards against oxidative stress by scavenging intracellular peroxides, whereas it also has been shown to stimulate inflammatory response by functioning as a chaperone protein. The potential in vivo link between PRDX1’s peroxidase activity and its pro-inflammatory activity remains elusive.
Methods: We generated peroxidase-dead PRDX1 variant mice by mutating its peroxidatic cysteine at 52 (Cys52) to serine, here referred to as PRDX1Cys52Ser. Trx-TrxR-NADPH coupled activity assay was applied to evaluate the peroxidase activity of global PRDX in PRDX1Cys52Ser variant mice. PRDX1Cys52Ser mice and their wild-type littermates were subjected to western diet or methionine and choline deficient diet feeding. NASH phenotypes were assessed through different analyses including physiological measurements, immunohistochemical staining, and quantitative PCR (qPCR). RNA sequencing, qPCR and western blotting were used to reveal and validate any changes in the signaling pathways responsible for the altered NASH phenotypes observed between WT and PRDX1Cys52Ser variant mice.
Results: PRDX1Cys52Ser variant mice showed impaired global PRDX peroxidase activity and reduced susceptibility to diet-induced NASH and liver fibrosis. Mechanistically, PRDX1 Cys52Ser variant suppressed NF-κB signaling and STAT1 signaling pathways that are known to promote inflammation and NASH.
Conclusion: The peroxidatic Cys52 of PRDX1 is required for its pro-inflammatory activity in vivo. This study further suggests that PRDX1 plays dual but opposing roles in NASH

overall_design: 8-week-old male WT and PRDX1Cys52Ser mice were fed a WD for 20 weeks before their liver tissues were collected for RNA-Seq

first: Zhonghao

last: Bai

first: Wen

last: Yin


title: Transcriptome data of Foxp3-Cre, Rbx1&Sag-deficient Treg cells from mice

first: Di

last: Wu

first: Yi

last: Sun


title: A novel 13q12 microdeletion associated with familial syndromic corneal dystropy

city: Ann Arbor

first: William

last: Presley

state: MI

address: 1137 Catherine St

department: Human Genetics

institute: University of Michigan

summary: We identified a family with a novel chromosome 13 microdeletion associated with a syndromic form of corneal opacification. In order to determine which genes in/around the microdeletion were contributing to the constellation of phenotypes, a corneal epithelial sample was obtained during a superficial keratectomy of the proband's 9-year-old brother.

overall_design: RNA was extracted from the corneal sample, sequenced, and gene expression levels compared to those of 10 control corneal samples from You et al. ("RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients." Sci Rep, 2018.)

first: Serpen

last: Jasmine Y.

first: Presley

last: William

first: Beil

last: Adelyn

first: Armenti

last: Stephen T

first: Johnson

last: Kayla

first: Mian

last: Shahzad I.

first: Innis

last: Jeffrey W.

first: Prasov

last: Lev


title: HDR-CRISPR promotes targeted genome editing with reduced mutational burden in primary human cells [Amp-seq]

city: Freiburg

first: Claudio

last: Mussolino

address: Breisacherstr. 115

institute: Institute for Transfusion Medicine and Gene Therapy

summary: We have established a technology to endorse DSB resolution via HDR with the goal of facilitating clinical transition of HDR-based editing strategies and increase safety. We have used high throughput sequencing as deposited here to assess safety of our platform

overall_design: We have performed Amplicon Sequencing to monitor gross genomic aberration between control samples and samples that have received our HDR-promoting tools

first: Antonio

last: Carusillo

first: Raul

last: Schäfer

first: Manuel

last: Rhiel

first: Daniel

last: Türk

first: Kay

middle: O

last: Chmielewski

first: Laura

last: Mosti

first: Geoffroy

last: Andrieux

first: Richard

first: Tatjana

middle: I

last: Cornu

first: Toni

last: Cathomen


title: HDR-CRISPR promotes targeted genome editing with reduced mutational burden in primary human cells [CAST-seq]

overall_design: We have performed CAST-seq to monitor gross genomic aberration between control samples and samples that have received our HDR-promoting tools


title: HDR-CRISPR promotes targeted genome editing with reduced mutational burden in primary human cells

overall_design: Refer to individual Series


title: Effects of Diphtheria Toxin and Compound 6p on HPKs (human primary keratinocytes)

city: Singapore

first: Franklin

last: ZHONG

state: Singapore

address: 11 Mandalay Road

country: Singapore

institute: NTU LKC School of Medicine

summary: This study investigates the effect of diphtheria toxin (DT) as an activator of ZAKalpha-dependent ribotoxic stress response and the human NLRP1 inflammasome, specifically in primary human epithelial cells. This RNAseq experiments in particular seeks to identify the genes that are induced by DT in a manner that is dependent on the kinase activity of ZAKalpha.

overall_design: HPKs are treated with the following conditions: 1) DMSO+ PBS; 2) DMSO+DT (150ng/mL), 3) Compound 6p (ZAK inhibitor)+PBS and 4) Compound 6p+DT (150ng/mL). All cells were harvested 4 hours after DT treatment.

last: Zhong


title: miRNA-1 promotes Acute Myeloid Leukemia cell pathogenesis through metabolic regulation

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah


title: A genome-wide genetic screen uncovers novel determinants of human pigmentation

city: Stanford

first: Tomek

last: Swigut

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

summary: To study the differentially expressed genes in lightly and darkly pigmented human skin melanocytes, we isolated melanocytes from light and dark skin samples and performed RNA-seq using Illumina platform.

overall_design: comparative gene expression analysis of dark and light colored melanocytes

first: Joanna

last: Wysocka


title: Faecalibacterium prausnitzii abrogates immunotherapy toxicity

city: Shanghai

first: Gao

last: Yaqi

address: 145 Middle Shandong Road

institute: Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China

summary: To elucidate whether Faecalibacterium prausnitzii has effects on intestinal toxicity induced by immune checkpoint inhibitors, we performed RNA-seq analysis of colon tissues of mice receiving DSS, DSS+ICB and DSS+ICB+F. prausnitzii gavage to compare the gene expression profiles.

overall_design: RNA-seq was performed on colon tissues of mice receiving DSS(N=5), DSS+ICB(N=5) and DSS+ICB+F. prausnitzii gavage(N=5)


title: miRNA-1 promotes Acute Myeloid Leukemia cell pathogenesis through metabolic regulation [miRNA]

summary: Acute myeloid leukemia (AML) is a heterogeneous and deadly disease characterized by uncontrolled expansion of malignant blasts. The current treatment for AML patients includes intensive chemotherapy and high-risk hematopoietic stem cell transplantation, highlighting the need for less toxic and more effective therapies. Altered metabolism and dysregulated microRNA (miRNA) expression profiles are characteristic of AML. However, there is a paucity of studies exploring how changes in the metabolic state of the leukemic cells regulate miRNA expression leading to altered cellular behavior. Here, we blocked pyruvate entry into mitochondria by deleting the Mitochondria Pyruvate Carrier (MPC1) gene in MV4-11 and Molm-14 human AML cell lines, which decreased Oxidative Phosphorylation (OXPHOS). The loss of MPC1 led to increased expression of miR-1 in both human AML cell lines tested. AML patient sample analysis showed that higher miR-1 expression correlates with reduced survival. Transcriptional and metabolic profiling of miR-1 overexpressing AML cells revealed that miR-1 increased OXPHOS, along with key metabolites that fuel the TCA cycle such as glutamine and fumaric acid. Inhibition of glutaminolysis decreased the elevated OXPHOS in miR-1 overexpressing MV4-11 cells, highlighting that miR-1 regulates OXPHOS through glutaminolysis. Further, the overexpression of miR-1 in AML cells exacerbated disease in a mouse xenograft model. Our work expands current knowledge within the field by uncovering novel connections between AML cell metabolism and miRNA expression that facilitates disease progression. Together, our work points to miR-1 as a potential new therapeutic target that can be used to disrupt AML cell metabolism and thus pathogenesis.

overall_design: Comparison miRNA seq analysis of MV4-11 control and MV4-11 MPC1 KO cells, Molm-14 control and Molm-14 MPC1 KO cells.

first: Arevik

last: Ghazaryan

first: Jared

last: Wallace

first: Soh

last: Lee


title: Transient naive reprogramming corrects hiPS cells functionally and epigenetically [ONT DNA-seq]

city: Perth

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

summary: Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. We found that reprogramming-induced epigenetic aberrations emerge midway through primed reprogramming, whereas DNA demethylation begins early in naive reprogramming. Using this knowledge, we developed a transient-naive-treatment (TNT) reprogramming strategy that emulates the embryonic epigenetic reset. We show that the epigenetic memory in hiPS cells is concentrated in cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1 and aberrant CpH methylation. TNT reprogramming reconfigures these domains to a hES cell-like state and does not disrupt genomic imprinting. Using an isogenic system, we demonstrate that TNT reprogramming can correct the transposable element overexpression and differential gene expression seen in conventional hiPS cells, and that TNT-reprogrammed hiPS and hES cells show similar differentiation efficiencies. Moreover, TNT reprogramming enhances the differentiation of hiPS cells derived from multiple cell types. Thus, TNT reprogramming corrects epigenetic memory and aberrations, producing hiPS cells that are molecularly and functionally more similar to hES cells than conventional hiPS cells. We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications and providing a novel system for studying epigenetic memory.

overall_design: Examination of potential bottlenecking between different classes of induced pluripotent stem cells through lentiviral insertion site mapping

first: Sam

last: Buckberry

first: Xiaodong

last: Liu

last: Poppe

first: Jia

last: Tan

first: Jose

last: Polo


title: RNA sequencing of TCF19 knockdown by siRNA in endometrial cancer cells

city: Ji’nan

first: Xinyue

last: Ma

state: Shandong

address: 107 West Wenhua Road

institute: Qilu Hospital of Shandong University

summary: In our study, TCF19 was found to be upregulated in microsatellite instability (MSI) endometrial cancer and  was associated with poor prognosis and immune exhaustion signature. Elevated TCF19 enhanced cell proliferation and migration, which promoted tumorigenicity under non-immunological background; Moreover, tumoral TCF19 expression could also promote CD8+T cell exhaustion in tumor immune microenvironment, which facilitated immune escape and tumor development. Therefore, TCF19 could be a promising biomarker and effective therapeutic target for MSI endometrial cancer.

overall_design: RNA-seq was performed on three experimental triplictes of TCF19 knockdown (siTCF19) and control (siNC) Ishikawa cells.

first: Qing

last: Zhang

first: Beihua

last: Kong


title: Role of TCF19 in endometrial cancer

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


title: Third Generation Quinoline-3-Carboxamide Transcriptional Disrupter of HDAC4, HIF-1α, and MEF-2 Signaling for Metastatic Castration-Resistant Prostate Cancer

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: The quinoline-3-carboxamide, Tasquinimod, is orally active as a maintenance therapy with an on-target mechanism-of-action via allosteric binding to HDAC4. This prevents formation of the HDAC4/NCoR1/HDAC3 complex, disrupting HIF-1α transcriptional activation and repressing MEF-2 target genes needed for adaptive survival signaling in the compromised tumor microenvironment (TME). In phase 3 clinical testing against metastatic castration-resistant prostate cancer (mCRPC), Tasquinimod (1 mg/day) increased time-to-progression, but not overall survival. Here, we document that, on this regimen, blood levels are 10-fold lower than the optimal concentration (≥2 μM) needed for anti-cancer activity, suggesting higher daily doses are needed. Unfortunately, we also demonstrate that Tasquinimod is an aryl hydrocarbon receptor (AHR) agonist, which binds with an EC50 of 1 μM to produce unwanted off-target side effects. Therefore, we screened a library of Tasquinimod analogs to maximize on-target vs. off-target activity. Using this approach, we identified ESATA-20, which has ~10-fold lower AHR agonism and >5-fold greater potency against prostate cancer patient-derived xenografts. This increased therapeutic index nominates ESATA-20 as a lead candidate for clinical development as an orally active 3rd generation quinoline-3-carboxamide analog that retains its on-target ability to disrupt HDAC4/HIF-1α/MEF-2-dependent adaptive survival signaling in the compromised TME found in mCRPC.

overall_design: RNA sequencing of prostate tumor patient-derived xenograft (PDX) models using Illumina TruSeq Library prep and sequenced on Illumina NovaSeq 6000.

first: John

middle: T

last: Isaacs

first: Susan

last: Dalrymple

first: Lizamma

last: Antony

first: D

last: Rosen

first: Peter

last: Nelson

first: Maya

last: Kostova

first: Iain

middle: A

last: Murray

first: Gary

last: Perdew

first: Samuel

last: Denmeade

first: W

middle: N

last: Brennen

first: Emmanuel

last: Akinboye


title: EZH2 Mediated Metabolic Rewiring Promotes High-grade Serous Ovarian Cancer Progression Independently of Histone Methyltransferase Activity II

first: Jianfeng

last: Chen

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Enhancer of zeste homolog 2 (EZH2), the key catalytic subunit of polycomb repressive complex 2 (PRC2), is overexpressed and exerts an oncogenic role in various cancers through catalytic-dependent or -independent pathways. However, the mechanisms contributing to high-grade serous ovarian cancer (HGSOC) are not well understood. Here, we showed that a subgroup of HGSOC patients with high EZH2 expression but low H3K27me3 level exhibited the worst prognosis. We demonstrated that induction of EZH2 degradation but not catalytic inhibition profoundly blocked ovarian cancer cell proliferation and tumorigenicity in vitro and in vivo. We further demonstrated that EZH2 transcriptionally upregulated IDH2 to potentiate metabolic rewiring by enhancing the tricarboxylic acid cycle (TCA cycle), which contributed to the progression of HGSOC. Together, these data reveal a novel oncogenic role of EZH2 in HGSOC, and provide potential therapeutic strategies in HGSOC by targeting EZH2 non-catalytic activity.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for EZH2, H3K27me3 and SUZ12 in OVCAR8 cells.

first: Jin

last: Hong


title: Chromatin Immunoprecipitation(ChIP)-seq of TCF19 in endometrial cancer cells

first: Xinyue

last: Ma

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) was performed in TCF19 over-expression and control Ishikawa cells using anti-TCF19 antibody.


title: miRNA-1 promotes Acute Myeloid Leukemia cell pathogenesis through metabolic regulation [mRNA]

first: Ryan

last: O'Connell

overall_design: Comparison mRNA seq analysis of MV4-11 control and MV4-11 miR-1 overexpressing cells, Molm-14 control and Molm-14 miR-1 overexpressing cells.

first: Arevik

last: Ghazaryan

first: Warren

last: Voth

first: Soh

last: Lee


title: EZH2 Mediated Metabolic Rewiring Promotes High-grade Serous Ovarian Cancer Progression Independently of Histone Methyltransferase Activity

summary: Despite EZH2 is overexpressed and exerts an oncogenic role in various cancer through catalytic-dependent or -independent manner, the mechanisms of EZH2 contributing to high-grade serous ovarian cancer (HGSOC) are incompletely understood. Here, we showed that a subgroup of HGSOC patients with high EZH2 expression but low H3K27me3 level exhibited worst prognosis. We demonstrated that EZH2 degradation but not catalytic inhibition profoundly lowered EZH2 protein and blocked cell proliferation and tumorigenicity in vitro and in vivo. Ectopic expression of EZH2 without SET domain (EZH2-∆SET), which is known to be essential for catalytic activity, restored the phenotypes of EZH2 degradation. Mechanistically, we identified that IDH2 was transactivated by EZH2 to impair metabolic rewiring by disrupting the TCA cycle, which contributed to the oncogenic role of EZH2 in OC. Together, these data reveal a novel carcinogenic role of EZH2 in HGSOC, and provide potential strategies in HGSOC by targeting EZH2 non-catalytic activity.

overall_design: RNA-seq for OVCAR8 treated with DZNep or doxycycline-induced EZH2 silence was performed (duplicate).

first: Jing

last: Tan


title: Transient naive reprogramming corrects hiPS cells functionally and epigenetically [WGBS 2]

last: Lister

overall_design: Examination of genome-wide DNA methylation in human embryonic stem cells and different classes of induced pluripotent stem cells

first: Sam

last: Buckberry

first: Xiaodong

last: Liu

first: Daniel

last: Poppe

first: Jia

middle: P

first: Jose

last: Polo


title: Transient naive reprogramming corrects hiPS cells functionally and epigenetically [ATAC-seq]

overall_design: Examination of genome-wide ATAC-seq in human embryonic stem cells and different classes of induced pluripotent stem cells


title: Small RNA profiling of aster yellows infected Catharanthus roseus plants

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

summary: Aster yellows phytoplasma strain Hyd35 (16SrI-B) in micropropagated periwinkle shoots in collection was used to produce infected plants in pots that were separated according to the diverse symptomatology i.e. phyllody and witches’ broom. Small RNA high-throughput sequencing (HTS) was then used to determine the small RNA pattern of these plants. Bioinformatics analysis revealed the presence of expression changes of different miRNA classes and the presence of phytoplasma derived small RNAs. These results could complement previous studies and serve as a starting point for small RNA omics in phytoplasma research

overall_design: Potted cuttings from one micropropagated clone of C. roseus infected with aster yellows phytoplasma(strain Hyd35, 16SrI-B) were sampled. RNA was extracted from six plants showing different phenotypes: three showing phyllody, three showing witches’ broom and three asymptomatic plants. Small RNA libraries were prepared from these 9 plants

first: Nicoletta

last: Contaldo

first: Yuri

last: Zambon

first: Zsuzsanna

last: Galbacs Nagyne

first: Fabio

last: Miloro

first: Assunta

last: Bertaccini


title: Transient naive reprogramming corrects hiPS cells functionally and epigenetically [RNA-Seq]

overall_design: Examination of gene expression differences between isogenic human embryonic stem cells and different classes of induced pluripotent stem cells


title: Transient naive reprogramming corrects hiPS cells functionally and epigenetically [WGBS]


title: Genome-wide RNA-seq from control vector- and GALNT3-overexpressed H2030 cell lines

city: DaeJeon

first: Mi Young

last: Kim

address: Biological science

institute: KAIST

summary:
Purpose: To identify downstream signaling pathways mediated by GALNT3 in lung cancer
Methods: RNAs isolated from H2030 cells overexpressing control vector (vec) and GALNT3 (OE) were analyzed by using an Illumina Nextseq 500
Conclusions: Our study represents the first transcriptomic profiles of effects of GALNT3 overexpression in lung cancer

overall_design: mRNAs prepared from control vector- and GALNT3-overexpressed H2030 cell lines were analyzed in duplicaters by Illumina Nextseq 500.

first: Mi

middle: S

last: Park

first: Mi-Young

first: Jae-seok

last: Roe


title: Alterations to the Hidradenitis Suppurativa Serum Proteome with Spleen Tyrosine Kinase Antagonism: Proteomic Results from a Phase 2 Clinical Trial.

status: Public on Aug 10 2023

city: Liverpool

first: John

last: Frew

address: Elizabeth St

department: Dermatology

institute: Liverpool Hospital

summary: Serum Proteomic Analysis of patients with Hidradenitis Suppurativa treated with Fostamatinib

overall_design: Phase 2 Clinical Trial  (NCT05040698)

first: J


title: DIRECT: Digital Microfluidics for Isolation-Free Shared Library Construction of Single-Cell DNA Methylome and Transcriptome

city: Xiamen

first: Xi

last: Zeng

state: Fujian

address: No.422, Siming South Road

institute: Xiamen University

summary: Integrated single-cell transcriptome and DNA methylome profiling has provided insight into the complex regulatory networks of cells. Existing methods are based on picking a single-cell and performing library construction in a tube, which is costly and cumbersome. Here, we propose DIRECT, a digital microfluidics-based method for simultaneous analysis of the methylome and transcriptome in a single library construction. The accuracy of DIRECT is demonstrated in comparison with bulk and single-omics data, and the high CpG site coverage of DIRECT allows for precise analysis of copy number variation information, enabling expansion of single cell analysis from two- to three-omics. By applying DIRECT to monitor the dynamics of mouse embryonic stem cell differentiation, the relationship between DNA methylation and changes in gene expression during differentiation was revealed. DIRECT enables accurate, robust, and reproducible single-cell DNA methylation and gene expression co-analysis at a lower cost and with greater efficiency, broadening the application scenarios of single-cell multi-omics analysis and revealing a more comprehensive and fine-grained map of cellular regulatory landscapes.

platform_organism:
Homo sapiens
Mus musculus

overall_design: In total, 29 K562 cell line samples, 6 HL-60 cell line samples and 16 mESC samples were analyzed. We examined genome-wide DNA methylation and gene expression profiles of K562 and HL-60 cells, including 13 single-cell K562 and 6 single-cell HL-60 samples with DIRECT, three single-cell K562 samples in tube and two bulk K562 samples. We analyzed DNA methylome of 3 K562 cells. We detected transcriptome of 8 K562 cells with normal dNTP and cytosine-methylated dNTP, respectively. Mouse embryonic stem cells were grown on 6-cm culture dishes with MEF feeder cells and cultured in a complete medium supplemented with leukemia inhibitory factor (LIF) to prevent differentiation. To induce undirectional differentiation, mESCs were dissociated and replated onto 0.1% gelatin-coated dishes, and cultured without LIF in a feeder-free manner for two passages. We collected mESCs at day 0 and differentiated cells at day 4.

first: Shaowei

last: Jiang

first: Zhixing

last: Zhong

first: Xiaoping

last: Yang

first: Qiuyue

last: Chen

first: Zhi

last: Zhu

last: Song

first: Chaoyong


title: Large-scale analysis of the integration of enhancer-enhancer signals by promoters

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute (NKI)

summary: Genes are often regulated by multiple enhancers. It is poorly understood how the individual enhancer activities are combined to control promoter activity. Anecdotal evidence has shown that enhancers can combine sub-additively, additively, synergistically, or redundantly. However, it is not clear which of these modes are more frequent in mammalian genomes. Here, we systematically tested how pairs of enhancers activate promoters using a three-way combinatorial reporter assay in mouse cells. By assaying about 69,000 enhancer-enhancer-promoter combinations we found that enhancer pairs generally combine near-additively. This behaviour was conserved across seven developmental promoters tested. Surprisingly, these promoters scale the enhancer signals approximately following a power-law, but the exponent of this response varies between promoters. A housekeeping promoter showed an overall different response to enhancer pairs, and a smaller dynamic range. Thus, our data indicate that enhancers mostly act additively, but promoters transform their collective effect non-linearly.

overall_design: Per EEP  library 1 iPCR sample was prepared and sequenced paired end. The  Klf2 library iPCR was sequenced twice, first on a MiSeq and then on a NovaSeq 6000.  1 pDNA sample was prepared per EEP library. For cDNA samples  3  Biological replicates were performed for each EEP library. All pDNA and cDNA samples were sequenced twice on a NovaSeq 6000

first: Miguel

last: Martinez-Ara

first: Federico

last: Comoglio


title: Integrative Multi-omics Analysis Reveals the Impact of Epigenetic Regulator Cfp1 on male meiosis

city: Seoul

first: Chanhyeok

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

institute: KIST (Korea Institute of Science and Technology)

summary: Spermatogenesis is a complex process involving meiosis in spermatocytes and dynamic epigenetic changes that ensure the inheritance of genetic traits. CXXC finger protein 1 (Cfp1), a component of the SETD1 methyltransferase complex, has a binding domain specific for unmethylated CpG sites. Previous studies have implicated Cfp1 in the epigenetic changes required for meiosis in spermatocytes, and its loss of function has been shown to result in male sterility. In this study, we aimed to gain a comprehensive understanding of Cfp1 function in spermatocytes by examining its genome-wide binding profile and the resulting changes in DNA methylation and H3K4me3, a histone modification associated with active gene transcription. We isolated Cfp1-depleted spermatocytes and performed H3K4me3 ChIP-seq and reduced-representation bisulfite sequencing (RRBS) analyses. By integrating these multi-omics datasets with Cfp1 ChIP-seq analysis, we identified genes directly regulated by Cfp1 and characterised the epigenetic changes associated with its regulation. Our analysis shows that Cfp1 not only directly affects the regulation of genes essential for meiosis, but also has a significant impact on the overall regulation of gene expression. The knowledge gained from studying the regulatory mechanisms of Cfp1 in spermatocytes provides valuable information about the reproductive process and contributes to our understanding of the underlying causes of infertility.

overall_design: To observe cfp1-induced changes in DNA methylation in spermatocytes, we used RRBS to generate high-throughput sequencing data to identify methylation differences.

first: Kwonho

last: Hong


title: Transient naive reprogramming corrects hiPS cells functionally and epigenetically [ChIP-seq]

first: Ryan

last: Lister

overall_design: Examination of H3K9me3 enrichment in human embryonic stem cells and different classes of induced pluripotent stem cells

first: Sam

last: Buckberry

first: Xiaodong

last: Liu

first: Daniel

last: Poppe

first: Jia

last: Tan

first: Jose

last: Polo


title: Effect of  rice fermentation and succinic acid on gene expression of human dermal fibroblasts irradiated with UVA

city: Chengdu

first: Yu

last: Li

address: Guoxue Alley, No.37

department: Dermatology and venereology

institute: West China Hospital, Sichuan University

summary: Skin aging caused by UV is called photoaging, which is characterized by deeper wrinkles accompanied by senescence of dermal fibroblasts and reduction of collagens. Rice fermentation, widely used in the cosmetics, has been reported to possess anti-aging benefits on skincare, however, its roles in the skin photoaging remains unclear. In this study, the effects of Maifuyin (a rice fermentation), and its ingredients succinic acid (SA) and choline on UVA-induced senescence in fibroblasts were evaluated. A mRNA sequencing technology (RNA-seq) was applied to study the effects of these ingredients on UVA-induced photoaging. In conclusion, these results highlight the potential use of Maifuyin and SA as promising agents for anti-photoaging applications.

overall_design: Human dermal fibroblasts (HDFs), derived from human skin specimens, were used for experiments between 5 and 15 passages. Processing with 1 mg/mL Maifuyin and 1 mg/mL succinic acid, HDFs were exposed to 2 J/cm2 UVA irradiation and incubated with new serum-free medium for 3 h. Next, cells were washed twice with PBS and mRNAs were isolated from cell cultures using the Trizol method. mRNA-sequecing (n = 3) were completed by Novogene Inc on the Illumina Genome Analyzer under strict quality control.

first: Miao

last: Guo

first: Li

first: Fan

last: yang

first: Lidan

last: Xioing


title: Identification of crucial modules and genes associated with backfat tissue development by WGCNA in Ningxiang pigs

city: Changsha

first: Chen

last: Chen

address: No. 8 Changlang Road, Furong District, Changsha City, Hunan Province

institute: Hunan Institute of Animal & Veterinary Science

summary: Fat deposition is a prominent economic trait and complex process in pigs. Ningxiang pig, one of the four famous indigenous breeds in China, is characterized by high fat content. The underlying gene expression pattern in different developmental periods of backfat tissue remains unclear, and the purpose of this investigation is to explore the potential molecular regulators of backfat tissue development in Ningxiang pigs. Histological analysis of backfat tissue showed that adipocyte area increased and adipocyte number decreased with the development of backfat tissue in different stages (60d, 120d, 180d, 240d, 300d, and 360d). Meanwhile, a total of 1024 differentially expressed genes were identified in five comparison groups (120d vs 60d, 180d vs 120d, 240d vs 180d, 300d vs 240d, and 360d vs 300d). And then strongly co-expressed genes in modules were clustered by Weighted gene co-expression network analysis (WGCNA). Among these modules, turquoise, red, pink, paleturquoise, darkorange, and darkgreen module had close correlation with 60d, 120d, 180d, 240d, 300d, and 360d developmental stage, respectively, while tan, black and turquoise module had intimate relation with backfat thickness, adipocyte area and adipocyte number, respectively. Furthermore, GO and KEGG enrichment were analyzed in each module, the gene co-expression network was constructed, and the hub genes were described. According to the co-expression network, 13 genes (ACSL1, ACOX1, FN1, DCN, CHST13, COL1A1, COL1A2, COL6A3, COL5A1, COL14A1, OAZ3, DNM1, and SELP) were recognized as hub genes. Further analysis revealed that ACSL1 and ACOX1 might perform considerable function in early developmental stage of backfat tissue before 60d. FN1, DCN, COL1A1, COL1A2, COL5A1, COL6A3, and COL14A1 have unignorable position around 120d developmental stage. Besides, the functional relevance associated with SELP and backfat thickness, DNM1 and adipocyte area needs to be elucidated. In addition, QCR analysis validated the strong consistency of genes expressions with RNA-seq data, manifesting the reliability and accuracy of our study. The present research preliminarily depicted the gene co-expression network for each period of backfat developmental stage in Ningxiang pigs, which not only help to understand the integrated mechanism underlying backfat tissue development and lipid metabolism, but also promotes the progress of genetic improvement in pigs.

overall_design: Eighteen castrated Ningxiang pigs in six developmental stages (60d, 120d, 180d, 240d, 300d and 360d) were used in this study. Six groups of pigs were half-sibs, and the three samples in each developmental stage were full-sibs. All the experimental pigs were reared under the standard environmental conditions. The backfat tissue at the position of the thickest point in shoulder were collected, and the sample was immediately frozen in liquid nitrogen for the further RNA-sequencing.

first: Huibo

last: Ren

first: Huali

first: Yuan

last: Deng

first: Qingming

last: Cui

first: Ji

first: Siyang

last: Zhang

first: Jine

last: Yu

first: Huiming

last: Wang

first: Xiaodan

first: Shiliu

last: Yang

first: Xionggui

last: Hu

first: Yinglin

last: Peng


title: Epigenome analysis of normal and colorectal cancer (CRC) samples

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

type: Methylation profiling by genome tiling array

summary:
Genome wide DNA methylation profiling of peripheral blood mononuclear cells(PBMCs) in normal and CRC samples. The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 820,000 CpGs in PBMC samples. Samples included 50 newly diagnosed CRC patients and 50 normal controls.
NOTE:Patients numbered "CRC" and "E-CRC" are from two wards of the same hospital and do not need to be treated differently in data analysis.

overall_design: Bisulphite converted DNA from the 100 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip.

first: Chuanxin


title: The transcriptional profile of 'Candidatus Epulopiscium viviparus' within Naso tonganus guts at different time points throughout its diurnal cycle

city: Ithaca

first: David

last: Sannino

state: New York

address: 123 Wing Drive

department: Microbiology

institute: Cornell University

summary: Transcriptome of 'Candidatus Epulopiscium viviparus' type B cells found in Naso tonganus guts. The purpose is to see how the transcriptome of type B changes throughout the day as its host feeding pattern changes.

overall_design: Samples are of type B cells isolated directly from the gut of Naso tonganus at early morning, mid morning, and evening time points. Each sample comes from a separate fish, thus they are biological replicates.

first: Francine

last: Arroyo

first: Wenbo

first: Esther

last: Angert


title: mRNA transcriptome data of normal ovarian stromal cells and tumor ovarian stromal cells

city: Dummerstorf

first: Vijay simha

last: Baddela

address: Wilhelm-Stahl-Allee 2

department: Reproductive biology

institute: Leibniz institute for farm animal biology

summary:
Stromal fibroblast cells were isolated from an unusually enlarged left-side ovary of a Holstein cow. Isolated stromal cells expressed several genes such as asporin and VCAM1 that are active in aggressive tumors.
Several functional pathways were modulated especially sirutin signaling pathway, oxidative phosphorylation and mitochindrial dysfunction.

overall_design: RNA from normal  and  tumor ovarian stromal cells were processed for microarray  analysis

first: Arpna

last: Sharma

first: Vijay Simha

first: Jens

last: Vanselow


title: GPX8 deficiency-induced oxidative stress reprogrammed m6A epitranscriptome of oral cancer cells

city: guangzhou

first: xun

last: chen

state: guangdong

address: Linyuanxi Road 55

institute: Sun yat-sen University

summary: Glutathione peroxidase 8 (GPX8) is a key regulator of redox homeostasis. Whether its antioxidant activity participates in the regulation of m6A modification is a crucial issue, which has important application value in cancer treatment. MeRIP-seq was used to explore the characteristics of transcriptome-wide m6A modification in GPX8-deficient oral cancer cells in this study. Oxidative stress caused by lack of GPX8 resulted in 1,279 hyper- and 2,287 hypo-methylated m6A peaks and 2,036 differentially expressed genes in GPX8-KO cells. Twenty-eight differentially expressed genes were related to the cell response to oxidative stress, and half of them changed their m6A modification. In GPX8-KO cells, m6A regulators IGF2BP2 and IGF2BP3 were upregulated, while FTO, RBM15, VIRMA, ZC3H13 and YTHDC2 were downregulated. After H2O2 treatment, the expression changes of RBM15, IGF2BP2 and IGF2BP3 were further enhanced. These data indicated that GPX8-mediated redox homeostasis regulated m6A modification, thereby affecting the expression and function of downstream genes. This study highlights the possible significance of GPX8 and the corresponding m6A regulatory or regulated genes as novel targets for antioxidant intervention in cancer therapy

overall_design: Transcriptome-wide methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were performed as previously described. Briefly, total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). PolyA RNA was purified using DynabeadsOligo (dT)25-61005 (Thermo Fisher, CA, USA) and cleavedinto about 100nt fragments using Magnesium RNA Fragmentation Module (NEB, USA). One portion of the RNA fragments was used as input and the other portion wasimmunoprecipitated with m6A-specific antibody (Synaptic Systems, Germany) to enrich m6A-methylated RNA fragments. RNA sequence library was prepared and purified, and the paired-end sequencing (PE150) of libraries was performed on Illumina NovaSeq™ 6000 platform (LC-Bio Technology CO., Ltd., Hangzhou, China), following the manufacturer’s protocol.

first: Xun

last: Chen

first: Lingyu

last: Yuan

first: Lejia

first: Liutao


title: PerturbSci-Kinetics: Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens

city: New York

first: Zihan

last: Xu

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: Here we described PerturbSci-Kinetics, a novel combinatorial indexing method for capturing three-layer single-cell readout (i.e., nascent transcriptome, whole transcriptome, sgRNA identities) across hundreds of genetic perturbations. Through PerturbSci-Kinetics profiling of pooled CRISPR screens, we were able to decipher the complexity of RNA dynamics (e.g., synthesis, splicing, and degradation) at both global and gene-specific levels. Our technique opens up the possibility to perform genome-wide perturbations across millions of single cells cost-effectively.

overall_design: A growth screen including 699 gRNAs targeting 228 genes and no-target

first: Andras

last: Sziraki

first: Jasper

last: Lee

first: Wei

last: Zhou

first: Junyue

last: Cao


title: TGF-β1 activates neutrophil signaling and transcription but not migration

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

summary: Tumor-associated neutrophils are found in many types of cancer and are often reported to contribute to negative outcomes. Several studies have shown that the presence of TGF-β in the tumor microenvironment contributes to the skewing of neutrophils to have a more pro-tumor phenotype. However, the direct effects of TGF-β on neutrophil signaling and migration are unclear. We sought to characterize TGF-β signaling in both primary human neutrophils and the neutrophil-like cell line HL-60 and determine whether TGF-β directly induces neutrophil migration. We found that TGF-β1 does not induce neutrophil migration in either a transwell or an underagarose migration assay. However, TGF-β1 does activate signals canonically through SMAD3 and noncanonically through ERK1/2 in neutrophils in a time and dose-dependent manner. Additionally, TGF-β1 present in the tumor-conditioned media (TCM) is responsible for SMAD3 activation. Moreover, we discovered that TCM from aggressive breast cancer cells induces neutrophils to secrete leukotriene B4 (LTB4), which is a lipid mediator important for amplifying neutrophil recruitment. However, we found that TGF-β1 alone does not induce secretion of LTB4. We next performed RNA-sequencing to evaluate the effects of TGF-β1 and TCM on the neutrophil transcriptome. We found that TGF-β1 and TCM result in changes in gene transcription in HL-60 cells, specifically of two pro-tumor genes OSM and VEGFA. Together, our findings characterize the effects of TGF-β1 on neutrophil signaling, migration, and gene expression that can be applied to understanding the changes in neutrophils that occur in the tumor microenvironment.

overall_design: We performed RNA-seq analysis using 2 cell lines, 2 time points, and 2 treatments each with their own media control

first: Lauren

middle: E

last: Hein

first: Carole

last: Parent

first: Craig

last: Johnson


title: Ahmed Scientific Advances 2023 data repository

city: Madison

first: Jack

middle: M

last: Shireman

state: WI

address: 1500 Highland Ave

department: Neurological Surgery

institute: UW-Madison

summary: Understanding of TMZ therapy during and after treatment in a mouse model

overall_design: single cell sequencing was conducted on mice both after and during in Vivo TMZ treatment

first: Atique

middle: U

last: Ahmed


title: Biological function and mechanism of circRNA in the occurrence and development of hepatocellular carcinoma

city: Nanning

first: Deyuan

last: Li

address: 22 Shuangyong Road, Nanning

institute: Guangxi Medical University

summary: In order to study the biological function and regulatory mechanism of circRNA in the occurrence and development of HCC, we collected cancer and adjacent tissues of 5 HCC patients, extracted total RNA and mixed samples of equal quality. RNA-seq was used to obtain the expression profiles of differential circRNA in HCC tissues, and the expression profiles were annotated and analyzed for differential expression.

overall_design: Comparison of gene expression profiles of RNA-seq data in HCC tissues and adjacent tissues.

first: Xiaoyun

last: Zeng

first: Meiliang

last: Liu

first: Mingshuang

last: Lai