title: Disruption of higher order nuclear condensates by a dominant negative FOXN1 mutation causes immunodeficiency

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: The transcription factor FOXN1 acts in a gene-dosage sensitive way as a master regulator of thymic epithelial cell development and maintenance enabling effective thymopoiesis. Its autosomal recessive loss of function is the molecular cause of the “nude” phenotype, a severe combined immunodeficiency caused by athymia. Here we report on  a spontaneously occurring, novel heterozygous FOXN1 mutation that initially permits regular thymus organogenesis but results in a failure of thymic maintenance beyond late stages of human gestation. Modeling the mutation in mice results in divergent disruptions of normal TEC subtype differentiation and function.  Transcriptionally inactive,  the mutant disrupts the formation of wild type FOXN1 homo-multimers and occupies canonical DNA binding sites, at which it operates in a dominant negative fashion to displace wild type FOXN1 from nuclear condensates. Comparing the interactome of the mutant and wild type FOXN1 identified binding partners that uniquely interact with wild type FOXN1 and are characteristic constituents of nuclear organelles required for transcription. Mutant FOXN1 moves in and out of condensates over a time-course indistinguishable from that of wild type FOXN1, suggesting that the mutation did not affect the molecular movement of FOXN1.  Thus, we have identified a clinically relevant gain of function mutation of FOXN1 that actively prevents the transcriptional activity of wild type FOXN1 and provides critical insight into the mechanism by which FOXN1 operates in controlling sustained gene expression necessary for normal thymic epithelial cell differentiation, maintenance and function.

overall_design: mTEC4D6 cell lines - RNA-seq: WT-FOXN1, d550-FOXN1, WT-FOXN1/d550-FOXN1 and empty control (n = 3 for each); ChIP-seq: WT-FOXN1, d550-FOXN1, WT-FOXN1-input and d550-FOXN1-input (n = 3 for each); mouse model - 10X gene expression: wt/wt-Foxn1 and d505/wt-Foxn1 (n = 3 for each at 5 weeks and 16 weeks of age)

first: Ioanna

last: Rota

first: Georg

last: Holländer


title: Down Syndrome Induced Senescence Disrupts the Nuclear Architecture of Neural Progenitors

status: Public on Oct 11 2021

city: Cambridge

first: Hiruy

last: Meharena

state: MA

address: 43 Vassar St

department: The Picower Institute for Learning and Memory

country: USA

institute: Massachusetts Institute of Technology

type: Expression profiling by high throughput sequencing

summary: We utilized human derived induced pluripotent stem cells (iPSCs) and iPSC derived neural progenitor cells (NPCs) from individuals with Down syndrome and sex matched controls to interrogate the cell type consequences of trisomy 21 (T21). We report the consequences of T21 on the spatial chromatin organization (Hi-C), lamina-associated domains (ChIP-seq), chromatin state (ATAC-seq), and transcriptome (RNA-seq)  in an isogenic pair (euploid: Iso-E and trisomic: Iso-T cells derived from the same individual), pair of male individuals with euploid (Ma-E) and trisomic (Ma-T), pair of female individuals with euploid (Fe-E) and trisomic (Fe-T). Our findings show that T21 induces chromosomal introversion, disrupts lamina-associated domains (LADs) and alters the genome-wide chromatin-accessibility of NPCs but not iPSCs. While the overall organization of A/B compartments and location of TAD-boundaries are conserved in NPCs harboring T21, we observe loss of chromatin-accessibility within the A-compartment that is associated with transcriptional downregulation, and increased long-range chromatin interactions in the B-compartment that is associated with transcriptional upregulation. We find that these architectural changes are similar to those observed in senescent cells, and our transcriptional analysis confirms that differentially expressed genes (DEGs) identified in NPCs harboring T21 are highly correlated with DEGs identified in oxidative stress induced senescent cells. Finally, we demonstrate that the senolytic drug combination of dasatinib and quercetin alleviates the genome-wide transcriptional disruption, as well as deficits in cellular migration and proliferation observed in NPCs harboring T21.

overall_design: Decoding the impact trisomy 21 (T21) on the 3D-genome organization, lamina-associated domains, epigenome and transcriptome of human derived induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs).

middle: S

first: Asaf

last: Marco

first: Li-Huei

last: Tsai


title: Gene expression profiles in GC B cells of wild-type and Bmi1 cKO mice during acute or chronic viral infection

city: Melbourne

first: Andrea

last: Di Pietro

state: VIC

address: 305 Grattan Street

department: Cancer Immunology program

country: Australia

institute: Peter MacCallum Cancer Centre

summary: To study how chronic viral infection disrupts B cell differentiation pathways and identify key intrinsic regulators in an endogenous polyclonal response, we used the comparative LCMV model. Wild-type or Bmi1 conditional know-out in B cells mice were infected with either the acute (WE) versus chronic (Docile) strains of LCMV, GC B cells (CD19+IgDloCD95+CD38loCD138-) isolated 14 days post-infection, and RNA-seq was undertaken

overall_design: 8 samples . Each group has at least 2 biological replicates.

first: Kim

last: Good-Jacobson

first: Christopher

middle: D

last: Scharer


title: GABAergic neuronal IL-4R mediates T cell effect on memory

status: Public on Oct 12 2021

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

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

overall_design: Refer to individual Series


title: NEURON-SPECIFIC CHROMOSOMAL MEGADOMAIN ORGANIZATION IS ADAPTIVE TO RECENT RETROTRANSPOSON EXPANSIONS

city: New York

first: Sandhya

last: Chandrasekaran

state: NY

address: 1470 Madison Avenue, 9-202, Hess Building

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here, we mapped cell-type specific chromatin domain organization in adult mouse cerebral cortex and report strong enrichment of Endogenous Retrovirus 2 (ERV2) repeat sequences in the neuron-specific heterochromatic 'B2NeuN+' megabase-scaling subcompartment. Comparative chromosomal conformation mapping in Mus spretus and Mus musculus revealed neuron-specific reconfigurations tracking recent ERV2 retrotransposon expansions in the murine germline, with significantly higher B2 megadomain contact frequencies at sites with ongoing ERV2 insertions in Mus musculus. Ablation of the retrotransposon silencer Kmt1e/Setdb1 (KO) triggered B2 megadomain disintegration and rewiring with open chromatin domains enriched for cellular stress response genes, along with severe neuroinflammation and proviral assembly of ERV2/Intracisternal-A-Particles (IAPs) infiltrating dendrites and spines. We conclude that neuronal megadomain architectures include evolutionarily adaptive heterochromatic organization which, upon perturbation, unleashes ERV proviruses with strong tropism within mature neurons.

sample_organism:
Mus musculus
Mus spretus

platform_organism:
Mus musculus
Mus spretus

overall_design: Chromatin configurations, histone modifications, RNA, and open chromatin profiles in wildtype and Setdb1 fl/fl x Camk2a-Cre mice; chromatin configurations in SPRET/EiJ and C57/BL6J mice; targeted de novo insertions in wildtype mice

first: Sergio

last: Espeso-Gil

first: Yong-Hwee

middle: E

last: Loh

first: Behnam

last: Javidfar

first: Bibi

last: Kassim

first: Yuhao

last: Dong

first: Yueyan

last: Zhu

first: Lucy

middle: K

last: Bicks

first: Prashanth

last: Rajarajan

first: Cyril

middle: J

last: Peter

first: Esperanza

last: Agullo-Pascual

first: Marina

last: Iskhakova

first: Molly

last: Estill

first: Li

last: Shen

first: Yan

last: Jiang

first: Schahram

last: Akbarian


title: Gene expression profiles in GC B cells during acute and chronic viral infection

first: Andrea

last: Di Pietro

summary: To study how chronic viral infection disrupts B cell differentiation pathways and identify key intrinsic regulators in an endogenous polyclonal response, we used the comparative LCMV model. Wild-type mice were infected with either the acute (WE) versus chronic (Docile) strains of LCMV, GC B cells (CD19+IgDloCD95+CD38loCD138-) isolated 14 days post-infection, and RNA-seq was undertaken

overall_design: 4 samples . Each group has at least 2 biological replicates.

first: Kim

last: Good-Jacobson

first: Christopher

last: Scharer

first: Tian

last: Mi


title: Using next generation sequencing to compare gene expression of wild type and Δcsp1 mutant of bacterial plant pathogen Xylella fastidiosa strain Stag's Leap

status: Public on Oct 10 2021

city: Parlier

first: Lindsey

last: Burbank

state: California

address: 9611 S Riverbend Ave

institute: USDA-ARS

summary: To investigate the role(s) of a cold shock protein homolog (Csp1) in plant pathogenic bacteria Xylella fastidiosa, we compared transcriptome profiles between wild type and a csp1 deletion mutant (Δcsp1) using long read Nanopore RNA sequencing.

overall_design: Examined mRNA profiles of 7 day old wild type and Δcsp1 X. fastidiosa cells grown on PD3 agar plates under standard conditions (28°C) and at low temperature conditions (15°C)

first: Wei

last: Wei

middle: P

first: Teresa

last: Sawyer


title: NRF1 Association with AUTS2-Polycomb Mediates Specific Gene Activation in the Brain

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

summary: Polycomb group (PcG) proteins are evolutionarily conserved chromatin-modifying factors that regulate gene expression to control tissue development. We previously discovered an AUTS2?Polycomb complex activates gene expression by recruiting Casein kinase 2 (CK2) and P300. But the mechanisms underlying the recruitment of AUTS2-PRC1 to chromatin and the physiological relevance of AUTS2-P300 interaction during neurodevelopment remain unknown. Here, we report that the transcription factor Nuclear Respiratory Factor 1 (NRF1) physically interacts with AUTS2 and overlaps with AUTS2 on chromatin binding. In a functional study combined with the single cell RNA-seq approach, we demonstrate that NRF1 is required for AUTS2 recruitment to chromatin, ncPRC1 associated active transcription in motor neuron and thereby modulates multipotent progenitors to motor neuron differentiation. Moreover, we discover that mutations within AUTS2 HX repeat region, which associate with RSTS phenotype disrupt AUTS2-P300 interaction and AUTS2 mediated transcriptional activation. Together, these findings reveal the underlying mechanism by which the AUTS2-containing ncPRC1 complex is recruited and activates transcription and mutations in the AUTS2 HX repeat region exert a dominant negative effect on AUTS2-P300 mediated transcriptional activation in RSTS.

overall_design: ChIP-seq for AUTS2-PRC1 complex and NRF1 in mouse brain, mESCc, in vitro differentiated motor neuron under WT, Auts2, Nrf1 knockout condition, as well as scRNA-seq in MN under WT, Auts2, Nrf1 knockout condition.

first: Sanxiong

last: Liu

first: Danny

last: Reinberg


title: Zygotic transcription of ZGA staged embryos [GRO-seq]

status: Public on Oct 13 2021

city: Freiburg

first: Michael

last: Rauer

address: Breisacherstr. 153

department: Medical Faculty

country: Germany

institute: University of Freiburg

summary: During embryogenesis, the genome shifts from transcriptionally quiescent to extensively active in a process known as Zygotic Genome Activation (ZGA). In Drosophila, the pioneer factor Zelda is known to be essential for the progression of development, still, it regulates the activation of only a small subset of genes at ZGA. However, thousands of genes do not require Zelda, suggesting that other mechanisms exist. By conducting GRO-seq, HiC and ChIP-seq in Drosophila embryos, we demonstrate that up to 65% of zygotically activated genes are enriched for the histone variant H2A.Z and independent of Zelda. H2A.Z enrichment precedes ZGA and Polymerase II loading onto chromatin. In vivo knock-down of maternally contributed Domino, a histone chaperone and ATPase, reduces H2A.Z deposition at transcription start sites, causes global downregulation of housekeeping genes at ZGA, and compromises the establishment of the 3D chromatin structure. We infer that maternal factors and H2A.Z are master regulators of the de novo establishment of transcriptional programs during ZGA via chromatin reorganization.

overall_design: GRO-seq of Ctrl and DomKD embryos at ZGA, 3 replicates per condition performed in two different batches (A and B)

first: Dafne

middle: A

last: Ibarra Morales

first: Nicola

last: Iovino


title: A Polycomb domain found in committed cells impairs differentiation when introduced into PRC1 in pluripotent cells (ChIP-seq, CUT&RUN datasets)

city: Boston

first: Robert

last: Kingston

address: 185 Cambridge Street, 7th Floor

department: Molecular Biology

institute: Massachusetts General Hospital

summary: The CBX family of proteins is central to proper mammalian development via key roles in Polycomb-mediated maintenance of repression. CBX proteins in differentiated lineages have chromatin compaction and phase separation activities that might contribute to maintaining repressed chromatin. The predominant CBX protein in pluripotent cells, CBX7, lacks the domain required for these activities. We inserted this functional domain into CBX7 in embryonic stem cells to test the hypothesis that it contributes a key epigenetic function. ESCs expressing this chimeric CBX7 were impaired in their ability to properly form embryoid bodies and neural progenitor cells and showed reduced activation of lineage-specific genes across differentiation. Neural progenitors exhibited a corresponding inappropriate maintenance of Polycomb binding at neural-specific loci over the course of differentiation. We propose that a switch in the ability to compact and phase separate is a central aspect of Polycomb group function during the transition from pluripotency to differentiated lineages.

overall_design: Embryonic stem cells expressing different versions of CBX7 (WT, CaPS, KO) were differentiated into embryoid bodies and neural progenitor cells. Localization of PRC1 and H3K27me3 was determined in ESCs and differentiated cells by ChIP-Seq and by CUT&RUN. ChIP-Seq peaks were called over input values, and CUT&RUN peaks were called over IgG control values. Replicates were averaged where present. All comparisons were made between experiments that were performed at the same time.

first: Elizabeth

last: Jaensch


title: Targeting BMI-1 in B cells restores effective humoral immune responses and controls chronic viral infection


title: Chromatin accessibility regions in GC B cells during acute and chronic viral infection

summary: To study how chronic viral infection disrupts B cell differentiation pathways and identify key intrinsic regulators in an endogenous polyclonal response, we used the comparative LCMV model. Wild-type mice were infected with either the acute (WE) versus chronic (Docile) strains of LCMV, GC B cells (CD19+IgDloCD95+CD38loCD138-) isolated 14 days post-infection, an ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) was undertaken.

overall_design: 8 samples. Each group has at least 4 biological replicates.


title: A Polycomb domain found in committed cells impairs differentiation when introduced into PRC1 in pluripotent cells


title: Next Generation Sequencing Facilitates Quantitative Analysis of Control and beta-catenin Deficient Cancer-associated Fibroblasts Transcriptomes

city: Cincinnati

first: Yuhang

last: Zhang

state: OH

address: 231 Albert Sabin Way

institute: University of Cincinnati

summary: D4M BrafV600E; Ptenlox5/lox5 melanoma cells mixed with uninduced control Fb (Ctnnb1+/+; Col1α2-CreER) or mutant bcat/Fb (Ctnnb1fl/fl; Col1α2-CreER) were injected intradermally into flanks of control Ctnnb1+/+; Col1α2-CreER or Ctnnb1 fl/fl; Col1α2-CreER mice, respectively. Tumors were allowed to grow to a volume of approximately 62.5 cubic millimeters when tamoxifen (TAM) was then administrated to induce β-catenin ablation in mutant bcat/Fb CAFs. Control CAFs or bcat/CAFs were collected from BrafV600E; Ptenlox5/lox5 melanoma tumors using PDGFRα as a marker for fibroblasts. Normal fibroblasts were collected from B6 mouse skin.

overall_design: mRNA profiles of normal fibroblasts; control CAF and bcat/CAF were generated by  Illumina HiSeq-based next generation sequencing in triplicate.

first: Linli

last: Zhou

first: Tianyi


title: DNA methylation profiles of cells commonly found in bronchoalveolar lavage

status: Public on Oct 09 2021

city: Parkville

first: Shivanthan

last: Shanthikumar

address: 50 Flemington Road

institute: Royal Children's Hospital

summary: Genome wide DNA methylation profiling of 4 cell populations purified from paediatic bronchoalveolar lavage samples. The cell types profiled are alveolar macrophages, granulocytes, lymphocytes and alveolar epithelial cells. Fluorescence-activated single cell sorting was used to purify the cell populations of interest using previously described methods (Shanthikumar, AJRCMB, 2020 ;63(2):152-159). Genome wide DNA methylation profiling was performed via the EPICArray. These data can be used for reference based deconvolution of cell proportion of bronchoalveolar lavage samples. DNA extracted from raw BAL (n=6) was also profiled using the EPICArray, allowing for validation of reference based deconvulution.

overall_design: Bisulphite converted DNA from a total of 20 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip. 14 samples are made up of alveolar macrophages (n=5), granulocytes (n=4), lymphocytes (n=3), and alveolar epithelial cells (n=2).  6 samples are raw BAL.

first: Jovana

last: Maksimovic


title: Direct analysis of the embryo-maternal interactions in a 3D biomimetic implantation niche

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: To decipher the crosstalk between the implanting mouse embryo and the maternal blood vessels we analysed the transcriptomes of the trophoblast and the endothelial cells using RNA-seq. Using laser-assisted microdissection, we isolated the mural trophectoderm of E4.5 (non-implanted embryo) and E4.75 blastocysts (attached to the uterine wall). As the invasive trophoblast giant cells (TGCs) at early egg cylinder stage (implanted embryo) are not accessible, we allowed the E4.5 mural TE to differentiate into TGCs in vitro for 3 days and then we proceeded with the transcriptional analysis. In addition, we analysed the transcriptome of the endothelial cells of the E5.5 decidua and the bEnd5 endothelial cell line. We found that the trophoblast activates the expression of a large repertoire of vascular receptors, ligands and cell adhesion molecules, compiling a network for communication with the maternal blood vessels.

overall_design: RNA sequencing analysis of endothelial cells the E5.5 decidua, bEnd5 endothelial cells, E4.5 mural trophectoderm, E4.75 mural trophectoderm and trophoblast giant cells (TGCs).

first: Ivan

last: Bedzhov

first: Niraimathi

last: Govindasamy

first: Hyun

middle: W


title: Combination of EZH2 inhibitor and STING agonist in melanoma cell lines

city: Beijing

first: Tianxiao

last: Xu

address: 52 Fucheng Road, Haidian District, Beijing

country: China

institute: Peking University Cancer Hospital

summary: In order to better understand the effects of combination treatment with EZH2 inhibitor and STING agonist in human melanoma cells, RNA sequencing was performed to explore transcriptome alteration.

overall_design: RNA sequencing in 2 melanoma cell lines with GSK126 or/and di-ABZI treatment

first: Jie

last: Dai

first: Jun

last: Guo


title: RNA sequencing of E. coli NCM3722 over the course of glucose to acetate growth transition

city: San Diego

first: Rohan

last: Balakrishnan

state: Ca

address: 9500 Gilman drive

department: Physics

institute: UCSD

summary: To understand the gene response during the glucose to acetate diauxic transition, we grew E. coli in minimal media with acetate and a small amount of glucose. Cells were collected and RNA was purified at different time points during the growth transition, including pre-shift (growth on glucose), 5 minutes, 15 minutes, 60 minutes and 120 minutes after glucose run-out, and steady state growth on acetate (post-shift).

overall_design: Time-course monitoring of E. coli transcriptome by performing 6 RNA-sequencing experiments during glucose to acetate growth transition.

first: Jonas

last: Cremer

first: Terence

last: Hwa


title: Calcium-Restricted Lipid Remodeling Drives Ferroptosis Resistance

city: Neuherberg

first: Joel

middle: Anton

last: Schick

address: Ingolstädter Landstr. 1

department: TOXI

institute: HMGU

summary: Ferroptosis is an iron-dependent form of cell death driven by biochemical and metabolic alterations resulting in oxidation within the lipid compartment. Calcium is a potent signaling molecule ascribed to diverse cellular processes including migration, neurotransmitter function, and cell death. Here we elucidate a crucial link between calcium homeostasis and ferroptotic cell death through the identification of the tetraspanin MS4A15. Ectopic MS4A15 expression specifically protects against ferroptosis by depleting endoplasmic reticulum stores. In an unexpected connection, prolonged calcium dysregulation stimulates fundamental remodeling to ferroptosis-resistant monounsaturated and plasmalogen lipid species. Application of this discovery revealed that augmenting luminal calcium sensitizes cancer cell lines previously refractory to ferroptosis. This finding provides a unique mechanistic basis for ferroptosis sensitivity and resolves a long-standing query into the role of calcium in oxidative cell death. Manipulating calcium homeostasis offers an unprecedented strategy for overcoming therapy resistance in cancer.

overall_design: Examination of differential expressed genes in Ms4a15 OE and parental MF cells

first: Shan

last: Xin


title: Single-cell mRNAseq human pulmonary arterial endothelial cells in healthy and pulmonary arterial hypertension

status: Public on Oct 08 2021

city: Cleveland

first: Bo

last: Hu

state: Ohio

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: We report the single cell transcriptomic profiles of isolated and cultured human pulmonary arterial endothelial cells. Details were published in Scientifc Reports | (2021) 11:14714

overall_design: Examination of the single-cell profiles of human pulmonary arterial endothelial cells from health and pulmonary arterial hypertension lungs.

first: Kewal

last: Asosingh

first: Serpil

last: Erzurum

first: Suzy

last: Comhair

first: Lori

last: Mavrakis

first: Dean

last: Horton

first: Ian

last: Taylor

first: Svyatoslav

last: Tkachenko

first: Weiling


title: Spatial discordances between mRNAs and proteins in the intestinal epithelium

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

summary: A cell’s proteome is an important determinant of its functional state, however the use of transcriptomes as reliable proxies for cellular proteomes is debatable. In the small intestine, nutrient absorbing enterocytes operate for four days as they migrate along villi, highly graded microenvironments. Spatial transcriptomics demonstrated profound zonation in enterocyte gene expression, but how this variability translates to protein content is unclear. Here, we used spatial sorting to generate global spatial maps of enterocyte proteins and mRNAs along the villus axis. We found that both were zonated, yet often spatially anti-correlated. We developed a Bayesian approach to infer protein translation and degradation rates from the combined spatial profiles, and demonstrate that space-independent protein-synthesis delays can explain the mRNA-protein discordances. Our work provides a proteomic spatial blueprint of the intestinal epithelium and highlights the importance of protein measurements for inferring states of tissue cells that operate outside of steady state.

overall_design: mRNA profiles of enterocytes from spatially stratified villi zones, EDTA isolated jejunum epithelial cells from mouse jejunum were sequenced in several batches in an Illumina NextSeq.

first: Yotam

last: Harnik

first: Lisa

last: Buchauer

first: Shani

last: Ben-Moshe

first: Yishai

last: Levine

first: Alon

last: Savidor

first: Raya

last: Eilam

first: Andreas

last: Moor

first: Shalev

last: Itzkovitz


title: Modulation of the human pancreatic ductal adenocarcinoma immune microenvironment by stereotactic body radiotherapy

city: Rochester

first: Bradley

last: Mills

address: 601 Elmwood Avenue

institute: University of Rochester

summary:
Purpose: Stereotactic body radiotherapy (SBRT) is an emerging treatment modality for pancreatic ductal adenocarcinoma (PDAC) that can effectively prime cytotoxic T cells by inducing immunogenic tumor cell death in preclinical models. SBRT effects on human PDAC have yet to be thoroughly investigated, therefore, this study aimed to characterize immunomodulation in the human PDAC tumor microenvironment following therapy.
Experimental Design: Tumor samples were obtained from patients with resectable PDAC. Radiotherapy was delivered a median of seven days prior to surgical resection, and sections were analyzed by multiplex IHC (mIHC), RNA-Seq, and T cell receptor sequencing (TCR-Seq).
Results: Analysis of SBRT-treated tumor tissue indicated reduced tumor cell density and increased immunogenic cell death relative to untreated controls. Radiotherapy promoted collagen deposition, however, vasculature was unaffected and spatial analyses lacked evidence of T cell sequestration. Conversely, SBRT resulted in fewer tertiary lymphoid structures and failed to lessen or reprogram abundant immune suppressor populations. Higher percentages of PD-1+ T cells were observed following SBRT, and a subset of tumors displayed more clonal T cell repertoires.
Conclusions: These findings suggest that SBRT augmentation of antitumor immunogenicity may be dampened by an overabundance of refractory immunosuppressive populations, and support the continued development of SBRT/immunotherapy combination for human PDAC.

overall_design: RNA-Seq performed on 13 untreated and 9 SBRT-treated (25 Gy in 5 oligofractions) PDAC resections a median of 7 days post-SBRT.

first: Scott

last: Gerber

middle: N


title: The lncRNA HERVH negatively regulates chromatin targeting and remodeling mediated by CHD7

first: Fei

last: Ji

address: 185 Cambridge St

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

overall_design: Refer to individual Series


title: 1-deoxysphingolipids bind to COUP-TF to modulate lymphatic and cardiac cell development

city: New Haven

first: Fabio

middle: R

last: Santori

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University

summary: We identified 1-deoxysphingosine as a ligand for NR2F1 and NR2F2. To prove physiological relevance after in vitro binding assay we investigated the role of NR2F1 and NR2F2 in cardiomyocyte differentiation. We also used different strategies to manipulate levels of 1-deoxysphingosines and canonical sphingosines in cardiomyocytes derived from human embryonic stem cells. Here we generated both single knockout of NR2F2 and double knockouts of NR2F1 and NR2F2 in human embryonic stem cell line H9. The differentiation of WT, KO and DKO lines into cardiomyocytes was then compared by single-cell RNA-seq analysis.

overall_design: Examination of cell clusters in WT, NR2F2 single knockout and NR2F1 and NR2F2 double knockout embryonic stem cells during the differentiation into cardiomyocytes

first: Natalia

middle: B

last: Ivanova

first: Guilin

last: Wang

first: Ho-Joon

last: Lee


title: RNA-seq of 25OHC-treated CD4+ T cells

city: Tokyo

first: Hayato

last: Takahashi

address: 35 Shinanomachi Shinjuku-ku

department: Dermatology

country: Japan

institute: Keio University School of Medicine

summary: IL-27 is an immunoregulatory cytokine whose essential function is to limit immune responses. We found that the gene encoding cholesterol 25-hydroxylase (Ch25h) was induced in CD4+ T cells by IL-27, enhanced by TGF-β, and antagonized by T-bet. Ch25h catalyzes cholesterol to generate 25-hydroxycholesterol (25OHC), which was subsequently released to the cellular milieu, functioning as a modulator of T cell response. Extracellular 25OHC suppressed cholesterol biosynthesis in T cells, inhibited cell growth, and induced nutrient-deprivation cell death without releasing high-mobility group box-1. This growth inhibitory effect was specific to actively proliferating cells with high cholesterol demand and was reversed when extracellular cholesterol was replenished. Interestingly, Ch25h expressing CD4+ T cells that received IL-27 and TGF-β signals became refractory to 25OHC-mediated growth inhibition in vitro. Nonetheless, IL-27 treated T cells negatively affected viability of bystander cells in a paracrine manner, but only if the bystander cells were in the early phases of activation. In mouse models of skin inflammation due to autoreactive T cells or chemically induced hypersensitivity, genetic deletion of Ch25h or Il27ra led to worsened outcomes. Thus, Ch25h is an immunoregulatory metabolic switch induced by IL-27 and dampens excess bystander T effector expansion in tissues through its metabolite derivative, 25OHC. This study reveals regulation of cholesterol metabolism as a modality for controlling tissue inflammation and thus represents a mechanism underlying T cell immunoregulatory functions.

overall_design: RNA-seq anslysis for 25OHC-treated CD4+ T cells. Naïve CD4+ T cells were treated with different concentrations of 25OHC (0, 10, 100, and 1000 nM). After 1, 2, or 3 days of 25OHC treatment, cells were collected, and subjected to RNA-seq.

first: Takashi

last: Sasaki

first: Hisashi

last: Nomura


title: miRNA sequence of astrocytes cocultured with U87 glioblastoma cells

city: Bronx

first: Sean

last: McCutcheon

address: 1410 Pelham Pwky S, Kennedy Center Rm. 840

department: Neuroscience

institute: Albert Einstein College of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: miRNA sequencing data from immortalized murine astrocytes cocultured with U87 cells to evaluate transfer of miRNA from GBM to astrocytes

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cx43 WT or KO immortalized murine astrocytes were coculture with GBM cell line U87 for 24 hours and separated via FACS. miRNA was isolated from cells in monoculture or cells separted post-coculture.

first: David

last: Spray


title: Liver p53-dependent gene expression 8hrs after CCl4 treatment

city: Glasgow

first: Holly

last: Hall

address: Garscube Estate, Switchback Road, Bearsden

country: United Kingdom

institute: Cancer Research UK Scotland Institute

summary: Liver samples were taken from mice with WT p53 or liver-specific loss of p53 at 8 hrs after treatment with the potent hepatotoxin CCl4 in order to analyse differences in p53-dependent gene expression during the early response to CCl4.

overall_design: mRNA profiles of p53 wild-type (Albumin-Cre; p53 WT) and liver p53-deficient (Albumin-Cre; p53FL/FL) liver samples at 8 hours after carbon tetrachloride (CCl4) treatment

first: Timothy

last: Humpton


title: A Regulatory network of microRNAs confers lineage commitment during early developmental trajectories of B and T lymphocytes.

city: Hyderabad

first: Jagan

last: Pongubala

state: Telangana

address: Gachibowli

department: Animal Biology

country: India

institute: University of Hyderabad

summary: The commitment of hematopoietic multipotent progenitors (MPPs) towards a particular lineage involves activation of cell-type-specific genes and silencing of genes that promote alternate cell fates. Although the gene expression programs of early-B and early-T lymphocyte development are mutually exclusive, we show these cell types exhibit significantly correlated microRNA profiles. However, their corresponding miRNA-targetomes are distinct and predominated by transcripts associated with NK, DC, and myeloid lineages, suggesting miRNAs function in a cell-autonomous manner. Combinatorial expression of microRNAs: miR-186-5p, miR-128-3p, and miR-330-5p in MPPs significantly attenuate their myeloid differentiation potential due to the repression of myeloid-associated transcripts. Depletion of these miRNAs caused a pronounced de-repression of myeloid lineage targets in differentiating early-B and early-T cells, resulting in a mixed-lineage gene expression pattern. De novo motif analysis combined with an assay of promoter activities indicate that B, as well as T lineage determinants, drive the expression of these miRNAs in lymphoid lineages. Collectively, we present a paradigm that miRNAs are conserved between developing B and T lymphocytes, yet they target distinct sets of promiscuously-expressed lineage-inappropriate genes to suppress alternate cell-fate options. Thus, our studies provide a comprehensive compendium of miRNAs with functional implications for B and T lymphocyte development.

overall_design: This study includes the miRNA-seq and Ago2-RIPseq profiles of Ebf1-/- progenitors, Early-B and Early-T cells; and H3K4me3 profiles of Ebf1-/- progenitors and Early-B cells. The Early-B cells were obtained by in vitro differentiation of Ebf1-/- progenitors by expressing transcription factor EBF1 (via MigR1-EBF1.ER vector), followed by culturing on OP9 stromal cells in presence of cytokines SCF, FLT3-L, IL-7;  and 4-O-Hydroxy-tamoxifen for 2 days. The Early-T cells were obtained by culturing Ebf1-/- progenitors on OP9-DL1 stroma for 5 days in presence of cytokines SCF, FLT3-L and IL-7, in vitro. For miRNA-seq, miRNA libraries were prepared from total RNA samples using TrueSeq small RNA library preparation kit (Illumina). For Ago2-RIPseq, the INPUT (total RNA) or Ago2-immunoprecipitated (Ago2-IP) RNA was used for preparation of mRNA libraries using NEBNext Ultra II Directional RNA Library Prep kit (NEB). For ChIPseq, the INPUT (genomic DNA) or immunoprecipitated DNA (IP-DNA) was used for preparation of libraries using NEBNext Ultra II DNA Library prep kit (NEB) as per manufacturer?s instructions. All samples were processed in replicates and high-throughput sequencing was carried out on Illumina's HiSeq 2500.

first: Sameena

last: Nikhat

first: Anurupa

last: Yadavalli

first: Arpita

last: Prusty

first: Priyanka

last: Narayan

first: Dasaradhi

last: Palakodeti

first: Cornelis

last: Murre


title: Liver p53-dependent gene expression 48hrs after Mdm2Ex5/6Δ (Mdm2tm2.1Glo) allele activation

summary: Liver samples were taken from mice homozygous for the Mdm2Ex5/6Δ (Mdm2tm2.1Glo) allele at 48 hrs post-AAV treatment to observe gene expression after ubiquitous p53 stabilisation.

overall_design: mRNA profiles of liver sampled from Mdm2Ex5/6Δ homozygous mice at 48 hours after treatment with either AAV-Cre to induce the allele or AAV-control.

first: Christos

last: Kiourtis


title: NADH Inhibition of SIRT1 Links Energy State to Transcription During Time-Restricted Feeding

city: San Francisco

first: Louis

last: Ptacek

state: CA

institute: University of California San Francisco

summary: In mammals, circadian rhythms are entrained to the light cycle and drive daily oscillations in levels of NAD+ a co-substrate of the class III histone deacetylase SIRT1 that associates with clock transcription factors. While NAD+ also participates in redox reactions, the extent to which NAD(H) couples nutrient state with circadian transcriptional cycles remains unknown. Here we show that nocturnal animals subjected to time-restricted feeding of a calorie-restricted diet (TRF-CR) only during nighttime display reduced body temperature and elevated hepatic NADH during daytime. Genetic uncoupling of nutrient state from NADH redox state through transduction of the water-forming NADH oxidase from Lactobacillus brevis (LbNOX) increases daytime body temperature and blood and liver acyl-carnitines. LbNOX expression in TRF-CR mice induces oxidative gene networks controlled by BMAL1 and PPARa and suppresses amino acid catabolic pathways. Enzymatic analyses reveal that NADH inhibits SIRT1 in vitro, corresponding with reduced deacetylation of SIRT1 substrates during TRF-CR in vivo. Remarkably, Sirt1 liver nullizygous animals subjected to TRF-CR display persistent hypothermia even when NADH is oxidized by LbNOX. Our findings reveal that the hepatic NADH cycle links nutrient state to whole-body energetics through the rhythmic regulation of SIRT1.

overall_design: 87 libraries were generated in this study. They include ChIP-Seq and RNA-Seq experiments to determine the effect of NADH and SIRT1 on transcription during time-restricted calorie restriction (CR). Replicates are indicated in the final position of the title of each library. Inputs for ChIP-Seq experiments consist of equimolar pools of replicates within each group. RNA-seq controls for PPARaKO are GSM3347582-5 within GSE118787.

first: Daniel

middle: C

last: Levine

first: Hsin-Yu

last: Kuo

first: Heekyung

last: Hong

first: Jonathan

last: Cedernaeas

first: Chelsea

last: Hepler

first: Alexandra

middle: G

last: Wright

first: Meredith

last: Sommars

first: Yumiko

last: Kobayashi

first: B

last: Marcheva

first: Peng

last: Gao

first: Olga

last: Ilkayeva

first: Chiaki

last: Omura

first: Kathryn

middle: M

last: Ramsey

first: Christopher

last: Newgard

first: Grant

last: Barish

first: Clara

last: Peek

first: Navdeep

last: Chandel

first: Milan

last: Mrksich

first: Joseph

last: Bass


title: Decoupling of degradation from deadenylation reshapes poly(A) tail length in yeast meiosis

city: Seattle

first: David

last: Wiener

state: Washington

department: School of Oceanography

institute: University of Washington

summary: Nascent mRNA is endowed with a poly(A) tail, which is subject to gradual deadenylation in the cytoplasm, followed by mRNA degradation. Deadenylation and degradation rates are typically correlated, rendering it difficult to dissect the individual determinants governing each of these processes. In addition, the mechanistic basis for the coupling between deadenylation and degradation and the extent to which the two can be decoupled are largely unknown. Here we developed an approach allowing systematic, robust and multiplexed quantification of poly(A) tails. Our results suggest that in yeast, exclusively during meiosis, mRNA deadenylation and degradation rates are decoupled. The decoupled regime in meiosis allowed us to discover transcript length as a major determinant of deadenylation rates and as a key  contributor to the reshaping of poly(A) tail lengths in meiosis. The meiosis-specific decoupling also led to unique positive associations between poly(A) tail length and gene expression. The decoupling of degradation from deadenylation is also strongly associated with a focal localization pattern of the RNA degradation factor Xrn1 and can be phenocopied by deletion of Xrn1 under non-meiotic conditions. Importantly, the association of transcript length with deadenylation rates is conserved across eukaryotes. This study uncovers a new factor that shapes deadenylation rate and discovers a unique context in which degradation is decoupled from deadenylation.

overall_design: Exp1: After induction of meiosis RNA was extracted at 1hr interval timepoints for 9Hrs. Exp2: Yeast cells after 1 and 7 Hrs in SPO were transferred to YPD and RNA was extracted after 5 and 20min incubation. Exp3:In Wt, ccr4Δ/Δ, pop2Δ/Δ, and xrn1Δ/Δ strains RNA was extracted in vegetative growth, premeiotic conditions and after 5Hrs in SPO. Exp4: RNA was extracted in control cells and degron-Xrn1 cells growing in YPD2% before and after degradation of Xrn1. Exp5: RNA was extracted in control cells and pCup1-Ccr4 cells growing in YPD2% before and after induction of Ccr4. For all experiments poly(A) tail length was quantified using mPAT-seq and gene expression using RNA-seq.

first: Yaron

last: Antebi

first: Schraga

last: Schwartz


title: Knockdown of lncRNA NR2F1-AS1 in gastric cancer cells

status: Public on Oct 07 2021

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: Our data showed that NR2F1-AS1 functions oncogenic roles in gastric cancer (GC), but the underlying molecular mechanism remains largely unknown to date. To explore the function of lncRNA NR2F1-AS1 in gastric cancer, loss-of-function and RNA sequencing studies were performed in SGC7901 cell line. The results showed that depletion of NR2F1-AS1 significantly decreased the expression of VAMP7. Interestingly, VAMP7 was also a target gene of miR-29a-3p. Our data showed that NR2F1-AS1 promotes GC progression through regulating miR-29a/VAMP7 axis.

overall_design: To reveal the potent downstream target genes of NR2F1-AS1 in gastric cancer, we transfected NR2F1-AS1-targeted siRNAs in SGC7901 cells. The potent target genes of NR2F1-AS1 were identified by deep sequencing, using Illumina HiSeq 4000.

first: Shanshan

last: Qin

first: Dandan

last: Li


title: BAC 1.2F5 macrophage  gene expression

first: Jeffrey

last: Segall

address: 1301 Morris Park Avenue

summary:
BAC 1.2F5 macrophages are derived from a clone of the BAC1 SV40 transformed murine macrophage cell line with strong responses to CSF1.  They have been shown to interact with breast cancer tumor cells in a paracrine loop.
We used microarrays to determine the basal gene expression and expression after incubation with CXCL1 and NRG1

overall_design: BAC 1.2F5 macrophages were cultured in αMEM with L-glutamine, 10% FBS, 3000 units/ml CSF-1 and then stimulated for 2 hours either with the same medium or medium containing in addition both 12 nM NRG1 and 50 ng/ml CXCL1, followed by isolation of  total RNA.


title: Single-Cell RNA-Sequencing Atlas of Bovine Caudal Intervertebral Discs: Discovery of Heterogeneous Cell Populations with Distinct Roles in Homeostasis

city: New York

first: Robert

last: Sebra

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: We investigated the heterogeneous cell populations composing Bovine Intervertebral Discs (IVDs) through single cell RNA sequencing technologies. The assay sequenced over 14,000 cells composing 5 bovine discs from 3 unique bovine tails. Through both established and custom analysis pipelines, we characterize cell heterogeneity between populations of Nucleus Pulposus and Annulus Fibrosus cells. We further characterize populations of Endothelial, Muscle, Immune, and Notochord.

first: James

last: Iatridis


title: Non-cell autonomous and spatiotemporal signaling from a tissue organizer orchestrates root vascular development

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

summary: During plant development, a precise balance of cytokinin is crucial for correct growth and patterning, but it remains unclear how this is achieved across different cell types and in the context of a growing organ. Here we show that in the root apical meristem, the TMO5/LHW complex increases active cytokinin levels via two cooperatively acting enzymes. By profiling the transcriptomic changes of increased cytokinin at single-cell level, we further show that this effect is counteracted by a tissue-specific increase in CYTOKININ OXIDASE 3 expression via direct activation of the mobile transcription factor SHORTROOT. In summary, we show that within the root meristem, xylem cells act as a local organizer of vascular development by non-autonomously regulating cytokinin levels in neighbouring procambium cells via sequential induction and repression modules.

overall_design: Single-cell RNA-seq experiments were performed on protoplast cells extracted from the root-tips of 6 day old Arabidopsis thaliana seedlings.

first: BaoJun

last: Yang

first: Max

last: Minne

first: Federica

last: Brunovi

first: Lenka

last: Plačková

first: Ivan

last: Petřík

first: Yanbiao

last: Sun

first: Jonah

last: Nolf

first: Wouter

last: Smet

first: Kevin

last: Verstaen

first: Jos

last: Wendrich

first: Thomas

last: Eekhout

first: Klára

last: Hoyerová

first: Gert

last: Van Isterdael

first: Jurgen

last: Haustraete

first: Anthony

last: Bishopp

first: Etienne

last: Farcot

first: Ondřej

last: Novák

first: Yvan

last: Saeys


title: Genome-wide maps of chromatin state and RNA-seq in WT and Dnmt3a KO BMDMs (bone marrow derived macrophages) [RNA-seq]

city: Boston

first: Peter

middle: Geon

last: Kim

address: 360 Longwood Ave, Lc8202

department: Hematology/Oncology

institute: Dana Farber Cancer Institute

summary: To identify soluble factors released from Dnmt3a KO macrophages that might drive differences in osteoclast differentiation, we performed RNA sequencing on unstimulated BMDMs from WT and Dnmt3a KO mice. To investigate the mechanistic basis for the inflammatory phenotype. of myeloid cells with loss of Dnmt3a,we performed reduced representation bisulfite sequencing (RRBS) on Dnmt3a KO and WT BMDMs to assess methylation changes. Concurrently, we performed ATAC-sequencing (ATAC-seq) to assess differences in chromatin accessibility between WT and Dnmt3a KO BMDMs in the context of changes in methylation. We performed chromatin immunoprecipitation sequencing (CHIP-seq) for Irf3 and Rela based on ATAC-seq analysis.

overall_design: RNA-seq in WT and Dnmt3a KO BMDMs on day 8-10 of differentiation


title: Single-cell analysis identifies dynamic gene expression networks that govern B cell development and transformation

city: Minneapolis

first: Todd

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Integration of external signals and B-lymphoid transcription factor activities orchestrate B cell lineage commitment through alternating cycles of proliferation and differentiation, producing a diverse repertoire of mature B cells. We use single-cell transcriptomics and proteomics to characterize B cell development. Here we show unique transcriptional signatures that refine the pre-B cell expansion stages into pre-BCR-dependent and pre-BCR-independent proliferative phases. These changes correlate with unexpected dynamic and reciprocal changes in expression of the transcription factor EBF1 and the RNA binding protein YBX3, that are defining features of the pre-BCR-dependent stage. Using pseudotime analysis, we further characterize the expression kinetics of different biological modalities across B cell development, including transcription factors, cytokines, chemokines, and their associated receptors. Our findings demonstrate the underlying heterogeneity of developing B cells and point to key developmental nodes linked to B cell transformation.

overall_design: Single-cell RNA-seq with HTO and ADT sequencing

first: Robin

last: Lee

first: Sarah

last: Munro

first: Rebecca

last: LaRue

first: Lynn

last: Heltemes-Harris

first: Michael

last: Farrar


title: Characterization of the genes that were regulated by feeding with C. acnes strains

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

summary: In the present study, we investigated the effect of Cutibacterium acnes on lifespan and susceptibility to infection with Staphylococcus aureus using Caenorhabditis elegans as a model animal. When adult C. elegans were fed C. acnes strains, the lifespan of the animals fed pathogenic C. acnes strain (HM-122) was significantly shorter than that of animals fed OP50 (control). In contrast, the lifespan of the animals fed commensal C. acnes strain (HM-555) was not significantly different from that of animals in the control group. Moreover, the worms fed the commensal C. acnes strain were more resistant to infection with S. aureus. Transcriptional profiling comparing HM-122-, HM-555- and control-fed animals suggested that genes related to “cuticle development involved in collagen and cuticulin-based cuticle molting cycle” were regulated by HM-122, and genes related to “defense response to gram-positive bacterium” were regulated by HM-555.

overall_design: Transcriptional profiling of three-day-old worms that were fed OP50 or C. acnes strains for six hours, by deep sequencing, using Illumina HiSeq.


title: Lnc-SLC15A1-1 Up-regulates CXCL10/CXCL8 Expression in Endothelial Cells by Sponging MicroRNAs

status: Public on Oct 06 2021

city: Taipei

first: yu chin

last: Huang

address: No.1 Jen Ai road section 1

country: Taiwan

institute: NTU

summary: The molecular factors that cause disproportional increase in CVD in the DM/chronic kidney disease (CKD) population are still unknown. HUVESs were treated with high glucose (HG) or HG superimposed uremic toxin indoxyl sulfate (IS). Lnc-SLC15A1-1 was significant different expression between these two condition. HUVECs were transfected with lnc-SLC15A1-1 overexpression vector then microarray was applied to evaluate the downstream regulated gene.

overall_design: HUVECs were transfected with  a lnc-SLC15A1-1 expression plasmid (pcDNA3.1(+)-lnc-SLC15A1-1) or empty vector (EV) as a control by employing the TransIT-X2 delivery system

first: Yu-Chin

first: Liang-Chuan

last: Lai

first: Pin‑Hao

last: Ko


title: Endogenous retroviruses mediate IFN-independent protection against HSV-2 infection

first: Maria

last: Tokuyama

institute: Yale University School of Medicine

summary: Endogenous retroviruses (ERVs) are genomic sequences that originated from retroviruses and are present in most eukaryotic genomes. Both beneficial and detrimental functions are attributed to ERVs, but whether ERVs contribute to antiviral immunity is not well studied. Here, we used herpes simplex virus type 2 (HSV-2) infection as a model and found that mice deficient in Toll-like receptor 7 (Tlr7-/-) that have high systemic levels of infectious ERVs are resistant to intravaginal HSV-2 infection, compared with wildtype C57BL/6 (B6) mice. We deleted the endogenous ecotropic murine leukemia virus (Emv2) locus on the Tlr7-/- background (Emv2-/-Tlr7-/-) and found that Emv2-/-Tlr7-/- mice lose protection against HSV-2 infection. Intravaginal application of purified ERVs prior to HSV-2 infection delays disease in both B6 and highly susceptible interferon-alpha receptor-deficient (Ifnar1-/-) mice.  We did not observe enhanced type I interferon (IFN-I) signaling in the vaginal tissues from Tlr7-/- mice or B6 mice treated with purified ERVs, and instead found enrichment in genes associated with extracellular matrix organization. Together, our results revealed an IFN-independent modulation of the vaginal epithelium by ERVs that protects mice against vaginal HSV-2 infection and delays disease.

overall_design: Bulk RNA-seq of polyA RNA obtained from whole vaginal tissues of uninfected or HSV-2 186 Syn+ infected wildtype B6, Tlr7-/-, Emv2-/-, and Emv2-/-Tlr7-/- mice.

first: Yong

last: Kong

first: Akiko

last: Iwasaki


title: Changes of gene expression patterns of mouse lung CD45- cells in response to IL-15/IL-15Ra complex whether or not they have MCMV-memory CD8 T cells

city: Daejeon

first: Galam

last: Leem

address: 291 Daehakro Yusunggu

country: South Korea

institute: KAIST

summary: We report the differences of gene expression pattern of 4 different groups of mouse lung CD45- cells (Naive mouse without IL-15/IL-15Ra complex, Naive mouse with IL-15/IL-15Ra complex, MCMV-infected mouse without IL-15/IL-15Ra complex, and MCMV-infected mouse with IL-15/IL-15Ra complex). We found that mouse with MCMV-memory CD8 T cells response to IL-15/IL-15Ra complex and the behaviors of cancer were changed compared to other groups.

overall_design: Compare gene expression pattern of 4 different groups of mouse lung CD45- cells (Naive mouse without IL-15/IL-15Ra complex, Naive mouse with IL-15/IL-15Ra complex, MCMV-infected mouse without IL-15/IL-15Ra complex, and MCMV-infected mouse with IL-15/IL-15Ra complex).

first: Eui-Cheol

last: Shin


title: Analysis of N6-methyladenosine Methylation Modification in Fructose-induced Non-alcoholic Fatty Liver Disease

city: Shanghai

first: Yunchen

last: Luo

address: shanghai hongkou

institute: Shanghai Jiao Tong University School of Medicine

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Blocking of CA-MSC-induced desmoplasia reprograms the tumor immune microenvironment and enhances cancer immunotherapy

city: Pittsburgh

first: Ronald

last: Buckanovich

state: Pennsylvania

address: 204 Craft Avenue

department: Department of Medicine

institute: University of Pittsburgh

summary:
We determined the immune cell composition and their gene expression, by performing single-cell RNA sequencing (scRNA-seq), in anti-PD-L1-treated 2F8cis tumors, a hot and immunoresponsive ovarian murine tumor model, and anti-PD-L1-treated 2F8cis/CA-MSC tumors. We also evaluated the ability of hedgehog inhibitor (HHi) therapy to reverse CA-MSC effects.
Adipose-derived mesenchymal stem cells (MSC) were cultured with 2F8cis, an ovarian mouse tumor cell line, to generate cancer-associated MSC (CA-MSC). 2F8cis tumor cell alone or 2F8cis/CA-MSCs co-cultured cells at ratio 1:1 were injected into C57BL/6J mice.   Tumor infiltrating CD45+ cells were isolated from anti-PD-L1-treated 2F8cis (Group 1, n=3), anti-PD-L1-treated 2F8cis/CA-MSCs (Group 2, n=3), anti-PD-L1+ IPI-926-treated 2F8cis/CA-MSCs (Group 3, n=3) tumors. Samples were labeled with different TotalSeq oligo-conjugated antibodies and loaded into the Chromium instrument (10x Genomics). The resulting barcoded cDNAs were used to construct libraries.  Single-cell cDNA libraries were then processed for RNA sequencing using an Illumina NextSeq-500 platform.
Anti-PD-L1-treated 2F8cis/CA-MSC tumors showed a high number of Monocytes and macrophages over-expressing Ccr2 and Tgfbi when compared to anti-PD-L1 responsive 2F8cis tumors. Our results also indicated that IPI-926 restored response to anti-PD-L1 therapy decresing the expression of Ccr2 and Tgfbi both in monocytes and macrophages.
Our study represents the first detailed analysis generated by RNA-seq technology of 2F8cis/CA-MSC+ enriched tumor transcriptomes, treated with anti-PDL1 alone or in combination with HHi, and compared with anti-PDL1-treated tumors. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

overall_design: mRNA profiles of the following groups: a) a-PDL1-treated 2F8cis tumors , b) anti-PDL1-treated 2F8cis/CA-MSC tumors, and c) anti-PDL1+HHi-treated 2F8cis/CA-MSC tumors.

first: Sandra

last: Cascio

first: Hatice

middle: U

last: Osmanbeyoglu

first: Linan

last: Zhang


title: Genome-wide maps of H3 and H4 acetylation in wild type and gds1 deletion strain of S.cerevisiae.

first: Stephen

last: Buratowski

state: MA

address: 240 Longwood Avenue

department: BCMP

institute: Harvard Medical School

summary: The goals of this study are to compare Next-Generation-Sequecing (NGS)-derived genome-wide occupancy of H3 and H4 acetylation  in S. cerevisiae wildtype and gds1 deletion strain.

overall_design: Examination of H3 and H4ac in wildtype and gds1 deletion yeast stains.

first: Yoo

last: Joo


title: Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law

city: Shenzhen

first: Lei

last: Li

state: --- Select a state ---

address: China

department: Institute of Systems and Physical Biology

institute: Shenzhen Bay Laboratory

summary: We investigated the cis-regulatory divergences in alternative splicing and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid mouse. By obtaining more than 240 million read pairs on average in each sample from 5 organs and ESC as well as published data in liver, we comprehensively analyzed the allelic splicing patterns across tissues in hybrid mice. We find that tissue-dependent regulation causing large splicing differences is highly conserved and likely functional, while splicing divergence mainly affects genes under relaxed selective constraints.  Although cis-divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform could tolerate more mutations, which explains the paradoxical sequence conservation pattern in their exonic versus intronic splicing site flanking regions. Finally, we demonstrated that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attributed such buffering effect to trans-regulatory splicing efficiency.

overall_design:
High-throughput RNA-seq data of 5 organs (cerebral cortex, heart, kidney, lung, and spleen) and ESC from Female F1 hybrid mice (female C57BL/6J x male SPRET/EiJ).
High-throughput RNA-seq data of fibroblast cells from F1 hybrid mice with and without Pladienolide B treatment.

first: Wei

last: Chen


title: Analysis of N6-methyladenosine Methylation Modification in Fructose-induced Non-alcoholic Fatty Liver Disease [MeRIP-Seq]

summary: Improvements in living standards have led to non-alcoholic fatty liver disease (NAFLD), one of the most common chronic liver diseases worldwide. Recent studies have shown that N6-methyladenosine (m6A), a type of RNA modification, is strongly associated with many important biological processes. However, the relationship between m6A methylation modifications and NAFLD remains poorly understood. In the present study, through methylated RNA immunoprecipitation sequencing and RNA transcriptome sequencing in high fructose diet-induced NAFLD mice, we found that hypermethylation-encoding genes were mainly enriched in lipid metabolism processes. We identified 266 overlapping and differentially expressed genes (DEGs) that changed at both the mRNA expression level and m6A modification level. Among them, 193 genes displayed increased expression and m6A modification, indicating that m6A RNA modifications tend to be positively correlated with NAFLD. We further compared the high fructose diet-induced NAFLD mouse model with leptin receptor-deficient mice and found that DEGs enriched in the lipid metabolism pathway were up-regulated in both groups. In contrast, DEGs associated with the immune inflammatory response were up-regulated in the high fructose diet group, but down-regulated in leptin receptor-deficient mice. Taken together, our results demonstrate that m6A methylation modifications may play an important role in the development of NAFLD.

overall_design: Male C57BL/6J mice aged 10-11 weeks were purchased from the Shanghai Laboratory Animal Company (SLAC, Shanghai, China). HFrD containing 10% kcal from fat, 70% kcal from carbohydrate, and 20% kcal from protein were purchased from Research Diets (D08040107, Research Diets, USA). After a 2-week intervention period in which mice were fed either a normal diet (ND) or HFrD, mice were anesthetized with 10% chloral hydrate.

first: Yan

last: Lu

first: Yongde

last: Peng


title: Analysis of N6-methyladenosine Methylation Modification in Fructose-induced Non-alcoholic Fatty Liver Disease [RNA-Seq]


title: Adropin expression correlates with aging-related neuropathology in the human brain and improves neuroinflammation and cognitive function in aging mice

city: St. Louis

first: Jinsong

state: MO

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

summary: The putative secreted domain of adropin (residues 34-76) is sufficient for biological activity when administered by ip. injection to mice, inducing changes in mitochondrial fuel selection of skeletal muscle. To investigate whether adropin administered also regulates the brain transcriptome, RNA seq was used in 18-month-old male B6 mice treated with synthetic peptide at a dose previously shown to be effective. Mice were split into two weight matched groups, acclimated to handling and then treated with peptide (90 nmol/kg/d) suspended in 0.9% saline plus 0.1% BSA over 4 weeks. Controls were treated with diluent; injections were given daily at 0900h. Applying a cut-off using a fold-change (FC) >1.5 and a p-value of <0.05 identified a small number of responsive genes (84 upregulated, 172 downregulated). Gene enrichment analysis indicated that peptide treatment primarily changed the expression of genes involved in tissue morphogenesis (e.g. “pattern specification process”, “embryo development”, “animal morphogenesis”). Possibly related to increases in cellular proliferation and differentiation, there was also evidence for increases in large molecule synthesis. For example, RNA metabolism (“positive regulation of RNA biosynthetic process”; “positive regulation of transcription by RNA polymerase II”) and ‘macromolecule synthesis” were affected by treatment.

overall_design: C57BL mice were purchased at 18 months of age from Jackson Laboratories (Bar Harbor, ME). Mice were acclimated to local conditions for 2 wk and then divided into two weight matched groups (n=15/group). The mice were treated with 90 nmol/kg/d adropin ( ABClonal Science, 98.66% purity) suspended in 0.9% sterile saline with 0.1% BSA. The peptide was resuspended daily prior to injection and administered as a single ip. injection (0.1ml volume) at 0900h. Controls received saline diluent only. Mice were weighed daily; after 2 weeks of injections, mice were subjected to behavioral testing. Treatment continued during behavioral testing. At completion, mice were fasted for 6h. Blood glucose (tail snip) levels were recorded using a glucometer; blood samples were collected for analysis of measurement of insulin by ELISA (Ultra Sensitive Mouse Insulin ELISA kit, Crystal Chem USA, IL, USA). Brain tissue samples were collected and snap frozen using liquid nitrogen and subsequently used for RNA-Seq.

first: Subhashis

last: Banerjee

first: Andrew

last: Butler


title: Metabolic gene regulation by Drosophila GATA transcription factor Grain

city: Helsinki

first: Krista

last: Kokki

address: Viikinkaari 9, Biocenter 1, Institute of Biotechnology P.O.Box. 56

department: Department of Biosciences (Genetics)

country: Finland

institute: University of Helsinki

summary: Nutrient-dependent gene regulation critically contributes to homeostatic control of animal physiology in changing nutrient landscape. In Drosophila, dietary sugars activate transcription factors (TFs), such as Mondo-Mlx, Sugarbabe and Cabut, which control metabolic gene expression to mediate physiological adaptation to high sugar diet. TFs that correspondingly control sugar responsive metabolic genes under conditions of low dietary sugar remain, however, poorly understood. We have used de novo motif prediction to uncover a significant over-representation of GATA-like motifs on the promoters of sugar-responsive genes in Drosophila larvae. GATA TF Grain was found to contribute to the regulation of sugar-responsive genes, and consequently to central carbon and lipid metabolism, primarily on low sugar diet. Grain targets include known sugar responsive TFs, cabut and smad on X (smox). Moreover, Grain promotes the expression of genes involved in de novo lipogenesis. Grain chromatin binding sites significantly converge with those of Sugarbabe. Grain and Sugarbabe both activate lipogenic genes, but display functional predominance on low and high sugar conditions, respectively. Collectively, our data provides evidence for a metazoan GATA transcription factor in nutrient-responsive metabolic regulation in vivo.

overall_design: 1st instar larvae were collected 24 hours after egg laying to plates with LSD (low sugar diet, 10% yeast) at a controlled density. Early 2nd instar larvae were transferred at 48 hours after egg laying to plates containing either LSD or HSD (high sugar diet, 10% yeast supplemented with 15% sugar). After 8 hours of diet exposure, 20 larvae per sample were collected and snap-frozen in liquid nitrogen.

first: Ville

last: Hietakangas


title: The LRRK2 G2019S mutation alters astrocyte-to-neuron communication via extracellular vesicles and induces neuron atrophy in a human iPSC-derived model of Parkinson’s disease

city: Quebec

first: Aurelie

last: de Rus Jacquet

state: QC

address: 2705 Boulevard Laurier

country: Canada

institute: Universite Laval

summary: Astrocytes are essential cells of the central nervous system, characterized by dynamic relationships with neurons that range from functional metabolic interactions and regulation of neuronal firing activities, to the release of neurotrophic and neuroprotective factors. In Parkinson’s disease (PD), dopaminergic neurons are a vulnerable population progressively lost during the course of the disease, but the effects of PD on astrocytes and astrocyte-to-neuron communication remains mostly unknown. This study focuses on the effects of the PD-related mutation LRRK2 G2019S in astrocytes, using patient-derived induced pluripotent stem cells. We report the alteration of extracellular vesicle (EV) biogenesis in astrocytes, and we identify the abnormal accumulation of key PD-related proteins within multi vesicular bodies (MVBs). We found that dopaminergic neurons internalize astrocyte-secreted EVs but LRRK2 G2019S EVs are abnormally enriched in the neurites and provide only marginal neurotrophic support to dopaminergic neurons. Thus, dysfunctional astrocyte-to-neuron communication via altered EV biological properties could participate in the progression of PD.

overall_design: Differential gene expression between wild-type and LRRK2 G2019S iPSC-derived astrocytes.

first: Erin

last: O'Shea

first: Jenna

middle: L

last: Tancredi

last: Lemire

first: Michael

last: DeSantis

first: Wei-Ping


title: Expression data from glioma stem cells (GSC), comparing the WT cells to those after ALDH1A3-KO

city: Mobile

first: Robert

middle: W.

last: Sobol

state: AL

address: 1660 Springhill Avenue

department: Mitchell Cancer Institute

institute: University of South Alabama

summary:
Elevated aldehyde dehydrogenase (ALDH) activity correlates with poor outcome for many solid tumors as ALDHs potentially regulate cell proliferation and chemoresistance of cancer stem cells (CSCs). ALDH1A3 is the dominant isomer of the ALDH gene family in Mesenchymal subtype of GSC cells and is highly upregulated compared to other subtype of GSCs. ALDH1A3 is an important enzyme in the synthesis of Retinoic Acid, which regulates various downstream pathways and the transcription of numerous genes. Microarray analysis of the GSCs before or after depletion of ALDH1A3 provides important information to determine the genes regulated by ALDH1A3 in the mesenchymal subtype of GSCs.
We used microarrays to analyze the transcriptome change after the depletion of ALDH1A3 in GSC-326 cells that express very high levels of ALDH1A3.

overall_design: We depleted ALDH1A3 in GSC-326 cells using the CRISPR/Cas9 technique with 3 diffirent gRNAs targeting different regions of the ALDH1A3 gene. Six ALDH1A3-KO single clones generated from 3 diffirent gRNAs have validated the  loss of ALDH1A3 protein expression. Total RNA was extracted from the six ALDH1A3-KO single clone cells and three ALDH1A3 wlid type control cells. The RNAs were then processed using the kits for the Affymetrix GeneAtlas system and labeled cRNAs were hybridized to Affymetrix Human Genome U219 Array Strip to profile the transcriptome change after the loss of ALDH1A3.

first: Jianfeng


title: super-ehancer landscape shaped by master regulator in liver metastasis of colorectal cancer [RNA-seq]

status: Public on Oct 05 2021

first: Huanlong

last: Qin

state: Shanghai

address: 301 Yan Chang Road

department: Gastrointestinal Surgery

institute: Shanghai Tenth People’s Hospital Affiliated to Tongji University

summary: We interrogated global super-enhancer landscape and sought to discover master regulators governing the liver metastasis of colorectal cancer (CRC). Using de novo analysis, we predicted motif enrichment of master transcription factor in super-enhancers. We show that transcription factor-binding sites of hepatocyte nuclear factor 1 (HNF1) family are enriched at super-enhancers identified in cell lines derived from liver metastases, but not those derived from primary tumors. Using ChIP-Seq of acetylated H3K27, the enrichment of HNF1 binding motifs in super enhancers was found in a cell line derived from xenografted liver metastasis but not the parental cell line. The prediction method was further extended to pancreatic cancer where liver metastasis is also a common finding, and a similar enrichment of HNF1 family motif in super-enhancers was found. We subsequently showed that HNF1A was prominently expressed and significantly upregulated in metastatic cell lines and clinical specimens of liver metastases. Collectively, our study implicates HNF1A as a master transcription factor involved in shaping global super-enhancer landscape in CRC liver metastasis.

overall_design: Examination of mRNA expression profile in parental and HNF1A knocked-out KM12SM cell lines

first: Chunmiao

last: Cai

first: Dexi

last: Bi

first: Hu

last: Liu


title: COMMD10 is critical for Kupffer cell survival and controls Ly6Chi monocyte differentiation and inflammation in the injured liver

city: Tel-Aviv

first: Chen

last: Varol

address: Tel-Aviv University

institute: The Research Center for Digestive Tract and Liver Diseases, Tel-Aviv Sourasky Medical Center and Sackler School of Medicine


title: Bulk RNAseq analysis reveals distinct differentiation traits of COMMD10-deficient Ly6Chi monocytes in the injured liver

summary: Hepatic macrophages play a central role in the initiation, progression and resolution of various liver diseases. Specifically, infiltrating Ly6Chi monocytes and their-derived macrophage (MoMFs) descendants prevail in acute or chronic liver injury, display marked transcriptional variance and provide crucial functional plasticity. A specific example of MoMFs are lipid associated macrophages (LAMs) involved in progression of metabolic liver disease (Remmerie et al., 2020). Recent studies have uncovered binary developmental trajectories of monocytes in the BM with Neutrophil-like (NeuMo) and dendritic cell (DC)-like (DCMo) monocytes (Weinreb et al., 2020; Yanez et al., 2017), hence further challenging our current comprehension of macrophage heterogeneity in the diseased liver. Yet, the molecular factors regulating their inflammatory versus restorative activity remains enigmatic. The COMMD (copper metabolism MURR1 domain) family includes 10 evolutionarily conserved proteins. Functions of COMMD proteins are still being defined, but they seem to play non-redundant roles in regulating transcription and protein trafficking. Utilizing conditional COMMD10 knockout mice we uncovered a role for COMMD10 in limiting inflammasome activation in Ly6Chi monocytes during experimental sepsis and colitis (Mouhadeb et al., 2018), and in supporting phagolysosomal biogenesis and maturation in KCs and BM-derived macrophages infected with Staphylococcus aureus (Ben Shlomo et al., 2019). Hence, these studies mark COMMD10 as a candidate mediator of monocyte and macrophage fate and immune responses. Here we studeid the effect of COMMD10-deficiency on Ly6Chi monocyte differentiation and inflammatory behaviour in the injured liver, using an acute model of acetaminophen-induced liver injury (AILI). Bulk RNAseq analysis of sorted Ly6Chi monocytes, comparing between COMMD10+ and COMMD10-deficient cells, revealed an increased differentiation bias of Ly6Chi monocytes towards NeuMo and LAM differentiation fates. Collectively, COMMD10 appears as an important regulator of Ly6Chi monocyte fate decisions and reparative behavior in the diseased liver.

overall_design: Here, we have performed Bulk RNAseq analysis of sorted Ly6Chi monocytes in acute model of Acetaminophen-induced liver injury (AILI), comparing between COMMD10-deficient and sufficient Ly6Chi monocytes. Ly6Chi monocytes were sorted during the necro-inflammatory phase at 24 hours following AILI from livers of LysMDCommd10 and weight matched littermate Commd10fl/fl controls.

first: Nathan

last: Gluck

first: Keren

last: Cohen


title: COMMD10 is required for homeostatic maintenance of Kupffer cells

summary: Most tissue-resident macrophages are established prenatally and self-maintain independently of bone marrow (BM) monocytes. Instructed by local cues, these cells adopt unique transcriptional modules that impart tissue-specific functional identity (Varol et al., 2015). In the liver, Kupffer cells (KCs) dominate the homeostatic macrophage pool. They reside in the sinusoidal vessels and in the space of Disse, interacting with hepatic stellate cells (HSC) and hepatocytes (Bonnardel et al., 2019), where they act as sentinels and perform specialized accessory functions involving iron and lipid metabolism (Scott and Guilliams, 2018).  Yet, the molecular cues governing KC differentiation and maintanence remain largly elusive. Embryonic lethality of COMMD10 deficiency has hampered the study of its function. Yet, utilizing conditional COMMD10 knockout mice we recently uncovered a role for COMMD10 in supporting phagolysosomal biogenesis and maturation in KCs and BM-derived macrophages infected with Staphylococcus aureus (Ben Shlomo et al., 2019). Here we show that COMMD10-deficient KCs adopt liver-specific identity. Strikingly, COMMD10-deficiency in KCs and in other tissue resident macrophages impedes their homeostatic survival, leading to their continuous replacement by Ly6Chi monocytes. Transcriptional analysis of COMMD10-deficiet KCs reveales a notable reduction in genes encoding for translation initiation- and ribosomal complex proteins, for ubiquitin and the proteasome protein complex, and for key proteins of the mitochondrial respiration chain. These transcriptional alterations allude to protein stress and mitochondrial dysfunction, and hint at the reason of their premature death.

overall_design: To target COMMD10 deficiency to KCs we crossed Clec4f+/cre mice (Scott et al., 2018) with Commd10fl/fl mice (Mouhadeb et al., 2018) (Clec4fCommd10, C57BL/6 background). Isolation of hepatic non-parenchymal cells was performed as previously described (Zigmond et al., 2014). KCs were defined as CD45+CD11bloF4/80+Ly6G-Ly6C- cells, also expressing the KC markers TIM4, VSIG4, CLEC2 and CLEC4F. KCs were sorted to high purity from steady state livers of 8 weeks old male Clec4fCommd10 and their littermate Commd10fl/fl controls, using the the BD FACSAriaTM FUSION cell sorter (BD Bioscience). A bulk adaptation of the MARS-Seq protocol (Jaitin et al., 2014; Keren-Shaul et al., 2019) was used to generate RNA-Seq libraries for expression profiling.


title: COMMD10-deficiency promotes 'neutrophil like' differentiation fate of bone marrow Ly6Chi monocytes

summary: Monocytes are circulating myeloid immune precursor cells that are generated in the bone marrow (BM). Upon their release into the circulation, monocytes are recruited to inflammatory sites, where they differentiate into monocyte-derived effector cells. In absence of overt inflammation, monocytes also extravasate into selected tissues, where they complement tissue-resident macrophage compartments. Recent studies have uncovered binary developmental trajectories of monocytes in the BM with Neutrophil-like (NeuMo) and dendritic cell (DC)-like (DCMo) monocytes differentiating downstream of granulocyte-macrophage progenitors (GMP) and macrophage-dendritic cell progenitors (MDP), respectively (Weinreb et al., 2020; Yanez et al., 2017). Yet, the molecular cues that dictate BM monocyte differentiation remain incompletely understood. The COMMD (copper metabolism MURR1 domain) family includes 10 evolutionarily conserved proteins. Functions of COMMD proteins are still being defined, but they seem to play non-redundant roles in regulating transcription and protein trafficking. Utilizing conditional COMMD10 knockout mice we uncovered a role for COMMD10 in limiting inflammasome activation in Ly6Chi monocytes during experimental sepsis and colitis (Mouhadeb et al., 2018), and in supporting phagolysosomal biogenesis and maturation in KCs and BM-derived macrophages infected with Staphylococcus aureus (Ben Shlomo et al., 2019). Hence, these studies mark COMMD10 as a candidate mediator of monocyte and macrophage fate and immune responses. Here we studied the effect of COMMD10-deficiency on Ly6Chi monocyte differentiation. We show that COMMD10-deficiency in steady state Ly6Chi monocytes promotes a differentiation bias towards NeuMo fate.

overall_design: Here, we have performed Bulk RNAseq analysis of Ly6Chi monocytes sorted from steady state BM, comparing between COMMD10-deficient and sufficient Ly6Chi monocytes. Ly6Chi monocytes were sorted from BM (femur and tibia) of LysMDCommd10 and weight matched littermate Commd10fl/fl controls.


title: Epigenetic landscape of Mammalian Brain M1 by Single Nucleus Methylation Sequencing [MM_M1]

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. Single nucleus methylation sequencing was applied to M1 regions of human and mouse brains. we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster.

overall_design: Apply snmC-seq2 to brain M1 regions to identify epigenomic landcape of the adult human and marmoset brains

first: Wei

last: Tian

first: Hanqing

first: Chongyuan

last: Luo

first: Anna

last: Bartlett

first: Fenna

last: Krienen

first: Rebecca

middle: D

last: Hodge

first: Jacinta

last: Lucero

last: Nery

first: Angeline

last: Rivkin

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Huaming

last: Chen

first: Sheng-Yong

last: Niu

first: M

last: Behrens

first: Guoping

last: Feng

first: Ed

last: Lein


title: Glycogen phase separation drives liver tumor initiation

city: Xiamen

first: Dawang

last: Zhou

state: Fujian

address: Xiang'an south rd, Xiang'an district

department: Life Science

institute: Xiamen University

summary: Glycogen is the largest soluble cytosolic macromolecule and considered as the principal storage form of glucose. Cancer cells generally increase their glucose consumption and rewire their metabolism towards aerobic glycolysis to promote growth. Here we report that glycogen accumulation is a key initiating oncogenic event and essential for malignant transformation. RNA-sequencing analysis reveals that G6PC, an enzyme catalyzing the last step of glycogenolysis, is frequently downregulated to augment glucose storage in pro-tumor cells. Accumulated glycogen undergoes liquid-liquid phase separation undergoes liquid-liquid phase separation, which results in the assembly of the laforin-Mst1/2 complex and consequently traps Hippo kinases Mst1/2 in glycogen liquid droplets to relieve their inhibition on Yap. Moreover, G6PC or another glycogenolysis enzyme PYGL deficiency in both human and mice result in glycogen storage disease with enlarged liver size and cancer development, phenocopying Hippo deficiency. Consistently, elimination of glycogen accumulation abrogates liver enlargement and cancer incidence, whereas increasing glycogen storage accelerates tumorigenesis. Thus, we concluded that glycogen not only provides nutrition and energy to the cells but also functions as a key initiating oncogenic metabolite, which physically blocks Hippo signaling through glycogen phase separation to augment pro-tumor cell initiation and progression.

overall_design: liver mRNA profiles of 3 glycogen stacked regions and their corresponding normal adjacent regions

first: Cheng

last: Nian

first: Junhong

last: Li

first: Lanfen


title: Epigenetic landscape of Mammalian Brain M1 by Single Nucleus Methylation Sequencing [M1_2]

first: Joseph

last: Ecker

first: Wei

last: Tian

first: Hanqing

last: Liu

first: Chongyuan

last: Luo


title: Cumulative in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse Hoxd cluster  [ChIP-seq]

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

summary: ChIP-seq analysis of CTCF wildtype in mouse embryonic posterior trunk and brain samples

first: Ana

last: Amândio

first: Leonardo

last: Beccari

first: Bénédicte

last: Mascrez

first: Jozsef

last: Zakany

first: Sandra

last: Gitto

first: Denis

last: Duboule


title: Molecular mechanisms of embryonic tail development in the self-fertilizing mangrove killifish Kryptolebias

status: Public on Oct 04 2021

city: Exeter

first: Paul

middle: Andrew

last: O'Neill

address: Stocker Road

department: Sequencing Service

institute: University of Exeter

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

overall_design: RNAseq of Kryptolebias marmoratus embryos, WT and mutants (shorttail and balltail)

first: Tetsuhiro

last: Kudoh

last: O'Neil


title: Genetic control of pluripotency epigenome informs differentiation bias in mouse embryonic stem cells

city: Bar Harbor

first: Christopher

last: Baker

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Genetically diverse pluripotent stem cells (PSCs) display varied, heritable responses to differentiation cues in the culture environment. By harnessing these disparities through derivation of embryonic stem cells (ESCs) from the BXD mouse genetic reference panel, along with C57BL/6J (B6) and DBA/2J (D2) parental strains, we demonstrate genetically determined biases in lineage commitment and identify major regulators of the pluripotency epigenome. Upon transition to formative pluripotency using epiblast-like cells (EpiLCs), B6 quickly dissolves naïve networks adopting gene expression modules indicative of neuroectoderm lineages; whereas D2 retains aspects of naïve pluripotency with little bias in differentiation. Genetic mapping identifies 6 major trans-acting loci co-regulating chromatin accessibility and gene expression in ESCs and EpiLCs, indicating a common regulatory system impacting cell state transition. These loci distally modulate occupancy of pluripotency factors, including TRIM28, P300, and POU5F1, at hundreds of regulatory elements. One trans-acting locus on Chr 12 primarily impacts chromatin accessibility in ESCs; while in EpiLCs the same locus subsequently influences gene expression, suggesting early chromatin priming. Consequently, the distal gene targets of this locus are enriched for neurogenesis genes and were more highly expressed when cells carried B6 haplotypes at this Chr 12 locus, supporting genetic regulation of biases in cell fate. Spontaneous formation of embryoid bodies validated this with B6 showing a propensity towards neuroectoderm differentiation and D2 towards definitive endoderm, confirming the fundamental importance of genetic variation influencing cell fate decisions.

overall_design: Bulk RNA-seq and ATAC-seq performed in ESCs and EpiLCs in biological replicates derived from C57BL/6J, DBA/2J and BXD mouse strains. ChIP-seq performed in biological replicate ESCs. Single cell RNA-seq performed in embryoid bodies.

first: Candice

last: Byers


title: Single cell RNAseq reveals distinct differentiation traits of COMMD10-deficient Ly6Chi monocytes in the injured liver

first: Chen

last: Varol

summary: Hepatic macrophages play a central role in the initiation, progression and resolution of various liver diseases. Specifically, infiltrating Ly6Chi monocytes and their-derived macrophage (MoMFs) descendants prevail in acute or chronic liver injury, display marked transcriptional variance and provide crucial functional plasticity. A specific example of MoMFs are lipid associated macrophages (LAMs) involved in progression of metabolic liver disease (Remmerie et al., 2020). Recent studies have uncovered binary developmental trajectories of monocytes in the BM with Neutrophil-like (NeuMo) and dendritic cell (DC)-like (DCMo) monocytes (Weinreb et al., 2020; Yanez et al., 2017), hence further challenging our current comprehension of macrophage heterogeneity in the diseased liver. Yet, the molecular factors regulating their inflammatory versus restorative activity remains enigmatic. The COMMD (copper metabolism MURR1 domain) family includes 10 evolutionarily conserved proteins. Functions of COMMD proteins are still being defined, but they seem to play non-redundant roles in regulating transcription and protein trafficking. Utilizing conditional COMMD10 knockout mice we uncovered a role for COMMD10 in limiting inflammasome activation in Ly6Chi monocytes during experimental sepsis and colitis (Mouhadeb et al., 2018), and in supporting phagolysosomal biogenesis and maturation in KCs and BM-derived macrophages infected with Staphylococcus aureus (Ben Shlomo et al., 2019). Hence, these studies mark COMMD10 as a candidate mediator of monocyte and macrophage fate and immune responses. Here we studeis the effect of COMMD10-deficiency on Ly6Chi monocyte differentiation and inflammatory behaviour in the injured liver, using an acute model of acetaminophen-induced liver injury (AILI). Single cell RNAseq analysis of sorted Ly6Chi monocytes, comparing between COMMD10+ and COMMD10-deficient cells, revealed increased differentiation bias of Ly6Chi monocytes towards NeuMo and LAM differentiation fates. Collectively, COMMD10 appears as an important regulator of Ly6Chi monocyte fate decisions and reparative behavior in the diseased liver.

overall_design: Here, we have performed single cell RNAseq analysis of sorted Ly6Chi monocytes in acute model of Acetaminophen-induced liver injury (AILI), comparing between COMMD10-deficient and sufficient Ly6Chi monocytes. Ly6Chi monocytes were sorted during the necro-inflammatory phase at 24 hours following AILI from LysMDCommd10 (Sample - LysM-4, 5229 cells) and Commd10fl/fl (two samples C10-1 and C10-3, 4860 and 8149 cells respectively) livers. Cells were counted and diluted to a final concentration in PBS supplemented with 0.04% BSA. Cellular suspension was loaded onto Next GEM Chip G and then ran on a Chromium Controller instrument to generate GEM emulsion (10x Genomics). Single-cell 3’ RNA-seq libraries were generated according to the manufacturer’s protocol (10x Genomics Chromium Single Cell 3’ Reagent Kit User Guide v3/v3.1 Chemistry). Final libraries were quantified using NEBNext Library Quant Kit for Illumina (NEB) and high sensitivity D1000 TapeStation (Agilent). Libraries were pooled according to targeted cell number, aiming for ~50,000 reads per cell. Pooled libraries were sequenced on a NovaSeq 6000 instrument using an SP 100 cycles reagent kit (Illumina).

first: Nathan

last: Gluck

first: Keren

last: Cohen


title: Retinal ganglion cell survival after severe optic nerve injury is modulated by crosstalk between JAK/STAT signaling and innate immune responses in the zebrafish retina

first: Jeffrey

last: Gross

state: PA

department: Ophthalmology

institute: University of Pittsburgh School Of Medicine

summary: The death of retinal ganglion cells(RGC) after the damage on optic nerve as a result of high intraocular pressure is the main reason of the irreversible blindness in glaucoma patients ,and mammals have very limited ability of maintaining the RGCs after optic nerve injury.Zebrafish,however,possess the ability of keep most RGCs from death after optic nerve injury.  The purpose of this study is to determine which gene or pathway mediate the RGC survival mechanism underlying.It is observed JAK/STAT signaling pathway as well as the innate immune response is activated after optic nerve injury(in this study,optic nerve transection).Pharmacological inhibition of JAK/STAT by intravitreal(IV) injection of JAK inhibitor,P6,induced the reduction of RGC survival while both local and systemic immune suppressor application result in the rescue of RGC survival.Moreover,phospho-STAT3(pSTAT3),which is an evidence of STAT3 activation,demonstrated elevation of expression level after ONT,and the trend of pSTAT3 expression change is consistent with the RGC survival rate change .JAK inhibition reduced pSTAT3 expression level and immune suppressor application elevated the pSTAT3 expression level on RGCs.  In summary,these data suggested JAK/STAT signaling pathway crosstalk with innate immune response create a dynamic balance in the mechanism of RGC survival.Interestingly,innate immune response which was used to be considered promoting tissue repair in other studies,proved to be suppressing RGC survival in this study.These data could be used as reference for future direction of neuroprotection in glaucoma treatment.

overall_design: RNA-seq from FACS-purified retinal ganglion cells post optic nerve transection and uninjured contralacteral eyes as control at 3 timepoints: 6,12 and 24 hours post injury(hpi). ONT+ for injured samples and ONT- for control

first: Si

last: Chen


title: RNA sequencing analysis of wild-type and BML-210 treated breast cancer EO771

city: Indianapolis

first: Xiongbin

last: Lu

state: Indiana

address: 980 W. Walnut Street, R3-C218D	MMGE

institute: Indiana University School of Medicine

summary: We investigated the molecular mechanism by which BML-210 enhanced the response of breast tumor cells to cytotoxic CD8+ T cells. For this purpose, we performed RNA sequencing and analyzed the genome-wide gene expression profiles to systematically identify transcriptom reprogramming in the BML-210-treated cells.

overall_design: Comparison of total RNA expression profile of wild-type and BML-210 treated breast cancer EO771

first: Xinna

last: Zhang

first: Zhuolong

last: Zhou


title: Single-cell analysis revealed the role of CD8+ effector T cells in preventing cardioprotective macrophage differentiation in the early phase of heart failure

city: Tokyo

first: Shintaro

last: Yamada

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

summary: Heart failure is a complex clinical syndrome characterized by insufficient cardiac function. It has been characterized that heart resident and infiltrated macrophages play important roles in the cardiac remodeling in response to cardiac pressure overload, however, role of T cells has not been well characterized. Here we show that CD8+T cell depletion resulted in the late stage heart protection, but induced cardioprotective hypertrophy at an early stage of heart failure caused by cardiac pressure overload. Single cell RNA sequencing analysis revealed that cardioprotective hypertrophy was characterized by an expression of mitochondrial genes and growth factor receptors genes. CD8+T cells regulated the conversion of cardiac-resident macrophages as well as infiltrated macrophages to cardioprotective macrophages which express growth factor genes including Areg, Osm and Csf1 at the early phase of cardiac pressure overload, which are essential for the myocardial adaptive response. Our results demonstrate a dynamic interplay between cardiac CD8+T cells and macrophages that is necessary for adaptation to cardiac stress, and they highlight the homeostatic functions of tissue macrophages.

overall_design: The hearts of WT mice or mice without Tcells were pressure over loaded, and cardiomyocytes were harvested two weeks later for single-cell RNA sequencing (scRNA-seq) analysis.

first: Kyoko

last: Komai

first: Minako

last: Ito

first: Seitaro

last: Nomura

first: Shigeyuki

last: Shichino

first: Manami

last: Katoh

first: Toshiyuki

last: Ko

first: Mana

last: Iizuka-Koga

first: Hiroko

last: Nakatsukasa

first: Akihiko

last: Yoshimura


title: Cumulative in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse Hoxd cluster

first: Lucille

last: Lopez-Delisle

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

overall_design: Refer to individual Series


title: Transcriptomic profiling of human stromal cells in mouse xenografts upon treatment with chemotherapeutic drug and/or the senolytic agent procyanidin C1

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Physical function declines in advanced age, portending disability, increased health expenditures, and clinical mortality. Cellular senescence leads to tissue dysfunction and contributes to the consequences of aging, but whether age-related pathologies including cancer can be alleviated by targeting senescent cells remains largely unclear. Long term retention of senescent cells in vivo, a process mainly attributed to high expression of BCL2 family proteins, causes chronical tissue damages mainly through the senescence-associated secretory phenotype (SASP). Indeed, senescent cells can be removed by several strategies, thus preventing appearance of chronic symptoms and prolonging healthspan. Strategies involving senolytics, which eliminate senescent cells by pharmacological actions, are recently emerging as a novel and prominent solution to ameliorate diverse age-related pathologies. Achieving the goal using synthetic or natural agents would generate a tremendous impact on the quality of life. We test the potential of procyanidin C1 (PCC1), a B type procyanidin flavonoid derived from plant sources including grape, apple and cocoa, in targeting senescent cells through inducing apoptosis and suppressing the pro-inflammatory phenotype. This study demonstrates the efficacy of PCC1 in restraining the SASP expression and minimizing the influence of senescent stromal cells in tumor microenvironment and provides a strong rationale for its future development in anti-aging industrial pipelines.

overall_design: Examination of in vitro efficacy of PCC1 in treating human senescent stromal cells. Experimental mice xenografted with human stromal cells (PCS27) and cancer epithelial cells (PC3) were treated with vehicle, mitoxantrone (MIT) or MIT/PCC1 as three independent corhorts in a 8-week preclinical regimen. Upon completion of treatment, mice were sacrificed and tumors were collected for further process. Stromal cells were isolated from tumor tissues by laser capture microdissection (LCM) and subject to RNA preparation, library construction and high throughput sequencing. This trial was performed beyond previous studies reporting their effects in treatment of disorders including but not limited to osteoporosis, osteoarthritis, atherosclerosis, cancer and neurodegenerative diseases including Alzheimer's and Parkinson's.

first: Qixia

last: Xu

first: Qiang

last: Fu