title: Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [ChIP-seq]

overall_design: Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) for PDS5A, PDS5B, cohesin and CTCF in cells mocked depleted or depleted of PDS5A/B


title: Single-Cell RNA-Sequencing reveals cellular heterogeneity and trajectories of lineage specification of mammary basal epithelial cells of WT and Fgd5-depeleted mice

status: Public on Oct 08 2022

city: Beijing

first: Tingting

last: Zhang

address: 1 Xian Nong Tan Street

country: China

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College

type: Expression profiling by high throughput sequencing

summary: We report the application of Single-Cell RNA-Sequencing technology for high-throughput profiling in mammary basal epithelial cells of WT and Fgd5-depeleted mice. By obtaining basal epithelial cells isolated from mammary gland of WT and Fgd5-depeleted mice, we performed Single-Cell RNA-Sequencing of basal epithelial cells. The scRNA-Seq libraries were prepared with Single Cell 3′ Reagent Kit v2 (10×Genomics) following the user guide provided. We found that FGD5 promotes mammary development by maintaining LGR5/SLPI/ID3 positive basal cell subsets.. We conclude that Single-Cell RNA-Sequencing would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Two samples from mammary basal epithelial cells of WT and Fgd5-depeleted mice

first: Ke

last: Li

first: Bing

last: Cui

first: Chenxi

last: Zhao


title: Effect of time-course forskolin (FSK) treatment versus rosiglitazone (Rosi) treatment on the chromatin accessibility landscape in a new immortalized mouse adipocyte progenitor (MAP) cell line (ATAC-Seq).

city: Indianapolis

first: Jisun

last: So

state: IN

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

country: USA

institute: Indiana University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
To investigate how the chromatin accessibility landscape is altered during biphasic FSK-induced browning in comparison with single-phase Rosi-induced browning,
We performed chromatin lanscape profiling using the nuclei sorted from MAP cells treated with vehicle (Control) or with FSK for mulitple time durations (4 hours, 1 day, or 3 days) or with Rosi for 3 days.

overall_design: Comparative chromatin accessibility profiling analysis of ATAC-seq data for MAP cells treated with vehicle, FSK 4h, FSK 1D, FSK 3D, and Rosi 3D (2 replicates per group).

first: Hyun

middle: C

last: Roh

first: Solaema

last: Taleb


title: Effect of time-course forskolin (FSK) treatment versus rosiglitazone (Rosi) treatment on the chromatin accessibility landscape in a new immortalized mouse adipocyte progenitor (MAP) cell line

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

overall_design: Refer to individual Series


title: Effect of time-course forskolin (FSK) treatment versus rosiglitazone (Rosi) treatment on gene expression in a new immortalized mouse adipocyte progenitor (MAP) cell line (RNA-Seq).

summary:
To characterize biphasic adipocyte browning induced by chronic FSK treatment and compare this process to Rosi-induced browning,
We performed gene expression profiling using MAP cells treated with vehicle or with FSK for mulitple time durations (4h, 1D, and 3D) or with Rosi for 3D.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MAP cells treated with vehicle, FSK 4h, FSK 1D, FSK 3D, and Rosi 3D (3 replicates per group).


title: SMAD2/3 mediate oncogenic effects of TGF-β in the absence of SMAD4

status: Public on Oct 09 2022

city: LYON

first: Laurent

last: Bartholin

state: AUVERGNE-RHONE-ALPES

address: 28 RUE LAENNEC

country: France

institute: Centre de Recherche en Cancérologie de Lyon

summary: The tumor suppressive effects of TGF-β are classically associated with the activation of the “canonical” SMAD-mediated pathway, whereas its oncogenic effects are largely attributed to its “non-canonical signaling”. We herein provide evidence of an oncogenic effect for SMAD2 and 3 in response to TGF-β in SMAD4-null cancer cells. Using the CRISPR/Cas9 technology, we report that simultaneous knockout of Smad2 and 3 in Smad4-negative pancreatic ductal adenocarcinoma (PDAC) cells compromises TGF-β-driven collective migration mediated by FAK and Rho/Rac signaling. Moreover, RNA-sequencing analyses highlight a TGF-β gene signature related to aggressiveness mediated by SMAD2 and 3 in the absence of SMAD4. Using PDAC patients cohorts, we reveal that SMAD4-negative tumors with high levels of (phospho)-SMAD2 are more aggressive and have a poorer prognosis. Thus, loss of SMAD4 tumor suppressive activity in PDAC is associated with oncogenic gain-of-function of SMAD2 and 3 and the onset of associated deleterious effects.

overall_design: SMAD2 and SMAD3 were inactivated in BxPC3 cells via Crispr-Cas9. Control and KO cells were then divided in two groups (4 replicates in each group), one treated with TGFB and one not. The experiment was conducted for 1h or 24h of treatment.

first: Adrien

last: Bertrand-Chapel

first: Cassandre

last: Caligaris

first: Sophie

last: Aires

first: Clara

last: Savary

first: Sylvie

last: Martel

first: Tanguy

last: Fenouil

first: Laurie

last: Tonon

first: Alain

last: Mauviel

first: Stéphanie

last: Sentis


title: DNA polymerase epsilon interacts with SUVH2/9 to mediate meiotic DSB associated gene silencing beyond DNA methylation in Arabidopsis [RNA-seq]

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

summary: Meiotic recombination is initiated from the SPORULATION 11 (SPO11)-triggered formation of double strand breaks (DSBs) that usually occur in open chromatin with active transcriptional features in many eukaryotes. However, gene transcription at meiotic DSB sites appears to be detrimental for repair, and the mechanisms for gene silencing at DSB sites are largely undefined, especially in plants. Here, we demonstrate that the largest DNA polymerase epsilon subunit POL2A interacts with SU(VAR)3-9 homologs SUVH2 and SUVH9. N-SIM (Structured Illumination Microscopy) observation shows that the colocalization of SUVH2 with meiotic DSB marker γ- H2AX is dependent on POL2A. RNA-seq of male meiocytes identifies that POL2A and SUVH2 jointly repress the expression of 865 genes, which have several known characteristics associated with meiotic DSB sites. Bisulfite-seq and small RNA-seq of male meiocytes support the idea that the silencing of these genes by POL2A and SUVH2/9 is likely independent of CHH methylation or 24-nt siRNA accumulation. Consequently, pol2a suvh2 suvh9 triple mutants have more severe defects in meiotic recombination and fertility compared with either pol2a or suvh2 suvh9. Taken together, our results not only identify a new epigenetic regulatory mechanism for gene silencing in male meiocytes, but also reveal new roles for DNA polymerase and SUVH2/9 beyond their classic functions in mitosis.

overall_design: Examination of gene expression in meiocytes and seedlings of mutants, such as pol2a-1, suvh2 suvh9 etc, and wild type plants

first: Cong

last: Wang

first: Yingxiang


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT and WT+CXCL14 mouse endothelial cells' Transcriptomes in mammary gland

first: Tingting

last: Zhang

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in  WT and WT+CXCL14 mammary endothelial cells  by using NGS-derived transcriptome profiling (RNA-seq).
Methods:  Recombinant mouse CXCL14 protein in 50 μL of PBS (50μg/kg) was injected into the tail vein every 3 days for 2 weeks. The mice in the control group were treated with an identical volume of PBS. The mice were sacrificed by excessive anaesthesia 14 days after cytokine administration. Mammary glands of 6-week-old female virgin mice were harvested and single-cell suspension was obtained by Collagenase III-mediated digestion of minced tissue, followed by trypsin-EDTA and DNaseI sequential incubation before filtering through 70 μm cell strainers. The following antibodies in 1:200 dilutions were used: rat anti-mouse CD16/CD32, FITC-conjugated hematopoietic lineage cocktail, APC-conjugated CD31. All analysis and sorting were performed using a FACS Aria III sorter. The purity of sorted population was routinely checked and ensured to be > 95%. WT and WT+CXCL14 endothelial cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with  following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including  GO enrichment analysis and KEGG .
Conclusions: Our study represents the first detailed analysis of WT and WT+CXCL14 endothelial cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: WT and WT+CXCL14 cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Ke

last: Li

first: Bing

last: Cui

first: Chenxi


title: Comparative transcriptome analysis reveals critical genes/pathways related yolk precursor synthesis in  livers of Guangxi Ma chicken with different egg laying rate

city: Nanning

first: Liangfeng

last: Huang

state: Guangxi

address: No. 100, East University Road

department: Animal Reproduction Institute

institute: Guangxi University

summary: Liver tissues of Guangxi Ma chicken from 32-week old with m performance, 50-week old with high and low laying performance, and 72-week old with high and low laying performance were collected and sequenced in quadruplicate using RNA-seq. The sequences were double-ended sequenced on the DNBSEQ sequencing platform. The sequence reads were quality controlled and then aligned with genomic sequences using HISAT2 program, quantified by featureCounts program, and gene expression levels were verified by qRT-PCR with SYBR Green detection. The results will be helpful to explore the factors that affecting laying performance from the perspective of yolk synthesis and provide a theoretical basis for improving the egg production of Guangxi Ma chicken.

overall_design: Liver mRNA profiles of Guangxi Ma chicken at 32-week old (C32),  50-week old with high (C50WH) and low (C50WL) laying performance, 72-week old with high (C72WH) and low (C72WL) laying performance.

first: Hanxiao

last: Wu

first: Hu

first: Yuanyuan

last: Hou

first: Jianing

last: Hu

first: Lin

first: Yangqing

last: Lu

first: Xingting

last: Liu


title: Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [Hi-C]

first: Guoyu

last: Chen

address: Xuhui District Yueyang Road 320

institute: PICB

summary: Cohesin regulates sister chromatids cohesion but also contributes to chromosome folding by promoting the formation of chromatin loops, a process proposed to be mediated by loop extrusion. PDS5 plays a crucial role in regulating the cohesin dynamic on chromatin, mainly through WAPL-mediated release activity and the opponent ESCO1/2-sororin dependent pathway. However, the exact function of PDS5 on cohesin-mediated chromatin looping remains ambiguous. Two versions of PDS5 exist in vertebrates, PDS5A and PDS5B. Here, we construct cells for rapid PDS5A or PDS5B degradation in PLC/PRF/5 cell line with the FKBP12F36V-dTAG degron system to perform loss of function studies. Combining Hi-C, ChIP-seq for cohesin regulators, and RNA-seq data, we describe the redundant and discrete roles of PDS5A and PDS5B in three-dimensional genome organization and gene expression.

overall_design: In situ Hi-C experiments performed in PDS5A/B-dTAG cells with DMSO or dTAG treatment

first: Dingdang

last: Yu


title: Interferon-gamma signaling promotes melanoma progression and metastasis

city: Sugar Land

first: Kumaraswamy Naidu

last: Chitrala

state: TX

address: 13850 University Blvd, SAB1 Room No: 214

department: Engineering Technology

institute: College of Technology, University of Houston

summary:
To investigate the effect of Interferon-gamma signaling on gene expression in melanoma cells
We performed gene expression analysis of mouse melanoma cell lines that have been treated with Interferon-gamma cytokine as compared with mock-treated controls.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for B16 and YUMM1.1 mouse melanoma cells exposed to 10 ng/ml recombinant mouse IFN-gamma for 48 hours in culture as compared to untreated control cells.

first: Bo

last: Zhou

first: Chitrala

last: Kumaraswamy Naidu

first: M

last: Raza Zaidi


title: Regulation of cohesin-mediated chromosome structure by PDS5 in mammals


title: Histone methylation antagonism drives tumor immune evasion in squamous cell carcinomas

city: New York

first: Chao

state: New York

address: 1130 Saint Nicholas Ave

department: Genetics & Development

institute: Columbia University Medical Center

summary: This work uncovers a druggable chromatin crosstalk that defines tumor innate immune response and enables immune evasion.

overall_design: 20 RNA-seq samples; 14 CUT&Tag samples

first: Yinglu

first: Elizabeth

middle: M

last: Goldberg

first: Xiao


title: Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation

city: Peking

first: Zhuoning

last: Zou

address: 30 Shuangqing Rd

department: School of Life Sciences

institute: Tsinghua University

summary: Translational regulation plays a critical role during oocyte-to-embryo transition including zygotic genome activation. However, the translatome during OET and molecular mechanisms underlying human ZGA remain largely uncharted. Here, we integrated ultra-low-input Ribo-seq with RNA-seq (R2-lite) to jointly profile the translatome and transcriptome from the same samples across 8 stages in human oocytes and early embryos. These data not only unveil conservation and divergence of the translation landscapes between human and mouse OET, but also identify critical regulators of human ZGA.

overall_design: Ultra-low-input Ribo-seq(Ribo-lite) with RNA-seq (R2-lite) was performed on human oocytes and early embryos. RNA-seq was performed on human embryos with knockdown of transcription factors or under drug treatment.  RNA-seq and Stacc-seq were performed on hESC overexpressing transcription factors.

first: Chuanxin

first: Qiuyan

last: Wang

first: Zhenzhen

first: Han

last: Zhao

first: Zi-Jiang

first: Wei

last: Xie


title: Evolution of hypervirulence during bloodstream adaptation of CA-MRSA strain USA300

first: Harm

middle: van

last: Bakel

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: The epidemic community-acquired methicillin-resistant S. aureus (CA-MRSA) clone USA300 has recently become a leading cause of hospital-associated bloodstream infections (BSI). Leveraging this recent introduction into hospitals and the limited genetic variation across the USA300 strains, we combined microbial comparative genomics with phenotypic analyses to discover adaptive mutations. USA300 isolates from BSI were found to have independently evolved single nucleotide variants in the transcriptional regulator sarZ. sarZ inactivation lead to altered expression of virulence factors, resulting in increased lethality in a murine model of BSI. Thus, USA300 strains can optimize their fitness in hospitals through evolution of higher virulence.

overall_design: To establish the SarZ regulon in the USA300 background we performed RNA-Seq experiments in sarZ wild-type, mutant and complement strains during logarithmic or stationary growth. The laboratory-constructed strains AH-LAC + vector, AH-LAC sarZ::bursa + vector, and AH-LAC sarZ::bursa + sarZWT were used. In addition we selected two clinical USA300 bloodstream infection (BSI) isolates with a wild-type (ER00573) and mutant sarZ locus (ER00594), and constructed sarZ deletion (sarZ::tet) and complement strains. Each strain was profiled, in triplicate, after culturing for 3h (logarithmic growth) and 5h (stationary phase) in 5mL tryptic soy broth (TSB).

first: Sophie

last: Dyzenhaus

first: Mitchell

middle: J

last: Sullivan

first: Bremy

last: Alburquerque

first: Adriana

last: van de Guchte

first: Marilyn

last: Chung

first: Yi

last: Fulmer

first: Richard

last: Copin

first: Juliana

middle: K

last: Ilmain

first: Anna

last: O’Keefe

first: Deena

middle: R

last: Altman

first: François-Xavier

last: Stubbe

first: Amy

last: Dupper

last: Shopsin

last: van Bakel

first: Victor

last: Torres


title: CEBPB-dependent transcriptome in NRF2-activated non-small cell lung cancer cell line A549 [RNA-seq]

city: Sendai

first: Hozumi

last: Motohashi

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University

summary: CEBPB was knocked down in A549 cells, and transcriptomic alterations were examined.

overall_design: RNA-seq analysis of A549 cells after CEBPB knockdown in two alternative siRNAs or control siRNA transfection

first: Keito

last: Okazaki

first: Hayato

last: Anzawa

first: Fumiki

last: Katsuoka

first: Kengo

last: Kinoshita

first: Hiroki

last: Sekine


title: CEBPB-dependent enhancer formation in NRF2-activated non-small cell lung cancer cell line A549 [ChIP-seq]

summary: CEBPB was knocked down in A549 cells, and H3K27ac deposition were examined.

overall_design: ChIP-seq analysis of H3K27ac antibody in A549 cells after CEBPB knockdown using two alternative siRNAs or control siRNA transfection


title: Transcriptome analysis of Bifidobacterium adolescentis P2P3 cultivated with resistant starch

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

summary: RNA-seq based transcriptome analysis was employed to understand the genome-wide expression patterns under cultivation with resistant starch (RS). To identify differentially expressed genes, we compared RS-induced transcriptome to non-RS transcriptome as sole carbon source.

overall_design: Eight libraries constructed: Each two replicates of growth conditions (GLC, SS, GRS, and RS ) in Bifidobacterium adolescentis P2P3

first: Dong-Hyun

last: Jung

first: Hyun-Hee

last: Lee

first: Young-Su

last: Seo

first: Cheon-Seok


title: RNA-seq analysis of the effect of overexpression of DsrA at 42°C on the transcriptome of E. coli wild-type and ∆dps strains

status: Public on Oct 07 2022

city: Hohhot

first: Jiaxin

last: Qiao

address: Zhao Jun road

institute: Inner mongolia university

summary: The bacteria were cultured in ABTG-CAA medium at 42°C until OD450=0.15-0.2. Cells were harvested for total RNA extraction and subsequent RNA-seq. Differential expression of various conditions was analyzed.

overall_design: RNA-seq contributor: Morigen

first: Weiwei

last: Zhu

first: Morigen

last: Morigen


title: Differentially expressed genes related to lymph node metastasis in advanced laryngeal squamous cell cancers

city: ANKARA

first: Ömer

last: Bayır

address: Gölbaşı

country: Turkey

institute: University of Health Sciences

summary: Understanding the molecular mechanisms and gene expression in laryngeal squamous cell carcinoma (LSCC) may explain its aggressive biological behavior and regional metastasis pathways. Better understanding of the molecular mechanisms underlying LSCC metastasis and the search for possible molecular targets seems promising. Interpreting the links between the differentially expressed genes in advanced stages can lead to a search for predictive markers that can also help determine the possible treatment routes. We designed this study to detect possible genetic alterations in a homogeneous group of patients with locoregionally advanced laryngeal cancer who underwent total laryngectomy and neck dissection. Patients with and without lymph node metastasis were selected to examine the differential gene expression in the normal mucosa, tumor, and lymph node tissues of each patient. Our main purpose was to identify the possible commonly expressed genes in this homogenous group of Turkish patients with locoregionally advanced laryngeal cancer. Second, we aimed to determine the predictive role of these genes in lymph node metastasis and overall prognosis.

overall_design: A total of 16 patients who had undergone total laryngectomy with neck dissection for advanced LSCC were randomly selected from our database: eight patients had lymph node metastasis (Group 1) and the other eight patients had no metastasis (Group 2). For each patient, paraffin-embedded tissue samples were collected from non-tumoral mucosa, tumoral lesions, and lymph node tissues. These tissue samples were used to extract RNA after cDNA synthesis, and microarray analysis was subsequently performed on each sample. Genetic alterations were determined in each specimen, and Groups 1 and 2 were compared and statistically analyzed.

first: Mehmet

middle: D

last: Aşık


title: Alcohol reverses the effects of KCNJ6 (GIRK2) noncoding variants on excitability of human glutamatergic neurons

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Synonymous and noncoding single nucleotide polymorphisms (SNPs) in the KCNJ6 gene, encoding G protein-gated inwardly rectifying potassium (GIRK2) channel subunit 2, have been linked with increased electroencephalographic frontal theta event-related oscillations (ERO) in subjects diagnosed with alcohol use disorder (AUD). To identify molecular and cellular mechanisms while retaining the appropriate genetic background, we generated induced excitatory glutamatergic neurons (iN) from iPSCs derived from four AUD-diagnosed subjects with KCNJ6 variants (‘Affected: AF’) and four control subjects without variants (‘Unaffected: UN’). Neurons were analyzed for changes in gene expression, morphology, excitability and physiological properties. Single cell RNA sequencing suggests that KCNJ6 AF variant neurons have altered patterns of synaptic transmission and cell projection morphogenesis. Results confirm that AF neurons express lower levels of GIRK2, have greater neurite area, and elevated excitability. Interestingly, exposure to intoxicating concentrations of ethanol induces GIRK2 expression and reverses functional effects in AF neurons. Ectopic overexpression of GIRK2 alone mimics the effect of ethanol to normalize induced excitability. We conclude that KCNJ6 variants decrease GIRK2 expression and increase excitability and that this effect can be minimized or reduced with ethanol.

overall_design: Pooled cultures of excitatory human neurons cultured on primary mouse glia were harvested and run through the 10X Genomics Chromium device for scRNAseq.  Each pool mixed cells from four subjects, with one group (first character of sample name=C, control) having major-allele KCNJ6 haplotype and the other group (first character of sample name=A, affected) with minor-allele haplotype.  One set of cultures from each group was exposed to intermitent ethanol (20 mM, 7 days; second character=7) and the other was untreated ( second character=C, control).  Libraries were prepared using the 10X Genomics 3' GEM Reagent Kit v3.1. After aligning reads with a mixed human and mouse reference index in cellranger, and merging samples in Seurat, mouse-specific clusters were removed, leaving only human cell data for analysis. Cells from individual subjects were identified using SNP profiles and demuxlet.

first: Dina

last: Popova

first: Petronio

last: Zalamea

first: Azadeh

last: Jadali

first: Kelvin

middle: Y

last: Kwan

middle: P


title: RNAseq of Bone Marrow-Derived Macrophages (BMDMs)

city: shanghai

first: shanshan

last: zhong

address: 320 Yueyang Rd

institute: Chinese Academy of Sciences (CAS)

summary: RNAseq for BMDMs (LKO and DKO)

overall_design: 6 samples include 3 samples (LKO) are control

first: Huiyong

last: Yin

first: Shanshan

last: Zhong


title: Arraystar Human m6A-mRNA&lncRNA Epitranscriptomic microarray analysis in adenomyosis and non-adenomyosis patients

status: Public on Oct 06 2022

city: Zhengzhou

first: Yan

last: Zhang

state: Henan

address: No. 1 Jianshe East Road, Erqi District

department: Department of Gynecology

institute: The First Affiliated Hospital of Zhengzhou University

summary: Adenomyosis mostly occurs in the females with reproductive age, and the pathogenesis is not clear. If we want to improve the diagnosis and treatment of adenomyosis, we must fully understand the specific molecular mechanism of adenomyosis. The Arraystar Human m6a-mRNA&lncRNA Epitranscriptomic microarray analysis was performed on endometrial specimens of 3 patients in the human adenomyosis group and 3 patients in the normal control group to compare and screen the m6A marker of adenomyosis, providing reference for clinical treatment.

overall_design: All  volunteers  were divided into 2 groups: Adenomyosis  group(adenomyosis patients) and Control group(non-adenomyosis patients), each containing 3 patients.

first: Liping

last: Han


title: Mutation in LBX1/Lbx1 precludes transcription factor cooperativity and causes congenital hypoventilation in humans and mice

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

country: Germany

institute: Berlin Institute of Health

summary: The respiratory rhythm is generated by the preBötzinger complex in the medulla oblongata, and is modulated by neurons in the retrotrapezoid nucleus (RTN), which are essential for accelerating respiration in response to high CO2. Here we identify a LBX1 frameshift (LBX1FS) mutation in patients with congenital central hypoventilation. The mutation alters the C-terminal but not the DNA-binding domain of LBX1. Mice with the analogous mutation recapitulate the breathing deficits found in humans. Furthermore, the mutation only interferes with a small subset of Lbx1 functions, and in particular with development of RTN neurons that coexpress Lbx1 and Phox2b. Genome-wide analyses in a cell culture model show that Lbx1FS and wild-type Lbx1 proteins are mostly bound to similar sites, but that Lbx1FS is unable to cooperate with Phox2b. Thus, our analyses on Lbx1FS (dys)function reveals an unusual pathomechanism; that is, a mutation that selectively interferes with the ability of Lbx1 to cooperate with Phox2b, and thus impairs the development of a small subpopulation of neurons essential for respiratory control.

overall_design: ChIP-seq of retinoic acid induced P19 cells expressing virally expressed Lbx1wt or Lbx1-frameshift constructs

first: Luis

last: Hernandez-Miranda

first: Carmen

last: Birchmeier


title: Functional effects on HUVEC of CD63+ and MHC class 1+ subsets of extracellular vesicle produced by wild type and CD47-deficient T cells

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

institute: nih

summary: The present study revealed that CD63+ and MHC-1+ EVs from CD47-deficient T cells are enriched in small non-coding RNAs relative to the respective EVs from WT cells. CD47-deficient T cells secrete more CD63+ and MHC-1+ EVs, but MHC-1+ EVs are selectively taken up more by human umbilical vein endothelial cells. Microarray analysis of endothelial cells treated with CD63+ or MHC-1+ EVs showed surface marker- and CD47-dependent changes in gene expression in the target cells. Gene set enrichment analysis identified CD47-dependent and surface marker-dependent effects of T cell EVs on VEGF and inflammatory signaling, cell cycle, and on lipid and cholesterol metabolism. Thus, subsets of T cell EVs differentially regulate endothelial cell metabolism and inflammatory and angiogenic responses.

overall_design: HUVEC (ATCC) were co-cultured with immunocaptured CD63+ and MHC-1+ EVs or control beads alone from Jurkat and JinB8 T cells for 3 days. The total RNA was extracted using miRNA easy kit equal amount of RNAs was subjected to global microarray analyses

first: A

middle: G

last: Elkahloun

first: Sukhbir

last: Kaur

first: David

last: Roberts


title: KCNJ6 variants associated with alcohol use disorder (AUD) in human induced neurons

first: Ronald

last: Hart

summary: Noncoding SNP variants in KCNJ6 have been linked with increased risk of alcohol use disorder (AUD) and the endophenotype EEG frontal theta event related oscillation (ERO) power.  We prepared iPSC from subjects with contrasting diagnosis of AUD and KCNJ6 variants (AF, affected) or unaffected with reference KCNJ6 (UN).  Induced neurons cultures were prepared from each iPSC line and harvested for RNAseq analysis.  In these bulk RNAseq analyses, we do not identify meaningful differences by KCNJ6 haplotype, we we can validate expression of the long (18kb) 3'UTR from the KCNJ6 gene, and identify several additional SNPs linked with the original three.  Additional studies used single cell RNAseq to isolate differentiated neurons from iN cultures and analysis of these samples found differences in neuron process formation and synaptic function, which were validated with morphometrics, immunocytochemistry, and electrophysiology.

overall_design: Unbiased RNA sequencing was performed on iPSC-derived human induced neurons (iN) from two groups: AF having a variant KCNJ6 haplotype associated with alcohol use disorder (AUD) and diagnosed with AUD, and UN having reference allele KCNJ6 haplotype and diagnosed with no AUD.

first: Mavis

last: Swerdel


title: NSUN2-mediated 5-methylcytosine enhances purine metabolism through ALYREF in retinoblastoma

first: Sipeng

last: Zuo

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary: 5-methylcytosine (m5C) RNA modification installed  by methyltransferase NSUN2 regulates gene expression and cell fate. Retinoblastoma (RB) is the most common primary intraocular tumor in children. However, the functional role of m5C modification in retinoblastoma remains unclear. Here, we show that 5-methylcytosine significantly promotes the progression of  retinoblastoma.  Retinoblastoma samples showed increased m5C levels, indicating a poor prognosis. Changes in global m5C modification were highly associated with tumor progression in vitro and in vivo. Mechanistically, NSUN2 stabilized the methylated PFAS mRNA, a tumor promoter in retinoblastoma. Our work uncovers a critical function for m5C methylation in retinoblastoma and provides additional insight into the understanding of  m5C modification.

overall_design: RNA-seq and MeRIP-seq for retinoblastoma cell lines (Y79) and one retina pigment epithelium cell line (ARPE-19)

first: Lin

last: Li

first: Peiwei

last: Chai

first: Linna

last: Lu

first: Xianqun

last: Fan


title: Growth in a multispecies biofilm results in remodelling of central metabolism

city: Singapore

first: Xianghui

last: Liu

address: 60 Nanyang Drive, SBS-01N-27

country: Singapore

institute: Nanyang Technological Univ. of Singapore

summary: Multispecies biofilms are the predominant form of bacterial growth in natural and human-associated environments. Although the pathways involved in monospecies biofilm have been well characterized, less is known about the metabolic pathways and emergent traits of a multispecies biofilm community. Here, we performed a transcriptome survey of the developmental stages of a 3-species biofilm community and combined it with quantitative imaging and growth experiments. We report the remodelling of central metabolism of two of the three species in this community. Specifically, we observed an increase in the expression of genes associated with glycolysis and pentose phosphate pathways in K. pneumoniae. Similarly, a decrease in the expression of the same pathways in P. protegens was observed along with an increase in expression of glyoxalate cycle genes when grown as a mixed species biofilm, suggesting reorganisation of metabolic pathways and metabolite sharing for the community biofilms. To test the possibility of cross-feeding for the community, planktonic growth experiments revealed that both the Pseudomonads grew well in TCA cycle intermediates, while K. pneumoniae grew poorly when given those carbon sources. Despite this poor growth in mono-culture, K. pneumoniae was still the dominant species in mixed species biofilms cultivated in TCA intermediates as the sole source of carbon. The biofilm growth data, combined with the transcriptomics data, suggests there is reorganisation of metabolism for the community members and may allow for cross-feeding that allows K. pneumoniae to dominate the community. We also demonstrated that sdsA1 of P. aeruginosa was induced upon exposure to the surfactant SDS and that this gene was essential in protecting mono and mixed species biofilms from surfactant stress. This also suggests that the community members can share defence mechanisms. Overall, this study describes a comprehensive transcriptomics level investigation of shared resources, metabolites and stress defence that may underpin the emergent properties of mixed species biofilm communities.

sample_organism:
Pseudomonas aeruginosa PAO1
Pseudomonas protegens Pf-5
Klebsiella pneumoniae KP-1

overall_design: Comparative gene expression profiling analysis of RNA-seq data for single, mixed species and SDS treatment.

first: Kai

last: Lee

first: Sujatha

last: Subramoni

first: Harikrishnan

middle: S

last: Nair

first: Krithika

last: Arumugam

first: Rikky

middle: W

last: Purbojati

first: Daniela

last: Moses

first: Stephan

last: Schuster

first: Staffan

last: Kjelleberg

first: Rohan

middle: H

last: Williams

first: Scott

middle: A

last: Rice


title: Profiling the intragenic toxicity determinants of the hok/Sok toxin-antitoxin system

city: Bordeaux

first: Nicolas

middle: J.

last: Tourasse

address: 146 rue Leo Saignat

department: INSERM U1212, CNRS UMR5320

institute: University of Bordeaux

summary: Here, we adapted and improved our FASTBAC-Seq method originally designed in Helicobacter pylori to investigate T1TAs in the model organism Escherichia coli. Our approach combines a life and death selection with deep-sequencing to assess the killing capability of a toxin and obtain an overview of single-nucleotide substitutions suppressing the toxin expression or activity in absence of its antitoxin.  As a proof of concept, we revisited the regulation of the plasmidic hok/Sok T1TA system.

overall_design: Amplicon DNA sequencing of bacterial strains transformed with mutated PCR libraries of the hok/Sok toxin-antitoxin system, either a wild-type hok/Sok locus, a hok/Sok locus with a mutated Sok promoter, or a hok/Sok locus with mutated hok and Sok promoters. Five biological replicates were sequenced for each PCR libraries (15 samples in total).

first: Anaïs

last: Le Rhun

first: Fabien

last: Darfeuille


title: Illumina methylEPIC arrays on Peruvian individuals with high (>10 ppm) or low (<1 ppm) total hair mercury, a proxy for methylmercury exposure

city: Portland

first: Caren

last: Weinhouse

state: OR

address: 3181 SW Sam Jackson Park Road L606

institute: Oregon Health & Science University

type: Methylation profiling by genome tiling array

summary: Methylmercury (MeHg) is an environmental pollutant of global public health concern. MeHg is associated with immune dysfunction but the underlying mechanisms are unclear. The most common route of MeHg exposure is through consumption of fatty fish that contain beneficial n-3 polyunsaturated fatty acids (PUFA) that may protect against MeHg toxicity. To better inform individual costs and benefits of fish consumption, we aimed to identify candidate epigenetic biomarkers of biological responses that reflect MeHg toxicity and PUFA protection.

overall_design: We profiled genome-wide DNA methylation using Illumina 850K methylEPIC arrays in whole blood from N=32 age- and sex-matched individuals: N=16 individuals with high (>10 mg/g or ppm) vs. N=16 individuals with low (<1 mg/g or ppm) total hair mercury (a proxy for methylmercury exposure).

first: William

last: Pan


title: p300/CBP sustains Polycomb silencing by non-enzymatic functions (RNA-seq on inhibitor-treated Drosophila S2 cells)

city: Stockholm

first: Mattias

last: Mannervik

address: Svante Arrhenius väg 20C

department: Dept. of Molecular Biosciences

country: Sweden

institute: Stockholm University

summary: Maintenance of appropriate cell states involves epigenetic mechanisms, including Polycomb group (PcG)-mediated transcriptional repression. While PcG proteins are known to induce chromatin compaction, how PcG proteins gain access to DNA in compact chromatin to achieve long-term silencing is poorly understood. Here we show that the p300/CBP co-activator is associated with two-thirds of PcG-regions and required for PcG occupancy at many of these in Drosophila and mouse cells. CBP stabilizes RNA polymerase II (Pol II) at PcG-bound repressive sites and promotes Pol II pausing independently of its histone acetyltransferase activity. CBP and Pol II pausing are necessary for RNA-DNA hybrid (R-loop) formation and nucleosome depletion at Polycomb Response Elements (PREs), whereas transcription beyond the pause region is not. These results suggest that non-enzymatic activities of the CBP co-activator have been repurposed to support PcG-mediated silencing, revealing how chromatin regulator interplay maintains transcriptional states.

overall_design: RNA-seq analysis of gene expression changes in Drosophila late embryonic Schneider 2 cells treated for 30 minutes with the CBP HAT pharmacological inhibitor C646 with and without a drug washout (WO) of 1 hr or 4 hr, relative to untreated cells.

first: George

last: Hunt

first: Ann

last: Boija


title: Methionine metabolism and the NOP2 methyltransferase are essential for MYC-Driven liver tumorigenesis

city: San Francisco

first: Sensen

last: Lin

state: CA California

address: HSW 760, UCSF Parnassus, 513 Parnassus Ave, San Francisco

institute: UCSF

summary: Hepatocellular carcinoma (HCC) represents the third leading cause of cancer-related death worldwide and has been increasing in recent years in developed nations1,2. The MYC oncogene or its paralogs are frequently amplified or overexpressed in particularly aggressive subtypes of cancer associated with stem cell-like features and worse clinical outcomes3,4, including in liver cancer5. Unfortunately, selective inhibitors that target MYC or its transcriptional program are not yet clinically available for therapy of HCC. Here, we identified methionine metabolism as a selective vulnerability for MYC but not RAS-driven liver cancers. MYC-driven liver cancer cells are methionine dependent and S-adenosylmethionine (SAM), the predominant methyl donor, partially rescues methionine depletion. A low methionine diet, or the methylation inhibitor 5-azacytidine limited MYC-driven tumor formation, but RAS-driven liver cancer was resistant to a low methionine diet. Metabolic tracing of methionine catabolism in MYC high cells identified increased m5C methylation of genomic DNA or ribosomal RNA. We identified NOP2, an rRNA m5C-methyltransferase as a MYC target gene. Knockdown of NOP2 selectively inhibited MYC liver cancer cell proliferation and in vivo tumorigenesis. Thus, methionine catabolism is critical for MYC-driven liver tumorigenesis and NOP2 may serve as a new therapeutic target in liver cancer.

overall_design: RNA seq of EC4 cells. MYC high and MYC low cells were cultured with either 10 µM or 200 µM methionine medium for 24 h, and RNA was isolated for deep sequencing. Four groups, MYC high methionine high, MYC low methionine high, MYC high methionine low, MYC low methionine low.

first: Vijay

last: Ramani

first: Andrei

last: Goga


title: p300/CBP sustains Polycomb silencing by non-enzymatic functions (ChIP-seq on inhibitor-treated mouse ES cells)

overall_design: Analysis of the genomic distribution of SUZ12 (PRC2) by ChIP-seq in mouse embryonic stem (ES) cells treated with the p300/CBP inhibitor C646 or DMSO for 1 hour.


title: p300/CBP sustains Polycomb silencing by non-enzymatic functions (ATAC-seq on inhibitor-treated Drosophila S2 cells)

overall_design: Analysis of chromatin accessibility by ATAC-seq in Drosophila late embryonic Schneider 2 cells treated with the CBP inhibitor C646.


title: Three dimensional sectioning and full length gene expression profiling of Patiria miniata

city: Menlo Park

first: Adam

last: Knight

state: CA

address: 1305 Obrien Dr

institute: pacbio

summary: The affinity of the echinoderm pentaradial body plan with that of the ancestral bilateral symmetry remains one of the biggest zoological puzzle. Here, we revisited this classical zoological problem using RNA tomography and HCR in situ hybridization in the sea star Patiria miniata.

overall_design: Young Patiria miniata (~2cm) sectioned into indiviual arms, each of which was cryo micro-sectioned into 8-22 sections across 3 sectionng dimensions (Proximo-disal, oral-aboral, and left-right) full length transcriptomic data was gathered on each section.  Addionally HRC insitu hybridizations were performed to provide higher resolution information for specific developementally imporant genes.

first: L

last: Formery

first: P

last: Peluso

first: I

last: Kohnle

first: K

last: Uhlinger

first: M

last: Pitel

first: J

last: Levine

first: D

last: Rokhsar

last: Rank

first: C

last: Lowe


title: m6A RNA methylation mediates NOD1/NF-kB signaling activation in the liver of piglets challenged with lipopolysaccharide

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: No. 6, Tongwei Road, Xuanwu District

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is the most abundant internal modification that widely participates in various immune and inflammatory responses, however, its regulatory mechanisms in the inflam-mation of liver induced by lipopolysaccharide in piglets remain largely unknown. In the present study, MeRIP-seq showed that 1166 and 1344 transcripts contained m6A methylation in control and LPS groups, respectively. The m6A methylation sites of these transcripts mainly distributes in the 5’ un-translated region (5’UTR), the coding sequence (CDS), and the 3’ untranslated region (3’UTR). In-terestingly, these genes were mostly enriched in the NF-κB signaling pathway, and LPS treatment significantly changed the m6A modification among NOD1, RIPK2, NFKBIA, NFKBIB and TNFAIP3 mRNAs.In conclusion, LPS activated the NOD1/NF-κB pathway at post-transcriptional regulation through changing m6A RNA methylation, and then promoted the overproduction of proinflammatory cytokines, ultimately resulting in liver inflammation and damage.

overall_design: Twelve male piglets in the growing stages (Duroc x Large White x Landrace) were assigned randomly to two treatment groups: the control (CON) group and the Lipopolysaccharide (LPS) group.

first: Menghui

last: Xu

first: Ruhao

last: Zhuo

first: Shengxiang

last: Tao


title: RNA sequencing of the mouse dentate gyrus in temporal lobe epilepsy

city: Indianapolis

first: Kunal

last: Gupta

address: 355 W 16th St

institute: Indiana Universitty

summary: To explore the transcriptome of the ipsilateral and contralateral dentate gyrus during the first 2-weeks of temporal lobe epileptogenesis. Wild-type C57BL/6J mice underwent unilateral intrahippocampal injection of kainate or saline. Dentate gyri were extracted 3-days, 7-days and 14-days after injection and processed for RNA-sequencing.

overall_design: Four 6-8 week-old wild-type C57BL/6J mice (2 male, 2 female) were included in each group (saline and kainate) at each time-point (3-days, 7-days, 14-days). Ipsilateral and contralateral dorsal dentate gyri were extracted from each mouse for RNA-sequencing.

first: Muriel

last: Mardones


title: p300/CBP sustains Polycomb silencing by non-enzymatic functions (ChIP-seq on RNAi-treated Drosophila S2 cells)

first: Mattias

last: Mannervik

overall_design: Analysis of the genomic distribution of CBP and the PcGs E(z) (PRC2) and Pho (PhoRC) by ChIP-seq in Drosophila late embryonic Schneider 2 cells treated with double-stranded RNA (dsRNA) targeting CBP or GFP for consecutive 72 h treatments. Anti-E(z) was a kind gift of Richard Jones, Southern Methodist University, USA and anti-Pho was a kind gift of Judith Kassis, National Institute of Health, USA.

first: George

last: Hunt

first: Ann

last: Boija


title: Choice of Template Delivery Mitigates the Genotoxic Risk and Adverse Impact of Editing in Human Hematopoietic Stem Cells (Targeted deep sequencing)

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Long-range gene editing by homology-directed repair (HDR) in hematopoietic stem/progenitor cells (HSPCs) often relies on viral transduction with recombinant adeno-associated viral vector (AAV) for template delivery. Here, we uncover unexpected load and prolonged persistence of AAV genomes and their fragments, which trigger sustained p53-mediated DNA damage response (DDR) upon recruiting the MRE11-RAD50-NBS1 (MRN) complex on the AAV inverted terminal repeats (ITRs). Accrual of viral DNA in cell-cycle-arrested HSPCs led to its frequent integration, predominantly in the form of transcriptionally competent ITRs, at nuclease on- and off-target sites. Optimized delivery of integrase-defective lentiviral vector (IDLV) induced lower DNA load and less persistent DDR, improving clonogenic capacity and editing efficiency in long- term repopulating HSPCs. Because insertions of viral DNA fragments are less frequent with IDLV, its choice for template delivery mitigates the adverse impact and genotoxic burden of HDR editing and should facilitate its clinical translation in HSPC gene therapy.

overall_design: The frequency and diversity of insertions/deletions (indels) generated at the target site upon NHEJ-mediated repair of the nuclease-induced DNA double strand break (DSB) can be used as surrogate readout of graft complexity. Moreover, integration of fragments derived from the DNA template can be integrated at the nuclease DNA DSB. Therefore, we performed targeted deep sequencing of the nuclease target site in hematopoietic organs of humanized hematochimeric mice.

first: Samuele

last: Ferrari

first: Aurelien

last: Jacob

first: Ivan

last: Merelli

first: Luigi

last: Naldini


title: mRNA-seq data for KMT2D HNSCC (follow-up)

city: Madison

first: Scot

middle: Carson

last: Callahan

state: WI

address: 600 highland ave

institute: UW Health

summary: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, with 5-year survival of ~50%. Genomic profiling studies have identified important somatic mutations in this disease which presents an opportunity for precision medicine. We demonstrate that KMT2D, a histone methyltransferase harbors somatic mutations in ~17% of HNSCC and is associated with 2-year recurrence in TCGA data. Consistent with algorithmic prediction of bring a driver tumor-suppressor event, its loss results in larger oral tumors in immune-proficient orthotopic models. Mechanistically, we find that KMT2D knockdown or KMT2D mutation causes loss of H3K4me1-marked enhancers harboring IRF7/9 binding sites, which is known to regulate interferon signaling. Indeed, KMT2D loss in human and murine cell lines deregulated transcriptional levels of cytokine expression and impacted numerous immune signaling pathways, including interferon signaling. Consistently, Kmt2d knockdown in murine tumors exhibited decrease in IFN-producing effector T cells and an increase in T-cells with an exhausted phenotype. Epistasis experiments showed that exogenous treatment with IFNabrogated the increased tumor growth in Kmt2d-deficient oral tumors. Together, these results support the role of KMT2D as a tumor suppressor in HNSCC that regulates the tumor microenvironment by modulating H3K4me1-marked enhancers controlling interferon signaling.

overall_design: 6 samples – 2 conditions of 3 replicates each. ***Please note that the raw sequence data cannot be provided due to these being old cell lines without proper consents. Please contact krai@mdanderson.org for the sequence data***

first: S

middle: C

last: Rai


title: Neferine treatment lower blood pressure in SHR

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of this study is to compare the differently expressed genes in abdominal aorta tissue of WKY and SHR as well as differently expressed genes in the abdominal aorta tissue of SHR with or without neferine treatment. The rat (n=15) were randomly divided into 3 groups: WKY,SHR, and SHR + neferine - H (high concentration) groups (n=6 for each group). Rat in WKY and SHR groups were intragastrically with double distilled water (dd H2O); while rat in SHR + SHR + neferine - H groups were  intragastrically with 10mg/kg/D of neferine for 10 weeks. Then the abdominal aorta were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with abdominal aorta of mice in 3 groups: WHY, SHR, SHR + neferine - H treated (n=5 for each group) to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Weiquan

last: Zeng

first: Xiuli

last: Zhang


title: p300/CBP sustains Polycomb silencing by non-enzymatic functions

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

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Refer to individual Series


title: Chip-seq data for KMT2D HNSCC

overall_design: ***Authors state: Please note that the raw sequence data cannot be provided due to these being old cell lines without proper consents. Please contact krai@mdanderson.org for the sequence data***

first: Zhiyi

last: Liu


title: Choice of Template Delivery Mitigates the Genotoxic Risk and Adverse Impact of Editing in Human Hematopoietic Stem Cells (RAAVIoli sequencing)

first: Daniela

last: Cesana

first: Andrea

last: Calabria


title: Choice of Template Delivery Mitigates the Genotoxic Risk and Adverse Impact of Editing in Human Hematopoietic Stem Cells


title: mRNA-seq data for KMT2D HNSCC

overall_design: 6 samples – 2 conditions of 3 replicates each. ***Authors state: Please note that the raw sequence data cannot be provided due to these being old cell lines without proper consents. Please contact krai@mdanderson.org for the sequence data***

first: Kunal


title: Transcriptional memory of dFOXO activity in early adulthood delays late life mortality [RNA-seq]

city: LONDON

first: MengJia

last: Li

state: Please Select

address: flat38 midhopse house, midhope street

country: United Kingdom

institute: University College London

summary: The study examined transcriptional memory after dFOXO induction in fat body and gut of young adult female fruit flies.

overall_design: foxo overexpression in the first three weeks in S106 D. melanogaster, followed by one week recovery.  polyA RNAseq.

first: Mengjia

first: Guillermo

middle: M

last: Corrales

first: Tatiana

last: Svermova

first: Adam

last: Dobson


title: Effect of the Idd2 locus of B10 origin on the transcriptome of B cell of NOD mice

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

country: Canada

institute: RPM Bioinfo Solutions

summary: Type 1 diabetes (T1D) is an autoimmune disease characterized by pancreatic beta-cell destruction. It is a complex genetic trait driven by over 30 genetic loci with parallels between humans and mice. The NOD mouse spontaneously develops autoimmune diabetes and is widely used to identify insulin-dependent diabetes (Idd) genetic loci linked to diabetes susceptibility. While many Idd loci have been extensively studied, the impact of the Idd2 locus on autoimmune diabetes susceptibility remains to be defined. To address this, we generated a NOD congenic mouse bearing B10 resistance alleles on chromosome 9 in a locus coinciding with part of the Idd2 locus and find that NOD.B10-Idd2 congenic mice are highly resistant to diabetes. Bone marrow chimera and adoptive transfer experiments show that the B10 protective alleles provide resistance in an immune cell-intrinsic manner. While no T cell-intrinsic differences between NOD and NOD.B10-Idd2 mice were observed, we find that the Idd2 resistance alleles limit the formation of spontaneous and induced germinal centers. Comparison of the B cell transcriptome profile from NOD and NOD.B10-Idd2 mice reveal that resistance alleles at the Idd2 locus affect the expression of specific MHC molecules, a result confirmed by flow cytometry. Altogether, these data demonstrate that resistance alleles at the Idd2 locus impair germinal center formation and influence MHC expression, both of which likely contribute to reduce diabetes incidence.

overall_design: 3 samples of isolated B and per mouse strain are analyzed. NOD cell samples serve as control.

first: Sylvie

last: Lesage

first: Felix

last: Lombard-Vadnais


title: Transcriptional memory of dFOXO activity in early adulthood delays late life mortality.


title: p300/CBP sustains Polycomb silencing by non-enzymatic functions (ChIP-seq on inhibitor-treated Drosophila S2 cells)

first: Mattias

last: Mannervik

overall_design:
Analysis of the genomic distribution of CBP and the PcGs dRING (PRC1), E(z) (PRC2) and Pho (PhoRC) by ChIP-seq in Drosophila late embryonic Schneider 2 cells treated for 30 minutes with the CBP HAT pharmacological inhibitor C646 or the inactive analog C37. Anti-E(z) was a kind gift of Richard Jones, Southern Methodist University, USA, anti-dRING was a kind gift of Yuri Schwartz, Umeå Universitet, Sweden and anti-Pho was a kind gift of Judith Kassis, National Institute of Health, USA.
Please note that each processed data was generated from both replicates and is linked to the corresponding *rep1 sample records.

first: George

last: Hunt

first: Ann

last: Boija


title: Transcriptional memory of dFOXO activity in early adulthood delays late life mortality [ATAC-seq]

overall_design: foxo overexpression in the first three weeks in S106 D. melanogaster, followed by one week recovery.  ATACseq


title: Memory-induced epigenome in Huntington's disease (HD) mice [ChIP-seq]

city: strasbourg

first: Charles

last: DECRAENE

address: 12 rue Goethe

department: UMR 7364 CNRS

institute: CNRS

type: Genome variation profiling by high throughput sequencing

summary: Evaluation of the effect of procedural  memory using the double-H maze (DH) on striatal epigenome in HD R6/1  mice

overall_design: ChIPseq data were generated using the striatum of WT and HD mice in resting condition (home cage, HC) and during procedural memory consolidation/recall.

first: Karine

last: Merienne

first: Rafael

last: Alcala-Vida

first: Jonathan

last: Seguin


title: Regeneration of the cerebral cortex by direct chemical reprogramming of macrophages into neuronal cells in acute ischemic stroke

status: Public on Oct 05 2022

city: Niigata

first: Itaru

last: Ninomiya

state: Niigata

address: 1-757 Asahimachi-dori, Chuoku

department: Neurology

institute: Brain Research Institute, Niigata University

summary: Ischemic stroke causes extensive neuronal cell death. Antithrombotic agents and rehabilitation are the primary treatment options but have limited efficacy. Therefore, to achieve radical neurological improvement, practical neuroregenerative technologies must be developed. Recently, direct chemical reprogramming using small molecules to transdifferentiate somatic cells into neurons has garnered much attention. We investigated the possibility of applying this technology for the treatment of ischemic stroke. During the acute phase of ischemic stroke, circulating monocytes increase chemotaxis and accumulate in the infarct area through the disrupted blood-brain barrier, where they differentiate into macrophages involved in inflammation and remodeling. Direct reprogramming of these monocyte-derived macrophages into neuronal cells in vivo is theoretically possible with the administration of small-molecule drugs. However, the efficacy of this neuroregenerative therapy cannot be verified because the optimal chemical compounds that convert macrophages into neurons have not yet been identified.

overall_design: Direct chemical reprogramming of infiltrated monocyte-derived macrophages into neurons in the infarct area is theoretically a promising regenerative therapy for ischemic stroke. However, the optimal combination of small molecules to transdifferentiate macrophages into neurons has not yet been discovered. Here, we identified the essential small molecules and demonstrated that their administration generates a new neuronal layer in the infarct cortex by converting macrophages into neuronal cells, ultimately improving neurological function.

first: Akihide

last: Koyama

first: Yutaka

last: Otsu

first: Masato

last: Kanazawa

first: Osamu

last: Onodera


title: Promotion of Melanoma Cells’ Proliferation by Cyclic Strain-ing through Regulatory Morphogenesis

city: Xi'an

first: Yingjun

last: Yang

state: Shaanxi

address: Weiyang University Park

institute: Shaanxi University of Science and Technology

summary:
To investigate the functions of cyclic straining in promotion of melanoma cells' proliferation.
We then performed gene expression profiling analysis using data obtained from RNA-seq of cells under different experiment condition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for B16 cells under cyclic straining or inhibitor treatment.

first: Siyuan

last: Huang


title: Baseline Clinical, Hormonal and Molecular Markers Associated with Clinical Response to IL-23 Antagonism in Hidradenitis Suppurativa

city: Liverpool

first: John

last: Frew

address: Elizabeth St

department: Dermatology

country: Australia

institute: Liverpool Hospital

summary:
Background: Hidradenitis Suppurativa is a complex inflammatory disease in which predicting therapeutic response remains challenging. Clinical trials of IL-23 antagonism have shown high variability leading to abandonment of various clinical trials. IL-23 is known to interact with sex hormones in. monocytes, dendritic cells, and T cells. Relationships of IL-23 clinical response in HS to hormonal and molecular markers of inflammation has not been previously assessed.
Objectives: To assess whether baseline clinical, hormonal, or molecular markers are associated with clinical response to IL-23 antagonism with Risankizumab in Hidradenitis Suppurativa.
Methods: 26 individuals with Hurley Stage 2/3 disease were administered Risankizumab 150mg Week 0,4,12. Baseline sex hormones and skin biopsies were taken. Clinical response at Week 16 assessed by the HiSCR, and differences between responders and non-responders assessed.
Results: Clinical response to IL-23 antagonism was associated with male gender, elevated total serum testosterone, and decreased levels of FSH. nCounter gene expression identified consistent differential expressed genes to previously published RNAseq datasets. Stratification by clinical responders/non responders identified differentially expressed genes included TRAT1, TPSAB1/2, LTA, IL17A, CXCR1 as well as hormonally responsive genes including PLPP4 and MAPK10. Immunohistochemistry identified elevated numbers of CD11c, IL-17A and IL-17F positive cells compared to non-responders. CD11c+ cells significantly correlated with serum levels of total testosterone and inversely correlated with serum FSH.

overall_design: Baseline Data, Nanostring nCounter Human Fibrosis V2.0 Panel

first: A

last: Flora

first: J


title: Memory-induced 3D chromatin architecture in Huntington's disease (HD) mice [4C-seq]

summary: Evaluation of the effect of procedural  memory using the double-H maze (DH) on striatal 3D chromatin architecture in HD R6/1 mice

overall_design: 4C-seq experiment (8 baits) in WT and R6/1 HD mice striatum at 14 weeks of age in resting condition (HC) and after 2 days of training in the double-H maze (DH)


title: FAM69C promotes stress granule assembly and suppresses inflammasome activation

city: 北京市

first: Zhongyan

last: Wu

address: 学院路38号北京大学医学部

institute: PKUISB

summary: Stress granule and inflammasome assembly determine contrasting fates of stressed cells. FAM69C is a brain-enriched kinase associated with neurodegenerative diseases, but its biological functions are still largely unknown. Here we show that FAM69C plays an important role in the regulation of stress responses through promoting stress granule assembly and suppressing inflammasome activation. In response to ATP, a common inflammasome activator, mouse primary microglia, and BV-2 cells form stress granules. FAM69C deficiency hastens inflammasome activation in mouse microglia, which is accompanied by inhibited stress granule assembly. FAM69C promotes the assembly of stress granules and halts protein translation under stress. Aged Fam69c knockout mice show increased neuroinflammation and ASC specks formation. We further find that FAM69C physically phosphorylates eIF2α and promotes stress granule assembly. Our data reveal that FAM69C promotes stress granule assembly under stress and suppresses inflammasome formation in microglia, suggesting that FAM69C may be a potential therapeutic target for neurodegenerative diseases.

overall_design: Cerebral cortex mRNA profiles of 12-month-old wild type (WT) and Fam69c-/- mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000.

first: Fan

last: Mei


title: Advanced physiological maturation of iPSC-derived human cardiomyocytes using an algorithm-directed optimization of defined media components

city: Toronto

first: Neal

middle: I

last: Callaghan

state: Ontario

address: 661 University Ave

department: Institute of Biomedical Engineering

institute: University of Toronto

summary: Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) hold tremendous promise for in vitro modeling to assess native myocardial function and disease mechanisms as well as testing drug safety and efficacy. However, current iPSC-CMs are functionally immature, resembling in vivo CMs of fetal or neonatal developmental states. The use of targeted culture media and organoid formats have been identified as potential high-yield contributors to improve CM maturation. This study presents a novel iPSC-CM maturation medium formulation, designed using a differential evolutionary approach with oxidative capacity as an objective metric for iterative optimization. Relative to gold-standard reference formulations, our approach significantly matured morphology, Ca2+ handling, electrophysiology, and metabolism, which was further validated by multi-omic screening, for cells in either pure or co-cultured microtissue formats. Together, these findings not only provide a reliable workflow for highly functional iPSC-CMs for downstream use, but also demonstrate the power of high-dimensional optimization processes in evoking advanced biological function in vitro.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iPSC-derived cardiomyocytes treated with 4 different media formulations, and for iPSC-derived biowire tissues cultured in C16 or RPMI+B27 media, with or without electrical stimulation

first: Lauren

middle: J

last: Durland

first: Wenliang

last: Chen

first: Uros

last: Kuzmanov

first: Maria

middle: Z

last: Miranda

first: Zahra

last: Mirzaei

first: Ronald

last: Ireland

first: Erika

last: Wang

first: Karl

last: Wagner

first: Michelle

last: Kim

first: Julie

last: Audet

last: Santerre

first: Anthony

middle: O

last: Gramolini

first: Filio

last: Billia

first: Milica

last: Radisic

first: Seema

last: Mital

first: James

last: Ellis

first: Peter

last: Backx

first: Craig

last: Simmons


title: A flexible model for correlated count data, with application to analysis of gene expression differences in multi-condition experiments

city: Chicago

first: Nicolas

last: Chevrier

state: Illinois

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: The University of Chicago

summary: Detecting differences in gene expression is an important part of RNA sequencing (RNA-seq) experiments, and many statistical methods have been developed for this aim. Most differential expression analyses focus on comparing expression between two groups (e.g., treatment vs. control). But there is increasing interest in multi-condition differential expression analyses in which expression is measured in many conditions, and the aim is to accurately detect and estimate expression differences in all conditions. We show that directly modeling the RNA-seq counts in all conditions simultaneously, while also inferring how expression differences are shared across conditions, leads to greatly improved estimates of expression differences, particularly when the power to detect expression differences is low in the individual conditions  (e.g., due to small sample sizes). We illustrate the potential of this new multi-condition differential expression analysis in analyzing data from a single-cell experiment for studying the effects of cytokine stimulation on gene expression. We call our new method “Poisson multivariate adaptive shrinkage,” and it is implemented in the R package poisson.mash.alpha, available at https://github.com/stephenslab/poisson.mash.alpha.

overall_design: Droplet-based scRNA-seq on PBMCs from unstimulated mice and mice injected with various cytokines and chemokines.

first: Michihiro

last: Takahama

first: Adam

last: Gruenbaum


title: The binding pattern of HOXA5 in the genome of extrahepatic cholangiocarcinoma cells

city: Wuhan

first: Fei

last: Xiong

state: Hubei

address: Jiefang Road No.1095

institute: Huazhong University of Science and Technology

summary: HOXA5 is a transcription factor in mammalian and can regulate cell differentiation, proliferation and apoptosis as well as tumorigenesis. However, little is known on whether and how HOXA5 can regulate the malignant behaviors of cholangiocarcinoma. The binding pattern of HOXA5 was evaluated by CUT & Tag assay. The differential peaks were analysed to assess the role of HOXA5 in the regulation of the key genes involved in cell proliferation and DNA replication.

overall_design: Immunoprecipitation was performed with anti-Flag antibodies. This dataset includes two CUT & Tag samples. One is TFK-1 cell sample that treated with HOXA5 overexpression vector and the other is TFK-1 cell sample that treated with normal control vector.

first: Bing

first: Yongjun

last: Chen


title: Transcriptome sequencing of Serpine1-overexpression MLE-12 cells

city: Shanghai

first: Dongting

last: yao

state: Shanghai

address: 徐汇区广元路145号科研楼4楼

institute: nternational Peace Maternity and Child Health Hospital of China Welfare Institution, School of Medicine

summary: To determine the function of Serpine1 in alveolar cells, the Serpine1 overexpression plasmid pCI-neo-Serpine1 was constructed and transfected into MLE-12 cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Serpine1-overexpression MLE-12 cells

last: Yao

first: Jiuru

last: Zhao

first: Zhiwei

last: Liu


title: Single-cell transcriptome analysis reveals T-cell exhaustion in denosumab-treated giant cell tumor of bone

city: Guangzhou

first: Meiling

last: Yang

address: No. 106, Zhongshan Road,Yuexiu District

institute: Guangdong Provincial People’s Hospital（Guangdong Academy of Medical Sciences）

summary: Denosumab (DMAB), a human monoclonal antibody against the receptor activator of the nuclear factor-kappa B ligand, is used for the treatment for unresectable giant cell tumor of bone (GCTB). However, little is known about the molecular and functional characteristics of GCTB-infiltrating lymphocytes after DMAB treatment. Here, we performed single-cell RNA sequencing and immunostaining assays to delineate the immune landscape of GCTB in the presence and absence of DMAB. We found that exhausted CD8+ T cells were preferentially enriched in DMAB-treated GCTB. A distinct M2-skewed type of tumor-associated macrophages (TAMs) comprises the majority of GCTB TAMs. We identified cytokines, including interleukin-10, and inhibitory receptors of M2 TAMs as important mediators of CD8+ T cell exhaustion. We further revealed that DMAB treatment notably increased the expression levels of periostin (POSTN) in GCTB cells. Furthermore, POSTN expression was transcriptionally regulated by c-FOS signaling and correlated with GCTB recurrence in patients after DMAB treatment. Collectively, our findings reveal that CD8+ T-cells undergo unappreciated exhaustion during DMAB therapy and that GCTB cell-derived POSTN educates TAMs and establishes a microenvironmental niche that facilitates GCTB recurrence.

overall_design: Primary giant cell tumor of bone tissues in the presence and absence of denosumab were used for single cell RNA sequencing by 10X Genomics

first: Wei

first: Changye

last: Zou


title: Transcriptome sequencing of the lung tissue of neonatal mice with Intrauterine inflammation

address: 徐汇区广元路145号科研楼4楼

summary: To  investigate the effects of IUI on lung development, and identify the key molecule involved in these effects and its epigenetic regulatory mechanism.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the lung tissue of neonatal mice with Intrauterine inflammation


title: HRasV12-induced senescence with WSTF overexpression

city: Boston

first: Zhixun

last: Dou

state: MA

address: 185 Cambridge Street, CPZN 4-234

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

overall_design: Refer to individual Series


title: The role HOXA5 in extrahepatic cholangiocarcinoma (Methylation)

summary: Homeobox A5 (HOXA5) is a transcription factor in mammalian and can regulate cell differentiation, proliferation and apoptosis as well as tumorigenesis. However, little is known on whether and how HOXA5 can regulate the malignant behaviors of cholangiocarcinoma. The methylation levels of HOXA5 were evaluated by methylation microarray and bisulfite sequencing PCR. We found that hypermethylation in the HOXA5 promoter down-regulated HOXA5 expression in extrahepatic cholangiocarcinoma (ECCA) tissues, which was correlated with worse overall survival. HOXA5 over-expression significantly inhibited the proliferation and tumor growth.

overall_design: A fresh extrahepatic cholangiocarcinoma cell sample (TFK-1) and a normal bile duct sample were used for methylation analysis and we found HOXA5 was hypermethylated in extrahepatic cholangiocarcinoma sample compared with normal control sample.

last: Wang


title: The role HOXA5 in extrahepatic cholangiocarcinoma


title: The role HOXA5 in extrahepatic cholangiocarcinoma (Expression)

summary: Homeobox A5 (HOXA5) is a transcription factor in mammals and can regulate cell differentiation, proliferation and apoptosis as well as tumorigenesis. However, little is known about whether and how HOXA5 can regulate the malignant behaviors of cholangiocarcinoma. The expression profiles were analyzed by RNA microarray. We found MXD1 was upregulated upon HOXA5 overexpression. Besides, p53 pathway was activated by HOXA5 overexpression.

overall_design: Fresh cell samples of extrahepatic cholangiocarcinoma cell line TFK-1, containing three cell samples treated by HOXA5 overexpression vectors and three normal control samples.


title: A single-cell transcriptomic atlas of the human ciliary body

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

summary: The ciliary body is required for the maintenance of intraocular pressure and immunity as well as vision accommodation. We report a comprehensive cell atlas of human ciliary body from single-cell RNA sequencing (scRNAseq)

overall_design: Ciliary body tissues from human donor eyes were dissected and dissociated to yeild single cell suspension. ScRNAseq was performed using a BD Rhapsody system, followed by analyses of cell clusters, specific gene expression profiling and ligand-receptor pairs

first: Feng

last: Zhang

first: Bingsheng

last: Lou

first: Lei

last: Zeng


title: Inhibiting the activation of MAPK (ERK1/2) in stressed Müller cells prevents photoreceptor degeneration

city: Sydney

first: Ling

last: Zhu

state: New South Wales

address: Save Sight Institute, Level 2, South Block, Sydney Eye Hospital, 8 Macquarie St

institute: the University of Sydney

summary: MAPK (ERK1/2) signalling was exclusively activated in Müller cells under stress, both ex vivo and in vivo. PD98059, a specific pERK1/2 inhibitor, inhibited the phosphorylation of ERK1/2 in Müller cells, reduced the gliotic marker glial fibrillary acidic protein (GFAP) and increased neuroprotective factor interphotoreceptor retinoid-binding protein (IRBP). Inhibition of pERK1/2 reduced retinal injury in photo-oxidative damaged mice assessed by optical coherence tomography (OCT). However, exactly how Müller cells and photoreceptors communicate under stress, as well as the signalling pathways involved, remains unclear. We explored the RNA and signalling pathway changes after MAPK deactivation in human retina explants by RNA sequence.

overall_design: 8 mRNA profiles of human retina explants cultured from 4 donors, including 2 groups with different treatments (DMSO and ERK1/2 inhibitor treatment)

first: Shaoxue

first: Ting

first: Joshua

last: Chu-Tan

first: Yingying

first: Kaiyu

last: Jin

first: Michele

last: Madigan

first: Nilisha

last: Fernando

first: Adrian

last: Cioanca

first: Fanfan

last: Zhou

first: Meidong

first: Xiaohui

last: Fan

first: Junjun

first: Riccardo

last: Natoli

first: Mark

last: Gillies


title: Immune and inflammation-related factors alteration as a biomarker for predicting prognosis and responsiveness to PD-1 monoclonal antibody in patients with recurrent cervical cancer

city: Jinan

first: Xihan

last: Liu

state: Shandong

address: Wenhuaxi Road #44

institute: Shandong University

summary: Purpose: We aimed to elucidate the potential mechanisms of effective responsiveness to PD-1 monoclonal antibody and evaluate more reliable biomarkers for improving the predictive utility of the dominant populations of recurrent cervical cancer (RCC) to receive immunotherapy.  Methods: Peripheral blood samples of PD-L1 positive patients with RCC treated with second-line PD-1 monoclonal antibody were collected prior to treatment initiation and after the treatment. Differentially expressed genes (DEGs) were analyzed between partial response (PR) patient and progressive disease (PD) patients.

first: Jin

last: Peng


title: Transcriptional constraint of EWS/FLI by an ETS transcription factor promotes Ewing sarcoma growth [PEDS0009 CUT&Tag]

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Room LC6115

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Pediatric cancers frequently harbor sentinel mutations involving transcription factors (TFs) that dysregulate normal development. A recurrent mechanism involves the ability of mutant TFs to co-opt cell lineage-specific, activating TFs to promote cancer growth. Ewing sarcoma, the second most common pediatric bone cancer, is defined by the presence of a 11;22 chromosomal translocation fusing the N-terminus of the EWS protein with the C-terminal DNA binding domain of an ETS (E26 Transformation Specific) TF family member, most commonly (85-90% of cases), FLI1. The EWS/FLI fusion exhibits the neomorphic ability to pioneer de novo enhancers at repeating 5’-GGAA-3’ motifs in the cell-of-origin, which has not been identified. To date, efforts to elucidate the key mechanisms by which EWS/FLI promotes oncogenesis have prioritized identifying the genes that are profoundly activated by EWS/FLI and highly expressed in Ewing sarcoma compared to other cancers, with particular focus on transcription factors capable of altering cell state. However, it is not known whether, globally, these genes constitute the most critical drivers of Ewing sarcoma cell growth. Here, we describe the results of an unbiased deletion screen revealing that the wild-type repressive ETS family TF, ETV6 (ETS Variant 6, or TEL), is a novel and most critical TF dependency specific to Ewing sarcoma. We demonstrate that the repressive activity of ETV6 constrains EWS/FLI gene activation at GGAA repeat enhancers to promote Ewing sarcoma cell growth.

overall_design: CUT&Tag (Kaya-Okur, et al., Nature Communications, 2019) was used to evaluate ETV6 binding in Ewing sarcoma using the newly derived CCLF_PEDS_0009_T (PEDS0009) cell line (Guenther et al., Clinical Cancer Research, 2019) in cells transduced with lentivirally-packaged CRISPR/Cas9 constructs.  All sgRNA sequences used in the Broad Institute AVANA CRISPR/Cas9 screen are available for download at the DepMap Portal (https://depmap.org). sgRNA sequences used to target ETV6 were taken from this screen. The sgETV6-1 forward sequence was 5’-GCAGCCAATTTACTGGAGCA-3’. The sgETV6-2 forward sequence was 5’-GCAGGGATGACGTAGCCCAG-3’. The sgETV6-3 forward sequence was 5’-GTGTGTGTATAGAGTTTCCA-3’. The sgETV6-4 forward sequence was 5’-GTTATGGTGCACATTATCCA-3’. For  control sgRNA, sgChr2.2 was used as a cutting control and targets a gene desert on Chromosome 2, 5’-GGTGTGCGTATGAAGCAGTG-3’. For ligation into the LentiCRISPRv2 plasmid, additional bases were added. 5’-CACCG-3’ was added to the beginning of the forward sequence. 5’-AAAC-3’ and 5’-C-3’ were added at the beginning and end of the reverse sequence, respectively.  Duplicate paired-end experiments were used to evaluate ETV6 binding in all cases. All CUT&Tag samples have matching Rabbit anti-mouse reference sample from the same batch and treatment condition.

first: Diana

last: Lu

first: Kimberly

last: Stegmaier


title: TGM2-Mediated Histone Transglutamination is Dictated by Steric Accessibility

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Histone monoaminylation is a new class of chromatin post-translational modification whereby glutamines are transamidated by tissue transglutaminase 2 (TGM2). Initial studies of these marks have identified serotonylation and dopaminylation on H3Q5, suggesting the modification is a marker of active chromatin. However, little work has been conducted to understand the regulation of TGM2-mediated monoaminylation of chromatin. Here, we employed a highly sensitive TGM2 assay using the small molecule biotin-cadaverine as an acyl-acceptor substrate. In doing so, we discovered that, in addition to H3Q5, H3Q19 and H2A.ZQ123 and Q124 are glutaminyl substrates for TGM2 in vitro. Modification of these residues occurs in a sequence independent manner, with the primary determining factor for substrate selectivity being steric accessibility. We demonstrated that moving substrate glutamines near the histone fold domain turns them into non-substrates. Furthermore, we found that steric accessibility of glutamines appears to be controlled by higher order chromatin structures. Using nucleosome arrays as substrates, we successfully showed that formation of chromatin fibers in vitro reduces levels of monoaminylation. We then successfully extended these findings to a cell based system, showing that TGM2 is not enriched in heterochromatin and that H3Q5 serotonylation and H3K9me3 are mutually exclusive marks. In total, our results strongly suggest that TGM2, and monoaminylation, are excluded from heterochromatin based on steric accessibility

overall_design: Adherent HeLa S3 cells were cultured in medium containing DMEM high glucose, 10% FBS and 1% P/S.

first: Bradley

last: Lukasak

first: Barbara

middle: E

last: Dul

first: Ian

last: Maze

first: Tom

last: Muir


title: Gasdermin D deficiency promotes antitumor immunity by upregulating Type I ISG program in Antigen-presenting cells in response to PD-L1 antibody treatment

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: The tumor immune microenvironment is complex in composition, function and dynamic, influencing the evolution of tumor, prognosis and response to immunotherapy. Recent studies have significantly advanced our knowledge of the roles of Gasdermin protein-mediated tumoral pyroptosis activated by caspases and granzymes from cytotoxic lymphocytes in facilitating the killing of tumor cells. However, the pyroptosis of immune cells in tumor microenvironment and their affecting the reprogram of the tumor microenvironment remains poorly understood. In this study, we find that Gasdermin D (GSDMD), among Gasdermin family proteins, is significantly positively correlated with the immune checkpoint signature, and inversely linked to the overall survival of cancer patients by the analysis with TCGA clinical data. Using conditional knockout of GSDMD together with immunofluorescence co-labeling and single-cell RNA sequencing (scRNA-seq), we demonstrate that GSDMD mainly on antigen-presenting cells (APCs) such as macrophages and dendritic cells (DCs) in tumor microenvironment, restrains anti-tumor immunity under the treatment of PD-L1 antibody. Loss of GSDMD in APCs enhanced Type I interferon-stimulated gene (ISG) program of such cells, which promotes antigen presentation of macrophages and DCs, and facilitates the production of CD8+ effector and functional T cell. We further demonstrate that GSDMD deficiency increases anti-tumor immunity in a cyclic GMP–AMP synthase (cGAS)-dependent manner. Moreover, pharmacological inhibition of GSDMD-mediated pyroptosis significantly improves anti-tumor immunity in combination with PD-L1 antibody immunotherapy. Together, our findings reveal an important role for GSDMD-mediated pyroptosis of APCs such as macrophages and DCs in regulating CD8+ T cell function and underscore the potential of GSDMD blockade in promoting anti-tumor immunity, which may help the development of cancer immunotherapy.

overall_design: To investigate the specific role of Gsdmd of DCs and macrophages in tumor immunity, we implanted subcutaneously B16F10 tumor cell into Gsdmdfl/fl Cx3cr1-cre and Cx3cr1-cre mice, anti-PD-L1 were intraperitoneally injected on day 4, 8. Tumors were collected on day 14 for single-cell RNA-seq. Single-cell RNA-seq data of tumor infiltrates immune cells were generated from twice independent experiments, in which experiment, cells were mixed from three Cx3cr1-cre and Gsdmdfl/fl Cx3cr1-cre mice.

first: Shuo

last: Yang

first: Yongbing


title: Transcriptional constraint of EWS/FLI by an ETS transcription factor promotes Ewing sarcoma growth [CUT&RUN]

overall_design: CUT&RUN (Skene and Henikoff, eLife, 2017) was used to evaluate FLI1 and H3K4me3 binding in Ewing sarcoma using the newly derived CCLF_PEDS_0009_T (PEDS0009) cell line (Guenther et al., Clinical Cancer Research, 2019) in cells transduced with lentivirally-packaged CRISPR/Cas9 constructs.  All sgRNA sequences used in the Broad Institute AVANA CRISPR/Cas9 screen are available for download at the DepMap Portal (https://depmap.org). sgRNA sequences used to target ETV6 were taken from this screen. The sgETV6-1 forward sequence was 5’-GCAGCCAATTTACTGGAGCA-3’. The sgETV6-2 forward sequence was 5’-GCAGGGATGACGTAGCCCAG-3’. The sgETV6-3 forward sequence was 5’-GTGTGTGTATAGAGTTTCCA-3’. The sgETV6-4 forward sequence was 5’-GTTATGGTGCACATTATCCA-3’. For  control sgRNA, sgChr2.2 was used as a cutting control and targets a gene desert on Chromosome 2, 5’-GGTGTGCGTATGAAGCAGTG-3’. For ligation into the LentiCRISPRv2 plasmid, additional bases were added. 5’-CACCG-3’ was added to the beginning of the forward sequence. 5’-AAAC-3’ and 5’-C-3’ were added at the beginning and end of the reverse sequence, respectively. Paired-end experiments were used to evaluate FLI1 and H3K4me3 binding. All CUT&RUN samples have matching IgG reference sample from the same batch and treatment condition. The samples were processed with a pipeline based upon the bulk-level method outlined in CUT&RUNTools 2.0 (Yu, F., Sankaran, V.G., and Yuan, G. CUT&RUN Tools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag analysis. Bioinformatics, 38(1), 2022, 252-254. https://github.com/fl-yu/CUT-RUNTools-2.0/blob/master/docs/INSTALL.md).


title: CD4 T cell ChIPseq (H3k27ac) and RARα

city: Ann Arbor

first: Chang

last: Kim

address: 109 Zina Pitcher

institute: University of Michigan

summary: H3k27ac assessment by ChIPseq was performed on 16h-activated naïve CD4+ T cells with variables of RARα expression and RA concentration.

overall_design: Naïve CD4 T cells isolated from WT, RARα KO and RARα TG mice, were examined by ChIPseq.

first: Leon

last: Friesen


title: Exploration of the genome-wide DNA binding of chicken p53 in LMH cells

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

summary: To investigate the genome-wide DNA binding of chicken p53, we overexpressed chicken p53 with a flag in LMH cells. We then performed genome-wide DNA binding analysis using data obtained from ChIP-seq of LMH cells.

overall_design: Comparative DNA binding profiling analysis of ChIP-seq data for DNA bound by p53 and input DNA of LMH cells with p53 overexpression. Four biological replicates for each condition have been done.

first: Shengwang


title: ATAC-seq of HRasV12-induced senescence with WSTF overexpression

first: Zhixun

last: Dou

summary: We discovered that WSTF is downregulated in senescent cells by autophagy degradation. Forced expression of WSTF inhibits senescence-associated secretory phenotype, via inhibition of chromatin accesibility over inflammatory genes.

overall_design: Primary IMR90 cells were stably expressing vector control or WSTF. The cells were then infected by HRasV12 retrovirus to induce senescence. Three replicates each were included in each conditon for ATAC-seq analyses.

first: Murat

last: Cetinbas

first: Ruslan

last: Sadreyev


title: CD4 T cell transcriptome and RARα

summary: Transcriptome assessment by RNAseq was performed on 24h-activated naïve CD4+ T cells with variables of RARα expression and RA concentration.

overall_design: Naïve CD4 T cells isolated from WT, RARα KO and RARα TG mice, were examined by bulk-RNA-seq.


title: ZBTB7A promotes virus-host homeostasis during human coronavirus 229E infection II

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: In this study, we define ZBTB7A as a driver of cellular survival during HCoV-229E infection.

overall_design: Huh7-dCas9 cells were expanded and 3×10^7 Huh7-dCas9 cells were transduced with the CRISPR activation sgRNA library (Calabrese set A, Addgene#92379) in two replicates. After 1 µg/mL puromycin selection, half of the cells were collected as control samples and the other half of cells were infected with HCoV-229E (MOI=0.02). Surviving cells were then harvested and the genomic DNA in control and surviving cells were extracted.  The sgRNA sequences were then amplified and sequenced.

first: Xinyu

last: Zhu

first: Joseph

middle: D

last: Trimarco

first: Courtney

last: Williams

first: Alejandro

last: Barrera

first: Timothy

last: Reddy


title: ZBTB7A promotes virus-host homeostasis during human coronavirus 229E infection

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


title: ZBTB7A promotes virus-host homeostasis during human coronavirus 229E infection I

overall_design: ZBTB7A-Huh7 cells and control-Huh7 cells were mock-infected or infected with HCoV-229E (MOI=1). Total RNA was collected at 1 DPI and prepared for sequencing.


title: CAR Density Influences Antitumoral Efficacy of BCMA CAR T Cells and Correlates with Clinical Outcome [RNA-seq]

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

country: Spain

institute: CIMA

summary: In this work, we address the impact of CAR density on the in vitro and in vivo functionality of BCMA-CAR T cells. Phenotypic, functional, transcriptomic and epigenomic studies at bulk and single cell level revealed different profiles between CAR T cells with high and low expression of the CAR molecule (CARHigh and CARLow T cells). We analyzed the phenotype of CARHigh and CARLow T cell populations before and after stimulation with tumor cells. Sorted CD4+ and CD8+ CARHigh and CARLow T cell populations from six different CAR T cell productions were profiled using high-throughput RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin (ATAC-seq). To better understand the heterogeneity of CAR T cells and the influence of CAR level on their transcriptomic profile, we performed single cell transcriptomic analysis on 43,981 CAR T cells from three independent productions.

overall_design: We have carried out a comprehensive study of the influence of CAR density in CAR T cell function. We have performed transcriptomic assays at bulk level in FACS-isolated subpopulations of CAR-T cells with different CAR densities.

first: Juan

middle: R

first: Paula

last: Rodriguez-Marquez

first: Felipe

last: Prosper-Cardoso

first: Mikel

last: Hernaez


title: CAR Density Influences Antitumoral Efficacy of BCMA CAR T Cells and Correlates with Clinical Outcome


title: CAR Density Influences Antitumoral Efficacy of BCMA CAR T Cells and Correlates with Clinical Outcome [scRNA-seq]

overall_design: We have carried out a comprehensive study of the influence of CAR density in CAR T cell function. We have performed single-cell RNA-seq and single-cell TCR repertoire sequencing of CAR T cells.


title: Exploration of the transcriptional regulation network of chicken p53 in LMH cells upon ILTV infection

summary:
To gain the in-depth insights into the transcriptional regulation network of chicken liver cancer cells, we sequenced the mRNA of LMH cells for further genome-wide gene expression analysis.
To investigate the transcriptional regulation network of chicken p53, we created conditions different in p53 activity for LMH cell lines upon ILTV infection. We then performed gene expression profiling analysis using data obtained from RNA-seq of LMH cells.

overall_design:
Examination of genome-wide gene expression was performed by RNA-seq.
Comparative gene expression profiling analysis of RNA-seq data for LMH control cells (DMSO treatment) and LMH cells upon different conditions of p53 activity (N, PFT-?, DMSO) upon ILTV infection. Four biological replicates for each condition have been done.

last: Liu


title: Transcriptomic analysis of the Arabidopsis leaf during the deetiolation

city: Hong Kong

first: Zizhen

last: Liang

address: The Chinese University of Hong Kong

institute: The Chinese University of Hong Kong

summary: We report the mRNA profiles of the Arabidopsis thaliana seedlings germinated for 7days in the dark, then treated with light for 0h, 1h, 2h, 4h, 8h and 12h.

overall_design: Examine of the transcriptomic level of the photosynthetic complex encoded by nuclear genes

first: Byung-Ho

last: Kang


title: Transcriptomic analysis of rice seedlings under cold stress engineered with rd29a:AtDREB1a

city: Ahmedabad

first: Bhuvan

last: Pathak

state: Gujarat

address: m303 School of Arts and Sciences, Ahmedabad University, Commerce Six Road

department: Biological and Life Sciences Division

country: India

institute: Ahmedabad University

summary: Purpose: The aim is to identify the downstream target genes of AtDREB1a under cold stress in rice and reveal the potential mechanism of cold tolerance

overall_design: The transcriptomic analysis was performed on the Cre-lox mediated multigene stacked rice lines expressing RD29A:AtDREB1a in Taipei-309 background (Pathak and Srivastava, 2020). The analysis was performed on the cold-stressed as well as room-temperature RD29A:AtDREB1a lines against the Cre-lox founder line, T5 (Srivastava and Ow, 2002) at cold-stress and room-temperature. The Cre-lox founder line (T5) is referred to as wild-type (WT) in this experiment.

first: Vibha

last: Srivastava


title: Transcriptional constraint of EWS/FLI by an ETS transcription factor promotes Ewing sarcoma growth [CUT&Tag]

first: Kenneth

last: Ross

overall_design: CUT&Tag (Kaya-Okur, et al., Nature Communications, 2019) was used to evaluate ETV6 binding in Ewing sarcoma the A673 cell line using both the parental A673 cell line with two different anti-bodies and  in A673 cells engineered to express FKBP12F36V-HA-ETV6 were treated with either DMSO control or dTAGV-1 for24 hours to induce ETV6 degradation. Duplicate paired-end experiments were used to evaluate ETV6 binding in all cases. All CUT&Tag samples have matching input DNA reference sample from the same batch and treatment condition.

first: Diana

last: Lu

first: Kimberly

last: Stegmaier


title: Transcriptomic analysis of paternal behaviors in prairie voles

city: Tallahassee

first: Mohamed

last: Kabbaj

state: Florida

address: 1115 W Call St

department: Biomedical Sciences

institute: Florida State University

summary: The importance of fathers' engagement in care and its critical role in the offspring’s cognitive and emotional development is now well established. Yet, little is known on the underlying neurobiology due to the lack of appropriate animal models. In the socially monogamous and bi-parental prairie vole (Microtus ochrogaster), while most virgin males show spontaneous paternal behaviors (Paternal), others display pup-directed aggression (Attackers). Here we took advantage of this phenotypic dichotomy and used RNA-sequencing in three important brain areas to characterize gene expression associated with paternal behaviors of Paternal males and compare it to experienced fathers and mothers. This strategy allowed the identification of spontaneous paternal behaviors independently from fatherhood and pair-bonding. While Paternal males displayed the same range and extent of paternal behaviors than experienced Fathers, the nucleus accumbens (NAc) and medial preoptic area (MPOA) transcriptomes mainly reflected pair-bonded status or sex differences, respectively. The lateral septum (LS) transcriptome, however, primarily reflected phenotypic differences between Paternal and Attackers and suggested the involvement of the mitochondria, RNA translation, and protein degradation processes. Altogether, these observations highlight a marked structure- and phenotype-specific pattern of gene expression underlying paternal behaviors in prairie voles and highlight similarities and differences from those underlying fatherhood.

overall_design: A total of 24 prairie voles were used: 6 Mothers (6 MPOA, 6 NAc, 6 LS libraries), 6 Fathers (6 MPOA, 6 NAc, 6 LS libraries), 6 Paternal (4 MPOA, 6 NAc, 6 LS libraries), and 6 Attackers (6 MPOA, 6 NAc, 5 LS libraries).

first: Florian

last: Duclot

first: Yan

first: Samantha

middle: K

last: Saland

first: Zuoxin

last: Wang


title: RNA-seq of WT and shrek1 kernels at 13DAP

city: Qingdao

first: hui

last: liu

address: 72 Binhai Road, Jimo, Qingdao, P.R. China

summary: To investigate the biological functions of SHREK1 in seed development, we compared the transcriptome profiles between the WT and shrek1 kernels at 13DAP by  RNA-seq.

overall_design: mRNA profiles of 13DAP kernels of WT and shrek1 were analyzed in triplicates using NGS.

first: Bao-Cai

last: Tan

first: Hui