title: Clonotypic analysis of T cells cultured in extracellular matrices of different viscoelasticies

summary: The efficacy of adoptive T cell therapy is highly dependent on the generation of T cell populations that are able to both provide immediate effector function and long-term protective immunity. Inspired by the emerging consensus that T cell phenotype and function are inherently linked to their tissue localization, we present an approach to generate functionally distinct T cell populations via the physical properties of their surrounding matrix. A collagen type I based extracellular matrix (ECM) was engineered to allow for independent tuning of matrix stiffness and viscoelasticity, two features that characterize the mechanical properties of tissues. To assess whether phenotypic differences imparted by matrix viscoelasticity are due to the selection and persistence of specific T cell clones, we performed single cell RNA-sequencing with TCR sequencing

overall_design: T cells cultured in fast-relaxing and slow-relaxing matrices, plate-cultured T cells and the parent T cell population were separately stained with TotalSeq C 0252 anti-human Hashtag 2 (Biolegend # 394663), TotalSeq C 0253 anti-human Hashtag 3 (Biolegend # 394665), TotalSeq C 0254 anti-human Hashtag 4 (Biolegend # 394667) and TotalSeq C 0251 anti-human Hashtag 1 (Biolegend # 394661), in addition to TotalSeq C 0063 anti-human CD45RA (Biolegend # 304163). After staining, the T cells were pooled together for sequencing.

first: Yutong

last: Liu

first: David

last: Mooney


title: Mitotic chromosomes scale to nucleo-cytoplasmic ratio and cell size in Xenopus

status: Public on May 02 2023

city: Worcester

first: Bastiaan

last: Dekker

state: Massachusetts

address: 368 Plantation street

department: Systems Biology

country: USA

institute: University of Massachusetts Medical School

summary: Hi-C on mitotic chromosomes in Xenopus system to study mitotic chromosome scaling by comparing replicated sperm vs stage 8 embryo chromosomes

first: Coral

middle: Y

last: Zhou

first: Martin

first: Hilda

last: Cabrera

first: Joel

last: Ryan

first: Job

first: Rebecca

last: Heald


title: Gene expression profiles of CD8+ T cells cultured in extracellular matrices of different viscoelasticies

city: Boston

first: Kwasi

last: Adu-Berchie

address: 3 Blackfan Circle

institute: Harvard University

type: Expression profiling by high throughput sequencing

summary: The efficacy of adoptive T cell therapy is highly dependent on the generation of T cell populations that are able to both provide immediate effector function and long-term protective immunity. Inspired by the emerging consensus that T cell phenotype and function are inherently linked to their tissue localization, we present an approach to generate functionally distinct T cell populations via the physical properties of their surrounding matrix. A collagen type I based extracellular matrix (ECM) was engineered to allow for independent tuning of matrix stiffness and viscoelasticity, two features that characterize the mechanical properties of tissues. To investigate how ECM viscoelasticity drives changes in the transcriptional landscape of T cells, scRNA-seq of CD8+ T cells cultured in fast relaxing and slow relaxing collagen matrices was performed

overall_design: CD8+ T cells were harvested from collagen gels, and live cells were enriched using a dead cell removal kit (Miltenyi #130-090-101). Single cell sequencing was performed using the Chromium Single Cell 3’ v3 platform (10x Genomics) on the NovaSeq S1.

middle: J


title: RNA-seq of muscles from young and aged ATF4 mKO mice and littermate controls

city: Iowa City

first: Matthew

last: Miller

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: To investigate the roles of ATF4 in skeletal muscle aging we generated muscle-specific ATF4 knockout (ATF4 mKO) mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of tibialis anterior muscles at 6-months and 22-months of age.

overall_design: Tibialis anterior mRNA profiles of 6-month-old and 22-month-old ATF4 mKO and control mice

first: Scott

middle: M

last: Ebert

first: Christopher

last: Adams


title: Reduced histone gene copy number disrupts Drosophila Polycomb function

city: Chapel Hill

first: Gregory

last: Matera

state: North Carolina

address: Genome Science Building

institute: University of North Carolina at Chapel Hill

summary:
The chromatin of animal cells contains two types of histones: canonical histones that are expressed during S phase of the cell cycle to package the newly replicated genome, and variant histones with specialized functions   that are expressed throughout the cell cycle and in non-proliferating cells. Determining whether and how canonical and variant histones cooperate to regulate genome function is integral to understanding how chromatin-based processes affect normal and pathological development. Here, we demonstrate that variant histone H3.3 is essential for Drosophila development only when canonical histone gene copy number is reduced, suggesting that coordination between canonical H3.2 and variant H3.3 expression is necessary to provide sufficient H3 protein for normal genome function. To identify genes that depend upon, or are involved in, this coordinate regulation we screened for hemizygous chromosome 3 deficiencies that impair development of flies bearing reduced H3.2 and H3.3 gene copy number. We identified two regions of chromosome 3 that conferred this phenotype, one of which contains the Polycomb gene, which is necessary for establishing domains of facultative chromatin that repress master regulator genes during development. We further found that reduction in Polycomb dosage decreases viability of animals with no H3.3 gene copies. Moreover, heterozygous Polycomb mutations result in de-repression of the Polycomb target gene Ubx and cause ectopic sex combs when either canonical or variant H3 gene copy number is also reduced.  We conclude that Polycomb-mediated facultative heterochromatin function is compromised when canonical and variant H3 gene copy number falls below a critical threshold.
To investigate whether H3.3A and/or H3.3B mRNA levels change in 12xHWT animals, we looked at differential gene expression profiles of 12xHWT and yw (200xWT) third instar larval brain cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from 12xHWT and yw (200xWT) Drosophila melanogaster third instar larval brain cells.

first: Jeanne-Marie

last: McPherson

first: Harmony

last: Salzler

first: Daniel

last: McKay

first: Robert

last: Duronio


title: Mast cell tolerance in the skin microenvironment to commensal bacteria is controlled by fibroblasts [single-cell RNA-seq]

city: San Diego

first: Anna

last: Di Nardo

address: 9500 Gilman Drive

department: Dermatology ACTRI

institute: UCSD

summary:
To investigate the cooperative function of dermal fibroblast and mast cell in inducing mast cell tolerance to commensals
We then performed gene expression profiling analysis using data obtained from SC RNA seq of mast cells, dermal fibroblast and  and mast cells in co culture with dermal fibroblasts  .

overall_design: Comparative gene expression profiling analysis of single cell  RNA-seq data for conditioned and not conditioned mast cells

first: Yu-Ling

last: Chang

first: Shahrzad

last: Alimohammadi

first: Kana

last: Masuda-Kuroki

first: Zhenping

last: Wang

first: Krishna

last: Sriram

first: Paul

middle: A

last: Insel


title: Transcriptomic differences in CCR10+ versus CCR10- regulatory T cells (Tregs)

city: Nashville

last: Alexander

state: TN

address: 1211 Medical Center Drive

institute: Vanderbilt University Medical Center

summary: We identified decreases in circulating CCR10+ Tregs in human hypertension. In order to better determine the phenotype of these cells, we performed bulk RNA sequencing of flow sorted human CCR10+ versus CCR10- Tregs from healthy control individuals. Results revealed evidence of increased T cell activation in CCR10+ Tregs.

overall_design: PMBCs from 3 healthy controls were isolated and flow sorted into distinct CCR10+ Treg and CCR10- Treg populations from each sample. Bulk RNA sequencing was performed on RNA extracted from each cell population from each donor.

first: Meena

last: Madhur


title: mRNA array in brain tissue samples of 5XFAD mice

city: Barcelona

first: Christian

middle: Griñán

last: Ferré

state: Barcelona

address: Joan XIII, s/n

department: Pharmacology, Toxicology and Therapeutic Chemistry

country: Spain

institute: University of Barcelona

summary: In Alzheimer's disease pathology, several neuronal processes are dysregulated by excitotoxicity including neuroinflammation and oxidative stress (OS). New therapeutic agents capable of modulating such processes are needed to foster neuroprotection. Here, the effect of an optimised NMDA receptor antagonist, UB-ALT-EV and memantine, as a gold standard, have been evaluated in 5XFAD mice. Following treatment with UB-ALT-EV, nor memantine, changes in the calcineurin (CaN)/NFAT pathway were detected. UB-ALT-EV increased neurotropic factors (Bdnf, Vgf and Ngf) gene expression. Treatments reduced astrocytic and microglial activation as revealed by GFAP and Iba-1 quantification. Interestingly, only UB-ALT-EV was able to reduce gene expression of Trem2, a marker of microglial activation and NF-κB. Pro-inflammatory M1-microglial phenotype (Il-1β, Ifn-γ, Ccl2 and Ccl3) markers were down-regulated in UB-ALT-EV-treated mice but not in memantine-treated mice. Interestingly, the anti-inflammatory markers of the M2-migroglial phenotype, chitinase-like 3 (Ym1) and Arginase-1 (Arg1), were up-regulated after treatment with UB-ALT-EV. Since iNOS gene expression decreased after UB-ALT-EV treatment, a qPCR array containing 84 OS-related genes was performed. We found changes in Il-19, Il-22, Gpx6, Ncf1, Aox1 and Vim gene expression after UB-ALT-EV. In sum, our results reveal a robust effect on neuroinflammation and OS processes after UB-ALT-EV treatment, surpassing the memantine effect in 5XFAD.

overall_design: The expression of 84 mature oxidative stress mRNAs in the brain of 5XFAD corresponding to the different study groups (Wild Type Control Control, 5XFAD Control and 5XFAD treated with UB-ALT-EV)

first: Júlia

last: Companys-Alemany

first: Mercè

last: Pallàs

last: Griñán-Ferré


title: Functional roles of STIM1::MXD3 in K562 myeloid leukemic cells and its impact on MYC transcriptional control [K562_STIM1-MXD3]

city: Hong Kong

first: Margaret HL

last: Ng

address: Prince of Wales Hospital

department: Department of Anatomical and Cellular Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: To investigate the functional significance of STIM1::MXD3, we overexpressed the fusion gene in K562 myeloid leukemia cells and analysed global gene expression changes using RNA-seq.

overall_design: Differential gene expression profiling analysis of RNA-seq data for K562 cells expressing STIM1::MXD3, wild-type MXD3 and the empty vector control.

first: Margaret

first: Chi-Keung

last: Cheng

first: Yuk-Lin

last: Yung


title: Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster [WGBS]

summary: Hibernation consist of alternating torpor/arousal phases, during which animals cope with repetitive hypothermia and ischemia-reperfusion. Due to limited transcriptomic and methylomic information for facultative hibernators, we here conducted RNA and whole genome bisulfite sequencing in liver of hibernating Syrian hamster (Mesocricetus auratus). Gene Ontology analysis was performed on 844 differentially expressed genes (DEGs) and confirmed the shift in metabolic fuel utilization, inhibition of RNA transcription and cell cycle regulation as found in seasonal hibernators. We show a so far unreported suppression of MAPK and PP1 pathways. Notably, hibernating hamsters showed upregulation of MAPK inhibitors (DUSPs and SPRYs) and reduced levels of MAPK induced transcription factors. Promoter methylation was found to modulate the expression of genes targeted by these transcription factors. In conclusion, we document gene regulation between hibernation phases, which may aid the identification of pathways and targets to prevent organ damage in transplantation or ischemia-reperfusion.

overall_design: Whole Genome Bisulphite Sequencing profiles for 9 Syrian Hamsters in the following hibernation stages: euthermic, torpor late and arousal early.

first: Marloes

last: Oosterhof

first: Louis

last: Coussement

first: Victor

last: Guryev

first: Vera

last: Reitsema

first: Jojanneke

last: Bruintjes

first: Maaike

last: Goris

first: Hjalmar

middle: R

last: Bouma

first: Tim

last: De Meyer

first: Marianne

middle: G

last: Rots

first: Robert

middle: H

last: Henning


title: Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections [3]

status: Public on May 04 2023

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Single-cell genetic and epigenetic analyses parse the brain’s billions of neurons into thousands of “cell-type” clusters, each residing in different brain structures. Many of these cell types mediate their unique functions by virtue of targeted long-distance axonal projections to allow interactions between specific cell types. Here we have used Epi-Retro-Seq to link single cell epigenomes and associated cell types to their long-distance projections for 33,034 neurons dissected from 32 different source regions projecting to 24 different targets (225 source→target combinations) across the whole mouse brain. We highlight uses of this large data set for interrogating both overarching principles relating projection cell types to their transcriptomic and epigenomic properties and for addressing and developing specific hypotheses about cell types and connections as they relate to genetics. We provide an overall synthesis of the data set with 926 statistical comparisons of the discriminability of neurons projecting to each target for every dissected source region. We integrate this dataset into the larger, annotated BICCN cell type atlas composed of millions of neurons to link projection cell types to consensus clusters. Integration with spatial transcriptomic data further assigns projection-enriched clusters to much smaller source regions than afforded by the original dissections. We exemplify these capabilities by presenting in-depth analyses of neurons with identified projections from the hypothalamus, thalamus, hindbrain, amygdala, and midbrain to provide new insights into the properties of those cell types, including differentially expressed genes, their associated cis-regulatory elements and transcription factor binding motifs, and neurotransmitter usage.

overall_design: In Epi-Retro-Seq, the retrograde viral tracer rAAV2-retro-Cre is injected in the target region in an INTACT mouse, turning on Cre-dependent nuclear-GFP expression in neurons that project to the injected target, throughout the mouse brain. The brain is then sectioned into eighteen 600-micron coronal slices, and the brain regions of interest are mannually dissected from each slice. Nuclei are sampled from 4 mice (2 male and 2 female) for each projection target. Nuclei from each of the dissected source regions are prepared, from which GFP+/NeuN+ nuclei (the GFP-labeled projection neurons) are isolated as single nuclei using fluorescence activated nuclei sorting (FANS) and assayed using snmC-Seq2/3 to profile their genome-wide DNA methylation signatures. Low-quality nuclei were removed.

first: Jingtian

last: Zhou

first: Zhuzhu

last: Zhang

first: May

last: Wu

first: Hanqing

last: Liu

first: Yan

last: Pang

first: Anna

last: Bartlett

first: Angeline

middle: C

last: Rivkin

first: Will

middle: N

last: Lagos

first: Elora

last: Williams

first: Cheng-Ta

last: Lee

first: Paula

last: Assakura Miyazaki

first: Andrew

middle: I

last: Aldridge

first: Qiurui

last: Zeng

first: J

middle: L

last: Salinda

first: Naomi

last: Claffey

first: Michelle

last: Liem

first: Conor

last: Fitzpatrick

first: Lara

last: Boggeman

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon

last: Nery

first: Rosa

last: Castanon

first: Neelakshi

middle: S

last: Patne

first: Minh

last: Vu

first: Mohammad

last: Rashid

first: Matthew

middle: W

last: Jacobs

first: Tony

last: Ito-Cole

first: Julia

last: Osteen

first: Sharon

last: Huang

first: António

last: Pinto-Duartec

first: Bertha

last: Dominguez

first: Jared

middle: B

last: Smith

first: Carolyn

last: O'Connor

first: Kuo-Fen

first: Eran

last: Mukamel

first: Xin

last: Jin

first: M

last: Behrens


title: Functional roles of RUNX1::ERG in K562 myeloid leukemia cells [K562_RUNX1-ERG]

first: Margaret HL

last: Ng

summary: To investigate the functional significance and transcriptional impacts associated with RUNX1::ERG, we overexpressed the fusion gene in K562 myeloid leukemia cells and analysed global gene expression changes using RNA-seq.

overall_design: Differential gene expression profiling analysis of RNA-seq data for K562 cells expressing RUNX1::ERG and the empty vector control.

first: Margaret

first: Chi-Keung

last: Cheng

first: Yuk-Lin

last: Yung


title: Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections [2]

status: Public on May 03 2023

first: Joseph

last: Ecker

first: Jingtian

last: Zhou

first: Zhuzhu

last: Zhang

first: May

last: Wu

first: Hanqing

last: Liu

first: Yan

last: Pang

first: Anna

last: Bartlett

first: Angeline

last: Rivkin

first: Will

last: Lagos

first: Elora

last: Williams

first: Cheng-Ta

last: Lee

first: Paula

last: Assakura Miyazaki

first: Andrew

last: Aldridge

first: Qiurui

last: Zeng

first: J

last: Salinda

first: Naomi

last: Claffey

first: Michelle

last: Liem

first: Conor

last: Fitzpatrick

first: Lara

last: Boggeman

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon

last: Nery

first: Rosa

last: Castanon

first: Neelakshi

last: Patne

first: Minh

first: Mohammad


title: Age-dependent cell stemness plasticity orchestrates postnatal functional maturity of ruminants

city: Hangzhou

first: Jiajin

last: Wu

state: Zhejiang

address: Yuhangtang road

country: China

institute: Zhejiang University

summary: Newborn ruminants are considered as functionally monogastric animals. The poorly understanding of tremendous cellular differences between newborn and completely ruminating stages hinders the improvement of health and performance of domestic ruminants. Here, unbiased single-cell RNA sequencing was performed on the rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, rectum, salivary gland, liver, and mammary gland from newborn and adult cattle. We created a comprehensive single-cell transcriptomic compendium covering 235,941 high-quality single cells and 78 cell types. The age-state cell atlases for each tissue type were also constructed to delineate the cell type composition dynamics at newborn and adult stages. We further created the Cattle Cell Landscape database (http://cattlecelllandscape.zju.edu.cn) to detailly display the informative results and to facilitate in effectively annotation of cattle cell type/subtypes for the broad research community. By measuring stemness states of epithelial cells across multiple tissue types, we revealed a multi-tissue representation of paradigm of cell stemness plasticity: the newborn forestomach (rumen, reticulum, and omasum) epithelial cells are more transcriptionally indistinct and stochastic compared with adult stage, which contrary to that of abomasum and intestinal tissues. Moreover, the rapid forestomach development during the early life of calves was driven by the epithelial progenitor-like cells with high activities of epigenetic modifying. A novel cell type STOML3+ cell was found to be newborn cattle-specific that plays an important role in stemness maintenance of its own and cholangiocyte in the hepatic microenvironment. These results provide novel insights into the cellular biology and postnatal ruminating maturity of ruminants

overall_design: Construction of the age-state cell atlases for 13 tissue types of cattle covering 30 single-cell RNA sequencing datasets.

first: Senlin

last: Zhu

first: Huizeng

last: Sun


title: RNA-seq of murine spleocytes

city: Leipzig

first: Marco

last: Herling

address: Johannisallee 32a

department: Department for Hematology, Cell Therapy, Hemostaseology, and Infectious Diseases

country: Germany

institute: University Clinic Leipzig

summary: Aberrant expression of the T-cell lymphoma/leukemia 1A (TCL1A) oncogene is a hallmark of chronic lymphocytic leukemia (CLL) and is associated with aggressive disease features. A better understanding of functional networks around TCL1A is required to develop new treatment approaches in CLL. Here, we identify the epigenetic modifying lysine-specific demethylase KDM1A as a nuclear interaction partner of the TCL1A protein in CLL B-cells. Interestingly, binding to TCL1A increased KDM1A?s demethylase activity. Moreover, higher KDM1A expression correlated with adverse clinical characteristics and shorter progression-free survival in CLL. Kdm1a knockdown (Kdm1a-KD) reduced leukemic burden and prolonged overall survival in a CLL mouse model accompanied by upregulation of p53 and pro-apoptotic pathways. RNA-seq analysis of differentially expressed genes upon Kdm1a-KD suggests that Kdm1a might act as a transcriptional repressor. In addition, ChIP experiments demonstrated an altered modification of H3K4me3 in Kdm1a-KD mice. Moreover, KDM1A expression in the microenvironmental had an impact on its support for CLL progression. In line, KDM1A inhibition by the pharmacologic compound C12 induced apoptosis and affected H3K4/9 target methylation levels in B-cell lines and CLL samples. Overall, we found a relevant pathogenetic role of KDM1A as a pro-oncogenic marker in CLL cells and their microenvironment. This provides a novel treatment rationale for targeting KDM1A in CLL.

overall_design:
We reported the gene expression changes in CLL mouse model upon KDM1A knockdown. An doxycycline-inducible KDM1A knockdown Eµ-TCL1A mouse model was established. Leukemic mice were treated with doxycycline to induce KDM1A knockdown.
RNA-seq of  splenic mononuclear cells from KDM1AKD;Eµ-TCL1A and Eµ-TCL1A

first: Qu

last: Jiang

first: Prerana

last: Wagle


title: Plasma exosomal miRNA profiles in pediatric fulminant myocarditis patients and healthy controls

city: Jinan

first: Xinyue

last: Zhang

address: 324，Jingwu Road

institute: Department of Pediatric Cardiology, Shandong Provincial Hospital, Shandong University

summary: The pathophysiology of fulminant myocarditis (FM) is significantly influenced by the interactions between immunological and myocardial cells, involving exosome-mediated intercellular microRNA (miRNA) signaling. To further investigate the pathogenesis of FM and discover diagnostic biomarkers, we have employed miRNA microarray expression profiling as a discovery platform.

overall_design: Plasma exosome miRNAs of 3 pediatric FM patients and 3 healthy volunteers were analyzed using a small RNA microarray analysis. The pathophysiological relevance and potentials as diagnostic biomarkers of the most significantly altered miRNAs were explored. To screen for FM-specific target genes, differentially expressed mRNAs in peripheral blood mononuclear cells (PBMCs) from pediatric FM patients were intersected with the miRNA target genes obtained from 5 different miRNA target gene predictive tools. The hub genes and their biological and mechanistic pathways related to inflammation and/or the immune system were identified. CeRNA networks of lncRNAs, circRNAs, miRNAs, and mRNAs between cardiomyocytes and PBMCs were finally established. Furthermore, we verified that the expression levels of four selected miRNAs were increased in plasma exosomes of pediatric FM patients compared to those in controls by qRT-PCR.

first: Bo

last: Han


title: Systematic comparison of experimental and human obstructive cholestasis reveals conservation of canonical pathway activation and biomarkers relevant for cholestatic liver disease [human data set]

first: Lindsey

last: Devisscher

address: Corneel Heymanslaan 10

summary: Cholelithiasis-induced cholestasis is one of the most common causes of hospitalization due to gastrointestinal disease, yet considerable knowledge gaps exist in the pathogenesis of this disease. This can partially be explained by inadequate characterization of experimental cholestasis models. Therefore, we compared the transcriptional profile of commonly used mouse models for obstructive cholestasis and benchmarked them to human disease to identify the model(s) best suited for cholelithiasis-induced cholestasis research and to uncover conserved mechanisms involved in human and murine cholestasis. Selected mouse models included bile duct ligation (BDL) surgery, 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet, associated with extra- and intrahepatic obstructive cholestasis, respectively, and a drug-induced cholestasis model relying on cyclosporin A (CsA), in an acute and chronic setting. Human samples were collected from patients with cholelithiasis-induced cholestasis of an acute and recurrent nature. RNA sequencing was performed on mouse and human liver tissue. Both the BDL and DDC models, but not the CsA model, were shown to be applicable for studying cholelithiasis-induced cholestasis, with transcriptomic profiles that highly correspond to acute cholestasis in human patients. In particular, the conservation of canonical pathways related to the inflammatory response and cytoskeleton organization, in which the Rho family GTPase is involved, were identified. This study furthermore revealed some promising mechanistic-based transcriptomic biomarkers relevant for murine and human cholestasis, which could potentially be useful for robust prediction and detection of diverse types of cholestatic liver disease.

overall_design: Fresh liver tissue was collected from 3 acute (HUMAC) and 4 recurrent (HUMREC) cholestasis patients. The respective control group consists of 3 human patients (HUMN) that were scheduled for a gastric bypass (without confirmed non-alcoholic fatty liver disease) or liver resection without clinical signs of cholestasis. RNA was extracted from the fresh liver tissue of cholestasis patients and paraffin embedded liver tissue from the patients without cholestasis.

first: Tim

last: Meese

first: Eva

last: Gijbels

first: Filip

last: Van Nieuwerburgh


title: Placental Cell Conditioned Media Modifies Hematopoetic Stem Cell Transcriptome In Vitro

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

summary: Background: Factors secreted from the placenta into maternal and fetal circulation are important for maternal and fetal development during pregnancy. Maternal hematopoietic stem cells maintain maternal blood supply. The placenta is an early site of fetal hematopoiesis, and placental hematopoietic stem cells are involved in the early stages of fetal blood cell differentiation. Cross-talk between placental cells and hematopoietic stem cells represents an important but understudied phenomenon of pregnancy. The impact of toxicant exposure on placental-immune cell communication is poorly understood. The goals of this study were to 1) determine if factors secreted from placental cells alter transcriptomic responses in hematopoietic stem cells in vitro and 2) if monoethylhexyl phthalate (MEHP), the major metabolite of the pollutant diethylhexyl phthalate, modifies these effects.  Methods: Using in vitro cell line models of hematopoietic stem cells (K-562) and placental syncytiotrophoblasts (differentiated BeWo), we treated K-562 cells for 24 hours with media conditioned by incubation with BeWo cells, media conditioned with BeWo cells treated with 10 µM MEHP, or unconditioned controls (n = 4 replicates for each group). We extracted K-562 cell RNA and performed RNA sequencing. We then conducted differential gene expression and pathway analysis by treatment group and accounted for multiple comparisons using false discovery rate (FDR).   Results: K-562 cells treated with BeWo cell conditioned media differentially expressed 173 genes (FDR<0.05 and fold-change>2.0), relative to vehicle control. Cells treated with BeWo media upregulated TPM4 2.4 fold (FDR=1.8x10-53) and S1PR3 3.3 fold (FDR=1.6x10-40) compared to controls. Upregulated genes were enriched for biological processes including stem cell maintenance (“somatic stem cell population maintenance”), cell proliferation (“positive regulation of endothelial cell proliferation”) and immune processes (“myeloid leukocyte cytokine production”). Downregulated genes were enriched for protein translation (“mitochondrial translation”) and transcriptional regulation (“RNA processing”). Cells treated with media from BeWo cells treated with MEHP upregulated (FDR<0.05) eight genes, including genes involved in fat/lipid metabolism (PLIN2, fold-change: 1.4; CPT1A, fold-change: 1.4) and iron uptake (TFRC, fold-change: 1.3), relative to the BeWo conditioned media treatment.  Conclusion: Hematopoietic stem cells are responsive to media that has been conditioned by placental cells, potentially impacting processes related to stem cell maintenance and proliferation, which may represent placental-immune communication important for development. The metabolite MEHP only had a modest impact on these responses at the single concentration tested. Future directions will investigate components of placental cell media (hormones, microvesicles, and proteins) contributing to hematopoietic cell signals.

overall_design: 3 treatment groups with 4 replicates: unconditioned media, BeWo conditioned media, MEHP + BeWo conditioned media

first: Sean

last: Harris

first: Anthony

last: Su

first: John

middle: F

last: Dou

first: Rita

last: Loch-Caruso

first: Elana

last: Elkin


title: Single cell analysis of the postnatal dorsal V-SVZ reveals a role for Bmpr1a-signaling in silencing pallial germinal activity

city: Lyon

first: Guillaume

last: Marcy

address: 8 avenue Rockefeller

country: France

institute: Universite Lyon 1

summary: The ventricular-subventricular zone (V-SVZ) is the largest neurogenic region of the postnatal forebrain, containing neural stem cells (NSCs) that emerge from both the embryonic pallium and subpallium. Despite of this dual origin, glutamatergic neurogenesis declines rapidly after birth, while gabaergic neurogenesis persists throughout life. We performed single-cell RNA-sequencing (scRNA-Seq) of the postnatal dorsal V-SVZ for unravelling the mechanisms leading to pallial lineage germinal activity silencing. We show that pallial NSCs enter a state of deep quiescence, characterized by high BMP-signaling, reduced transcriptional activity and Hopx expression, whilst in contrast, subpallial NSCs remain primed for activation. Induction of deep quiescence is paralleled by a rapid blockade of glutamatergic neurons production and differentiation. Finally, manipulation of Bmpr1a demonstrates its key role in mediating these effects. Together, our results highlight a central role of BMP-signaling in synchronizing quiescence induction and blockade of neuronal differentiation to rapidly silence pallial germinal activity after birth.

overall_design: Single cell profiles of microdissected dorsal subventricular zone of postnatal day 2, 12 and 22 wild type mice. Samples were collected independently using the 10x Chromium Single Cell Controller and libraries were prepared according to 10x Genomics protocol.

first: Louis

last: Foucault

first: Olivier

last: Raineteau


title: Screening regulated pathway and genes expression in intestinal GVHD patients

city: Suzhou

first: xiaoliang

last: yu

state: Jiangsu

address: Chongwen Road

institute: Suzhou Institute of Systems Medicine

summary: Colon biopsies samples were collected after GVHD diagnosis，total RNA was extracted and deep sequenced to compare the gene expression  profiles among Normal and acute intestinal GVHD patients

overall_design: Duplicated 3 control samples,3 acute GVHD patients' colon samples were sequneced and compared

first: Xiaoliang

last: Yu

first: Sudan

last: He

first: Siying

last: Liu


title: Human iPSC can be differentiated in vitro to articular cartilage or to osteogenic organoids via the endochondral ossification transdifferentiation pathway

city: Parkville

first: Shireen

last: Lamande

state: Victoria

address: Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

summary: The ability to generate chondrocytes and osteoblasts from induced pluripotent stem cells (iPSCs) will provide insights into skeletal development and genetic skeletal disorders and generate cells for regenerative medicine applications. Here we describe a method that directs iPSC-derived sclerotome to chondroprogenitors in 3D pellet culture then to articular chondrocytes or, alternatively, along the growth plate cartilage pathway to become hypertrophic chondrocytes that can transdifferentiate to osteoblasts. Osteogenic organoids deposit and mineralize a collagen I extracellular matrix (ECM), mirroring in vivo endochondral bone formation. We have identified gene expression signatures at key developmental stages including chondrocyte maturation, hypertrophy and transdifferentiation to osteoblasts, and show that this system can be used to model genetic cartilage and bone disorders.

overall_design: Comparative RNAseq of iPSCs at different timepoints as they are differentiating to growth plate chondrocytes. Comparative RNAseq of articular vs growth plate chondrocytes. Comparative RNAseq of hypertrophic growth plate chondrocytes and osteoblasts/osteocytes. Data for two iPSC lines is presented.

last: Lamandé

first: Elizabeth

last: Ng

first: Edouard

last: Stanley

first: Andrew

last: Elefanty

last: Bateman


title: Gene Expression Profiling of leukemic blasts/ mesenchymal stem cells (MSC) derived from bone marrow of Indian patients with Acute Myeloid Leukemia (AML) and profiling of AML xenograft post-treatment with human MSC in mice model

city: Navi Mumbai

first: Jyoti

middle: Anand

last: Kode

state: Maharashtra

address: Kharghar

department: Kode Lab

country: India

institute: Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre

summary:
Heterogeneity and variable survival outcomes of Acute Myeloid Leukemia (AML), suggest that yet undiscovered genes and pathways contribute to AML. Mesenchymal stem cells (MSC), an important component of bone marrow/ stromal microenvironment has been shown to contribute to development and progression of various cancers. Current study was aimed at characterizing MSC from AML bone marrow (BM) and evaluate their therapeutic potential in controlling survival of AML leukemic blasts. MSCs were isolated and cultured from BM of high-risk AML patients. MSC were also obtained from BM of bi-lineage leukemia (ETP-ALL) patients as control MSC from precursor stage of leukemia. MSC derived from uninvolved BM (UnBM) of lymphoma patients were used as normal MSC control. Leukemic blasts were derived from BM of AML and ETP-ALL patients. Patient derived AML-MSC exhibited characteristic profile of MSC Type-II CD90+CD45lo expressing high percent of TLR3 than TLR4 receptors, indicating pro-tumorigenic nature. Gene expression profiles of freshly derived leukemia blasts, AML cell line and AML MSC exhibited deregulated and overactivated Aurora Kinase pathway and inflammasome innate immune pathway. These two pathways are known to be upregulated in many solid and hematological cancers. Further we observed few tumor suppressor genes were downregulated in these groups. In vitro, AML MSC supported survival of leukemic blasts and increased chemoresistance to standard anticancer drugs. Hence AML MSC and ETP-ALL MSC were treated with immunomodulatory drug cocktail (IMiD) containing TLR3 antibody, TLR4 ligand and CXCR4 antagonist peptide (Gift from Kyoto University, Japan), designated as MSC-IMiD. It was observed that MSC-IMiD reduced chemoresistance of leukemic blasts to certain extent in vitro. Further we evaluated if leukemia BM derived MSC, MSC culture supernatant or MSC-IMiD can provide therapeutic benefit to control growth of AML xenograft in mouse model. Human gene expression profile was mapped in human-mouse xenograft made as subcutaneous tumor in immunodeficient NOD-SCID mice model from AML cell line KG1. Comparison was done of all treated groups with tumor bearing control gene expression data. It was interesting to note that MSC and MSC-IMiD could reduce tumor growth in 50% of mice tested. Mice treated with MSC culture supernatant exhibited reduction in tumor growth at par with that seen in Adriamycin treated positive control group. Deregulation of Aurora kinase pathway, inflammasome pathway genes and tumor suppressor genes was found to be reversed in residual tumor tissue of mice treated with MSC and MSC culture supernatant. This gene expression profiling study has helped understanding pathways involved in chemoresistance and immune suppression observed in AML. Moreover, this study has provided leads that MSC or its conditioned media can be explored further to control abnormal myelopoiesis in AML and develop targeted therapy.

Funding source:
Grant ID:  53/13/2013/CMB/BMS.
Grantee:  Jyoti Kode
Grant title: Understanding the cross-talk between mesenchymal stromal cells and leukemic stem cells in Acute Myeloid Leukemia: Implications in disease biology and therapy.
Name of the funding source: Indian Council of Medical Research, Government of India, India.

first: Manasi

last: Nagare

first: Manju

last: Sengar

first: Navin

last: Khattry

first: Sachin

last: Punatar

first: Anant

last: Gokarn

first: Shubhada

last: Chiplunkar


title: constructing condylar organoid to explore its difference to the traditional two-dimensional (2D) culture condylar chondrocyte

status: Public on May 01 2023

city: Wuhan

first: Yang

middle: xue

last: wen

address: No. 237, Luoyu Road, Hongshan District

institute: Wuhan University

summary: An organoid culture system can better recapitulate the cellular structure, function, and interaction between cells and the extracellular matrix (ECM) than the traditional two-dimensional (2D) culture system. We here constructed a condylar cartilage organoid and utilized it to explore the regulatory role of primary cilia at the organoid level. RNA sequencing unveiled the differences of transcriptomics between the condylar cartilage organoid and 2D culture chondrocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for condylar organoid and 2D cultured condylar chondrocyte

first: Liu

last: Zhan

first: Zhou

last: Haoyu

first: Sa

last: Guoliang

last: Xuewen


title: Differences in PD-1+CD57- CD8+ T cells versus other CD8+ memory T cells and in control versus hypertensive individuals

first: Matthew

last: Alexander

summary: The primary goal was to determine the phenotype of PD-1+CD57- CD8+ T cells compared to other CD8+ memory T cells based on single cell RNA sequencing. Peripheral blood mononuclear cells (PBMCs) from control and hypertensive samples were included. Secondary analyses include comparing gene expression changes in these cells between control and hypertensive individuals.

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated from 4 healthy control and 4 hypertensive individuals, stained with hashtags and extracellular antibodies, and loaded onto the 10X Genomics controller for single cell sequencing. Antibodies were used for targeting PD-1+CD57- CD8+ memory T cells. The 4 healthy control samples were hashed together and 4 hypertensive samples were hashed together.

first: Meena

last: Madhur


title: Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster [RNA-Seq]

first: Jeroen

last: Galle

summary: Hibernation consist of alternating torpor/arousal phases, during which animals cope with repetitive hypothermia and ischemia-reperfusion. Due to limited transcriptomic and methylomic information for facultative hibernators, we here conducted RNA and whole genome bisulfite sequencing in liver of hibernating Syrian hamster (Mesocricetus auratus). Gene Ontology analysis was performed on 844 differentially expressed genes (DEGs) and confirmed the Liver, shift in metabolic fuel utilization, inhibition of RNA transcription and cell cycle regulation as found in seasonal hibernators. We Liver, show a so far unreported suppression of MAPK and PP1 pathways. Notably, hibernating hamsters Liver, showed upregulation of MAPK inhibitors (DUSPs and SPRYs) and reduced levels of MAPK induced transcription factors. Promoter methylation was found to modulate the expression of genes targeted by these transcription factors. In conclusion, we document gene regulation between hibernation phases, which may aid the identification of pathways and targets to prevent organ damage in transplantation or ischemia-reperfusion.

overall_design: RNA Sequencing profiles  for 9 Syrian Hamsters in the following hibernation stages: euthermic, torpor late and arousal early.

first: Marloes

last: Oosterhof

first: Louis

last: Coussement

first: Victor

last: Guryev

first: Vera

last: Reitsema

first: Jojanneke

middle: J

last: Bruintjes

first: Maaike

last: Goris

first: Hjalmar

last: Bouma

first: Tim

last: De Meyer

first: Marianne

last: Rots

first: Robert

last: Henning


title: A core of differentially methylated CpG loci in gMDSCs isolated from neonatal and adult sources

city: Boston

first: Ze

last: Zhang

state: MA

address: 375 Longwood Ave

department: Medical Oncology & Population Sciences

institute: Harvard Medical School

summary: Using the Illumina EPIC array to measure DNAm of gMDSCs and neutrophils from diverse neonatal and adult blood sources, we found 189 differentially methylated CpGs between gMDSCs and neutrophils with a core of ten differentially methylated CpGs that were consistent across both sources of cells. Genes associated with these loci that are involved in immune responses include VCL, FATS, YAP1, KREMEN2, UBTF, MCC-1, and EFCC1. In two cancer patient groups that reflected those used to develop the methylation markers (head and neck squamous cell carcinoma (HNSCC) and glioma), all of the CpG loci were differentially methylated, reaching statistical significance in glioma cases and controls, while one was significantly different in the smaller HNSCC group. Our findings indicate that gMDSCs have a core of distinct DNAm alterations, informing future research on gMDSC differentiation and function.

overall_design: Bisulphite converted DNA from fourteen gMDSC cells were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4

first: Isabella

last: Berglund-Brown

first: Emily

last: Nissen

first: Devin

last: Koestler

first: Rondi

last: Butler

first: Melissa

last: Eliot

first: James

last: Padbury

first: Lucas

last: Salas

first: Annette

middle: M

last: Molinaro

first: Brock

last: Christensen

first: John

middle: K

last: Wiencke

first: Karl

middle: T

last: Kelsey


city: Saskatoon

first: Brian

last: Eames

state: Saskatchewan

address: 107 Wiggins Road

department: Anatomy and Cell Biology

country: Canada

institute: University of Saskatchewan

summary: LCM-RNA-Seq data obtained from Xenopus tropicalis chondrocytes and osteoblasts at different stages of differentiation -immature chondrocytes and mature (hypertrophic) chondrocytes- isolated from the ceratohyal. Osteoblasts isolated from the mandible (dentary bone).

overall_design: Chondrocyte and osteoblast mRNA profiles of wild type Xenopus tropicalis

first: B

first: Jason

last: Nguyen


title: Chronic hypercapnia-induced gene expression profiles in the brain

city: Milwaukee

first: Kirstyn

last: Grams

state: Wisconsin

address: 8701 W Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

summary: To test the hypothesis that increasing severity of chronic hypercapnia elicits distint gene expression profiles in important brainstem regions of cardiorespiratory control, three groups of goats (female; n=6/group) were exposed either 14 days of room air (RA), 14 days of 6% inspired CO2 (mild CH), or 7d of 6% InCO2 followed by 7d of 8% InCO2 (moderate CH). Following 14 days of exposure 4 target sites were collected (3 brainstem/1 cortical) for gene expression profiling analysis using bulk-tissue RNA-sequencing. Comparisons were made across all target sites comparing room air animals to either mild or moderate CH.

overall_design: Comparative gene expression analysis of RNA-seq data from 4 brain regions (mPFC, NTS, VRC, RTN) collected from animals (n=6/condition) exposed one of  3 different conditions (normal room air,mild CH, or moderate CH). Comparisons were made for RA vs. Mild or RA vs. Moderate CH across all 4 brain regions.

first: Angela

last: Mathison

first: Michael

last: Zimmerman

first: Amanda

last: Miller

first: Jenica

last: Abrudan

first: Jaime

last: Wendt Andrae


title: Different gene expression in cisplatin chemo-resistant or sensitive of esophageal squamous carcinoma patients.

city: Guangzhou

first: Yujing

last: He

state: guangdong

address: No.1023-1063 South Shatai Road, Baiyun District, Guangzhou City, Guangdong Province

department: thoracic

institute: nanfang hospital

summary:
To investigate mRNA expression difference  in cisplatin  chemo-sensitivity in esophageal squamous carcinoma patients.
We performed gene expression profiling analysis using data obtained from RNA-seq of 6 different patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cisplatn chemo-resistant or sensitive in esophageal squamous cacinoma patients.

first: S

last: Rao


title: S-lactoyl modification of KEAP1 by a reactive glycolytic metabolite activates NRF2 signaling

last: Bollong

state: California

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

summary: KEAP1, a cytoplasmic repressor of the oxidative stress responsive transcription factor NRF2, senses the presence of electrophilic agents by modification of its sensor cysteine residues. In addition to xenobiotics, several reactive metabolites have been shown to covalently modify key cysteines on KEAP1, although the full repertoire of these molecules and their respective modifications remains undefined. Here, we report the discovery of sAKZ692, a small molecule identified by high throughput screening that stimulates NRF2 transcriptional activity in cells by inhibiting the glycolytic enzyme pyruvate kinase. sAKZ692 treatment promotes the buildup of glyceraldehyde 3-phosphate, a metabolite which leads to S-lactate modification of cysteine sensor residues of KEAP1, resulting in NRF2 dependent transcription.  This work identifies a novel posttranslational modification of cysteine derived from a reactive central carbon metabolite and helps further define the complex relationship between metabolism and the oxidative stress sensing machinery of the cell.

overall_design: To identify the transcriptional program activated by the small molecule NRF2 activator sAKZ692, we evaluated the transcriptional signature of compound treatment (20 µM, 24 hours) relative to DMSO in the IMR32 cell line.

first: Lara

last: Ibrahim

first: Yeonjin

last: Ko


title: Gene expression and mutation profiles in HRR mutated recurrent ovarian cancers

city: Seongnam-si

first: Je-Gun

last: Joung

address: 335, Pangyo-ro, Bundang-gu

country: South Korea

institute: CHA University

summary: RNA sequencing and whole-exome sequencing data were obtained from 30 platinum-resistant recurrent ovarian cancer samples.

overall_design:
Pretreatment tumors samples from fresh-frozen tissue were obtained for whole-transcriptome sequencing and whole-exome sequencing. RNA and DNA samples were sequenced on HiSeq 2500 sequencing platform. For RNA-seq, sequencing reads were aligned to the human reference genome (GRCh37) by using STAR aligner. Expected counts of reads mapped into genes were estimated and transformed into TPM values by RSEM. For whole exome sequencing, sequenced reads were aligned to the reference human genome (GRCh37) using the Burrows-Wheeler Aligner (BWA). After pre-processing using the Genome Analysis Toolkit (GATK), variants were called by Mutect2.
>>>Raw data for human samples not available due to patient privacy concerns<<<

first: Jung

middle: Y

last: Lee


title: Rewiring of master transcription factor cistrome during high-grade serous ovarian cancer development [Hi-C]

city: San Antonio

first: Kate

last: Lawrenson

address: 7703 Floyd Curl Dr.

institute: Cedars Sinai Medical Center

summary: The transcription factors MECOM, PAX8, SOX17 and WT1 are candidate master regulators of high-grade serous ‘ovarian’ cancer (HGSC), yet their cooperative role in the hypothesized tissue of origin, the fallopian tube secretory epithelium (FTSEC) is unknown. We generated 26 epigenome (CUT&TAG, CUT&RUN, ATAC-seq and HiC) data sets and 24 profiles of RNA-seq transcription factor knock-down followed by RNA sequencing in FTSEC and HGSC models to define binding sites and gene sets regulated by these factors in cis and trans. This revealed that MECOM, PAX8, SOX17 and WT1 are lineage-enriched, super-enhancer associated master regulators whose cooperative DNA-binding patterns and target genes are re-wired during tumor development. All four TFs were indispensable for HGSC clonogenicity and survival but only depletion of PAX8 and WT1 impaired FTSEC cell survival. These four TFs were pharmacologically inhibited by transcriptional inhibitors only in HGSCs but not in FTSECs. Collectively, our data highlights that tumor-specific epigenetic remodeling is tightly related to MECOM, PAX8, SOX17 and WT1 activity and these transcription factors are targetable in a tumor-specific manner through transcriptional inhibitors.

overall_design: Hi-C for fallopian tube secretory epithelial cell line  (FT246,FT282) and two high-grade serous ovarian cancer cell line (KURAMOCHI,OVCAR4)

first: Robbin

last: Nameki


title: Analysis of donor pancreata defines the transcriptomic signature and microenvironment of early neoplastic lesions.

first: Marina

last: Pasca di Magliano

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

summary: The adult healthy human pancreas has been poorly studied given lack of indication to obtain tissue from the pancreas in the absence of disease and rapid postmortem degradation. We obtained pancreata from brain dead donors thus avoiding any warm ischemia time. We found that neoplastic lesions occur frequently in healthy organs, in donors as young as in their 3rd decade of life. Using the 10X Genomics Platform, we performed single cell RNA sequencing on 6 donor pancreata, 5 of which we separately sequenced tissue from the pancreas head and tail, for a total of 11 sequencing runs.  This is a robust single-cell dataset of healthy, nonpathologic pancreas tissue and includes acinar, ductal, and non-epithelial cells (myeloid cells, fibroblasts, endothelial cells, lymphocytes). We compared this dataset of normal pancreata to single cell sequencing of tumor samples previously published in Steele, et al, Nature Cancer 2020, (raw fastq in dbGap phs002071) realigned to GRCh38 reference genome (CellRanger 6.0).  This GEO series contains the raw and filtered feature matrices for the donor pancreata as well as the realigned tumor samples.  Supplementary files contain the aggregate feature matrices and the metadata of the donor pancreata samples and the tumor samples.

overall_design:
Briefly, the donor pancreas was dissected by a clinically-trained pancreatobiliary surgeon. The organ was dissected into head, body, and tail, with portions of each placed into DMEM media with 1%BSA/10μM Y27632.  Tissue was minced into 1mm3 pieces, then digested with 1 mg/mL collagenase P for 20-30 min at 37°C with gentle agitation.  Digested tissue was rinsed three times with DMEM/1%BSA/10μM Y27632, then filtered through a 40μm mesh.  Resulting cells were submitted to the University of Michigan Advanced Genomics Core for single cell sequencing using the 10x Genomics Platform.
<<< Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns. >>>

first: Eileen

last: Carpenter

first: Ahmed

last: Elhossiny


title: Effect of cisplatin in depletion MAGEA6 expression  of esophageal cancer cells

summary:
To investigate  cisplatin  chemo-sensitivity in established KYSE 150/510 cell lines in which each target gene has been knocked out by CRISPR-Cas9.
We performed gene expression profiling analysis using data obtained from RNA-seq of 8 different cells by three biological replicate.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KYSE 150/510 cells  which targeted gene (sgMAGEA6) or treatment of cisplatin.


title: Systematic comparison of experimental and human obstructive cholestasis reveals conservation of canonical pathway activation and biomarkers relevant for cholestatic liver disease [mouse data set]

city: Ghent

first: Lindsey

last: Devisscher

institute: Ghent University

summary: Cholelithiasis-induced cholestasis is one of the most common causes of hospitalization due to gastrointestinal disease, yet considerable knowledge gaps exist in the pathogenesis of this disease. This can partially be explained by inadequate characterization of experimental cholestasis models. Therefore, we compared the transcriptional profile of commonly used mouse models for obstructive cholestasis and benchmarked them to human disease to identify the model(s) best suited for cholelithiasis-induced cholestasis research and to uncover conserved mechanisms involved in human and murine cholestasis. Selected mouse models included bile duct ligation (BDL) surgery, 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet, associated with extra- and intrahepatic obstructive cholestasis, respectively, and a drug-induced cholestasis model relying on cyclosporin A (CsA), in an acute and chronic setting. Human samples were collected from patients with cholelithiasis-induced cholestasis of an acute and recurrent nature. RNA sequencing was performed on mouse and human liver tissue. Both the BDL and DDC models, but not the CsA model, were shown to be applicable for studying cholelithiasis-induced cholestasis, with transcriptomic profiles that highly correspond to acute cholestasis in human patients. In particular, the conservation of canonical pathways related to the inflammatory response and cytoskeleton organization, in which the Rho family GTPase is involved, were identified. This study furthermore revealed some promising mechanistic-based transcriptomic biomarkers relevant for murine and human cholestasis, which could potentially be useful for robust prediction and detection of diverse types of cholestatic liver disease.

overall_design: Cholestasis was induced in C57BL/6 mice, either by performing a bile duct ligation surgery, administering 15 mg/kg bodyweight cyclosporin A dissolved in olive oil via oral gavage or by feeding 0.1 % wt/wt 3,5-diethoxycarbonyl-1,4-dihydrocollidine (n=4). Control mice were subjected to sham surgery, olive oil via oral gavage or control diet. Liver samples were collected after 7 and 28 days in all models and subsequently subjected to RNA sequencing analysis (n=4).

first: Tim

last: Meese

first: Eva

last: Gijbels

first: Filip

last: Van Nieuwerburgh


title: Single Cell Multiome of isogenic HIV-1-infected Jurkat T cells

city: New Haven

first: Ya-Chi

last: Ho

state: Connecticut

address: 295 Congress Avenue,BCMM 354E

institute: Yale University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: HIV-1 integration introduces ectopic transcription factor binding sites into host chromatin. We postulate that the integrated provirus serves as an ectopic enhancer that recruits additional transcriptional factors to the integration locus, increases chromatin accessibility, changes 3D chromatin interactions, and enhances both retroviral and host gene expression. We used 4 well-characterized HIV-1-infected cell line clones having unique integration sites and low to high levels of HIV-1 expression. Using single-cell DOGMA-seq, which captured the heterogeneity of HIV-1 expression and host chromatin accessibility, we found that HIV-1 transcription correlated with HIV-1 accessibility and host chromatin accessibility. HIV-1 integration increased local host chromatin accessibility within ~5–30 kb distance. CRISPRa and CRISPRi-mediated HIV-1 promoter activation and inhibition confirmed integration site-dependent HIV-1-driven changes of host chromatin accessibility. HIV-1 did not drive chromatin confirmation changes at the genomic level (by Hi-C) or the enhancer connectome (by H3K27Ac HiChIP). Using 4C-seq to interrogate HIV-1-chromatin interactions, we found that HIV-1 interacted with host chromatin ~100–300 kb from the integration site. By identifying chromatin regions having both increased transcription factor activity (by ATAC-seq) and HIV-1-chromtain interaction (by 4C-seq), we identified enrichment of ETS, RUNT, STAT, and ZNF transcription factor binding that may mediate HIV-1-host chromatin interactions. Our study found that HIV-1 promoter activity increased host chromatin accessibility, increased HIV-1-host chromatin interactions in an integration site dependent manner, within the existing chromatin boundaries without impacting broader host chromatin structure.

overall_design: Unstimulated Jurkat CD4+ T cells with or without an HIV-1 provirus were profiled.

first: Jack

last: Collora


title: Transcriptomic analysis of tumour-associated macrophages in wildtype and Colec11-/- mice

city: Xi'an

first: Jiaxing

last: Wang

state: Shaanxi

address: 157 West Fifth Road

department: Second Affiliated Hospital

institute: Xi'an Jiaotong University

summary: Collectin-11 (CL-11) is a recently described soluble C-type lectin, which has distinct roles in embryonic development, host defence, autoimmunity and fibrosis. Here we show that CL-11 also plays an important role in promoting melanoma growth. Colec11 deficient mice engrafted with B16 melanoma cells displayed significantly reduced tumour burden compared with WT mice. Cellular and molecular analyses showed that melanoma tumour in Colec11-/- mice had: i) lower levels of angiogenesis and tumour cell proliferation, ii) less immunosuppressive tumour microenvironment characterised by high lymphocyte to myeloid infiltrate ratio, increased infiltration of CD8+ T cells into the tumour core, high levels of anti-tumour cytokines/chemokines, reprogramming macrophages to M1 phenotype.

overall_design: mRNA profiles of tumour-associated macrophages in wildtype and Colec11-/- mice


title: p53-dependent transcription in hTERT-RPE1 cells

city: Baltimore

first: Fred

last: Bunz

state: Maryland

address: 1550 Orleans Street

department: Radiation Oncology

institute: Johns Hopkins University

summary:
We investigated the genes that were most strongly activated by p53 in this immortalized human cell line following treatment with the MDM2 inhibitor nutlin-3a.
To identify genes that were activated by p53, we comparatively analyzed parental cells and isogenic derivatives. Wild type, p53-knockout and cells harboring a heterozygous p53 A276P mutation were assessed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hTERT-RPE1 cells and its derivatives (p53-/- and p53+/A276P).

first: Bunz

last: Fred

first: Miciak

last: Jessica


title: PCDH19 regulation of neural progenitor cell differentiation suggests asynchrony of neurogenesis as a mechanism contributing to PCDH19 Girls Clustering Epilepsy

city: Adelaide

first: Mark

middle: A

last: Corbett

state: South Australia

address: Adelaide Health and Medical Sciences, University of Adelaide, North Tce

department: Adelaide Medical School

institute: University of Adelaide

summary: PCDH19-Girls Clustering Epilepsy (PCDH19-GCE) is a childhood epileptic encephalopathy characterised by a spectrum of neurodevelopmental problems. PCDH19-GCE is caused by heterozygous loss-of-function mutations in the X-chromosome gene, Protocadherin 19 (PCDH19) encoding a cell-cell adhesion molecule. Intriguingly, hemizygous males are generally unaffected. As PCDH19 is subjected to random X-inactivation, heterozygous females are comprised of a mosaic of cells expressing either the normal or mutant allele, which is thought to drive pathology. Despite being the second most prevalent monogeneic cause of epilepsy, little is known about the role of PCDH19 in brain development. In this study we show that PCDH19 is highly expressed in human neural stem and progenitor cells (NSPCs) and investigate its function in vitro in these cells of both mouse and human origin. Transcriptomic analysis of mouse NSPCs lacking Pcdh19 revealed changes to genes involved in regulation of neuronal differentiation, and we subsequently show that loss of Pcdh19 causes increased NSPC neurogenesis. We reprogramed human fibroblast cells harbouring a pathogenic PCDH19 mutation into human induced pluripotent stem cells (hiPSC) and employed neural differentiation of these to extend our studies into human NSPCs. As in mouse, loss of PCDH19 function caused increased neurogenesis, and furthermore, we show this is associated with a loss of human NSPC polarity. Overall our data suggests a conserved role for PCDH19 in regulating mammalian cortical neurogenesis and has implications for the pathogenesis of PCDH19-GCE. We propose that the difference in timing or heterochrony of neuronal cell production originating from PCDH19 wildtype and mutant NSPCs within the same individual may lead to downstream asynchronies and abnormalities in neuronal network formation, which in-part predispose the individual to network dysfunction and epileptic activity.

overall_design: Cultured neurospheres from Pcdh19 knock out, wild type or a mosaic mix of cells, from these two genotypes compared at day 0 and day 4 of differentiation.  Three technical replicates per genotype and per timepoint were measured.

first: Claire

last: Homan

first: Stephen

last: Pederson

first: Thu-Hein

last: To

first: Chuan

last: Tan

first: Sandra

last: Piltz

first: Ernst

last: Wolvertang

first: Paul

middle: Q

last: Thomas

first: Lachlan

last: Jolly

first: Jozef

last: Gecz


title: Systematic comparison of experimental and human obstructive cholestasis reveals conservation of canonical pathway activation and biomarkers relevant for cholestatic liver disease

first: Lindsey

last: Devisscher

address: Corneel Heymanslaan 10

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Sensory ataxia and cardiac hypertrophy caused by neurovascular oxidative stress

first: Thomas

last: Michel

address: 75 Francis Street

institute: BWH/HMS

summary: In our chemogenetic neurovacular mouse model, DRGs transcriptomic analysis was performed by RNA-seq; Oxidative stress is associated with cardiovascular and neurodegenerative disease. We created transgenic chemogenetic mouse lines expressing yeast D-amino oxidase (DAAO) in endothelial cells and neurons. DAAO generates hydrogen peroxide (H2O2) in target tissues when mice are provided with D-amino acids, causing oxidative stress. DAAO-TGCdh5 transgenic mice express DAAO under control of the putatively endothelial-specific Cdh5 promoter. We provided these mice with D-alanine¬– expecting a vascular phenotype– but found that the mice develop sensory ataxia and neurodegeneration in dorsal root ganglia (DRG), associated with transgene expression within DRG neurons; electron microscopy revealed distorted mitochondria. DAAO-TGCdh5 mice also develop cardiac hypertrophy in response to chemogenetic oxidative stress, and we discovered transgene expression in parasympathetic nodose ganglia innervating the heart. We developed and characterized another transgenic line expressing DAAO under control of a different endothelial cell-specific Tie2 promoter. DAAO-TGTie2 mice express the transgene in endothelium but not neurons, and develop neither ataxia nor cardiac hypertrophy. The combination of ataxia, mitochondrial dysfunction, and cardiac hypertrophy is similar to findings in patients with Friedreich's Ataxia. Our observations confirm that neurovascular oxidative stress is sufficient to cause sensory ataxia and cardiac hypertrophy, and identify the DAAO-TGCdh5 mouse as a potentially informative animal model for Friedreich’s Ataxia.

overall_design: RNA-seq of mouse DRGs neuronal tissue. The DRGs neuronal tissue samples were studied and have a set of raw data files, analysis and expression matrix.  The total samples were 12 (6 control and 6 treatment). There were 6 replicates for control and 6 for treatment.

first: Shambhu

last: Yadav


title: Gene expression profile at single cell level of liver cells from the mouse liver under normal and 24 hour fasting condition

city: Cincinnati

first: Yunguan

last: Wang

state: oh

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: Because IGFBP2 labeling increased substantially with fasting, we used single nuclear transcriptomics to explore zonation as a function of nutrition, revealing that the zonal division of labor shifts dramatically with fasting.

overall_design: 6 week old C57BL/6 mice were purchased from Jackson Laboratory and maintained until 8 weeks of age. For fasting group, mice were fasted for 24 hours before hepatocyte isolation.  Littermates with ad libitum feeding were collected at the same time. For each sample, two biological replicates (n = 2 mice) were collected and combined.

first: Yu-Hsuan

last: Lin

first: Hao

last: Zhu


title: Mast cell tolerance in the skin microenvironment to commensal bacteria is controlled by fibroblasts [LTA]

city: San Diego

first: Anna

last: Di Nardo

address: 9500 Gilman Drive

institute: UCSD

summary:
To investigate the cooperative function of dermal fibroblast and mast cell in inducing mast cell tolerance to commensals
We then performed gene expression profiling analysis using data obtained from RNA-seq of mast cells, and mast cells conditioned by dermal fibroblasts before and after treatments with commensal bacteria supernatants.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for conditioned and not conditioned mast cells

first: Yu-Ling

last: Chang

first: Shahrzad

last: Alimohammadi

first: Kana

last: Masuda-Kuroki

first: Zhenping

first: Krishna

last: Sriram

last: Insel


title: Gene expression analysis in untreated or 1 mM iAs (6-120 hours post fertilization; hpf), pooled (10) whole larvae 5 days post fertilization (dpf): wild-type TAB14 compared to as3mt mutant larvae [whole lavae]

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: This study was carried out to compare the changes in gene expression in whole larvae  120 hours post fertilization zebrafish larvae in response to whole body mutation of the arsenic methylation gene (as3mt) - 8 bp deletion in exon 3 with and without 6-120 hpf exposure to 1 mM sodium arsenite (iAs).

overall_design: The Sadler lab generated a whole body mutation of as3mt in zebrafish using CRISPR. This line a missense mutaion with a premature stopcodon (8 bp deletion in exon 3). This experiment was conducted by natural spawnings between an incross of F2 homozgyous as3mt knockouts in an WT-ABNYU background in comparsion with wild-types (WT-TAB14). Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection, embryos were divided into 10 mL wells, 20 embryos per well in embryo medium (Zebrafish Information Network). 1 mM iAs was added to treatment groups at 6 hpf. At approximately 119 hpf, pools of 10 whole larvae were collected for each condition (WT or as3mt mutant and 0 or 1 mM iAs: four groups) and immediately placed into 500 uL of TRIzol (Thermo Fisher, 15596026). RNA from was extracted per standard TRIzol/Chloroform method and concentreated and DNAse treated (RNase-Free DNase Set; Qiagen) using RNeasy Mini Spin column kit (Qiagen) and resuspended in 30 uL of DNase/RNase free water. For library preparation, high quality of total RNA was QCed using a bioanalyzer (Agilent 2100; Agilent Technologies, Santa Clara, CA, USA). RNA was then quantified by Qubit flurometer. Next, RNA quality was measured on a Bioanalyzer (Agilent) and the only RNA with RIN score >7 were used for library preparation.mRNA library was prepared using Illumina TruSeq V2 RNA sample Prep Kit (San Diego, CA) according to the manufacturer’s protocol. Briefly, 100 ng of total mRNA was poly-A purified, fragmented, and first-strand cDNA reverse transcribed using random primers. Following second-strand cDNA synthesis, end repair, addition of a single A base, TrueSeq adapter-index was ligated to cDNA libraries, and PCR amplification of 12 cycles was done for enrichment, producing a 350-400 bp fragment including adapters. The fragment sizes and purity of the libraries were confirmed by analyzing on a Bioanalyzer 2100 (Agilent Technologies). The quantities of the libraries required for RNA-seq were determined by real-time qPCR using a KAPA library quantification kit for the NEBNext Ultra II Directional RNA Library Prep kit for Poly A. Enriched cDNA libraries were sequenced using the Illumina NextSeq550 (Illumina).

first: Patrice

last: Delaney

last: Edepli


title: Differential gene expression profile analysis of parental, Cas9-p15 control, and MELK knockout cells

city: HOUSTON

first: Chandra

last: Bartholomeusz

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: Triple-negative breast cancer (TNBC) has high relapse and metastasis rates and a high proportion of cancer stem-like cells (CSCs), which possess self-renewal and tumor initiation capacity. MELK (maternal embryonic leucine zipper kinase), a protein kinase of the Snf1/AMPK kinase family, is known to promote CSC maintenance and malignant transformation. Our study showed that MELK knockdown using siRNA or MELK inhibition using the MELK inhibitor MELK-In-17 significantly reduced invasiveness, reversed epithelial-to-mesenchymal transition (EMT), and reduced CSC self-renewal and maintenance in TNBC cells. Nude mice injected with CRISPR MELK-knockout MDA-MB-231 cells exhibited suppression of lung metastasis and improved overall survival compared with mice injected with control cells. Furthermore, MELK-In-17 suppressed 4T1 tumor growth in syngeneic BALB/c mice. Our findings indicate that MELK supports metastasis by promoting EMT and the CSC phenotype in TNBC. In our microarray analysis, we identified potential downstream targets of MELK, including STAT5 and NF-kB target genes, as well as genes involved in tumor progression and metastasis (i.e., EMT, angiogenesis, hypoxia, and apical junction). EMT was the most strongly enriched hallmark among genes highly expressed in Cas9-p15 control cells, further confirming that EMT is a major factor contributing to MELK-induced metastasis in TNBC. We also identified a direct physical interaction partner (PRKAB2) of MELK and a set of intermediate proteins (CDC25B, EZH2, FOXM1, JUN, MAP3K5, PRKAB1, PRKAB2, and SMAD2), suggesting that these proteins are key components of MELK-induced signal transduction.

overall_design: RNA was extracted from parental, Cas9-p15 control, and MELK KO MDA-MB-231 cells. RNA was hybridized onto Affymetrix Human Transcriptome Arrays (version 2.0). Raw gene expression data were read into R using the BioC-package affy, normalized using the Robust MultiArray (RMA) algorithm, and log2-transformed. Probes with normalized expression values exceeding log2(100) in at least 25% of the arrays were filtered for further analysis. In addition, redundancy in probes mapping to the same gene was removed by retaining only the probe with the largest reported variation in gene expression measured by standard deviation. In total, 10,059 unique genes were included for final analysis.


title: Transcritomic analysis in untreated and sodium arsenite treated (96-120 hours post fertilization; hpf) in pooled (12-15) zebrafish larval livers 5 days post fertilization (dpf): wild-type TAB5 compared to as3mt mutant larvae

summary: This study was carried out to compare the changes in  gene expression in 5 dpf zebrafish larval livers in response to mutation of the arsenic methylation gene (as3mt) - 8 bp deletion in exon 3 with and without 1 mM sodium arsenite treatment (96-120 hpf)

overall_design: The Sadler lab generated a whole body knockout of as3mt in zebrafish using CRISPR. This line a missense mutaion with a premature stopcodon (8 bp deletion in exon 3). This experiment was conducted by natural spawnings between an incross of F2 homozgyous as3mt knockouts in an WT-ABNYU background in comparsion with wild-types (WT-TAB5). Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection, embryos were divided into 10 mL well, 20 embryos per well in embryo medium (Zebrafish Information Network). 1 mM iAs was added to treatment groups at 96 hpf. At approximately 119 hpf, pools of 12-15 livers were microdissected from each condition (WT or as3mt mutant and 0 or 1 mM iAs: four groups) and immediately placed into 500 uL of TRIzol (Thermo Fisher, 15596026). RNA from was extracted per standard TRIzol/Chloroform method and concentreated and DNAse treated (RNase-Free DNase Set; Qiagen) and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water (Thermo Fisher Scientifc) and DNaseI treated (ThermoFisher). For library preparation, high quality of total RNA was QCed using a bioanalyzer (Agilent 2100; Agilent Technologies, Santa Clara, CA, USA). RNA was then quantified by Qubit flurometer. Next, RNA quality was measured on a Bioanalyzer (Agilent) and the only RNA with RIN score >7 were used for library preparation.mRNA library was prepared using Illumina TruSeq V2 RNA sample Prep Kit (San Diego, CA) according to the manufacturer’s protocol. Briefly, 100 ng of total mRNA was poly-A purified, fragmented, and first-strand cDNA reverse transcribed using random primers. Following second-strand cDNA synthesis, end repair, addition of a single A base, TrueSeq adapter-index was ligated to cDNA libraries, and PCR amplification of 12 cycles was done for enrichment, producing a 350-400 bp fragment including adapters. The fragment sizes and purity of the libraries were confirmed by analyzing on a Bioanalyzer 2100 (Agilent Technologies). The quantities of the libraries required for RNA-seq were determined by real-time qPCR using a KAPA library quantification kit for the NEBNext Ultra II Directional RNA Library Prep kit for Poly A. Enriched cDNA libraries were sequenced using the Illumina NextSeq550 (Illumina).


city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

type: Non-coding RNA profiling by high throughput sequencing

summary: To test if CWC15 is required for miRNA accumulation, an artificial miRNA (amiRCWC15) targeting 5’ UTR (Untranslated region) was used to knockdown the transcript levels of CWC15. Next, to test the effect of CWC15 on miRNA accumulation at global levels, flower inflorescences of four-week old col-0 and amiRCWC15 were collected, and total RNA was extracted by Trizol for Illumina deep sequencing analyses of miRNA profile.

overall_design: Comparative miRNA expression profiling analysis for amiRCWC15 mutant and Col-0 wildtype.

first: Bangjun

last: Zhou

first: Bin

last: Yu


title: RNAPolII CUT&Tag profiles of MDA-MB-231 cell line with repression of CDK genes and PRMT5

city: La Jolla

first: Brenton

last: Munson

state: CA

address: 9500 Gilman Drive, MC 0688

department: Bioengineering

institute: University of California San Diego

summary: A clonal doxycycline inducible dCas9-KRAB MDA-MB-231 cell line to control repression of CDK genes and PRMT5. On day 1 of the experiment cells were infected with lentiviruses containing the appropriate targeting/NTC sgRNAs driven by the human U6 promoter at an MOI of ~3 for each virus to ensure all cells were transduced. Cells were transduced in DMEM + 10% FBS with the addition of 8 μg/mL polybrene. 16 hours after the time of transduction, media was changed to DMEM +10% FBS. 24 hours after this, the cell culture media was switched to DMEM + 10%FBS containing 2μg/mL puromycin to ensure no uninfected cells remain. 48 hours after this, cell culture media was changed to DMEM + 10%FBS containing 2 μg/mL puromycin and 1 μg/mL doxycycline to induce dCas9-KRAB expression. 48 hours after this, cells were processed for CUT&Tag library prep following the manufacturer's recommendations.

overall_design: CUT&Tag was used to examine the location of RNA Polymerase II around transcript start sites in MDA-MB-231 cells upon repression of CDK7, CDK9, CDK12, with and without simultaneous repression of PRMT5.

first: Trey

last: Ideker

first: Prashant

last: Mali


title: Optic nerve hypoplasia iPSC derived retinal ganglion cells exhibit differential gene expression with potential relevance to disease etiology

city: Los Angeles

first: David

last: Cobrinik

address: 4546 Sunset Blvd.

department: Ophthalmology

institute: Children's Hospital Los Angeles

summary:
To investigate gentic contributions to optic nerve hypoplasia, induced pluripotent stem cells were produced from 3 patients and 3 controls.
The iPSCs were differentiated to retinal organoids from which differential gene expression was performed on FACS isolated retinal ganglion cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iPSC derived retinal ganglion cells from 3 ONH patients and 3 controls, each in triplicate. Where possible each sample of  the triplicates was from different iPSC clones from the same donor.

first: Jennifer

middle: G

last: Aparicio

first: Mark

last: Borchert


title: Necrocide 1 Mediates Necrotic Cell Death and Immunogenic Response in Human Cancer Cells

city: Shanghai

first: jing

last: zhang

address: South Chongqing road 280

institute: Shanghai Jiaotong university school of medicine

summary: Many anticancer agents induce apoptosis, mitotic catastrophe or cellular senescence. Here, we report the functional characterization of an experimental inducer of tumor necrosis factor (TNF)-independent necrosis, necrocide-1 (NC1). NC1 (but not its stereoisomer) killed a panel of human cancer cells (but not normal cells) at nanomolar concentrations and with a non-apoptotic, necrotic morphotype, both in vitro and in vivo. NC1-induced killing was not inhibited by caspase blockers, anti-apoptotic BCL2 overexpression or TNFα neutralization, suggesting that NC1 elicits a bona fide necrotic pathway. However, pharmacological or genetic inhibition of necroptosis, pyroptosis and ferroptosis failed to block NC1-mediated cell death. Instead, NC1 elicited reactive oxygen species (ROS) production by mitochondria, and elimination of mitochondrial DNA, quenching of mitochondrial ROS, as well as blockade of mitochondrial permeability transition with cyclosporine A, interfered with NC1-induced cell death. NC1 induced hallmarks of immunogenic cell death incurring calreticulin (CALR) exposure, ATP secretion and high mobility group box 1 (HMGB1) release. Taken together, these data identify a previously uncharacterized signaling cascade leading to an immunogenic variant of mitochondrion-regulated necrosis, supporting the notion that eliciting regulated necrosis may constitute a valid approach for anticancer therapy.

overall_design: Human breast cancer cells MCF-7 were treated by 50 nM NC1 for 6 hours, then RNA were extracted for sequencing

first: Jing

first: Christina

last: Trojel-Hansen

first: Jianghuang

last: Wang


title: Acetate controls endothelial-to-mesenchymal transition during atherosclerosis

first: Xiaolong

last: Zhu

address: 300 George


title: Acetate controls endothelial-to-mesenchymal transition during atherosclerosis [2]

summary: To investigate the gene expression profiling during endothelial-to-mesenchymal transition , and identify the main changes in metaboltic and EndoMT related genes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUAECs cells in different conditions: normal condition, TGFbeta stimulation, or Acss2 Knockdown treatment.

first: Michael

last: Simons


city: Wuhan

first: Chen-Yu

state: Hubei

address: 299 Bayi Road, Wuchang District

institute: Wuhan University

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K27ac and H3K9me3 in liver tissues from high fat  and regular chow diet mice.High fat diet group :H2、H3、H4;Regular chow diet group:N3、N4、N5.

first: La-Ying

first: Zi-Qi

last: Mu

first: Min

last: Wu

first: Lian-Yun

last: Li


title: Acetate controls endothelial-to-mesenchymal transition during atherosclerosis [1]


title: TNF-α activates RELA expression via TNFRSF1B to upregulate OPA1 expression and inhibit chondrogenic differentiation of human adipose stem cells

city: Guiyang

first: ZHEN

last: YANG

state: Guizhou

address: Jiaxiu South Road； Baoshan South Road

institute: Medical College of Guizhou University/Guizhou Provincial People's Hospital (People's Hospital of Guizhou University)

summary:
Tumour necrosis factor-alpha (TNF-α), one of the pro-inflammatory cytokines mediating the local inflammatory process in joints, has an inhibitory effect on cartilage formation and has a detrimental effect on stem cell-based cartilage regeneration for the treatment of osteoarthritis (OA). However, the mechanisms behind this inhibitory effect are still poorly understood. Mitochondria are important organelles that play a vital role in maintaining the structure and function of the cell. Our study aimed to investigate the role and mechanisms of regulation of mitochondrial fusion and fission in the chondrogenic differentiation of human adipose stem cells (hADSCs) in the absence and presence of TNF-α.
Affmetrix PrimeViewTM chips for gene expression profiling.

overall_design: The results of the previous experiments were summarized by observing that the expression levels of OPA1, DNM1L, mitochondrial morphology, and ROS levels were significantly different in the Chondro-TNF-α group compared to the Chondro group at 7 days of chondrogenic differentiation. Therefore, we prepared hADSCs from the Chondro group and Chondro-TNF-α group into cartilage differentiation at 7 days as well as hADSCs from the control group (differentiation 0 d) for gene expression profiling.

first: JiaJia

last: Guo

first: Wang

last: Ye


title: The high affinity Fc receptor provides a unique scaffold for directing T cells against solid cancers

city: Tel Aviv

first: Alon

last: Richter

address: Ramat Aviv

department: Pathology

country: Israel

institute: Tel Aviv University

summary: The pioneering design of chimeric antigen receptors T-cells (CAR-T) therapy has revolutionized treatments of refractory lymphomas and demonstrated the potential in reprogramming the immune system. Nonetheless, exhaustion, cytotoxicity and suppressive tumor microenvironment limit their efficacy in solid tumors. Moreover, the high sensitivity f CART cells dictate directing it against antigens exclusively expressed on tumor cells. Recently, we characterized a novel subset of tumor-infiltrating CD4 + T-cells that express the high-affinity FcγRI receptor and are capable of antibody-mediated cell cytotoxicity. Here, we provide further analysis of their biology and prevalence in human diseases. We also provide evidences for the presence of CD8 + T cells expressing FcγRI in tumors. While endogenous FcγRI is expressed on exhausted and non-proliferative T cells, ectopic expression in naïve T cells endow them with ADCC capacities. Based on the FcγRI structure, we engineered a novel receptor, allowing T-cells to target tumor cells using antibody intermediates, without the need of TCR recognition. Antibodies provides an ideal mean to discriminate between cells that express high and physiological levels of antigens. Modifications to FcγRI signaling can tune the activation threshold required to elicit T cell cytotoxicity. Here, we further demonstrate the principles and considerations underlying the improvement of the signals transmitted through it. Overall, this work describes the benefits of separating the antigen-binding receptor from the signaling chain and suggests FcRI as a scaffold for cell therapy to overcome CAR T limitations in the treatment of solid tumors.

overall_design: Gene profile comparison between CD64 positive and negative CD4+ T cells from two patients with tonsillitis

first: Diana

last: Rasoulouniriana

first: Yaron

last: Carmi


title: Targeting CD43 optimizes cancer immunotherapy through reinvigorating anti-tumor immune response in colorectal cancer

city: Guangzhou

first: Xinyu

state: Guangdong

address: Zhongshan 2nd Road

department: Department of Immunology

institute: Sun-yat sen University

summary:
We report a novel immune molecule, CD43, that can regulate the tumor immune microenvironment (TIME) and serves as a promising target for CRC immunotherapy.
The correlation of CD43 expression with CRC patient prognosis was revealed by public data analysis. CD43 KO CRC cell lines were generated by CRISPR-CAS9 technology, and a syngenetic murine CRC model was established to investigate the in vivo function of CD43.To elucidate the TIME more precisely, tumors were harvested at Day 21 postinoculation in vivo, and single-cell suspensions of tumor tissues were generated for transcriptome sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Vec-MC38 and CD43-KO MC38 tumors.

first: Yiyi

first: Yan

last: Liao

first: Yingzhao

first: Xiumei

first: Hai

last: Hong

first: Wei

last: Yi

first: Jun

last: Chen


title: Gene expression profiles of CRISPR-Cas9 pertubed single cell in triple negative breast cancer cell lines.

first: Brenton

last: Munson

summary: Crop-seq was used to examine the role cyclin-dependent kinases have on the transcriptome of triple negative breast cancer.

overall_design: Three triple negative breast cancer cell lines were transduced with a sgRNA library targeting all cyclin-dependent kinases and select associated epigentic factors. The resulting perturbed cell populations underwent single cell sequencing using the 10X Genomics platform.

first: Trey

last: Ideker

first: Prashant

last: Mali


title: Investigation of Thymic TCRd+ cells

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We profiled total DNs, DN1s, and gd T cells by scRNA-seq in fresh murine thymic resections

overall_design: scRNA-seq of Total DNs, DN1s, and gd T cells

first: Michela

last: Frascoli


title: Chromatin remodeler Fun30 promotes efficient DSB end resection and recombination during yeast meiosis

city: Emeryville

first: Pei-Ching

last: Huang

address: 1545 Park Ave

institute: Metagenomi

summary: Resection, nucleolytic processing of DSB ends is necessary to generate 3' single-stranded DNA tails (ssDNA) for homologous recombination (HR). Meiotic recombination initiated by Spo11 induced double-strand breaks (DSBs) is essential for the accurate segregation of homologous chromosomes. After cleavage, Spo11 stays covalently linked to the DSB ends, which requires MRX/Sae2 incision on broken molecules to allow following Exo1-mediated resection. Exonuclease I activity is inhibited by nucleosome bound DNA in vitro. To ensure resection proceeds, resection machineries must overcome chromatin barrier.  Here we show that in the absence of Fun30, an SNF2-like ATPase, resection tract lengths shortened, albeit less severe than exo1-nd (with more longer resection tracts than that in exo1nd), across all DSB hotspots, suggesting that Fun30 is required for meiotic resection. Additive resection defect in fun30Δ exo1-nd (nuclease dead) compared to exo1-nd mutant indicates that Fun30 regulates MRX/Sae2 nicking positions. We also observed extremely short resection tracts in the double mutants are mostly confined to NDR, suggesting initial nicking step is blocked by nucleosomes.

overall_design: 15 samples total: two biological replicate S1Seq maps of S.cerevisiae for each genetic background at 4hr after meiotic induction except sae2D.

first: Hajime

last: Murakami

first: Scott

last: Keeney


title: Paf1 complex subunit Rtf1 stimulates H2B ubiquitylation by interacting with the highly conserved N-terminal helix of Rad6

city: Pittsburgh

first: Karen

last: Arndt

state: PA

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

summary: Histone modifications coupled to transcription elongation play important roles in regulating the accuracy and efficiency of gene expression. The mono-ubiquitylation of a conserved lysine in H2B (K123 in Saccharomyces cerevisiae and K120 in humans) occurs co-transcriptionally and is required for initiating a histone modification cascade on active genes. H2BK123 ubiquitylation (H2BK123ub) requires the RNA polymerase II (RNAPII)-associated Paf1 transcription elongation complex (Paf1C). Through its Histone Modification Domain (HMD), the Rtf1 subunit of Paf1C directly interacts with the ubiquitin conjugase Rad6, leading to the stimulation of H2BK123ub in vivo and in vitro. To understand the molecular mechanisms that specifically target Rad6 to its histone substrate, we identified the site of interaction for the HMD on Rad6. Using in vitro crosslinking followed by mass spectrometry, we localized the primary contact surface for the HMD to the highly conserved N-terminal helix of Rad6. Using a combination of genetic and biochemical experiments, we identified separation-of-function mutations in RAD6 that greatly impair H2BK123 ubiquitylation but not other Rad6 functions. Finally, by employing RNA-sequencing as a sensitive approach for comparing mutant phenotypes, we show that mutating either side of the proposed Rad6-HMD interface yields strikingly similar transcriptome profiles that extensively overlap with those of a mutant that lacks the site of ubiquitylation in H2B. Our results fit a model in which a specific interface between a transcription elongation factor and a ubiquitin conjugase guides substrate selection toward a highly conserved chromatin target during active gene expression.

overall_design: Differential gene expression analysis based on RNA-seq data from S. cerevisiae (S288C). Three biological replicates were sequenced per strain (genotype). A total of eight strains were included: two wild-type strains (RAD6 RTF1 and RAD6-13xMyc 3x-HA-RTF1), two rad6∆ strains (rad6∆ RTF1 and rad6∆ 3xHA-RTF1), htb1-K123R htb2-K123R, rtf1-108-110AAA, rad6-R6Q and rad6-R6A,M10A. Kluyveromyces lactis cells were used for spike in.

first: Tasniem

last: Fetian

first: Brendan

last: McShane

first: Nicole

last: Horan

first: Donya

middle: N

last: Shodja

first: Jason

middle: D

last: True

first: Amber

last: Mosley


title: Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections [4]

status: Public on May 05 2023

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Single-cell genetic and epigenetic analyses parse the brain’s billions of neurons into thousands of “cell-type” clusters, each residing in different brain structures. Many of these cell types mediate their unique functions by virtue of targeted long-distance axonal projections to allow interactions between specific cell types. Here we have used Epi-Retro-Seq to link single cell epigenomes and associated cell types to their long-distance projections for 33,034 neurons dissected from 32 different source regions projecting to 24 different targets (225 source→target combinations) across the whole mouse brain. We highlight uses of this large data set for interrogating both overarching principles relating projection cell types to their transcriptomic and epigenomic properties and for addressing and developing specific hypotheses about cell types and connections as they relate to genetics. We provide an overall synthesis of the data set with 926 statistical comparisons of the discriminability of neurons projecting to each target for every dissected source region. We integrate this dataset into the larger, annotated BICCN cell type atlas composed of millions of neurons to link projection cell types to consensus clusters. Integration with spatial transcriptomic data further assigns projection-enriched clusters to much smaller source regions than afforded by the original dissections. We exemplify these capabilities by presenting in-depth analyses of neurons with identified projections from the hypothalamus, thalamus, hindbrain, amygdala, and midbrain to provide new insights into the properties of those cell types, including differentially expressed genes, their associated cis-regulatory elements and transcription factor binding motifs, and neurotransmitter usage.

overall_design: In Epi-Retro-Seq, the retrograde viral tracer rAAV2-retro-Cre is injected in the target region in an INTACT mouse, turning on Cre-dependent nuclear-GFP expression in neurons that project to the injected target, throughout the mouse brain. The brain is then sectioned into eighteen 600-micron coronal slices, and the brain regions of interest are mannually dissected from each slice. Nuclei are sampled from 4 mice (2 male and 2 female) for each projection target. Nuclei from each of the dissected source regions are prepared, from which GFP+/NeuN+ nuclei (the GFP-labeled projection neurons) are isolated as single nuclei using fluorescence activated nuclei sorting (FANS) and assayed using snmC-Seq2/3 to profile their genome-wide DNA methylation signatures. Low-quality nuclei were removed.

first: Jingtian

last: Zhou

first: Zhuzhu

last: Zhang

first: May

last: Wu

first: Hanqing

last: Liu

first: Yan

last: Pang

first: Anna

last: Bartlett

first: Angeline

middle: C

last: Rivkin

first: Will

last: Lagos

first: Elora

last: Williams

first: Cheng-Ta

last: Lee

first: Paula

last: Assakura Miyazaki

first: Andrew

middle: I

last: Aldridge

first: Qiurui

last: Zeng

first: J

middle: L

last: Salinda

first: Naomi

last: Claffey

first: Michelle

last: Liem

first: Conor

last: Fitzpatrick

first: Lara

last: Boggeman

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Cynthia

last: Valadon

last: Nery

first: Rosa

last: Castanon

first: Neelakshi

last: Patne

first: Minh

last: Vu

first: Mohammad

last: Rashid

first: Matthew

last: Jacobs

first: Tony

last: Ito-Cole

first: Julia

last: Osteen

first: Sharon

first: António

last: Pinto-Duartec

first: Bertha

last: Dominguez

first: Jared

last: Smith

first: Carolyn

last: O'Connor

first: Kuo-Fen

first: Eran

last: Mukamel

first: Xin

last: Jin

first: M

last: Behrens


title: Transcriptomic analysis reflects the different lung injury patterns of E-cigarette components VEA and PG in mice

city: jeongeup

first: seonghoon

last: yoon

address: baekhak 1 gil 30

institute: Korea Institute of Toxicology

summary: Recently, thousands of cases of E-cigarette or vaping product use-associated lung injury (EVALI) were reported. But the lung toxicity of each E-cigarette components were still poorly defined. Major components of E-cigarette were nicotine, flavoring, vitamin E acetate (VEA), propylene glycol (PG) and vegetable glycerin (VG). In our previous study, we determine the different lung injury patterns in PG and VEA exposed mice; fibrotic injury in PG and asthmatic injury in VEA. In this study, we performed the transcriptomic analysis that could reflect different lung injury patterns caused by PG and VEA in lung tissues using RNS-Sequencing and bioinformatics tools. A combination of P-value <0.05 and fold change ≥1.5 was used to identify differently expressed genes (DEGs).   Gene-expression data showed different gene-alteration patterns in the PG and VEA groups. Supervised analysis revealed that 1,193 PG and 1,795 VEA induced-specific genes, and functional analysis revealed that PG-specific genes were involved in TNC-related chronic obstructive pulmonary diseases, whereas VEA-specific genes were involved in asthma-related chronic lung injury. The results of transcriptomic analysis were consistent with lung histopathology results. These findings indicated that E-cigarette component-specific changes in gene expression closely reflected E-cigarette component pathological changes in E-cigarette component-induced lung injury.

overall_design: C57BL/6, 826 and 1,100 mg/mL of Propylene glycol (Sigma, P4347), 3.12, 6.25 and 12.5 mg/mL of Vitamin E acetate (Sigma, T3376), Intratracheal instillation, 50 uL/1time, 1time/1day, 14day-repeated treatment, Secrificed at day 15, RNA extraction form lung tissue after BALF

first: Sung-Hoon

last: Yoon

first: Mi-Kyung

last: Song

first: Dong

last: Kim

first: Kyuhong

last: Lee