title: TLR2 in γδ T cells is required for metabolic support of IL-17A ocular mucosal immune response to a commensal bacterium [RNA-seq]

city: Bethesda

first: Vijay

last: Nagarajan

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

summary: The ocular surface is colonized by commensal microbiota, which tune the local mucosal immune response. However, the mechanisms underlying the induction of an IL-17 response by γδ T cells in response to ocular commensal bacteria, particularly Corynebacterium mastitidis (C. mast), have not been fully investigated. Here, we demonstrated that intrinsic TLR2 activation in γδ T cells by commensal microbiota is required for their IL-17A production and fatty acid oxidation.  We also identified IκBζ, a transcription factor whose expression is upregulated by TLR2 signaling, as a key regulator to enhance the expression of genes responsible for IL-17A production and FAO program. This study highlights the role of TLR2-mediated transcriptional regulation in targeting effector cytokines and metabolic programs to support IL-17A responses to commensal bacteria.

overall_design: WT C57BL/6J mice were purchased from Jackson Laboratory. TLR2-/-, TCRβ-/-, and CD45.1 C57BL/6J mice originally from Jackson were bred at NIH. Vγ6 transgenic mice were generously provided by Paul E. Love; TLR2-/-Vγ6 transgenic mice, and TLR2-/- TCRβ-/- mice were crossed and bred at NIH. For most in vivo and in vitro animal studies, male and female mice aged 6-10 weeks were used. All mice were housed under NIH SPF conditions. All mice received tear wash and were confirmed with no microbiome on the ocular surface before the experiment. All mouse studies were performed in full compliance with IACUC-approved protocols (NEI-690) and institutional guidelines. C. mast was initially isolated from conjunctival homogenates that were plated on TSA + 5% blood agar plates kept at 37℃ in anaerobic conditions for 7 days. After original isolation, C. mast was propagated using TSA with 5% blood agar plates at 37℃ in an aerobic chamber. Further, C. mast was grown in blood heart infusion broth with 1% Tween 80 aerobically with shaking at 37℃.

first: Wenjie

last: Zhu

first: Vijayaraj

first: Jing

last: Guo

first: Zixuan

last: Peng

first: Amy

last: Zhang

first: Jie

last: Liu

first: Mary

last: Mattapallil

first: Yingyos

last: Jittayasothorn

first: Anthony

last: St. Leger

first: Reiko

last: Horai

first: Xiaoyan

last: Xu

first: Rachel

last: R Caspi


title: Maternal Adiposity Alters Transcriptomic and Epigenomic Neurodevelopmental Landscapes in the Fetal Hippocampus (RNA-Seq)

status: Public on May 15 2024

city: Oklahoma City

first: Willard

last: Freeman

state: OK

address: 834 NE 13th St

department: GHD

country: USA

institute: Oklahoma Medical Research Foundation

type: Expression profiling by high throughput sequencing

summary: To investigate the effects of maternal adiposity and leptin on fetal brain development, fetal hippocampal brain tissue was collected at 0.9 term for bulk RNA Seq analysis

overall_design: Comparative fetal baboon (0.9 term) hippocampal RNA-Seq analysis from dams with different adiposity and leptin levels

first: Ashley

middle: A

last: Cheyney

first: Adam

middle: M

last: Kulpa

first: Sarah

middle: R

last: Ocanas

first: Kevin

last: Pham

first: Hunter

last: Porter

first: Theo

last: Cohen

first: Nicole

last: Reuter

first: Alisha

last: Preno

first: Sunam

last: Gurung

first: David

last: Stanford

first: Martin-Paul

last: Agbaga

first: James

middle: F

last: Papin

first: Dean

last: Myers


title: A Japanese herbal medicine, Hochuekkito (TJ-41), has anti-inflammatory effects on the COPD mouse model

city: Tokyo

first: Masaaki

last: Yuki

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

department: Respiratory medicine

country: Japan

institute: The University of Tokyo

summary: We assessed the anti-inflammatory and systemic effects of TJ-41 on the COPD mouse model induced by porcine pancreatic elastase (PPE) and lipopolysaccharide (LPS).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of both mice-treated PBS and mice-treated PPE and LPS.

first: Akihisa

last: Mitani


title: TLR2 in γδ T cells is required for metabolic support of IL-17A ocular mucosal immune response to a commensal bacterium [ATAC-seq]

first: Vijay

last: Nagarajan

state: Maryland

type: Genome binding/occupancy profiling by high throughput sequencing

first: Wenjie

last: Zhu

first: Vijayaraj

first: Jing

last: Guo

first: Zixuan

last: Peng

first: Amy

last: Zhang

first: Jie

last: Liu

first: Mary

last: Mattapallil

first: Yingyos

last: Jittayasothorn

first: Anthony

last: St. Leger

first: Reiko

last: Horai

first: Xiaoyan

last: Xu

first: Rachel

last: R Caspi


title: Maternal Adiposity Alters Transcriptomic and Epigenomic Neurodevelopmental Landscapes in the Fetal Hippocampus

first: Willard

last: Freeman

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of 52 hpf mbd5 KO & KD embryos  and 7 dpf mb5 KO & OE larves

city: Shanghai

first: Jianhua

address: NO.2005,Songhu Road,jiangwan campus

country: China

institute: Fudan university

summary: To dissect the molecular function of mbd5 in zebrafish embryonic development, we carried out transcriptomic analyses at those two developmental stages.

overall_design: Gene expression profiles of mbd5 KD & KO and siblings at 52 hpf, mbd5 KO & OE and siblings at 7 dpf were generated by deep sequencing with Illumina HiSeq X Ten platform


title: RNA sequencing of WT or BTLA KO CAR T cells following chronic-antigen stimulation

city: Philadelphia

first: Puneeth

last: Guruprasad

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary:
RNA-seqeuncing of mock-electroporated (wild-type) anti-CD19 CAR T cells or BTLA-knockout anti-CD19 CAR T cells following repeated stimulation with OCI-Ly18 (CD19+ DLBCL cell line)
Analyzed data used in Fig 7j

overall_design: anti-CD19 WT or BTLA KO human CAR T cells from 2 healthy donors were co-cultured with OCI-Ly18, a diffuse large B cell lymphoma cell line. Additional OCI-Ly18 (effector:target ratio = 0.25) was fed into the co-culture on days  3, 7, 10, and 12. On day 15, CAR T cells had cleared all tumor cells, as confirmed by flow cytometeric analysis.


title: Maternal Adiposity Alters Transcriptomic and Epigenomic Neurodevelopmental Landscapes in the Fetal Hippocampus (Bisulfite-Seq)

summary: To investigate the effects of maternal adiposity and leptin on fetal brain development, fetal hippocampal brain tissue and DNA was collected at 0.9 term for targeted EM-Seq analysis

overall_design: Comparative fetal baboon (0.9 term) hippocampal targeted EM-Seq analysis from dams with different adiposity and leptin levels

first: Ashley

last: Cheyney

first: Adam

last: Kulpa

first: Sarah

last: Ocanas

first: Kevin

last: Pham

first: Hunter

last: Porter

first: Theo

last: Cohen

first: Nicole

last: Reuter

first: Alisha

last: Preno

first: Sunam

last: Gurung

first: David

last: Stanford

first: Martin-Paul

last: Agbaga

first: James

last: Papin

first: Dean

last: Myers


title: TLR2 in γδ T cells is required for metabolic support of IL-17A ocular mucosal immune response to a commensal bacterium

first: Vijay

last: Nagarajan


title: Gene expression profile of human liver MAIT cells from patients with biliary atresia

city: Guangzhou

first: Zhenhua

last: Luo

state: Guangzhou

address: Number 58, zhongshan er road, Yuexiu,

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: To investigate gene expression profile of human liver MAIT cells from patients with biliary atresia, we isolated human liver MAIT cells from liver tissues of patients with biliary atresia and from adjacent non-tumor liver tissues of hepatoblastoma patients (as control) at the time of diagnosis, and subjected for bulk RNA sequencing.

overall_design:
MAIT cells were enriched from liver mononuclear cells from adjacent non-tumor tissues of hepatoblastoma patients or liver tissues of biliary atresia patients. Vα7.2+ CD3+ MAIT cells were isolated using BV510-conjugated anti-TCRVα7.2 antibody (3C10; BioLegend) and PerCP/Cyanine5.5-conjugated anti-CD3 antibody (HIT3a; BioLegend) by fluorescence-activated cell sorting (BD Biosciences).Total RNA was extracted from sorted MAIT cells using TRIzol Reagent (Invitrogen) for subsequent RNA sequencing.
Raw data not provided due to patient privacy issues.


title: Chemical genetics in Caenorhabditis elegans identifies anticancer compound chaetocin and p300/CBP as modulators of metal response genes

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: We recently used a genome-wide screen to demonstrate that numr-1/2 is activated by disruption of RNA metabolism. To investigate numr-1/2 regulation and identify modulators of nucleic acid metabolism, we screened over 40,000 compounds and extracts from commercial and natural product libraries for numr-1/2p::GFP activation. Fungal toxin chaetocin was the most potent and least toxic numr-1/2 inducer.  RT-qPCR demonstrates that chaetocin induces numr-1/2 and another stress-responsive SR-like protein gene (W03G1.5) in C. elegans over 50-fold within 45 minutes without affecting expression of canonical heat shock, osmotic stress, endoplasmic reticulum stress, mitochondrial stress, or detoxification response genes.  Chaetocin does not activate other metal-responsive genes and actually reduces expression of metallothionein gene mtl-2 and fluorescence of mtl-2p::GFP consistent with repression of mtl-2 transcription.  Along with a similar HMTase inhibitor from the same fungal origin - Chetomin, and two synthetic S-methyl-products of Chaetocin and Chetomin, respectively, we tested the expression profile at 5h and 12h post treatment at 500 nM concentration in HCT116 colorectal carcinoma cell line. Both S-methyl-products showed no significant activity or any detectable statistically significant changes in expression compared to the vehicle control. The parent compounds induced a number of expression changes consistent with effects on the stress-response genes in HCT116 cells.

overall_design: HCT116 cells were seeded in 6-well plates at 2 × 10^5 cells/well in Dulbecco's Modified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (Sigma) and 1% Antibiotic-Antimycotic solution (Gibco), left overnight to attach and acclimate and treated with solvent control (DMSO, 0.5%), chaetocin, chetomin or their respective sulfide-depleted analogs  to final concentration of 500 nM . After 5 H or 12 H incubation with compounds or solvent, RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer instructions. Illumina RNA library construction and sequencing were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core, University of Florida (UF) .

first: Kalina

last: Atanasova

first: Ranjala

last: Ratnayake

first: Hendrik

last: Luesch

first: Keith

middle: P

last: Choe


title: Maternal Adiposity Alters Transcriptomic and Epigenomic Neurodevelopmental Landscapes in the Fetal Hippocampus (Targeted EM-Seq)

first: Willard

last: Freeman

first: Ashley

last: Cheyney

first: Adam

last: Kulpa

first: Sarah

last: Ocanas

first: Kevin

last: Pham


title: Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [Osr2OE_vs_Vector_CutnTag_CD8]

city: Xiamen

first: Dawang

last: Zhou

state: Fujian

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

department: Life Science

institute: Xiamen University

summary: The alteration in extracellular matrix (ECM) architecture and stiffness becomes one of the hallmarks of cancer. Whether the mechanical property of ECM contributes to the functionality of CD8+ T cells, a key component of anti-tumor response, remains largely unknown. Here we report that mechanical stress drives T cell exhaustion program via Osr2, a transcription factor that had been poorly investigated in T cells. Osr2 is highly and selectively induced in CD8+ T cells when encountering stiff matrix or mechanical force signaling (MFS). Integrated genetic and multi-omics analyses reveals that Osr2 is enriched in the terminal exhausted tumor infiltrating lymphocytes and its expression is modulated by the combined TCR and MFS mediated by Piezo1/Calcium/CREB axis. Importantly, depletion of Piezo1 or Osr2 alleviates T cell exhaustion, which is associated with enhanced anti-tumor immunity mediated by antigen specific T cells or CAR-T cells in solid tumor models. On the contrary, forced Osr2 expression in CD8+ T cells augment their exhaustion and dampens tumor control. In agreement with these observations, high Osr2 expression is correlated with poor prognosis in multiple human malignancies. Mechanistically, Osr2 recruits HDAC3, which in turn establishes epigenetic reprogramming to suppress cytotoxic genes expression and to promote CD8+T cell exhaustion. Thus, our results unravel a mechanical signaling cascade centered by Osr2 that serves as a key driver for CD8+ T cell exhaustion and suggest that mechanical checkpoints could be promising targets for cancer immunotherapy.

overall_design: CUT&Tag analysis of CD8+ T cells isolated from spleens followed by activation and transduction with retroviruses encoding Osr2 (Osr2OE) or control GFP.

first: Junhong

last: Li

first: Yongqiang

last: Hou

first: Lanfen

last: Chen


title: Gene expression profile at single cell level of human peripheral blood mononuclear cells cocultured with rotavirus treated or PBS treated human cholangiocyte cell line H69.

summary: Biliary atresia (BA) is an devastating pediatric cholangiopathy and the leading indication for liver transplant in children worldwide. An in vitro cell system for investigating BA is still lacking. We develop an in vitro cell culture system to mimic immune dysfunction of biliary atresia by coculturing human peripheral blood mononuclear cells (PBMC) with rotavirus treated or PBS treated human cholangiocyte cell line H69. Single cell RNA sequencing analysis of PBMC after coculture was applied to validate the efficacy and fidelity of cell system.

overall_design:
Human peripheral blood mononuclear cells (PBMC) from healthy donor were coculture with rotavirus (RRV) treated or DMEM medium (control) treated human cholangiocyte cell line H69. Living CD45+ cells were sorted for single cell RNA sequencing.
>>>Raw data for human samples not available due to ethical concerns<<<

first: Luo

last: Zhenhua


title: Heritable human Polycomb silencing is locus-dependent and requires H2AK119ub1 self-propagation

city: Boston

first: Danesh

last: Moazed

state: MA

address: 240 longwood avenue

department: Cell Biology

institute: Harvard Medical School

summary: Heritable gene silencing is essential for the development of multicellular organisms. Polycomb repressive complexes 1 and 2 (PRC1 and 2) catalyze and recognize histone H2A lysine 119 mono-ubiquitination (H2AK119ub1) and histone H3 lysine 27 trimethylation (H3K27me3), respectively, to mediate heritable gene silencing, but the mechanism of inheritance is not fully understood. Using an inducible gene silencing strategy, we show that the epigenetic inheritance of Polycomb silencing in human cells is strongly dependent on local DNA sequences and chromatin environment. In addition, we find that inheritance is not strictly dependent on H3K27me3 recognition and can be partially achieved by H2AK119ub1 catalysis and recognition, independently of H3K27me3. These findings demonstrate that locus specific features and H2AK119ub1 play key roles in inheritance of Polycomb silencing in human cells.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27me3 and Flag for Rescue Constructs Integrated into HEK293FT cells with a 5xtetO-H2B-CITRINE reporter inserted at chr11 (near WT1 gene) or chr 3 (near TFRC gene).

first: Tiasha

last: Shafiq


title: Age-related blood transcriptional regulators affect disease progression in pediatric multiple sclerosis

city: Ramat Gan

first: Michael

last: Gurevich

address: Tel Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

summary:
The more aggressive clinical disease course of Pediatric Onset Multiple Sclerosis(POMS) as compared to Adult Onset Multiple Sclerosis(AOMS) during the first year disease is supported by higher inflammatory potential promoted by transcriptional level of age-associated genes and transcription factors involved in Cell Cycle, B Cell proliferation and senescent mechanisms.
Herein, we compared the blood mononuclear cell transcriptome of POMS and AOMS patients during first year disease. Pediatric Healthy and Adult subjects (PHC, AHC) were used as controls. Correlation analysis of the gene expression with the radiological sign, upstream regulators analysis and clinical assesment were also evaluated.

overall_design: A total of 38 MS patients (22 POMS and 16 AOMS) and 21 Healthy controls( 11 PHC and 10 AHC) were analyzed.

first: Eitan

last: Shavit

first: Shay

last: Menascu

first: Anat

last: Achiron


title: MBD5, a m5C RNA reader, regulates histone ubiquitylation in development and function

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St, Room E319B

institute: University of Chicago

summary: Methyl-CpG-binding domain (MBD)-containing proteins are readers of epigenetic information. The founding member, MeCP2, mutated in the Rett Syndrome, binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy, autism spectrum disorders (ASD), and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development, erythrocyte differentiation, iron metabolism, and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes (e.g., hbae3), iron-regulated genes (e.g., fth1), and ASD-related genes (e.g., gabbr2), by binding to 5-methylcytosine (m5C) modified mRNAs, interacting with and stabilizing Additional Sex Combs Like 1 (ASXL1), a component of the Polycomb Repressive Deubiquinase (PR-DUB) complex, to facilitate removal of the repressive monoubiquitin mark at histone H2A (H2A-K119Ub), thereby facilitating gene activation. Together, these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo.

overall_design:
[Dataset 1] 6 samples. Triplicates for ribo-minus RNA-Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino
[Dataset 2] 16 samples. Duplicates for CLIP-seq experiments from 48-78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC

first: Zhongyu

last: Zou

first: Xiaoyang

last: Dou


title: Long Noncoding RNA LIRIL2R Modulates FOXP3 Levels and Suppressive Function of Human CD4+ Regulatory T Cells by Regulating IL2RA

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6A

department: Turku Bioscience

country: Finland

institute: University of Turku


title: Differential dynamic plasma miRNA profiles during the peri-implantation period in patients with different reproductive outcomes following embryo transfer

first: Hong

last: Zeng

state: Hunan

address: 87 Xiangya Street

department: Reproductive medicine center

institute: Xiangya Hospital Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the differential dynamic plasma miRNA profiles during the peri-implantation period in patients with different reproductive outcomes following embryo transfer. 10 negative pregnancy (NP) patients, 10 biochemical pregnancy loss (BPL) patients, and 10 clinical pregnancy (CP) patients were enrolled for miRNA-seq in this study. Peripheral blood samples were collected at three time-points (ET0, ET11, and ET14) from BPL patients and CP patients, and samples were collected at two time-points (ET0 and ET11) from NP patients. Small RNA libraries were constructed using peripheral plasma RNA. miRNA-seq was used to investigate the differential dynamic peripheral miRNA changes between the three groups during the peri-implantation period.

overall_design: We prospectively recruited a cohort undergoing embryo transfer (ET). Peripheral llood samples were collected on ET day before ET (ET0), 11 days after ET (ET11), and 14 days (ET14) after ET. The patients were divided into the negative prengancy (NP), biochemical pregnancy loss (BPL), and clinical pregnancy (CP) groups according to serum hCG levels. Ten patients in each group were randomly selected for miRNA-seq.

first: Lang

last: Shen

first: Yu

last: Fu

first: Song

last: Quan


title: In vitro priming of human mesenchymal stromal/stem cells into 3D capillary-like structures : Implication of the Src/JAK/STAT3 signaling pathway in vasculogenic mimicry

status: Public on May 14 2024

city: Montreal

first: Borhane

last: Annabi

state: Quebec

address: 2101 Jeanne-Mance

department: Chemistry

country: Canada

institute: Université du Québec à Montréal

summary: Background: Mesenchymal stromal/stem cells (MSC) can enhance the neovascularization processes required for wound healing and are widely used as an autologous source of progenitor cells in stem cell-based therapies. However, incomplete MSC differentiation towards a vascular endothelial cell phenotype questions their involvement in an alternative process to angiogenesis, namely vasculogenic mimicry (VM), and the signal transducing events that regulate their in vitro priming into 3D capillary-like structures. Methods: Human MSC were primed on top of Cultrex matrix in order to recapitulate an in vitro 3D phenotype of VM. Total RNA was extracted, and differential gene expression assessed through RNA-Seq analysis and RT-qPCR. Transient gene silencing was achieved using specific siRNA. AG490, Tofacitinib, and PP2 pharmacological effects on VM 3D structures were analyzed using the Wimasis software. Results: In vitro VM occurred within 4 hours and was prevented by the JAK/STAT3 inhibitors AG490 and Tofacitinib, as well as by the Src inhibitor PP2. RNA-Seq highlighted STAT3 as a signaling hub contributing to VM when transcripts from 3D cultures were compared to those from 2D monolayers. Concomitant increases in IL6, IL1b, CSF1, CSF2, STAT3, FOXC2, RPSA, FN1, and SNAI1 transcript levels suggest the acquisition of a combined angiogenic, inflammatory and epithelial-to-mesenchymal transition phenotype in 3D cultures. Increases in STAT3, FOXC2, RPSA, Fibronectin, and Snail protein expression were confirmed in 3D cultures. STAT3 and RPSA gene silencing abrogated in vitro VM. Conclusions: In vitro VM priming of MSC into 3D structures requires Src/JAK/STAT3 signaling. This molecular evidence supports a clinically feasible MSC-mediated pseudo-vasculature process that could temporarily sustain grafts through VM until the host vasculature is able to infiltrate and remodel injured tissues.

overall_design:
To investigate the impact of 3D cultures over 2D cell monolayers on the transcriptional profile associated to capillary-like structure formation.
We then performed gene expression analysis using data obtained from RNA-Seq of cells cultured on 3D (Cultrex) vs 2d (monolayers on plastic).

first: Marie-Eve

last: Roy

first: Carolane

last: Veilleux


title: Quantitative analysis of wild type and set2 mutant transcriptomes

city: Singapore

first: Ying

last: Li

state: --- Select a state ---

address: 14 Medical Dr, Singapore

country: Singapore

institute: Cancer Science Institute of Singapore

summary: RNA-seq on total RNA of wild type (WT) and set2 mutant (set2d). To determine the changes in transcriptome profile when set2 gene is delete in comparision to WT cells.

overall_design: The transcriptome profile of log phase asynchronous WT and set2d cells were generated by RNA-seq, in duplicate, using Illumina HiSeq 2000

first: K

middle: K

last: Lim

first: E

middle: S

last: Chen

first: Henry

last: Yang


title: SOX2-OT induced by PAI-1 promotes triple-negative breast cancer cells metastasis

city: Nanjing

first: Wenwen

last: Zhang

state: Jiangsu

address: 68 Changle Road

institute: Nanjing Medical University

summary: Triple-negative breast cancer (TNBC) has a relatively aggressive biological behavior and poor outcome. Our published study showed that PAI-1 could induce the migration and metastasis of TNBC cells. However, the underlying mechanism by which PAI-1 regulates TNBC metastasis has not been addressed. Using microarray analysis of lncRNA expression profiles, we identified a lncRNA SOX2-OT, which is by induced by PAI-1 and could function as an oncogenic lncRNA in TNBC.

overall_design: We treated MDA-MB-231 cells with or without recombinant human PAI-1 or PAI-1 small-molecule inhibitor PAI-039, then used microarray analysis to obtain the lncRNAs expression profiles. Biological replicates: 3 control replicates, 3 transfected replicates.

first: Xiaoxiang

last: Guan


title: Integration of ATAC and RNA-Sequencing identifies chromatin and transcriptomic signatures in classical and non-classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA]

city: Muenster

first: Kleio

last: Petratou-Busswinkel

address: Röntgenstraße 16

country: Germany

institute: Institute for Cardiovascular Organogenesis and Regeneration

summary: Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation, and notochord sheath cells, which serve as non-classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research, the genetic regulation of bone formation, as well as mechanisms of transcriptional control of entpd5a, remain largely unknown. Here, using a newly generated transgenic line, we isolate classical and non-classical osteoblasts from zebrafish embryos and performed both ATAC-Seq and RNA-Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation, Hox family factors are involved in governing spinal ossification via non-classical osteoblasts. We further present a resource-driven analysis of the entpd5a promoter, experimentally validating the ATAC-Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio-temporally regulated promoter/enhancer interactions taking place in the entpd5a locus.

overall_design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head (classical) and trunk (non-classical) osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC-Seq and RNA-Seq and analysed data at first individually, to establish open chromatin regions and gene expression profiles, respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.

first: Petratou

last: Kleio

first: Schulte-Merker

last: Stefan


title: Genome-wide characterization of effects of LINC01021 on p53-regulated gene expression in CRC cells

city: Munich

first: Markus

last: Kaller

address: Thalkirchner Strasse 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University Munich

summary: We studied the effect of CRISPR/Cas9-mediated deletion of LINC01021 on genome-wide RNA expression changes after ectopic activation of p53 in CRC cells by RNA-Seq analyses

overall_design: RNA expression profiles with and without ectopic activation of p53 in colorectal cancer cells with and without deletion of LINC01021

first: Heiko

last: Hermeking


title: A multi-adjuvant nanovaccine platform based on targeted delivery of specific antigens for cancer immunotherapy

city: Hubei

first: 文

last: 李

address: Wuhan

institute: Wuhan University

summary: Cance vaccines have become a milestone in immunotherapy, but inadequate activation rate of antigen presenting cells (APCs) and low delivery efficiency of specific antigen have widely limited their clinical application. Here we design an engineered vaccine platform based on targeted delivery of specific antigens to activated APCs. This vaccine platform is implemented by loading stimulator of interferon genes agonist and tumor lysate protein with calcium phosphate as adjuvants, and coating the surface with mannose-modified liposomes. By loading different types of tumor antigen proteins, this nanovaccine platform successfully achieves tumor immunotherapy in breast and colon cancer bearing mice. In addition, personalized nanovaccine prepared from surgically removed tumor lysate proteins also significantly suppresses postsurgical distant tumor. Through the design of nanovaccine platform, we provide an efficient multi-adjuvant delivery platform for multiple types of tumor antigens, and also offer more ideas for personalized vaccine immunization. This nanovaccine platform has great prospects for transformation due to the designability and simplicity for the preparation.

overall_design: DC2.4 cells were co-cultured with mLCAP (cGAMP: 85.8 ng mL-1, lysate protein: 63.6 μg mL-1) for 24 h. Total RNA was extracted using RNAiso plus reagent (TaKaRa Biomedical Technology Co., Ltd), and then RNA quality was determined by 5300 bioanalyzer (Agilent). RNA purification, reverse transcription, library construction, and sequencing were performed at Genecreate Biotechnology Co., LTD. (Wuhan, China) in accordance with the manufacturer's instructions. Cell transcriptomic data analysis was performed on the Genecreate Biotechnology cloud platform (China).

first: Wen

first: Qiu-Ling


title: Transcriptome of Foxa1/Foxa2-deficient colon [RNA]

city: PHILADELPHIA

first: Avital

last: Swisa

state: PA

summary: FOXA1 and FOXA2 are essentail transcription factors for proper gut development. In adults, they have a role in the differentiation of intestinal secretory cell lineages and were also reporeted to directly activate Muc2 transcription. Here we show that deletion of Foxa1 and Foxa2 in mouse intestinal epithelium leads to a downregulation of glycosylation genes in the colon and to a massive change of the colonic surface glycans. In turn, the microbiome composition shifts dramatically and spontaneous inflammatory bowel disease ensued. We conclude that vertebrates shape a favorable microbiome by establishing a glycocalyx to nurture specific bacterial taxa through control of the epithelial glycosylation program by the FoxA transcription factors.

overall_design: Colonic mRNA profile of 9-18 month old control and Foxa1/2-deficient mice. From each mouse, proximal and distal segments were analyzed.

first: Julia

last: Kieckhaefer

first: Hannah

last: Kolev

first: Klaus

middle: H

last: Kaestner


title: FBXO5 degrades DOK6 to enhance cell mechanics and sensitivity to Temozolomide

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

institute: Tianjin Medical University

summary: stable CRISPR/Cas9 sgRNA-expression U251 cells were treated with 200nM or 1500nM temozolomide for 72 hours, and then, we screened temozolomide-resistance genes by negative selection and temozolomide-sensitive genes by positive selection

overall_design: Examination of differentially expressed sgRNAs in nagative group and positive group with control.

first: Chao

last: Wang

first: Mengqi


title: FOXA1 and FOXA2 binding profile in mouse colon [ChIP]

summary: FOXA1 and FOXA2 are essentail transcription factors for proper gut development. In adults, they play a role in the differentiation of intestinal secretory cells and were also reporeted to directly activate Muc2 transcription. Here we show that FOXA1 and FOXA2 bind near goblet cell genes, and are specifically enriched near glycosylation genes. Deletion of these transcription factors in mouse intestine leads to a downregulation of glycosylation genes in the colon and to a massive change of the colonic surface glycans. I turn, the microbiome composition shifts dramatically and spontaneous inflammatory bowel disease ensued. We conclude that vertebrates shape a favorable microbiome by establishing a glycocalyx to nurture specific bacterial taxa through control of the epithelial glycosylation program by the FoxA transcription factors.

overall_design: ChIP-seq for FOXA1 and FOXA2 on isolated colonic crypts from wild type C57BL/6 male mice.


title: single nuclei transcriptomics of colonic epithelium

summary: FOXA1 and FOXA2 are essentail transcription factors for proper gut development. In adults, they play a role in the differentiation of intestinal secretory cells and were also reporeted to directly activate Muc2 transcription. Here we show that deletion of Foxa1 and Foxa2 in mouse intestinal epithelium leads to a downregulation of glycosylation genes in the colon and to a massive change of the colonic surface glycans, which in turn leads to dysbiosis and to inflammatory bowel disease. In order to associate this phenotype with a specific colonic lineage, we generated cell specific gene sets by performing single nuclei RNA-seq on colonic tissue from control mice. Gene set enrichment analysis demonstrated major changes in Goblet cell genes following Foxa1/2 deletion, including glycosylation genes. However, other lineages were also affected. We concluded that vertebrates shape a favorable microbiome by establishing a glycocalyx to nurture specific bacterial taxa through control of the epithelial glycosylation program by the FoxA transcription factors.

overall_design: Single nuclei RNA-seq of distal colon from two wild type mice.


title: Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [YODA1_vs_DMSO_CutnTag_CD8]

first: Dawang

last: Zhou

overall_design: CUT&Tag analysis of CD8+ T-cells activated by anti-CD3/CD28, with or without YODA1 treatment.

first: Junhong

last: Li

first: Jinjia

first: Lanfen


title: GLI1+ cells contribute to vascular remodeling in hypoxia- and cigarette smoke-induced pulmonary hypertension

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: The precise origin of newly formed alpha smooth muscle actin-positive (ACTA2+) cells appearing in non-muscularized vessels in the context of pulmonary hypertension (PH) is still debatable, although it is believed that they predominantly derive from pre-existing vascular smooth muscle cells (VSMCs). Here, Gli1Cre-ERT2; tdTomatoflox mice were used to lineage-trace GLI1+ cells in the context of PH using two independent models of vascular remodeling (VR) and reverse remodeling (RR): hypoxia and cigarette-smoke exposure (SE). Hemodynamic measurements, right ventricular hypertrophy assessment, flow cytometry, and histological analysis of thick lung sections followed by state-of-the-art 3D reconstruction and quantification using Imaris software were used to investigate the contribution of GLI1+ cells to neo-muscularization of the pulmonary vasculature. The data show that GLI1+ cells are abundant around distal, non-muscularized, vessels during steady state, and that this lineage contributes to around 50% of newly formed ACTA2+ cell around these normally non-muscularized vessels. During RR, cells derived from the GLI1+ lineage are largely cleared in parallel to the reversal of muscularization. Partial ablation of GLI1+ cells greatly prevented VR in response to hypoxia and attenuated the increase in RVSP and right heart hypertrophy. Single-cell RNA sequencing (scRNA-seq) on sorted lineage-labeled GLI1+ cells revealed an Acta2high fraction of cells with pathways in cancer and MAPK signaling as potential players in reprogramming these cells during VR. Analysis of human lung-derived material suggests that GLI1 signaling is overactivated in both Group 1 and Group 3 PH and can promote proliferation and myogenic differentiation. Our data highlight GLI1+ cells as an alternative cellular source of VSMCs in PH and suggest that these cells and the associated signaling pathways represent an important therapeutic target for further studies.

overall_design: Fresh flow cytometry sorted GLI1+ cells from Gli1CreERT2; tdTomatoflox mouse lung tissue from hypoxia conditions were then processed to scRNA-seq

first: Xuran

last: Chu

first: Saverio

last: Bellusci

first: Elie

last: El Agha


title: Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [Osr2KO_vs_WT_scRNA_CD8]

summary: The alteration in extracellular matrix (ECM) architecture and stiffness becomes one of the hallmarks of cancer. Whether the mechanical property of ECM contributes to the functionality of CD8+ T cells, a key component of anti-tumor response, remains largely unknown. Here we report that mechanical stress drives T cell exhaustion program via Osr2, a transcription factor that had been poorly investigated in T cells. Osr2 is highly and selectively induced in CD8+ T cells when encountering stiff matrix or mechanical force signaling (MFS). Integrated genetic and multi-omics analyses reveals that Osr2 is enriched in the terminal exhausted tumor infiltrating lymphocytes and its expression is modulated by the combined TCR and MFS mediated by Piezo1/Calcium/CREB axis. Importantly, depletion of Piezo1 or Osr2 alleviates T cell exhaustion, which is associated with enhanced anti-tumor immunity mediated by antigen specific T cells or CAR-T cells in solid tumor models. On the contrary, forced Osr2 expression in CD8+ T cells augment their exhaustion and dampens tumor control. In agreement with these observations, high Osr2 expression is correlated with poor prognosis in multiple human malignancies. Mechanistically, Osr2 recruits HDAC3, which in turn establishes epigenetic reprogramming to suppress cytotoxic genes expression and to promote CD8+T cell exhaustion. Thus, our results unravel a mechanical signaling cascade centered by Osr2 that serves as a key driver for CD8+ T cell exhaustion and suggest that mechanical checkpoints could be promising targets for cancer immunotherapy.

overall_design: Single cell transcriptional features of WT and OSR2-/- OT-I T cells following adoptive co-transfer into MC38-OVA bearing hosts for 14 days.

last: Zhang

first: Yongqiang

last: Hou

last: Chen


title: Cross-species analysis uncovers the mitochondrial stress response in the hippocampus as a shared mechanism in mouse early life stress and human depression

city: Groningen

first: Bente

middle: Marianne

last: Hofstra

address: Antonius Deusinglaan 1, Building 3211; PO Box 30001, CB50

department: Genetics

country: Netherlands

institute: University medical center Groningen

summary: Depression, or major depressive disorder, poses a significant burden for both individuals and society, affecting approximately 10.8% of the general population. This psychiatric disorder leads to approximately 800,000 deaths per year. A combination of genetic and environmental factors such as early life stress (ELS) increase the risk for development of depression in humans, and a clear role for the hippocampus in the pathophysiology of depression has been shown. Nevertheless, the underlying mechanisms of depression remain poorly understood, resulting in a lack of effective treatments. To better understand the core mechanisms underlying the development of depression, we used a cross-species design to investigate shared hippocampal pathophysiological mechanisms in mouse ELS and human depression. Mice were subjected to ELS by a maternal separation paradigm, followed by RNA sequencing analysis of the adult hippocampal tissue. This identified persistent transcriptional changes linked to mitochondrial stress response pathways, with oxidative phosphorylation and protein folding emerging as the main mechanisms affected by maternal separation. Remarkably, there was a significant overlap between the pathways involved in mitochondrial stress response we observed and publicly available RNAseq data from hippocampal tissue of depressive patients. This cross-species conservation of changes in gene expression of mitochondria-related genes suggests that mitochondrial stress may play a pivotal role in the development of depression. Our findings highlight the potential significance of the hippocampal mitochondrial stress response as a core mechanism underlying the development of depression. Further experimental investigations are required to expand our understanding of these mechanisms

overall_design: Mice were exposed to 4 hours of maternal separation per day between PND 10-17. Hippocampi were disected at 10 weeks of age and transcription profiling was conducted on these hippocampi.

first: Emmy

middle: E

last: Hoeksema

first: Dineke

last: Verbeek

first: Martien

middle: J

last: Kas


title: Effect of depletion of NR4A3 on vascular calcification [RNA-seq]

city: Shanghai

first: Wenqi

last: Ma

state: Shanghai

address: 227 Chongqing South Road, Huangpu District, Shanghai, China

institute: Shanghai Jiaotong University

summary: Medial arterial calcification is a chronic systemic vascular disorder distinct from atherosclerosis and is commonly observed in patients with chronic kidney disease (CKD), diabetes mellitus, and aging individuals. We previously showed that orphan nuclear receptor NR4A3 is a key regulator in the progression of apolipoprotein (apo) A-IV-induced atherosclerosis; however, little is known about its role in vascular calcification. NR4A3 expression was upregulated in calcified aortic tissues from CKD mice or 1,25(OH)2VitD3 overload-induced mice, and in human calcified aorta. NR4A3 deficiency preserved VSMCs contractile phenotype, inhibited the expression of osteoblast differentiation-related genes, and reduced calcium deposition in the vasculature.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT VSMC and NR4A3 VSMC

first: Kangni

last: Jia

first: Haomai

last: Cheng

first: Xiaoxiang

last: Yan


title: Effect of depletion of NR4A3 on vascular calcification [CUTtag_H3K18LA]


title: GLI1+ cells contribute to vascular remodeling in hypoxia- and cigarette smokeinduced pulmonary hypertension

summary: The precise origin of newly formed alpha smooth muscle actin-positive (ACTA2+) cells appearing in non-muscularized vessels in the context of pulmonary hypertension (PH) is still debatable, although it is believed that they predominantly derive from pre-existing vascular smooth muscle cells (VSMCs). Here, Gli1Cre-ERT2; tdTomatoflox mice were used to lineage-trace GLI1+ cells in the context of PH using two independent models of vascular remodeling (VR) and reverse remodeling (RR): Hypoxia and cigarette-smoke exposure (SE). Hemodynamic measurements, right ventricular hypertrophy assessment, flow cytometry, and histological analysis of thick lung sections followed by state-of-the-art 3D reconstruction and quantification using Imaris software were used to investigate the contribution of GLI1+ cells to neo-muscularization of the pulmonary vasculature. The data show that GLI1+ cells are abundant around distal, nonmuscularized vessels during steady state, and that this lineage contributes to around 50% of newly formed ACTA2+ cell around these normally non-muscularized vessels. During RR, cells derived from the GLI1+ lineage are largely cleared in parallel to the reversal of muscularization. Partial ablation of GLI1+ cells greatly prevented VR in response to hypoxia and attenuated the increase in RVSP and right heart hypertrophy. Single-cell RNA sequencing (scRNA-seq) on sorted lineage-labeled GLI1+ cells revealed an Acta2high fraction of cells with pathways in cancer and MAPK signaling as potential players in reprogramming these cells during VR. Analysis of human lungderived material suggests that GLI1 signaling is overactivated in both Group 1 and Group 3 PH and can promote proliferation and myogenic differentiation. Our data highlight GLI1+ cells as an alternative cellular source of VSMCs in PH and suggest that these cells and the associated signaling pathways represent an important therapeutic target for further studies.

overall_design: human Pulmonary Artery Smooth Muscle Cells (hPASMCs) treated or not with GLI antagonist (GANT61), 20uM, 24 hours

first: Stefano

last: Rivetti


title: The ATHB2 microProtein affects plant development and the shade avoidance response (PEAT)

city: Umeå

first: Stephan

last: Wenkel

address: Parallellvägen 21

country: Sweden

institute: Umeå Plant Science Center

summary: Plants display remarkable adaptability to varying light conditions, crucial for their optimal growth and development. Here, we investigate the functional significance of ATHB2-miP, a microProtein arising from an alternative transcript of the ATHB2 gene, in both white light and shade environments, supported by comprehensive phenotyping experiments. ATHB2, a homeodomain-leucine zipper transcription factor, is known for its involvement in growth regulation. By employing genetic, transcriptomic analyses, and phenotyping experiments, we dissect the regulatory role of ATHB2-miP. Transcriptomics unravel genes differentially induced and repressed upon ATHB2-miP expression, elucidating its impact on growth-related pathways. Notably, ATHB2-miP's expression responds to shade conditions, suggesting its role in light-mediated responses. Our research underscores ATHB2-miP's multifaceted contribution to plant growth and development, emphasizing its potential as a pivotal player in light-responsive gene regulation.

overall_design: We conducted transcriptomics, phenotyping studies, genetic analyses and protein interaction experiments on mutant lines generated by CRISPR-Cas9 where the microProein was deleted, a t-knockout line of the full ATHB2 gene and a line overexpressing the microProtein under the control of a 35S promoter.

first: Ashleigh

last: Edwards

first: Maurizio

last: Chiurazzi


title: Effect of depletion of NR4A3 on vascular calcification [CUT&Tag_NR4A3]


title: The ATHB2 microProtein affects plant development and the shade avoidance response

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

overall_design: Refer to individual Series


title: Small molecule TERT activator prevents aging and cognitive decline [ChIP-seq]

city: Houston

first: Hong Seok

last: Shim

state: TX

institute: MD Anderson Cancer Center

summary: We discovered a novel small-molecule TERT activating compound (TAC) that selectively enhances TERT transcription in human and mouse adult somatic cells. Our findings also provide the novel mechanism of TAC-mediated TERT up-regulation and elucidate the impact of TERT induction on regulatory factors governing aging.

overall_design: Profiling of histone modifcation and TF binding in human somatic cells.

first: Hong


title: Effect of TAC on human and mouse cells [RNA-seq]

summary:
Genome-wide transcriptomics were used to discover the MoA of the small-molecule TERT activator compound.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative gene expression profiling analysis of RNA-seq data for vehicle- or TAC-treated cells

first: Jiexi

last: Li


title: Cutting down steroid biosynthesis through SIRT6 induced H3K56ac deacetylation Fuels the osteogenic commitment of MSCs (ChIP-Seq)

city: Chengdu

first: XUEYANG

last: LIAO

state: Sichuan

address: NO.14 3rd section of Renminnan Road

institute: Sichuan university

summary: To detect the mechanism underlying osteogenic commitment and proliferation rate change of HDPCs driven by MDL-800, we performed ChIP-seq analysis to detect the recruitment of genes on H3K9ac and H3K56ac in MDL-800 pre-treated HDPCs.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K9ac and H3K56ac for DMSO, MDL-800(agonist for SIRT6 deacetylase) pre-treated HDPCs.

first: Xueyang

last: Liao

first: Ling

last: Ye


title: Cutting down steroid biosynthesis through SIRT6 induced H3K56ac deacetylation Fuels the osteogenic commitment of MSCs (RNA-Seq)

summary: To detect the mechanism underlying osteogenic commitment and proliferation rate change of HDPCs driven by MDL-800, we performed gene expression profiling analysis for HDPCs with DMSO or MDL-800 pre-treatment under normal or osteogenic differentiation conditions.

overall_design: Gene expression profiling analysis of RNA-seq data for HDPCs with DMSO or MDL-800(agonist for SIRT6 deacetylase) pre-treatment under normal or osteogenic differentiation conditions.


title: Cutting down steroid biosynthesis through SIRT6 induced H3K56ac deacetylation Fuels the osteogenic commitment of MSCs


title: RNA-seq analysis of the cerebellum of SCA7 mice treated with AAV expressing shRNA targeting Atxn7

city: Illkirch

first: Yvon

last: Trottier

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 1258 - University of Strasbourg

summary: Spinocerebellar ataxia type 7 (SCA7) belonging to a family of autosomal dominant cerebellar ataxias (ADCAs) is pathomechanistically associated with the group of polyglutamine expansion disorders which include SCA 1-3, 6, 7 and 17, and Huntington’s disease. These rare diseases share a common mutational feature that is the expansion of CAG repeat sequence in disease causing genes. These mutations lead to neuronal accumulation of expanded polyglutamine proteins and selective patterns of neurodegeneration. SCA7 is caused by a polyglutamine expansion in ATAXIN-7 (ATXN7), a subcomponent of co-activatory transcriptional complex SAGA and primarily affects the cerebellum, retina and brainstem. Currently, only treatments alleviating symptoms are available to patients. Allele-selective lowering of mutant polyQ proteins promises to have high therapeutic outcomes and safety profiles. In this study, PhP.eB  adeno-associated virus (AAV PhP.eB) was used to deliver several shRNAs targeting expanded CAG repeats that were tested for their safety and efficacy to lower the mATXN7 level in the brain. The SCA7140Q/5Q knock-in mice that expresses a mutated Atxn7 allele harboring an expansion of 140 CAG triplet repeats and the wild type mouse allele with 5 CAGs were used in the study. Our SCA7 140Q/5Q KI mouse model remarkably recapitulates cardinal features of SCA7 and bears the potential for pre-clinical trials (Niewiadomska-Cimicka et al., J.Neurosci., 2021). We showed that systemic injection of the AAV-shA4, the most allele-selective and safe reagent of our collection, results in improvement of motor phenotypes as indicated in open field test, and partial correction of transcriptional alterations in the cerebellum of SCA7 mice.

overall_design: Cerebellar transcriptional profiling (RNA-seq) of a knock-in mouse model of Spinocerebellar Ataxia Type 7 (SCA7) treated with shRNA targeting Atxn7 delivered in AAV PhP.eB.

first: Anna

last: Niewiadomska-Cimicka

first: Celine

last: Keime

first: Maciej

last: Figiel


title: Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function.

city: Wuhan

first: Junpeng

last: Zhan

state: Hubei

address: 1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

sample_organism:
Zea mays subsp. mexicana
Zea luxurians
Zea mays subsp. parviglumis
Zea mays subsp. mays


title: Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [YODA1_vs_DMSO_RNA_CD8]

city: Xiamen

first: Dawang

last: Zhou

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

institute: Xiamen University

overall_design: RNA-seq analysis of CD8+ T-cells activated by anti-CD3/CD28, with or without YODA1 treatment.

first: Jinjia

last: Zhang

first: Junhong

first: Lanfen

last: Chen


title: The ATHB2 microProtein affects plant development and the shade avoidance response (RNA-Seq)

first: Stephan

first: Ashleigh


title: CD36 Triggers a non-classical lipid metabolic Program promoting Immune Escape and Resistance to HMA therapy in AML

city: shanghai

first: hezhou

last: guo

address: Shanghai, P. R. China.  No. 197 Rui Jin Er Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary:
To investigate the effect of decitabine on CD36/NFkB/TLR signaling pathway in MV4-11 cells, and to explore the CD36-dependent signaling pathway regulated by decitabine.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at two different treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cells under decitabine/vehicle treatment and its KD derivatives

first: Hezhou

last: Guo

first: Ruixue

last: Feng


title: Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [TIL_scRNA_CD8]

overall_design: Single cell transcriptional features of WT OT-I T cells following adoptive co-transfer into MC38-OVA bearing hosts for 14 days.


title: Fusobacterium nucleatum upregulates the immune inhibitory receptor PD-L1 in intestinal epithelial cells via the activation of ALPK1

status: Public on May 13 2024

city: Utrecht

first: Marcel

last: de Zoete

address: Heidelberglaan 100

institute: UMC Utrecht

summary: Fusobacterium nucleatum is a Gram-negative oncobacterium that is associated with colorectal cancer. The molecular mechanisms utilized by F. nucleatum to promote colorectal tumor development have largely focused on adhesin-mediated binding to the tumor tissue and on the pro-inflammatory capacity of F. nucleatum. However, the exact manner in which F. nucleatum promotes inflammation in the tumor microenvironment and subsequent tumor promotion remains underexplored. Here, we show that both live F. nucleatum and sterile F. nucleatum-conditioned medium promote CXCL8 release from the intestinal adenocarcinoma HT-29 cell line. We determined that the pro-inflammatory response was ALPK1-dependent in both HEK293 and HT-29 cells and that the released F. nucleatum molecule had characteristics that match those of the pro-inflammatory ALPK1 ligand ADP-heptose or related heptose phosphates. In addition, not only F. nucleatum but also other Fusobacterium species such as F. varium, F. necrophorum and F. gonidiaformans promoted an ALPK1-dependent pro-inflammatory environment, indicating that ADP-heptose or related heptose phosphates secretion is a conserved feature of the Fusobacterium genus. By performing transcriptional analysis of ADP-heptose stimulated HT-29 cells, we found several inflammatory and cancer-related pathways to be differentially regulated, including DNA mismatch repair genes and the immune inhibitory receptor PD-L1. Finally, we show that stimulation of HT-29 cells with F. nucleatum resulted in an ALPK1-dependent upregulation of PD-L1. These results aid in our understanding of the mechanisms by which F. nucleatum can affect tumor development and therapy and pave the way for future therapeutic approaches.

overall_design: To investigate the effect of ADP-heptose on cancer cells, we stimulated HT-29 cells with ADP-heptose and flagellin. We then performed gene expression analysis on HT-29 stimulated with ADP-heptose, flagellin or non stimulated in triplicates

first: Coco

last: Duizer


title: CD36 impacts the expression of genes in MV4-11 cells

overall_design: Next Generation Sequencing Facilitates Quantitative Analysis of control MV4-11 cells and CD36 knockout MV4-11 cells


title: Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [Osr2OE_vs_Vector_RNA_CD8]

overall_design: RNA-seq analysis of CD8+ T cells isolated from spleens followed by activation and transduction with retroviruses encoding Osr2 (Osr2OE) or control GFP.

last: Li


title: Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [Osr2OE_vs_Vector_ATAC_CD8]

overall_design: ATAC-seq analysis of CD8+ T cells isolated from spleens followed by activation and transduction with retroviruses encoding Osr2 (Osr2OE) or control GFP.


title: Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [YODA1_vs_DMSO_ATAC_CD8]

overall_design: ATAC-seq analysis of CD8+ T-cells activated by anti-CD3/CD28, with or without YODA1 treatment.


title: Microneedle-mediated Delivery of Immunomodulators Restores Immune Privilege in Hair Follicles and Reverses Immune-Mediated Alopecia

city: Boston

first: Jamil

last: Azzi

address: 221 Longwood ave

department: Transplantation Research Center

institute: Brigham and Women's Hospital

summary: Disorders in the regulatory arm of the adaptive immune system result in autoimmune-mediated diseases. While systemic immunosuppression is the prevailing approach to manage them, it fails to achieve long-lasting remission due to concomitant suppression of the regulatory arm and carries the risk of heightened susceptibility to infections and malignancies. Alopecia Areata is a condition characterized by localized hair loss due to autoimmunity. The accessibility of the skin provides an opportunity for local rather than systemic intervention to avoid broad immunosuppression. We hypothesized that expansion of endogenous regulatory T cells (Tregs) at the site of antigen encounter can restore the immune balance and generate a long-lasting tolerogenic response. We therefore utilized a hydrogel microneedle (MN) patch for delivery of CCL22, a chemoattractant for Tregs, and IL-2, a Treg survival factor to amplify them. In an immune-mediated murine model of alopecia, we showed local bolstering of Treg numbers leading to sustained hair regrowth and attenuation of inflammatory pathways. In a humanized skin transplant mouse model, we confirmed expansion of Tregs within human skin without engendering peripheral immunosuppression. The MN patch offered high-loading capacity and shelf-life stability for prospective clinical translation. By harmonizing immune responses locally, we aspire to reshape the landscape of autoimmune skin disease management.

overall_design: We performed bulk RNA-sequencing of RNA isolated from AA-like skin lesions from  three different experimental groups (untreated, treated with empty MNs, and treated with IL-2+CCL22 loaded MNs).

first: Nour

last: Younis

first: Núria

last: Puigmal

first: Abdallah

last: El Kurdi

first: Andrew

last: Badaoui

first: Dongliang

first: Claudia

last: Morales

first: Anis

last: Saad

first: Diane

last: Cruz

first: Nadim

last: Al Rahy

first: Andrea

last: Daccache

first: Triana

last: Huerta

first: Christa

last: Deban

first: Ahmad

last: Halawi

first: John

last: Choi

first: Pere

last: Dosta

first: Christine

last: Lian

first: Natalie

last: Artzi


title: Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [Osr2KO_vs_WT_RNA_CD8]

first: Dawang

last: Zhou

overall_design: Transcriptional features of WT and OSR2-/- OT-I T cells following adoptive co-transfer into MC38-OVA bearing hosts for 14 days.

first: Junhong

last: Li

first: Jinjia

last: Zhang

first: Lanfen

last: Chen


title: Trefoil factor 2 expressed by the murine pancreatic acinar cells is required for the development of islets and for beta cell function during aging

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: Exocrine-to-endocrine crosstalk in the pancreas is crucial to maintain beta cell function. However, the molecular mechanisms underlying this crosstalk are largely undefined. Trefoil factor 2 (Tff2) is a secreted factor known to promote the proliferation of beta cells in vitro, but its physiological role in vivo in the pancreas is unknown. Also, it remains unclear which pancreatic cell type expresses Tff2 protein. We therefore created a mouse model with a conditional knockout of Tff2 in the murine pancreas. We find that the Tff2 protein is preferentially expressed in acinar but not ductal or endocrine cells. Tff2 deficiency in the pancreas reduces beta cell mass on embryonic day 16.5. However, homozygous mutant mice are born without a reduction of beta cells and with acinar Tff3 compensation by day 7. When mice are aged to 1 year, both male and female homozygous and male heterozygous mutants develop impaired glucose tolerance without affected insulin sensitivity. Perifusion analysis reveals that the second phase of glucose-stimulated insulin secretion from islets is reduced in aged homozygous mutant compared to controls. Collectively, these results demonstrate a previously unknown role of Tff2 as an exocrine acinar cell-derived protein required for maintaining functional endocrine beta cells in mice.

overall_design: Bulk mRNA-sequencing results of murine embryonic day 16.5 pancreatic tissue from control (Tff2fl/fl) versus conditional Tff2 KO (Pdx1:Cre;Tff2fl/fl) samples were compared and analyzed. In addition, bulk mRNA-sequencing results of isolated islets from 1-year-old control (Tff2fl/fl) versus conditional Tff2 KO (Pdx1:Cre;Tff2fl/fl) samples were compared and analyzed.

first: Jose

last: Ortiz

first: Min-Hsuan

first: Xiwei

last: Wu

middle: T


title: Cancer-associated MDM2 W329G mutant attenuates ribosomal stress-mediated p53 responses to promote cell survival and glycolysis

city: New York

first: Dr. Liang

last: Lei

state: NY

address: 1130 St. Nicholas Ave

department: Pathology and Cell Biology

institute: Columbia University

summary: Although amplification/overexpression is the predominant mechanism for the oncogenic properties of MDM2, an increasing number of MDM2 somatic missense mutations were identified in cancer patients with the recent advances in sequencing technology. Here, we characterized an MDM2 cancer-associated mutant variant W329G identified from patient samples that contain a wild-type p53 gene. We found that the MDM2 W329G mutant was resistant to the inhibitory effect of ribosomal protein L11 (RPL11) on MDM2-mediated p53 ubiquitination and degradation, in line with its defect on RPL11 binding. Using isogenic U2OS cells with or without endogenous mdm2 W329G mutation, we demonstrated that the expression of classic p53 targets induced by ribosomal stress signals was reduced in mutant cells. RNA-seq analysis revealed that upon 5-FU treatment, the p53 response was significantly impaired. Also, the 5-FU-mediated repression of genes in cell cycle progression and DNA replication was diminished in W329G mutant-containing cells. Physiologically, U2OS W329G cells were more resistant to cell growth inhibition induced by ribosomal stress and exhibited higher glycolytic rates upon 5-FU treatment. Together, our data indicated that cancer-associated MDM2 W329G mutant attenuates ribosomal stress-mediated p53 responses to promote cell survival and glycolysis.

overall_design: To investigate the effect of MDM2 W329G mutation in p53 regulation, we established isogenic U2OS wild-type and MDM2 W329G cells using Crispr/Cas9-based genome editing. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells treated with DMSO or 5-FU (50 µM) for 24 hours. Two independent experiments were performed and RNA-seq data were generated by two different vendors. Comparative gene expression profilling analysis of RNA-seq data were carried out between 5-FU treated U2OS wild-type and MDM2 W329G cells as well as DMSO treated U2OS wild-type and MDM2 W329G cells.

first: Sally

last: Lien

first: Thomas

last: Whitbread

first: Shiva

middle: O

last: Shastri

first: Jamie

last: Contreras

first: Ruiying

last: Zhao

first: Yan

last: Zhu


title: Spermine-induced DNA methylation change in human macrophages

city: Hangzhou

first: Hongde

state: Zhejiang

address: 150 Fucheng Road

institute: Hangzhou Institute of Medicine, Chinese Academy of Sciences

summary: Polyamines, crucial molecules involved in cell proliferation and growth, play a pivotal role in cancer development and progression. Within the tumor microenvironment, macrophages, key components of the immune system, exhibit a complex relationship with polyamines. Evidence suggests that polyamines can modulate macrophage polarization, influencing their functional phenotypes. Here, we detected the gene DNA methylation changes in spermine-stimulated human macrophages isolated from PBMCs and TAMs.

platform_organism: Mycobacterium tuberculosis variant bovis

platform_organism: Mycobacterium avium subsp. paratuberculosis

platform_organism: Mycobacterium tuberculosis variant microti

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium

platform_organism: Francisella tularensis subsp. tularensis

platform_organism: Francisella tularensis subsp. holarctica

platform_organism: Francisella tularensis subsp. mediasiatica

overall_design: Bisulphite converted DNA from the 4 samples were hybridised to human 850K llumina Infinium MethylationEPIC BeadChip .

first: Yinghua

first: Hai

last: Hu


title: Ubiquitylation of Pol II controls early stages of the transcription cycle [TT-seq]

city: Cambridge

first: Ana

last: Tufegdzic Vidakovic

state: Cambridge

address: Cambridge Biomedical Campus, Francis Crick Ave

country: United Kingdom

institute: MRC-LMB

summary: Control of RNA Polymerase II (Pol II) through ubiquitylation is essential for the DNA-damage response. Here we reveal a distinct ubiquitylation pathway in human cells that targets excessive and defective Pol II molecules at the initial stages of the transcription cycle. This pathway, mediated by ARMC5CUL3 ubiquitin ligase, drives homeostatic Pol II turnover, and is further enhanced when early stages of transcription - initiation and pausing - are perturbed. Upon ARMC5 loss, Pol II accumulates in the free pool and in the promoter-proximal zone, but is not permitted into elongation. We identify Integrator subunit 8 (INTS8) as a gatekeeper preventing the release of excess Pol II molecules into gene bodies. Combined loss of ARMC5 and INTS8 has strong detrimental effects on cell growth, with ARMC5 loss exacerbating transcriptional defects seen in INTS8-depleted cells. These findings uncover that ARMC5CUL3 and INTS8 form a collaborative checkpoint, monitoring the quantity and quality of transcription complexes before they are licensed into elongation.

overall_design: To study how ARMC5 loss confers partial resistance to XBP inhibition by triptolide we generated ARMC5 KO cells in HEK293 Trex flp In background. We treated WT and ARMC5 KO cells with triptolide at 300 nM for 2 h. 4SU was added 15 minutes prior to harvesting in all samples. To study the function of INTS8 on the ARMC5 KO background we depleted INTS8 with siRNA targeting INTS8 48 h prior to triptolide treatment.

first: Iván

last: Shlamovitz

first: Andrew

last: Zeller

first: Roberta

last: Cacioppo

first: Alastair

last: Crisp

last: Vidaković


title: Transthyretin orchestrates vitamin B12-induced stress resilience

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: Background: Chronic stress significantly contributes to mood- and anxiety disorders. Previous data suggest a correlative connection between vitamin B12 supplementation, depression, and stress resilience. However, the underlying mechanisms are still poorly understood.  Methods: Using the chronic variable stress mouse model coupled with RNA-sequencing, we determined vitamin B12-induced transcriptional changes related to stress resilience. By viral-mediated gene transfer and in vivo epigenome editing, we reveal a functional pathway linking vitamin B12, DNA methylation, and depressive-like symptoms. Results: We identified Transthyretin (Ttr) as a sex-specific key target of vitamin B12 action in chronic stress. Accordingly, TTR expression was increased postmortem in the prefrontal cortex of male, but not female, depressed patients. Virally altered Ttr in the prefrontal cortex functionally contributed to stress- and depression-related behaviors, changes in dendritic spine morphology, and gene expression. In stressed mice, vitamin B12 reduced DNAme in the Ttr promoter region. Importantly, using in vivo epigenome editing to alter DNAme in the brains of living mice for the first time, we establish a direct causal link between DNAme on Ttr and stress-associated behaviors.  Discussion: In summary, using state-of-the-art techniques, this study uncovers a mechanistic link between cobalamin supplementation, Ttr, and markers of chronic stress and depression, encouraging further studies into dietary interventions for mood disorders.

overall_design: Total mRNA sequenced for 12 brain (prefrontal cortex) samples from 14 weeks old, male mice, 4 weeks after stereotaxic surgery to infect PFC by 1) empty Adeno-associated virus constructs (GFP control), 2) AAVs to overexpress (OE) Ttr, 3) AAVs or knockdown (KD) Ttr.

first: Gregor

last: Stein

first: Janine

last: Aly

first: Annamaria

last: Manzolillo

first: Lisa

last: Lange

first: Iqra

last: Hussain

first: Elizabeth

last: Heller

first: Susana

last: Cubillos

last: Ernst

first: Christian

last: Hübner

first: Gustavo

last: Turecki

first: Steve

last: Hoffmann

first: Olivia

last: Engmann


title: RNA-seq expression analysis of liver, adipose, skeletal muscle, heart, and pancreatic islets from DO founder strain mice fed high-fat, high-sugar diet. [skeletal muscle]

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

summary: RNA-seq was performed on samples of frozen tissue (liver, adipose, skeletal muscle, heart, and pancreatic islets) from the eight founder stains for the Diversity Outbred mice. The mice were fed a high-fat, high-sugar diet to sensitize them to the development of diabetes.

overall_design: transcription profiling by high-throughput sequencing design

first: Candice

middle: N

last: Baker


title: RNA-seq expression analysis of liver, adipose, skeletal muscle, heart, and pancreatic islets from DO founder strain mice fed high-fat, high-sugar diet. [Islet]


title: Platform-based gene regulation by an endoderm-specific lncRNA via stabilizing nuclear speckles

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

summary: Nuclear speckles (NSs), one of the key non-membrane nuclear bodies, participate in transcription, RNA processing, and chromatin organization, yet their precise functions and mechanisms in vivo remain elusive. Here we show that Falcor, an endoderm-specific long non-coding RNA (lncRNA), is necessary and sufficient for maintaining structural integrity of NSs in mouse liver cells. Disruption and reinstatement of NSs by Falcor coordinately regulate more than one thousand genes, including those related to metabolic processes. Falcor locates in the core of NSs, and interacts with Zinc finger CCCH domain-containing protein 11A (ZC3H11A), thereby facilitating phase separation to maintain NSs' structure. Furthermore, specific knockout of Falcor in the mouse liver uncovered its pivotal role in governing metabolic homeostasis, and its absence affords protection against diet-induced liver steatosis, obesity, and metabolic disorders. Collectively, our study demonstrated essential roles of Falcor in NSs maintenance and regulating metabolic homeostasis, which imply the importance of lineage-specific lncRNAs in “platform-based” gene regulation via NSs during pathophysiological processes.

overall_design: To test the functions of Falcor in NSs, we knocked down its gene expression through short hairpin RNA (shRNA)-based RNA interference (RNAi) in mouse AML12 hepatocytes.To further investigate the collaboratively regulatory role of Falcor and ZC3H11A on downstream genes, we conducted RNA-seq analysis on AML12 cell lines with the conventional shRNA-based knockdown of Falcor or ZC3H11A.Next, we explored the functions of Falcor under normal physiological conditions. We further explored the effect of Falcor on metabolism under pathological conditions.

first: Qianfeng

last: Wang

first: Shibin

last: Hu

first: Bo

last: Wen


title: RNA-seq expression analysis of liver, adipose, skeletal muscle, heart, and pancreatic islets from DO founder strain mice fed high-fat, high-sugar diet. [Adipose]


title: Ubiquitylation of Pol II controls early stages of the transcription cycle [ChIP-seq]

first: Ana

last: Tufegdzic Vidakovic

overall_design: We aimed to study how ARMC5 loss affects Pol II occupancy on chromatin and how is a partial resistance to XBP inhibition by triptolide achieved in ARMC5 KO cells in HEK293 Trex flp In background. We treated WT and ARMC5 KO cells with triptolide at 300 nM for 2 h. We then performed double cross-linking, first we incubated the washed cells with disuccinimidyl glutarate (DSG) for 15 minutes, followed by washing and incubation with formaldehyde. Immunoprecipitation was performed against total Pol II (D8L4Y Antibody) and Serine 5 phosphorylated Pol II (3E8 Antibody).

first: Andrew

last: Zeller

first: Iván

last: Shlamovitz

last: Vidaković


title: Effect of AsiDNA and belinostat on gene expression in U87 cells. [RNA-Seq]

city: salt lake city

first: Mahesh

middle: Babu

last: Chandrasekharan

state: Utah

address: 2000 circle of hope room 3715

department: Radiation Oncology

institute: University of Utah SOM

summary: An effective long-term inhibition of multiple DNA repair signals is required to design a novel and effective therapeutic for glioblastoma (GBM), a highly DNA repair ‘addicted’ cancer. AsiDNA, a double-strand DNA break (DSB) mimetic, is an innovative approach that shuts down the entire DNA repair system in cancer cells by sequestering DSB repair factors. We showed that inhibition of class I histone deacetylases (HDACs) dislodges repair factors from sites of DNA damage. We therefore tested whether AsiDNA and pan HDAC inhibitor Belinostat combination can impart a chromatin-based long-term DNA damage and impair DNA repair in GBM cells. In order to understand the long-term effects of AsiDNA on DNA repair, we treated U87 cells with AsiDNA for 6 days followed by 6 days recovery from the drug. We used this protocol to create long-term AsiDNA treated cells (LTAU87) according to the clinical trial protocol. We performed RNA-Seq with LTAU87 cells and MTU87 (mock treated U87; control) in the presence and absence of belinostat.

overall_design: Comparative gene expression analysis was performed following exposure of glioblastoma cells to AsiDNA and belinostat.

first: Srividya

last: Bhaskara


title: Determine whether AsiDNA and belinostat alter chromatin accessbility genome-wide in glioblastoma cells. [NicE-Seq]

summary: An effective long-term inhibition of multiple DNA repair signals is required to design a novel and effective therapeutic for glioblastoma (GBM), a highly DNA repair ‘addicted’ cancer. AsiDNA, a double-strand DNA break (DSB) mimetic, is an innovative approach that shuts down the entire DNA repair system in cancer cells by sequestering DSB repair factors. We showed that inhibition of class I histone deacetylases (HDACs) dislodges repair factors from sites of DNA damage. We therefore tested whether AsiDNA and pan HDAC inhibitor Belinostat combination can impart a chromatin-based long-term DNA damage and impair DNA repair in GBM cells. We performed mass spectrometry with chromatin isolated from AsiDNA and Belinostat and found that Belinostat reduces histone H1.2 levels. To this end, we assessed whether AsiDNA and Belinostat alter histone H1.2 occupancy genome-wide. In order to understand the long-term effects of AsiDNA on DNA repair, we treated U87 cells with AsiDNA for 6 days followed by 6 days recovery from the drug. We used this protocol to create long-term AsiDNA treated cells (LTAU87) according to the clinical trial protocol. We performed NicE-seq with LTAU87 cells and MTU87 (mock treated U87; control) in the presence or absence of belinostat treatment in order to address whether they alter the global chromatin structure.

overall_design: NicE-seq analysis following exposure of glioblastoma cells to AsiDNA and/or Belinostat. Library construction was performed as described by Ponnaluri et al [Genome Biology 18, 122 (2017)] by biotin labeling of chromatin digested with Nt.CviPII (NEB R0626S).

first: Chin

last: Hang Gyeong

first: Sen

last: Sagnik

first: Pradhan

last: Sriharsa


title: RNA-seq expression analysis of liver, adipose, skeletal muscle, heart, and pancreatic islets from DO founder strain mice fed high-fat, high-sugar diet. [heart]


title: Determine whether AsiDNA and belinostat alter H1.2 occupancy genome-wide. [ChIP-Seq]

summary: An effective long-term inhibition of multiple DNA repair signals is required to design a novel and effective therapeutic for glioblastoma (GBM), a highly DNA repair ‘addicted’ cancer. AsiDNA, a double-strand DNA break (DSB) mimetic, is an innovative approach that shuts down the entire DNA repair system in cancer cells by sequestering DSB repair factors. We showed that inhibition of class I histone deacetylases (HDACs) dislodges repair factors from sites of DNA damage. We therefore tested whether AsiDNA and pan HDAC inhibitor Belinostat combination can impart a chromatin-based long-term DNA damage and impair DNA repair in GBM cells. We performed mass spectrometry with chromatin isolated from AsiDNA and Belinostat and found that Belinostat reduces histone H1.2 levels. To this end, we assessed whether AsiDNA and Belinostat alter histone H1.2 occupancy genome-wide. In order to understand the long-term effects of AsiDNA on DNA repair, we treated U87 cells with AsiDNA for 6 days followed by 6 days recovery from the drug. We used this protocol to create long-term AsiDNA treated cells (LTAU87) according to the clinical trial protocol. We performed H1.2 ChIP-Seq with LTAU87 cells and MTU87 (mock treated U87; control) in the presence and absence of belinostat in order to address whether they alter the global chromatin structure.

overall_design: Histone H1.2 ChIP-Seq analysis following exposure of glioblastoma cells to AsiDNA and Belinostat.


title: Regulation of Microglia-Mediated Neuroinflammation Post-Intracerebral Hemorrhage by Gut Microbiota and Short-Chain Fatty Acid Metabolism

city: hangzhou

first: Xuchao

last: He

state: zhejiang

address: 88 jiefang RD

institute: zhejiang university

summary: Intracerebral hemorrhage (ICH) induces alterations in the gut microbiota composition, significantly impacting neuroinflammation post-ICH. However, the impact of gut microbiota absence on neuroinflammation following ICH-induced brain injury remain unexplored. Here, we observed that the gut microbiota absence was associated with reduced neuroinflammation, alleviated neurological dysfunction, and mitigated gut barrier dysfunction post-ICH. In contrast, recolonization of microbiota from ICH-induced SPF mice by transplantation of fecal microbiota (FMT) exacerbated brain injury and gut impairment post-ICH. Additionally, microglia with transcriptional changes mediated the protective effects of gut microbiota absence on brain injury, with Apoe emerging as a hub gene. Subsequently, Apoe deficiency in peri-hematomal microglia was associated with improved brain injury. Finally, we revealed that gut microbiota influence brain injury and gut impairment via gut-derived short-chain fatty acids (SCFA).

overall_design: To investigate the complex modulatory effects of the gut microbiota on microglia following intracerebral hemorrhage, we established a intracerebral hemorrhage collagenase model and corresponding sham surgery controls using antibiotic cocktail-treated ABX mice, germ-free mice, and SPF mice. Subsequently, on days 3 and 7 post-cerebral hemorrhage, we performed RNA sequencing on the microglia surrounding the hematoma using flow cytometry-based cell sorting, and analyzed the RNA-Seq data to obtain gene expression profiles.

first: Xiongjie

last: Fu

first: Yin

last: Li

first: Lin


title: Inhalation exposure to CMIT/MIT in Drosophila melanogaster

city: Jeongeup

first: Yoon

last: Cho

state: Jeollabuk-do

address: 30, Baekhak 1-gil

country: South Korea

institute: Korea Institute of Toxiology

summary: The fly is a powerful tool for studying complex biological processes, with more than 60% of genes associated with various diseases and genetic similarities to humans. Based on the genetic advantages of this model organism, our study aims to perform a toxicogenic assessment of human health impact induced by the CMIT/MIT (chloromethyl-Methylisothiazolone).

overall_design: The flies of both sexes were exposed to CMIT/MIT aerosol for 1 hour at 330 mg/m3. Previous observations indicate that the survival rate of flies exposed to CMIT/MIT at this concentration is approximately 81.5% on average for days 1,2, and 7. To study into the molecular and transcriptional alteration underlying this response, we analyzed the RNA Seq-based transcriptome profiles of CMIT-MIT exposed flies on day 1, 2, and 7 with 1.5-fold change > and p < 0.05.

first: Min-Seok

last: Kim


title: Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (ChIP-Seq)

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

summary: To investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with three human H2A.Z proteins to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants even though Arabidopsis and human H2A.Z N-terminal tail sequences are divergent, while the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants. Furthermore, H2A.Z.1 almost completely re-establishes normal H2A.Z chromatin occupancy in h2a.z plants and restores the expression of more than 84 % of misexpressed genes. Finally, our hypothesis that the N-terminal tail of Arabidopsis H2A.Z is not crucial for its overall function was supported by the ability of N-terminal end truncations of Arabidopsis HTA11 to largely rescue the defects of h2a.z mutants.

overall_design: ChIPseq on biological duplicates of WT, h2a.z + AtHTA11, and h2a.z + HsH2A.Z.1 Arabidopsis leaf tissue (third and/or fourth pair of rosette leaves)

first: Paja

last: Sijacic

first: Dylan

last: Holder

first: Ellen

middle: G

last: Krall

first: Courtney

last: Willett

first: Maryam

last: Foroozani


title: Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development

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

overall_design: Refer to individual Series


title: Myeloid-specific ferritin light chain deletion does not confer renal protection in sepsis-associated acute kidney injury

city: Birmingham

first: SUBHASHINI

last: BOLISETTY

state: AL

address: 1918 University Blvd,, MCLM 523

institute: University of Alabama at Birmingham

summary: Sepsis-associated acute kidney injury (SA-AKI) is a key contributor to the life threatening sequalae attributed to sepsis. Mechanistically, SA-AKI is a consequence of unabated myeloid cell activation and oxidative stress that induces tubular injury. Iron mediates inflammatory pathways directly and through regulating the expression of myeloid-derived ferritin, an iron storage protein comprised of ferritin light (FtL) and ferritin heavy chain (FtH) subunits. Previous work revealed myeloid FtH deletion leads to a compensatory increase in intracellular and circulating FtL and is associated with amelioration of SA-AKI. We designed this study to test the hypothesis that loss of myeloid FtL and subsequently, circulating FtL will exacerbate the sepsis-induced inflammatory response and worsen SA-AKI. We generated a novel myeloid-specific FtL knockout mouse (FtLLysM-/-) and induced sepsis via cecal ligation and puncture or lipopolysaccharide endotoxemia. As expected, serum ferritin levels were significantly lower in the knockout mice, suggesting that myeloid cells dominantly contribute to circulating ferritin. Interestingly, while sepsis induction led to a marked production of pro- and anti-inflammatory cytokines, there was no statistical difference between the genotypes. There was a similar loss of kidney function, as evident by a rise in serum creatinine and cystatin C, and renal injury identified by expression of kidney injury molecule-1 and neutrophil gelatinase associated lipocalin. Finally, RNA sequencing revealed upregulation of pathways for cell cycle arrest and autophagy post-sepsis, but no significant differences were observed between genotypes, including in key genes associated with ferroptosis, an iron-mediated form of cell death. The loss of FtL did not impact sepsis-mediated activation of NFkB or HIF-1a signaling, key inflammatory pathways associated with dysregulated host response. Taken together, while FtL overexpression was shown to be protective against sepsis, loss of FtL did not influence sepsis pathogenesis.

overall_design: All mice were on the C57/BL6 background.  Male wildtype or FtL deletion mice were unstressed (baseline) or administered LPS at a dose of 8 mg/kg BW. 24 hours after injection, samples were collected and analyzed.

first: Subhashini

last: Bolisetty

first: James

middle: D

last: Odum

first: Juheb

last: Akhter


title: Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (WT, h2a.z, h2a.z + AtHTA11 RNA-Seq)

overall_design: RNA-seq from total RNA of the following plants: WT, h2a.z, h2a.z + AtHTA11. For h2a.z plants, aboveground tissue from three different plants was harvested and individually processed to extract total RNA. For all other genotypes, five individual leaves (third or fourth pair of rosette leaves) were collected from 5 different plants. The leaves were ground in liquid nitrogen and split into three equal replicates to extract total RNA.


title: Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (WT, h2a.z + HsH2A.Z. RNA-Seq)

overall_design: RNA-seq from total RNA of the following plants: WT, h2a.z + HsH2A.Z. Five individual leaves (third or fourth pair of rosette leaves) were collected from 5 different plants. The leaves were ground in liquid nitrogen and split into three equal replicates to extract total RNA.


title: Distinct metabolic responses to heme in inflammatory human and mouse macrophages - Role of nitric oxide

city: Hannover

first: Stephan

last: Immenschuh

state: Deutschland

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine and Transplant Engineering

institute: Hannover Medical School

summary: Activation of inflammation is tightly associated with metabolic reprogramming in macrophages. The iron-containing tetrapyrrole heme can induce pro-oxidant and pro-inflammatory effects in murine macrophages, but has been associated with polarization towards an anti-inflammatory phenotype in human macrophages. In the current study, we compared the regulatory responses to heme and the prototypical Toll-like receptor (TLR)4 ligand lipopolysaccharide (LPS) in human and mouse macrophages with a particular focus on alterations of cellular bioenergetics. In human macrophages, bulk RNA-sequencing analysis indicated that heme led to an anti-inflammatory transcriptional profile, whereas LPS induced a classical pro-inflammatory gene response. Co-stimulation of heme with LPS caused opposing regulatory patterns of inflammatory activation and cellular bioenergetics in human and mouse macrophages. Specifically, in LPS-stimulated murine, but not human macrophages, heme led to a marked suppression of oxidative phosphorylation and an up-regulation of glycolysis. The species-specific alterations in cellular bioenergetics and inflammatory responses to heme were critically dependent on the availability of nitric oxide (NO) that is generated in inflammatory mouse, but not human macrophages. Accordingly, studies with an inducible nitric oxide synthase (iNOS) inhibitor in mouse, and a pharmacological NO donor in human macrophages, reveal that NO is responsible for the opposing effects of heme in these cells. Taken together, the current findings indicate that NO is critical for the immunomodulatory role of heme in macrophages.

overall_design: To assess the comparative effects of heme and LPS on RNA expression, bulk transcriptomics was performed in human monocyte-derived macrophages (hMDMs) from four individual donors treated with either heme or LPS

first: Pooja

last: Pradhan

first: Vijith

last: Vijayan

first: Bin

last: Liu

first: David

last: DeLuca

first: Christoph

last: Nikolin

first: Robert

last: Greite

first: Beatriz

last: Martinez-Delgado

first: Sabina

last: Janciauskiene

first: Roberto

last: Motterlini

first: Roberta

last: Foresti


title: RNA-seq expression analysis of liver, adipose, skeletal muscle, heart, and pancreatic islets from DO founder strain mice fed high-fat, high-sugar diet. [liver]

first: Gary

last: Churchill

middle: A

first: Candice

last: Baker


title: A Lactate-induced SREBF2-dependent genetic program drives an immunotolerant dendritic cell population during cancer progression [scRNAseq_mouse]

city: Durham

first: Brent

last: Hanks

state: North Carolina

address: 308 Research Dr

department: Medicine

institute: Duke University

summary: Dendritic cells (cDCs) are essential mediators of anti-tumor immunity. Cancers have developed mechanisms to render DCs dysfunctional within the tumor microenvironment. Utilizing CD63 as a unique surface marker, we demonstrate that mature regulatory DCs (mregDCs) suppress DC antigen cross-presentation while driving TH2 and regulatory T cell differentiation within tumor-draining lymph node tissues. Transcriptional and metabolic studies show that mregDC functionality is dependent upon the mevalonate biosynthetic pathway and the master transcription factor, SREBP2. Melanoma-derived lactate activates DC SREBP2 in the tumor microenvironment (TME) and drives mregDC development from conventional DCs. DC-specific genetic silencing and pharmacologic inhibition of SREBP2 promotes anti-tumor CD8+ T cell activation and suppresses melanoma progression. CD63+ mregDCs reside within the sentinel lymph nodes of melanoma patients. Collectively, this work describes a tumor-driven SREBP2-dependent program that promotes CD63+ mregDC development and function while serving as a promising therapeutic target for overcoming immune tolerance in the TME.

overall_design: scRNAseq of dendritic cells (DCs) sorted from the tumor draining lymph node or non-draining lymph node of Tyrosinase-driven Cre Recombinase BRAFV600E, PTEN-/- mice on a C57Bl6 background, as well as Dcs sorted from the inguinal lymph node of non-tumor bearing wildtype mice. Additionally, scATACseq was performed on DCs sorted from the tumor draining lymph node of Tyrosinase-driven Cre Recombinase BRAFV600E, PTEN-/- mice. scRNAseq was also performed on dendritic cells sorted from the sentinel lymph node of human melanoma patients in addition to spatial transcriptomics of the sentinel lymph node of human melanoma patients.

first: Michael

last: Plebanek

first: Yue

last: Xue

first: Y-Van

last: Nguyen

first: Nicholas

middle: C

last: DeVito

first: Xueying

last: Wang

first: Alisha

last: Holtzhausen

first: Georgia

middle: M

last: Beasley

first: Balamayooran

last: Theivanthiran


title: A Lactate-induced SREBF2-dependent genetic program drives an immunotolerant dendritic cell population during cancer progression [scRNAseq_human]

middle: P


title: A Lactate-induced SREBF2-dependent genetic program drives an immunotolerant dendritic cell population during cancer progression


title: A Lactate-induced SREBF2-dependent genetic program drives an immunotolerant dendritic cell population during cancer progression [scATAC-seq]


title: A Lactate-induced SREBF2-dependent genetic program drives an immunotolerant dendritic cell population during cancer progression [Spatial transcriptomics]


title: Vegetable omega-3 and omega-6 fatty acids differentially modulate the antiviral and antibacterial immune responses of Atlantic salmon

city: St. John's

first: Albert

last: Caballero Solares

state: NL

address: 0 Marine Lab Road

department: Ocean Sciences

institute: Memorial University of Newfoundland

summary:
This study explored how the omega-6 to omega-3 fatty acid ratio in low-fish oil aquafeeds influences Atlantic salmon's antiviral and antibacterial immune responses. Atlantic salmon were fed aquafeeds rich in soy oil (high in omega-6) or linseed oil (high in omega-3) for 12 weeks and then challenged with bacterial (formalin-killed Aeromonas salmonicida; Asal) or viral-like (polyriboinosinic polyribocytidylic acid; pIC) antigens.
The mRNA levels of 46 immune-relevant genes in the head kidneys of the salmon were analyzed via quantitative real-time polymerase chain reaction (RT-qPCR).

overall_design: RT-qPCR profiling. Total RNA samples from Atlantic salmon fed two different experimental diets, intraperitoneally injected with either phosphate-buffered saline (PBS), a bacterin (Asal), or a viral mimic (pIC), and sampled at 6 and 24 h post-injection.

last: Caballero-Solares

first: Khalil

last: Eslamloo

first: Jennifer

middle: R

last: Hall

first: Tomer

last: Katan

first: Mohamed

last: Emam

first: Xi

first: Richard

last: Taylor

first: Christopher

last: Parrish

first: Matthew

middle: L

last: Rise


title: Batf3-dendritic cells and 4-1BB/4-1BB ligand axis are required at the effector phase within the tumor microenvironment for PD-1/PD-L1 blockade efficacy

city: Chicago

first: Thomas

last: Gajewski

state: IL

address: 929 E 57th St

institute: University of Chicago

summary: The cellular source of positive signals that reinvigorate T cells within the tumor microenvironment (TME) for the therapeutic efficacy of PD-1/PD-L1 blockade has not been clearly defined. We now show that Batf3-lineage dendritic cells (DCs) are essential in this process. Flow cytometric analysis, gene-targeted mice, and blocking antibody studies revealed that 4-1BBL was a major positive costimulatory signal provided by these DCs within the TME, that translated to CD8+ T cell functional reinvigoration and tumor regression. Immunofluorescence and spatial transcriptomics on human tumor samples revealed clustering of Batf3+ DCs and CD8+ T cells, which correlated with anti-PD-1 efficacy.  In addition, proximity to Batf3+ DCs within the TME was associated with CD8+ T cell transcriptional states linked to anti-PD-1 response. Our results demonstrate that Batf3+ DCs within the TME are critical for PD-1/PD-L1 blockade efficacy, and indicate a major role for the 4-1BB/4-1BBL axis during this process.

overall_design: Spatial transcriptomics (Visium, 10X) was performed on two primary invasive bladder carcinoma samples (B1 and B5) and ten additional primary invasive bladder carcinoma samples at higher resolution (Visium CytAssist, 10X). Samples B12 and B13 were sequenced in the same capture area. These samples were separated based on the tissue coordinates in R. Samples B17 and B18 were obtained from the same tumors as samples B5 and B1, respectively, and were also placed in the same capture area. These data were separated using non-overlapping alignments generated with the Loupe Browser (10X). With the aim to understand how close proximity to Batf3-lineage dendritic cells (DC1s) affect the CD8+ T cells in the tumor microenvironment, the data were used to compare the transcriptome of the spots that contained CD8+ cells (CD8A or CD8B and CD3) that were close or distant from spots that contained DC1s (Batf3, Clec9A or XCR1 and ITGAX).

first: Andrea

last: Ziblat

first: Brendan

last: Horton

first: Emily

middle: F

last: Higgs

first: Ken

last: Hatogai

first: Anna

last: Martinez

first: Danny

last: Kim

first: Jason

middle: W

last: Shapiro

first: Randy

last: Sweis


title: Comprehensive mRNA-sequencing-based characterization of three HEK-293 cell lines during an rAAV production process for Gene Therapy Applications

city: Orth and der Donau

first: Carolin Isabel

last: Kahlig

address: Uferstrasse 15

country: Austria

institute: Takeda

summary:
Human embryonal kidney cells (HEK-293) are the most common host cells used for transient recombinant adeno-associated virus (rAAV) production in pharmaceutical industry. To better cover the expected gene therapy product demands in the future, different traditional strategies such as cell line sub-cloning and/or addition of chemical substances to the fermentation media have been used to maximize titers and improve product quality. A more effective and advanced approach to boost yield can be envisaged by characterizing the transcriptome of different HEK-293 cell line pedigrees with distinct rAAV productivity patterns to subsequently identify potential gene targets for cell engineering. In this work, the mRNA expression profile of three HEK-293 cell lines, resulting in various yields during a fermentation batch process for rAAV production, was investigated to gain basic insight into cell variability and eventually to identify genes that correlate with productivity. Mock runs using only transfection reagents were performed in parallel as a control. We found significant differences in gene regulatory behaviors between the three cell lines at different growth and production stages. The evaluation of these transcriptomics profiles combined with collected in-process control parameters and titers shed some light on potential cell engineering targets to maximize transient production of rAAV in HEK-293 cells
Comparison of three HEK-293 suspension cell lines transcriptomics during an AAV production process

overall_design: Two factor design over time: the two factors are the cell line and the transfection status. 4 Biological replicates per condition.

first: Martina

last: Pistek

first: Carolin

first: Juan

middle: H

last: Bort