title: Next generation sequencing to do comparative transcriptome profiling of long bones from young and old mice

status: Public on Dec 15 2023

city: Nashville

first: Ananya

last: Nandy

state: Tennessee

address: 2215 Garland Ave

department: Clinical Pharmacology

institute: VUMC

summary: The goal of this study is to do a global transcriptiome profiling by NGS (RNA-seq) of RNA from long bone (Femur) of young (2 months) and aged (22 months) mice to understand how the bone function and their regulations are different between these two groups. Since loss of bone is prevalent with aging, we tried to find out what all genes related to bone function are affected at the expression level with aging. Using this gene expression data, we further tried to establish a relation between the pathways and regulators that contribute to this loss of function with biological replicates.

overall_design: RNAseq analysis from long bones of young and old mice samples. There were 10 total samples.

first: Elizabeth

last: Ruedy


title: The miR-183/96/182 Cluster Regulates Sensory Innervation, Resident Myeloid Cells and Functions of the Cornea Through Cell type-specific Target Genes

status: Public on Dec 20 2023

city: Detroit

first: Shunbin

last: Xu

state: MI

address: 540 E Canfield St, Scott Hall 8133/8137

department: Opthalmology, Visual and Anatomical Sciences

country: USA

institute: Wayne State University, School of Medicine

type: Expression profiling by high throughput sequencing

summary: The miR-183/96/182 cluster (miR-183C) is specifically expressed in sensory neurons and immune cells and modulates corneal immune/inflammatory response to bacterial infection. To uncover the roles of miR-183C in corneal homeostasis through its regulation of sensory neurons of the trigeminal ganglia (TG) and innate myeloid cells, we created miR-183C conventional knockout (KO), and sensory nerve-specific (SNS-CKO) and myeloid cell-specific conditional knockout (MS-CKO) mice. We performed 3'RNA sequencing in the TG and corneas of these knockout mice and their wild type (WT)-control littermates. To study specific functions of miR-183C in corneal resident myeloid cells (CRMCs), we isolated Csf1r-EGFP+ CRMCs from conventional KO and MS-CKO and their WT control mice. By comparison of the gene expression profiles of the KO or CKO vs their corresponding WT mice, we identified a series of differentially expressed genes. Bioinformatic analyses uncovered tissue- and/or cell-type-specific target genes of miR-183C. Functional annotation of the target genes revealed functions of miR-183C in TG and CRMCs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of TG, cornea and CRMCs of male young adult (8-12 weeks old) miR-183C KO, SNS-CKO and MS-CKO and their WT control mice.

first: Naman

last: Gupta

first: Mallika

last: Somayajulu

first: Katherine

last: Gurdziel

first: Giovanni

last: LoGrasso

first: Haidy

last: Aziz

first: Sharon

last: McClellan

first: Ahalya

last: Pitchaikannu

first: Manoranjan

last: Santra

first: Muhammed Farooq Abdul

first: Linda

middle: D

last: Hazlett


title: NGS-based miRNome reveals regulation in the miR-34/miR-449 cluster targetome in sinonasal cancers [miRNA-seq]

status: Public on Dec 28 2023

city: Verona

first: Marzia

last: Rossato

address: Strada Le Grazie 15

department: Biotechnology

country: Italy

institute: University of Verona

type: Non-coding RNA profiling by high throughput sequencing

summary: Using NGS-based miRNome, followed by AGO2-RIP-seq, the miR-34c and miR-449a and their direct targets were identified as factors involved in the development and progression of sinonasal cancers (SNCs). Both miR-34c and miR-449a were independent prognostic biomarkers and were associated with patient outcome.

overall_design: AGO2-RIP-seq, to identify the miR-34c/miR-449a  targetome

first: Marco

last: Tomasetti

first: Massimo

last: Re


title: Consequences of chromatin replication onRNAPII activity and transcriptional outcome [ChOR_G1]

status: Public on Dec 26 2023

city: Seville

first: Cristina

last: González-Aguilera

state: Seville

address: Avenida Américo Vespucio, 24

country: Spain

institute: CABIMER - CSIC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In the nucleus of the eukaryote cell, the genetic material is organized in the form of chromatin where DNA associates with nucleosomes, formed by an octamer of histone proteins, to provide the correct environment to regulate gene expression, maintain cellular identity and avoid disease. Despite the important role of chromatin organization in cellular function, in each cell division chromatin is totally disorganized. Nucleosomes are evicted ahead of the replication fork and will have to be recycled together with newly synthetized histones to maintain nucleosome density in the two daughter strands. This produce changes in chromatin accessibility and a dilution in epigenetic information. To date, it is not clear how these chromatin and epigenetic changes can affect gene expression. Here, we have used the cutting-edge technology ChOR-seq (Chromatin Occupancy after Replication and sequencing) and ChrRNA-seq (Chromatin-associated RNA-seq) to investigate the distribution and abundance of the RNA Polymerase II (RNAPII) in newly replicated chromatin and nascent RNA levels in human cells.

overall_design: Analysis of total RNAPII and S2P RNAPIIdistribution and abundance in newly replicated and mature chromatin by ChOR-seq in HeLa S3 cells.All experiments were done in duplicates. Replicated chromatin was labelled in early S. Chromatin of Drosophila melanogaster S2 cells were used as spike-in.

first: Federica

last: Bruno

first: Cristóbal

middle: C

last: Guisado

middle: G

last: Aguilera


title: Effect of depletion of Tfam on gene expression in stimulated B cells

status: Public on Dec 13 2023

city: Madrid

first: Nuria

last: Martínez-Martín

address: Nicolás Cabrera 1

institute: CBMSO-CSIC

summary: The germinal centre (GC) reaction requires a unique bioenergetic supply. Although mitochondria are remodelled upon antigen stimulation, mitochondrial function in B cells is still poorly understood. To gain a better understanding of the role of mitochondria in B cell function, we generated a mice that lack, specifically in B cells, TFAM, a transcription factor necessary for mitochondrial biogenesis. TFAM knock-out (KO) mice displayed a blockage of the GC reaction and established an immune response featured by the differentiation of activated B cells towards memory B cells and aged-related B cells, hallmarks of an aged immune response. Unexpectedly, GC blockage in TFAM KO mice did not cause defects in the bioenergetic supply but this phenotype was associated with a defect in remodelling of the lysosomal compartment in B cells. Therefore, these results may describe a new mitochondrial function for antigen presentation during the GC reaction, the abrogation of which may be the basis of an aged immune response.

overall_design: To investigate the impact of Tfam deletion in activated B cells, we sorted and stimulated in vitro B cells from WT and Tfamfl/fl Mb1Cre+ (KO) mice. RNA was purified and we performed gene expression profiling analysis using data obtained from RNAseq of 4 different mice for each genotype (WT and KO).

first: Marta

last: Iborra-Pernichi

first: Belen

last: S Estrada


title: Consequences of chromatin replication on RNAPII activity and transcriptional outcome [EdU-seq]

overall_design: Analysis of replicated regions associated to the study of the transcriptional outcome after chromatin replication by chromatin-associated RNA sequencing (ChrRNA). Two replicates of samples were performed.


title: Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

summary: While DNA N6-methyl-deoxyadenosine (6mA) is abundant in bacteria and protists, its presence and function in mammalian genomes have been less clear. We present Direct-Read 6mA sequencing (DR-6mA-seq), an antibody-independent method to measure 6mA at base-resolution with high sensitivity. DR-6mA-seq employs a unique mutation-based strategy to reveal 6mA sites as misincorporation signatures without any chemical or enzymatic modulation of 6mA. We validated DR-6mA-seq through successful mapping of the well-characterized G(6mA)TC motif in the E. coli DNA and identified 6mA sites in the mammalian mitochondrial DNA. As expected, when applying DR-6mA-seq to mammalian systems, we found that genomic DNA (gDNA) 6mA abundance is in general low in most mammalian tissues and cells; however, we did observe distinct gDNA 6mA sites in mouse testis and glioblastoma cells. DR-6mA-seq provides an enabling tool to detect 6mA at single-base resolution with high sensitivity for a comprehensive understanding of DNA 6mA in eukaryotes.

sample_organism:
Escherichia coli
Mus musculus
synthetic construct
Escherichia coli K-12

overall_design: Three biological replicates were generated.

first: Xinran

last: Feng

first: Lisheng

last: Zhang

first: Chuan

last: He


title: Expression data from lncRNA AL078604.2 and LINC01269 knockdown in MDA-MB-231, MDA-MB-468 and SKBR3 breast cancer cell lines

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 11F11, 5850 College Street

department: Pathology

country: Canada

institute: Dalhousie University

summary:
Breast cancer subtype-specific lncRNAs AL078604.2 and LINC01269 were knockdown in breast cancer cell lines
LncRNA AL078604.2 was knockdown by an anti-AL076804.2 antisense oligonucleotides (ASOs) in triple-negative breast cancer cell lines MDA-MB-231 and MDA-MB-468 breast cancer cells. LncRNA LINC01269 was knockdown by an anti-LINC01269 ASOs in HER2+ SKBR3 breast cancer cells. To ensure the initial presence of AL078604.2 and LINC01269 in their respective cell lines, qPCR analysis was performed to confirm their expression levels prior to knockdown experiments. The effectiveness of knockdown was confirmed by qPCR analysis, which validated the reduction in AL078604.2 and LNC01269 expression in their corresponding cell lines following ASO treatment.

overall_design: To investigate the impact of lncRNA AL078604.2 on the transcriptome of triple-negative breast cancer, microarray analyses were conducted on MDA-MB-231 and MDA-MB-468 cell lines. Cells were treated with either control ASO or anti-AL078604.2 ASO1 for 48 hours. A parallel investigation was carried out to evaluate the effect of lncRNA LINC01269 on gene expression in HER2+ breast cancer cells. SKBR3 cells were treated with control ASO and anti-LINC01269 ASO for 48 hours. Following the ASO treatment, the cells were collected and preserved in TRIzol reagent for subsequent RNA purification. The purified RNA samples were then sent to The Centre for Applied Genomics (TCAG), located at The Hospital for Sick Children in Toronto, Canada. The RNA samples underwent reverse transcription into complementary DNA (cDNA) and were subsequently hybridized to the Affymetrix Human Gene 2.0 ST microarray platform. The collected data was initially obtained in raw CEL format and subsequently processed using the Transcriptome Analysis Console (Affymetrix).

first: P

first: J

last: Venkatesh

first: M

last: Wasson


title: Translational control of skeletal muscle mass by the transcriptional repressor BCL6

first: Christopher

last: Futtner

state: Il

address: 303 E. Superior St, Lurie 7-220

department: Endocrinology

summary: Using mRNA-seq and ChIP-seq in muscle tissue, we found that BCL6 controls a broad range of anabolic targets, directly suppressing eukaryotic translation initiation factor 4E-binding protein 1 (Eif4epb1) and myostatin (Mstn) while enhancing insulin-like growth factor 1 (Igf1) and androgen receptor (Ar). Consistent with these gene regulatory effects, skeletal muscle ablation of Bcl6 increased physical association of the translation initiation factor eIF4E with its inhibitor EIF4E-BP1 and ribosomal sequencing in vivo revealed reduced translation efficiency.

overall_design: Genome-wide maps of chromatin state, gene expression, and translation efficiency in skeletal muscle in wild-type, control, and Bcl6 knock-out mice.

first: Grant

last: Barish

first: Krithika

last: Ramachandran


title: NK cells propagate T cell immunity following in situ tumor vaccination

status: Public on Dec 21 2023

city: Madison

first: Zachary

middle: Scott

last: Morris

state: Wisconsin

address: 1111 Highland Ave., WIMR Tower 1, Room 3131

department: Human Oncology

institute: University of Wisconsin-Madison

summary: We report an in situ vaccination, adaptable to nearly any type of cancer, that combines radiotherapy targeting one tumor and intratumoral injection of this site with tumor-specific antibody and interleukin-2 (IL-2; 3xTx). In a phase I clinical trial, administration of 3xTx (with an immunocytokine fusion of tumor-specific antibody and IL-2, hu14.18-IL2) to subjects with metastatic melanoma increases peripheral CD8+ T cell effector polyfunctionality. This suggests the potential for 3xTx to promote antitumor immunity against metastatic tumors. In poorly immunogenic syngeneic murine melanoma or head and neck carcinoma models, 3xTx stimulates CD8+ T cell-mediated antitumor responses at targeted and non-targeted tumors. During 3xTx treatment, natural killer (NK) cells promote CTLA4+ regulatory T cell (Treg) apoptosis in non-targeted tumors. This is dependent on NK cell expression of CD86, which is upregulated downstream of KLRK1. NK cell depletion increases Treg infiltration, diminishing CD8+ T cell-dependent antitumor response. These findings demonstrate that NK cells sustain and propagate CD8+ T cell immunity following 3xTx

overall_design: A preclinical model of tumor-bearing mice was developed to investigate systemic anti-tumor immune activation upon combinatorial treatment modalities. Primary and secondary tumors (MOC2) were engrafted by subcutaneous injection into the right and left flanks, respectively. Treatment was applied to primary tumors while secondary tumors were excised 12 days post trreatment and processed for RNA-seq transcriptional profiling

first: Won Jong

last: Jin

first: Justin

last: Jagodinsky

first: Jessica

middle: M

last: Vera

first: Paul

middle: A

last: Clark

first: Cindy

middle: L

last: Zuleger

first: Amy

middle: K

last: Erbe

first: Irene

last: Ong

first: Trang

last: Le

first: Kaitlin

last: Tetreault

first: Tracy

last: Berg

first: Alexander

last: Rakhmilevich

first: KyungMann

last: Kim

first: Michael

last: Newton

first: Mark

middle: R

last: Albertini

last: Sondel

middle: S


title: m6A RNA modification of TERRA lncRNA drives R-Loop formation and is required for telomere maintenance in ALT tumors [I]

city: Gothenburg

first: Tanmoy

last: Mondal

state: Västra Götaland

address: Bruna Stråket 16

department: Department of Clinical Chemistry and Transfusion Medicine

country: Sweden

institute: University of Gothenburg

type: Methylation profiling by high throughput sequencing

summary: Telomerase-negative tumors can maintain telomere length by alternative lengthening of telomeres (ALT) but the mechanism of telomere maintenance in ALT cells is not well understood. A significant portion of the relapse Neuroblastoma (NB) tumors are positive for ALT which suggests better dissecting the ALT mechanism could provide novel therapeutic opportunities. TERRA RNA which is derived from the telomere ends is localized to telomeres in R-loop dependent manner and is essential for telomere maintenance. In the present study, we provide evidence that RNA modification at the N6 position of internal adenosine (m6A) in TERRA RNA by methyl transferase METTL3 is essential for telomere maintenance in ALT cells and loss of TERRA m6A/METTL3 leads to accumulation of DNA damage over telomere. Our data suggest that m6A modification in TERRA RNA is required for R-loop formation and telomere targeting of TERRA. We observed that R-loop enriched TERRA is abundantly m6A modified and m6A mediated recruitment of hnRNPA2B1 to TERRA RNA is essential for R-loop formation. Together our study suggests that m6A-mediated R-loop formation could be a widespread mechanism utilized by other chromatin-interacting lncRNAs. We also show treating ALT positive NB cells with small molecule METTL3 inhibitor leads to compromised telomere targeting of TERRA and accumulation of DNA damage over telomere, suggesting METTL3 inhibition could be a therapeutic opportunity for ALT positive NB.

overall_design: m6A RNA immunoprecipitation (m6A-RIP seq) using Illumina short-reads and direct RNA Nanopore sequencing in U2OS and NB cells.

first: Roshan

last: Vaid

first: Akram

last: Méndez


title: Race-specific coregulatory and transcriptomic profiles associated with DNA methylation and androgen receptor in prostate cancer [RNA-Seq]

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: Prostate cancer incidence and related mortality are disproportionately higher in African American (AA) men than European American (EA) men, but the molecular mechanisms contributing to racial disparities are not fully elucidated. To identify molecular factors that can contribute to disease biology in prostate cancer from AA and EA men, we utilized a multi-omics approach to measure and integrate DNA methylation with gene expression changes. We compared and contrasted results from adjacent non-tumor and tumor tissues from AA and EA men. We found that hypermethylated regions are enriched for PRC2 and H3K27me3 pathways and EZH2/SUZ12 cofactors in a race-independent manner. On the other hand, hypomethylated regions in prostate tumors from AA men were enriched for olfactory/ribosomal pathways as well as distinct cofactors such as CTCF and KMT2A. DNA methylation at transcription start sites and 5’-UTR at GATA3, an androgen receptor (AR) coregulator, is associated with decreased gene expression in prostate tumors of AA men. Our analysis also showed an inverse correlation between DNA methylation and RNA expression of AR transcriptional targets, such as TRIM63, in prostate tumors of AA men. Our observations suggest a dysregulation of the AR signaling pathway in prostate cancer from AA men. To determine whether targeting AR results in race-specific gene expression changes, we utilized a prostate-cancer-specific Boolean network. Our simulation revealed that prolonged AR inhibition results in significant dysregulation in TGF-β, IDH1, and cell cycle pathways in prostate cancer of AA men. We expanded our observation of gene expression changes in the Boolean network and investigated RNA-sequencing data to better understand overall transcriptional alterations occurring in prostate tumors from AA and EA men. We found that gene expression changes related to microtubules, a subset of immune-related, and TMPRSS2-fusion pathways were dysregulated in prostate tumors of AA men and corresponded with progression-free survival of AA men. Altogether, the current study dissects complex signaling networks that are clinically actionable in prostate cancer from AA and EA men.

overall_design: 58 AA (31 Tumors and 27 adjacent) and 63 EA (31 Tumors and 32 adjacent) collected samples

first: Swathi

last: Ramakrishnan

last: Cortes-Gomez

first: Spencer

last: Rosario

first: Se

middle: J

first: Donald

middle: E

last: Mager

first: Kristopher

last: Attwood

first: Sarah

last: Athans

first: Qiang

last: Hu

first: Jianmin

last: Wang

first: Anna

last: Woloszynska


title: m6A RNA modification of TERRA lncRNA drives R-Loop formation and is required for telomere maintenance in ALT tumors

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

overall_design: Refer to individual Series


title: Disturbed flow in the juxta-anastomotic area of an arteriovenous fistula correlates with endothelial loss, acute thrombus formation and neointimal hyperplasia

status: Public on Dec 08 2023

city: New Haven

first: Yuichi

last: Ohashi

state: CT

address: 10 Amistad Street #414J

department: Surgery

institute: Yale University School of Medicine

summary:
Background: Clinical failure of arteriovenous fistulae (AVF) is frequently due to juxta-anastomotic neointimal hyperplasia (JANIH). Although the mouse AVF model recapitulates human AVF maturation, previous studies focused on the outflow vein distal to the anastomosis. We hypothesized that the juxta-anastomotic area (JAA) has increased NIH compared to the outflow vein.

Method: AVF were created in C57BL/6 mice without or with chronic kidney disease (CKD). Temporal and spatial changes of the JAA were examined using histology and immunofluorescence. Computational techniques were used to model the AVF. RNA-seq and bioinformatic analyses were performed to compare the JAA with the outflow vein. The jugular vein to carotid artery AVF model was created in Wistar rats.

Result: The neointima in the JAA shows increased volume compared to the outflow vein. Computational modeling shows increased volume of disturbed flow at the JAA compared to the outflow vein. Endothelial cells are immediately lost from the wall contralateral to the fistula exit, followed by thrombus formation and JANIH. Gene Ontology (GO) enrichment analysis of the 1862 differentially expressed genes (DEG) between the JANIH and the outflow vein identified 525 overexpressed genes. The rat jugular vein to carotid artery AVF showed changes similar to the mouse AVF.

Conclusion: Disturbed flow through the JAA correlates with rapid endothelial cell loss, thrombus formation, and JANIH; late endothelialization of the JAA channel correlates with late AVF patency. Early thrombus formation in the JAA may influence later development of JANIH.

overall_design: All animal experiments were performed in strict compliance with federal guidelines and with approval from the Institutional Animal Care and Use Committee of the Yale University. Mice were 9 to 11 weeks of age when the surgeries were performed. Anesthesia was administered using 2% to 2.5% isoflurane, and extended-release buprenorphine (Ethiqa XR; North Brunswick, NJ, USA) was administered subcutaneously with a dosage of 3.25 mg/kg body weight for intraoperative and postoperative analgesia. Briefly, after exposing the IVC and aorta, an aortocaval fistula was created by puncturing the distal aorta into the IVC using a 25-gauge needle, as described previously.(Yamamoto et al., 2013)  Visualization of pulsatile arterial blood flow in the IVC was used to assess initial technical success of AVF creation. The abdomen was then closed in two layers using running 6-0 sutures. On postoperative day 7, the anastomotic neointimas (combined from 4 mice) and outflow veins (combined from 2 mice) were carefully harvested.

first: Hualong

last: Bai

first: Alan

last: Dardik


title: Transcriptome analysis reveals the mechanism of bovine lactoferrin against lipopolysaccharide-induced acute lung injury

status: Public on Dec 19 2023

city: Shijiazhuang

first: Yantao

last: Li

address: No.389, Zhongshan East Road, Shijiazhuang City

department: Department of Critical Care Medicine

country: China

institute: The First Affiliated Hospital of Hebei University of Chinese Medicine

summary: Lactoferrin (LF) is an iron-binding multifunctional cationic glycoprotein secreted by exocrine glands and neutrophils in mammals. In this study, we created a mouse model of lipopolysaccharide (LPS)-induced acute lung injury and explored the anti-inflammatory effect and mechanism of bovine lactoferrin (bLF) in acute lung injury using the RNA sequencing (RNA-seq) technology and transcriptome analysis.

overall_design: A total of 24 mice were randomly divided into 4 groups (n = 6): control, LPS (lipopolysaccharide, 50 μL, 1 μg/μL), bLF (bovine lactoferrin, 200 mg/kg/day), and treatment (LPS+bLF). After 14 days of modeling, lung tissues of 12 mice from the control, LPS, bLF, and LPS+bLF groups (n = 3) were used for RNA-seq analysis. mRNA library construction and transcriptome sequencing (RNA-seq) were performed by the BGI Institute of Life Sciences (Shenzhen, China).

first: Zhigang

last: Cai


title: UNC93B1 variants underlie TLR7-dependent autoimmunity

status: Public on Dec 14 2023

city: Munich

first: Johanna

last: Klughammer

address: Feodor Lynen Str 25

country: Germany

institute: Gene Center LMU

summary: UNC93B1 is critical for trafficking and function of nucleic acid-sensing Toll-like receptors (TLRs) TLR3, TLR7, TLR8, and TLR9, which are essential for antiviral immunity. Overactive TLR7 signaling induced by recognition of self-nucleic acids has been implicated in systemic lupus erythematosus (SLE). Here, we report UNC93B1 variants (E92G and R336L) in four patients with early-onset SLE. Patient cells or mouse macrophages carrying the UNC93B1 variants produced high amounts of TNF-α and IL-6 and upon stimulation with TLR7/TLR8 agonist, but not with TLR3 or TLR9 agonists. E92G causes UNC93B1 protein instability and reduced interaction with TLR7, leading to selective TLR7 hyperactivation with constitutive type I IFN signaling. Thus, UNC93B1 regulates TLR subtype-specific mechanisms of ligand recognition. Our findings establish a pivotal role for UNC93B1 in TLR7-dependent autoimmunity and highlight the therapeutic potential of targeting TLR7 in SLE.

overall_design:
PBMCs of patients with mutations in the UNC93B1 gene as well as healthy controls were analyzed using 10x Chromium singel-cell RNA sequencing.
***Submitter declares that the raw data will be deposited in EGA due to patient privacy concerns.***

first: Min Ae

last: Lee-Kirsch


title: Transcriptome profiling of expanding pancreas progenitors derived from the H1 human pluripotent stem cells using TGFb inhibition

status: Public on Dec 07 2023

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

institute: TU Dresden

summary: The analysis revealed several candidate signaling pathways to be modulated in order to derive a reproducible procedure for the expansion of pancreatic progenitors derived from human pluripotent stem (hPS) cells

overall_design:
Pancreas progenitors were analyzed as soon as they were derived from differentiating hPS cells. Independently derived cell populations that expanded occasionally were analyzed after five (p5) and after 10 (p10) passages
CINI is a condition tested for the expansion as described in the paper. CINI is Condition INItial.

first: Ioannis

last: Giannios

first: Daniela

last: Pezzolla


title: Intestinal carbapenem-resistant Klebsiella pneumoniae undergoes complex transcriptional reprogramming following immune activation

city: Genève

first: Clément

last: David

state: Canton de Genève

address: Rue Michel-Servet 1

department: PATIM

country: Switzerland

institute: Université de Genève

summary: Carbapenem-resistantKlebsiella pneumoniae(CR-Kp) is significant threat to public health worldwide. The primary reservoir for CR-Kp is the intestinal tract, where the bacterium is usually present at low density, but can bloom following antibiotic treatment, mostly in hospital settings. The impact of disturbances in the intestinal environment on the fitness, survival, expansion, and drug susceptibility of this pathogen is not well-understood. Nevertheless, gaining such knowledge could lead to innovative intervention strategies for addressing colonization and infection. Here, we adopted anin vivomodel to examine the transcriptional adaptation of a CR-Kp clinical isolate to immune activation in the intestine. We report that as early as 6 hours following host treatment with anti-CD3 antibody, CR-Kp underwent rapid transcriptional changes including downregulation of genes involved in sugar utilization and amino acid biosynthesis, and upregulation of genes involved in amino acid uptake and catabolism, antibiotic resistance, and stress response. In agreement with these findings, the concentration of oxidative species and amino acids was increased in the mouse intestine following treatment. Genes encoding for proteins containing the domain of unknown function (DUF) 1471 were particularly upregulated, however their deletion did not impair CR-Kp fitness in vivoupon immune activation. Transcription factor enrichment analysis identified the global regulator cAMP-Receptor Protein CRP as a potential orchestrator of the observed transcriptional signature. In keeping with the recognized role of CRP in regulating utilization of alternative carbon sources, CRP deletion in CR-Kp resulted in strongly impaired gut colonization, but this effect was not amplified by immune activation. Thus, following intestinal colonization, which occurs in a CRP-dependent manner, CR-Kp can rapidly respond to immune cues by implementing a well-defined and complex transcriptional program whose direct relevance towards bacterial fitness remains cryptic. Further analyses utilizing this model may identify key factors to tackle the intestinal stage of CR-Kp colonization.

overall_design:
We investigated the molecular programs adopted by CR-Kp in the gut lumen and the relation of this pathobiont with the immune system.
To do so, we performed trancriptional profiling using data obtained from intestinal CR-Kp ST-258 in mice subjected to acute immune activation. We also performed transcriptional profiling of the cecal tissue of these mice.

first: Clement

first: Aleksander

last: Czauderna

first: Liqing

last: Cheng

first: Marion

last: Lagune

first: Hea-Jin

last: Jung

first: Sohn

last: Kim

first: Eric

last: Pamer

first: Liang

last: Chen

first: Simone

last: Becattini


title: Unstableregulatory and autoreactive effector T cells in patients with FOXP3 mutations

city: Stanford

first: Jason

last: Nideffer

state: CA

address: 240 Pasteur Drive

department: Medicine

institute: Stanford University

summary: Studies of the monogenic autoimmune disease immunodysregulation polyendocrinopathy enteropathy X-linked syndrome (IPEX) have elucidated the essential function of the transcription factor FOXP3 and thymic-derived regulatory T cells (Tregs) in controlling peripheral tolerance. However, the presence and the source of autoreactive T cells in IPEX remain undetermined. Here, we investigated how FOXP3 deficiency affects the T cell receptor (TCR) repertoire and Treg stability in vivo and compared T cell abnormalities in patients with IPEX to those in patients with autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy syndrome (APECED). To study Tregs independently of their phenotype and to analyze T cell autoreactivity, we combined Treg-specific demethylation region analyses, single-cell multi-omic profiling, and bulk TCR sequencing. We found that patients with IPEX, unlike patients with APECED, have expanded autoreactive T cells originating from both autoreactive effector T cells (Teffs) and Tregs. In addition, a fraction of the expanded Tregs lost their phenotypic and functional markers including CD25 and often also FOXP3.  Functional experiments with CRISPR/Cas9-mediated FOXP3 knock-out Treg and Tregs from patients with IPEX indicated that the patients’ Tregs gain a Th2 skewed Teff-like function, which is consistent with immune dysregulation observed in these patients. Analyses of FOXP3 mutation-carrier mothers and a patient with IPEX after hematopoietic stem cell transplantation, indicated that Tregs expressing non-mutated FOXP3 prevent the accumulation of autoreactive Teffs and unstable Tregs. Collectively, we describe Treg instability and Teff autoreactivity in patients with IPEX. These findings could be directly used for diagnostic and prognostic purposes and for monitoring the effects of immunomodulatory treatments.

overall_design: The study report scRNA seq, cell surface protein, and TCR data from CD4+ T cells from 3 healthy donors (HDs) and 3 patients with IPEX. The samples were hash tagged (1 HD and 1 IPEX), and analyzed ex vivo or after TCR stimulation.

first: Šimon

last: Borna

first: Esmond

last: Lee

first: Akshaya

last: Ramachandran

first: Bing

last: Wang

first: Jeanette

last: Baker

first: Melissa

last: Mavers

first: Uma

last: Lakshmanan

first: Mansi

last: Narula

first: Amy

last: Garrett

first: Janika

last: Schulze

first: Sven

last: Olek

first: Louis

last: Marois

first: Yael

last: Gernez

first: Monica

last: Bhatia

first: Hey

last: Chong

first: Jolan

last: Walter

first: Maleewan

last: Kitcharoensakkul

first: Abigail

last: Lang

first: Megan

last: Cooper

first: Alice

last: Bertaina

first: Maria

last: Roncarolo

last: Meffre

first: Rosa

last: Bacchetta


title: Prophilactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction.

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Senescent cells accumulate in organisms over time as a result of tissue damage and impaired immune surveillance and are thought to contribute to age-related tissue decline1,2. In agreement, genetic ablation studies reveal that elimination of senescent cells from aged tissues can ameliorate various age-related pathologies, including metabolic dysfunction and decreased physical fitness3-7. While small-molecule drugs capable of eliminating senescent cells (known as ‘senolytics’) partially replicate these phenotypes, many have uncertain mechanisms of action and all require continuous administration to be effective. As an alternative approach, we previously developed a cell-based senolytic therapy based on chimeric antigen receptor (CAR) T cells targeting uPAR, a cell-surface protein upregulated on senescent cells, and showed these can safely and efficiently eliminate senescent cells in young animals and reverse liver fibrosis8. We now show that uPAR-positive senescent cells accumulate during physiological aging and that they can be safely targeted with senolytic CAR T cells in aged animals. Treatment with anti uPAR CAR T cells ameliorates metabolic dysfunction by improving glucose tolerance and exercise capacity in physiological aging as well as in a model of metabolic syndrome. Importantly, the beneficial effects of senolytic CAR T cells are long lasting; single administration of a low dose is sufficient to achieve long-term therapeutic and preventive effects.

overall_design: Liver, gonadal adipose tissue and pancreas of 4 aged mice (20 months old; 2 females and 2 males) was dissociated into single cell suspension and subsequently stained for surface uPAR expression. Cells were FACS sorted into uPAR+ and uPAR- populations for each of the organs. After cell sorting the two females and the two males of each organ and population were pooled together so that each organ would have a replicate consisting of 2 pooled male samples and 2 pooled female samples. Single-cell RNAseq was then carried out using 10X Genomics 3' Gene Expression chemistry.

first: Corina

last: Amor

first: Jonathan

last: Preall


title: Effect of methionine-chorine-deficient diet (MCD) in murine liver

status: Public on Dec 06 2023

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

country: Japan

institute: Kochi University

type:
Expression profiling by array
Non-coding RNA profiling by array

platform_organism:
Mus musculus
synthetic construct


title: Separating the impact of flocculation upon global gene transcription in a yeast Cyc8 mutant

status: Public on Dec 05 2023

city: Dublin 2

first: Alastair

last: Fleming

address: College Green

department: Microbiology Dept.

country: Ireland

institute: Trinity College Dublin

summary: The transcriptome from a S. cerevisiae tup1 deletion mutant was one of the first comprehensive yeast transcriptomes published. Subsequent transcriptomes from tup1 and cyc8 mutants firmly established the Tup1-Cyc8 complex as predominantly acting as a repressor of gene transcription. However, transcriptomes from tup1/cyc8 gene deletion or conditional mutants would all have been influenced by the striking flocculation phenotypes that these mutants display. In this study, we have separated the impact of flocculation from the transcriptome in a cyc8 conditional mutant to reveal those genes (i) subject solely to Cyc8p dependent regulation, (ii) regulated by flocculation only, and (iii) regulated by Cyc8p and further influenced by flocculation. We reveal an improved Cyc8p transcriptome that includes newly identified Cyc8p-regulated genes that were masked by the flocculation phenotype and excludes genes which were indirectly influenced by flocculation and not regulated by Cyc8p. Furthermore, we show evidence to suggest that flocculation exerts a complex and potentially dynamic influence upon global gene transcription. These data should be of interest to future studies into the mechanism of action of the Tup1-Cyc8 complex and to those involved in understanding the development of flocculation and its impact upon cell function.

overall_design: We carried out RNA-Seq analysis to compare the transcriptomes of a flocculating Cyc8 conditional mutant (Flo+ Cyc8-AA) and a non-flocculating Cyc8 conditional mutant (Flo- Cyc8-AA)

first: Brenda

last: Lee

middle: B


title: Identification of genes targeted by miR-501 in two gastric cancer cell lines.

status: Public on Dec 02 2023

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

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

summary: This study aimed to explore the downstream genes targeted by miR-501 in GC.

overall_design: To reveal the genes downregulated by miR-501, we transfected GC cell lines with miR-501 mimics and negative control siRNAs. The transcriptome sequencing studies were performed by deep sequencing, using Illumina HiSeq 4000.

first: Shanshan

last: Qin

first: Dandan

last: Li


title: DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues

city: Boston

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

type: Genome binding/occupancy profiling by array

summary: Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) in eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyzed 92 human HD mutants, including disease-associated variants and variants of unknown significance (VUS), for their effects on DNA binding activity. Many of the variants altered DNA binding affinity and/or specificity. Structural analysis identified 14 novel specificity-determining positions, 5 of which do not contact DNA. The same missense substitution at analogous positions within different HDs exhibited different effects on DNA binding activity. Variant effect prediction tools perform moderately well in distinguishing variants with altered DNA binding affinity, but poorly in identifying those with altered binding specificity. Our results highlight the need for biochemical assays of TF coding variants and promote dozens of variants for further investigations into their pathogenicity and the development of clinical diagnostics and precision therapies.

overall_design: 123 homedomains were assayed by protein binding microarray (PBM).

first: Kian

middle: H

last: Kock

first: Patrick

last: Kimes

first: Sachi

middle: I

last: Iiyama

first: Sabrina

last: Phanor

first: James

middle: T

last: Anderson

first: Gayatri

last: Ramakrishnan

first: Colin

last: Lipper

first: Dongyuan

last: Song

first: Jesse

middle: V

last: Kurland

first: Julia

last: Rogers

first: Raehoon

last: Jeong

last: Blacklow

first: Rafael

last: Irizarry

first: Martha

last: Bulyk


title: Effect of methionine-chorine-deficient diet (MCD) on whole gene expression in murine liver [mRNA]

first: Shuji

last: Sakamoto

summary:
It is known that administration of MCD induces a severe state of hepatic fibrosis in mice.
To attempt to elucidate molecular mechanism of hepatic fibrosis, we performed  whole transcriptome analysis by microarray using RNAs prepared from liver of wild-type mice fed with normal diet (ND) or MCD.

overall_design: RNAs were prepared from liver of wild-type male C57BL/6J mice fed with ND or MCD. Single-stranded cDNAs derived from the RNAs were hybridized with a Mouse Gene 2.1 ST Array Strip (ThermoFisher Scientific). The array was scanned by the GeneAtlas system (Affymetrix) to measure the intensities of the microarray spots.

first: Takuma

last: Higuchi


title: Unified analysis of DNA methylation, hydroxymethylation and chromatin accessibility through targeted DNA labeling [RNA-seq]

status: Public on Dec 01 2023

city: Vilnuis

first: Kotryna

last: Kvederaviciute

address: Universiteto str. 3

country: Lithuania

institute: Vilnius University

summary: We performed differentiation of mouse ESC (mESC) into a population of radial-glial neuronal progenitor cells (NPC) and later into terminally differentiated glutamatergic pyramidal neuron cells (NC).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E14TG2a cells at 3 developmental stages (mouse ESC, neuronal progenitors and terminally differentiated glutamatergic pyramidal neurons) in two biological replicates.

last: Skardžiūtė

last: Kvederavičiūtė

first: Inga

last: Pečiulienė

first: Milda

last: Narmontė

first: Janina

last: Ličytė

first: Saulius

last: Klimašauskas

first: Edita

last: Kriukienė


title: Unified analysis of DNA methylation, hydroxymethylation and chromatin accessibility through targeted DNA labeling


title: m6A RNA modification of TERRA lncRNA drives R-Loop formation and is required for telomere maintenance in ALT tumors [II]

first: Tanmoy

last: Mondal

overall_design: m6A RNA immunoprecipitation (m6A-RIP seq) using Illumina short-read sequencing in NB samples.

first: Roshan

last: Vaid

first: Akram

last: Méndez


title: Distinct transcriptomic profile of satellite cells contributes to preservation of neuromuscular junctions in extraocular muscles of ALS mice

status: Public on Dec 11 2023

city: Arlington

first: Ang

last: Li

state: TX

address: 655 W Mitchell St, SEIR 244

department: Kinesiology

institute: University of Texas at Arlington

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neuromuscular disorder characterized by progressive weakness of almost all skeletal muscles, whereas extraocular muscles (EOMs) are comparatively spared. While hindlimb and diaphragm muscles of end-stage SOD1G93A (G93A) mice (a familial ALS mouse model) exhibit severe denervation and depletion of Pax7+satellite cells (SCs), we found that the pool of SCs and the integrity of neuromuscular junctions (NMJs) are maintained in EOMs. In cell sorting profiles, SCs derived from hindlimb and diaphragm muscles of G93A mice exhibit denervation-related activation, whereas SCs from EOMs of G93A mice display spontaneous (non-denervation-related) activation, similar to SCs from wild-type mice. Specifically, cultured EOM SCs contain more abundant transcripts of axon guidance molecules, including Cxcl12, along with more sustainable renewability than the diaphragm and hindlimb counterparts under differentiation pressure. In neuromuscular co-culture assays, AAV-delivery of Cxcl12 to G93A-hindlimb SC-derived myotubes enhances motor neuron axon extension and innervation, recapitulating the innervation capacity of EOM SC-derived myotubes. G93A mice fed with sodium butyrate (NaBu) supplementation exhibited less NMJ loss in hindlimb and diaphragm muscles. Additionally, SCs derived from G93A hindlimb and diaphragm muscles displayed elevated expression of Cxcl12 and improved renewability following NaBu treatment in vitro. Thus, the NaBu-induced transcriptomic changes resembling the patterns of EOM SCs may contribute to the beneficial effects observed in G93A mice. More broadly, the distinct transcriptomic profile of EOM SCs may offer novel therapeutic targets to slow progressive neuromuscular functional decay in ALS and provide possible ‘response biomarkers’ in pre-clinical and clinical studies.

overall_design: Skeletal muscles from different body regions exhibit different degree of vulerability to ALS, with hindlimb (HL) muscles like TA and EDL most severely affected and extraocular muscles (EOMs) least affected. We observed an association between the severity of NMJ degeneration and peri-NMJ SC depletion in HL, diaphragm (Dia) and EOMs in end-stage G93A mice. To investigate whether there is a mechanistic link between the two phenomena, we FACS-isolated HL, Dia, EOM SCs from end-stage G93A mice and their wildtype (WT) littermates to compare the transcriptome of SCs cultured under expansion and differentiation conditions using RNA-Seq. Additionally, we previously showed that feeding G93A mice with NaBu supplmenetation expanded their life span. Since NaBu is an HDAC inhibitor capable of changing the epigenetic landscape, we compared the transcriptome of G93A Dia, HL SCs with or without 3-day NaBu treatment.

first: Jingsong

last: Zhou


title: Unified analysis of DNA methylation, hydroxymethylation and chromatin accessibility through targeted DNA labeling [TOP-Seq]

summary: Epigenetic regulation depends on complex interactions between different epigenetic factors, such as DNA methylation and chromatin accessibility. As the gene activation potential cannot be predicted by looking at chromatin accessibility or DNA modification alone, methods capable of relating multiple factors are highly desirable. Existing methods for combined chromatin accessibility and DNA modification analysis rely on bisulfite sequencing, which has a number of well known drawbacks. We developed a novel cost-efficient method for simultaneous profiling of DNA methylation and hydroxymethylation within open chromatin loci. Our approach is based on chemo-enzymatic covalent tagging of unmodified (uCG) and hydroxymethylated (5hmC) CG sites along with GC sites in native chromatin, which are then mapped by tag-selective sequencing. Validation of the technology on model DNA systems and mammalian cells demonstrated a great applicability of this method for epigenomic studies. We employed the technology for tracking chromatin dynamics combined with changes of two different cytosine states, unmodified and hydroxymethylated, during differentiation of embryonic stem cells (ESC) which revealed extensive chromatin dynamics and DNA modification changes across gene bodies of development-associated genes at early transition from ESC. Strong DNA demethylation in the ESC-to-neuron differentiation pathway proceeds independently from cell transcriptional programs and highlights the value of separate 5hmC and 5mC analysis in understanding cell fate decisions.

overall_design: We performed differentiation of mouse ESC (mESC) into a population of radial-glial neuronal progenitor cells (NPC) and later into terminally differentiated glutamatergic pyramidal neurons (NC). 1*105 nuclei extracted from three developmental stages cells were used for double uCG- and GC-, 5hmC- and GC-azide and triple CG-, GC-alkyne, and 5hmC-azide labeling reactions.


title: Neoadjuvant durvalumab plus radiation versus durvalumab alone in stages I-III non-small cell lung cancer: survival outcomes and molecular correlates of a randomized phase II trial

status: Public on Nov 26 2023

first: Olivier

last: Elemento

address: 1305 York Ave

department: Biochemistry

institute: Weill Cornell Medicine

summary: Randomized phase II trial patients with early-stage non-small cell lung cancer were treated with either two preoperative cycles of the anti-PD-L1 antibody durvalumab alone or combined with immunomodulatory doses of stereotactic radiation. We report, based on transcriptome analyses of resected tumors, a correlation between an increase of immune pathway genes and freedom from recurrence.

overall_design: RNA-seq studies of resected tumors to identify biomarkers of recurrence in a clinical trial of immune checkpoint blockade therapy in the treatment of non-small cell lung cancer.

first: Nasser

last: Altorki

first: Timothy

last: McGraw

first: Vivek

last: Mittal

first: Alain

last: Borczuk


title: Probe to gene expressions in HIV infected CD4 T cells in the presence of CDK, caspase inhibitors and Nef

status: Public on Nov 23 2023

city: Rockville

first: Peter

last: Sun

state: MD

address: 5625 Fishers lane

department: Division of Intramural Research

institute: National Institute of Allergy and Infectious Diseases

summary:
HIV-1 infection selectively alters gene expressions of CD4 T cells. To understand the effects of HIV to the expressions of CDK and caspase pathway genes in the presence and absence of Nef, we infected CD8-depleted PBMC from healthy donors with HIV-1 BAL  in the presence of BB-94, PD-0332991, QVD-OPH or DMSO control, or with Nef-sufficient, Nef-deficient Vpu-sufficient, Vpu-deficient NL4-3 strain of HIV-1.  On day 6 of infection, cells were enriched for CD4 T cells for gene expression profile analyses by RNA sequencing.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 16 different treated CD4 T cells.

overall_design: All treatments are done in duplicates with DMSO controls. Infections with Nef-sufficient (wildtype), deficient, deficient NL4-3 HIV were also carried out in duplicates.

first: Jason

last: Segura

middle: D


title: Study of the effects of AZA and its combination with autophagy inhibitor, spautin-1 on the transcriptome of AML cell lines [II]

status: Public on Nov 29 2023

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: AZA treatment in AML cell lines led to a delayed expression of ERE transcripts. Autophagy inhibition resulted in a greater abundance of ERE transcripts, triggered pro-inflammatory responses, and improved the cytotoxic activity of AZA.

overall_design: AML cell lines were treated with indicated treatments and cells were collected on Day4

first: N

last: Noronha

first: G

last: Ehx

first: C


title: Effect of methionine-chorine-deficient diet (MCD) on microRNA expression in murine liver [miRNA]

first: Shuji

last: Sakamoto

summary:
It is known that administration of MCD induces a severe state of hepatic fibrosis in mice. Recently, many microRNAs (miRNAs) with pro- or anti-fibrotic properties have been identified during hepatic fibrosis.
To attempt to elucidate molecular mechanism of hepatic fibrosis involved in miRNA fnction, we performed comprehensive analysis of miRNA expression by microarray using RNAs prepared from liver of wild-type mice fed with normal diet (ND) or MCD.

overall_design: RNAs were prepared from liver of wild-type male C57BL/6J mice fed with ND or MCD. Biotin-labeled RNA were hybridized with a miRNA 4.1 Array Strip (ThermoFisher Scientific). The array was scanned by the GeneAtlas system (Affymetrix) to measure the intensities of the microarray spots.

first: Takuma

last: Higuchi


title: Transcriptome profiling of expanding pancreas progenitors derived from the H1 human pluripotent stem cells using a combination of mitogenic signals, RA signalling suppression and selective inhibition of the TGFb and Wnt signalling pathways

first: Anthony

last: Gavalas

summary: The expansion procedure strengthened the pancreas progenitor identity while efficiently repressed endocrine differentiation and liver fate as well as acinar and duct differentiation programs

overall_design:
Pancreas progenitors were analyzed as soon as they were derived from differentiating hPS cells (p0). Independently derived and expanding cell populations were analyzed after five (p5) and after 10 (p10) passages
6 is a condition tested for the expansion as described in the paper. C6 is Condition 6.

first: Manuj

last: Bandral

first: Luka

last: Jarc


title: Gene expression profile at single cell level of bone marrow mononuclear cells from MDS patients with secondary venetoclax-based therapy failure

status: Public on Nov 30 2023

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Myelodysplastic syndromes (MDS) are incurable neoplasms that arise from early hematopoietic stem cells (HSCs). We used single cell RNA sequencing (scRNA-seq) to evaluate mechanisms of resistance to venetoclax-based therapies.

overall_design: Bone marrow mononuclear cells were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Juan

last: Rodriguez-Sevilla

first: Simona

last: Colla


title: Lineage regulators TFAP2C and NR5A2 function as bipotency activators in totipotent embryos

city: Beijing

first: Lijia

last: Li

address: Haidian District

department: School of Life Science

institute: Tsinghua University

summary: During the first lineage segregation, a mammalian totipotent embryo differentiates into inner cell mass (ICM) and trophectoderm (TE). However, how transcription factors (TFs) regulate this earliest cell fate decision in vivo remains elusive, with their regulomes primarily inferred from cultured cells. Here, we investigated the TF regulomes during the first mouse lineage specification across 6 stages, spanning the pre-initiation, initiation, commitment, and maintenance phases. Unexpectedly, we found TFAP2C, a trophoblast regulator, bound and activated both early TE and ICM genes at the totipotent (2-8-cell) stages (“bipotency activation”). Tfap2c deficiency caused downregulation of early ICM genes, including Nanog, Nr5a2, Tdgf1, and early TE genes, including Tfeb and Itgb5 in 8-cell embryos. Transcription defects in both ICM and TE lineages were also found in blastocysts, accompanied by increased apoptosis and reduced cell numbers in ICMs. Upon trophoblast commitment, TFAP2C left early-ICM genes but acquired binding to late-TE genes in blastocysts where it co-bound with CDX2, and later to extra-embryonic ectoderm (ExE) genes where it cooperatively co-occupied with the former ICM regulator SOX2. Finally, “bipotency activation” in totipotent embryos also applied to a pluripotency regulator NR5A2 which similarly bound and activated both ICM and TE lineage genes at the 8-cell stage. These data reveal a unique transcription circuity of totipotency underpinned by highly adaptable lineage regulators.

overall_design: By employing CUT&RUN, RNA-seq, and ATAC-seq, we systematically examined the genome wide TFAP2C, CDX2 and SOX2 chromatin binding and transcriptional functions in mouse early embryos.

first: Fangnong

last: Lai

first: Wei

last: Xie


title: Transcriptome-wide analysis of hidradenitis suppurativa

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: The aim of this study was to obtain a better understanding of the molecular background of hidradenitis suppurativa (HS). Global transcriptome analysis of lesional and perilesional skin identifies numerous differentially expressed genes that display unique expression pattern in HS. Genes, whose expression is dysregulated in the skin of patients suffering from HS are novel biomarker candidates and potential therapeutic targets for HS.

overall_design: RNA-seq was performed to analyse transcriptome of perilesional and lesional skin of five hidradenitis suppurativa patients and six controls.

first: Weronika

last: Szukala

first: Agata

last: Lichawska-Cieslar

first: Piotr

last: Krajewski

first: Maria

last: Kulecka

first: Izabela

last: Rumienczyk

first: Michał

first: Łukasz

last: Matusiak

first: Jolanta

last: Jura

first: Jacek

middle: C

last: Szepietowski


title: Effect of STAT1 gain of function R274Q on gene expression in CD4+ T cells from STAT1 GOF/CMV Cre and wild type C57BL/6J control mice

status: Public on Nov 22 2023

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary:
To investigate the effect of STAT1 gain of function on gene expression in CD4+ T cells, we sorted  TCRβ+CD4+ CD44+ T cells from the spleens of
STAT1 gain of function (STAT1 GOF/CMV Cre) and wild type C57BL/6J control mice of the same sexe  by cell sorting.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TCRβ+CD4+ CD44+ T cells  in STAT1 GOF/CMV Cre and wild type C57BL/6J control mice.

first: Bettelli

last: Estelle

first: Palle

last: Pushpalatha


title: Differential in vivo labeling with barcoded antibodies allows for simultaneous transcriptomic profiling of airway, lung tissue and intravascular immune cells

status: Public on Nov 20 2023

city: Gaithersburg

first: Yang

last: Song

address: 1 MedImmune Way

institute: AstraZeneca

summary: We used single-cell RNA sequencing (scRNA-seq) paired with DNA-barcoded antibodies to see if it allows to distinguish immune cells in different anatomical compartments in the lung akin to flow cytometry. To do this, we infected Balb/c animals with non-typeable Haemophilus influenzae (NTHi) and administered barcoded anti-CD45 antibody intratracheally and intravenously to label airway and vascular immune cells respectively. We isolated and sequenced neutrophils from the lung as these cells undergo transendothelial migration upon inflammation. We sequenced 5,543 neutrophils and found 3 different major clusters of neutrophils based on barcoded CD45 antibodies.

overall_design: Single-cell RNA sequencing with feature barcodes was performed on lung neutrophils from Balb/c animals infected with NTHi for 48-hours. For this experiment, cells were stained with 32 DNA-barcoded antibodies

first: Barbara

last: Christina Mindt

first: John

last: Kim

first: Troy

last: Warren

first: Antonio

last: DiGiandomenico


title: Study of the effects of AZA and its combination with autophagy inhibitor, spautin-1 on the transcriptome of AML cell lines

status: Public on Nov 24 2023

first: Claude

last: Perreault

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

overall_design: Refer to individual Series


title: RNA sequencing analysis of unilateral orchidectomy, bilateral orchidectomy, and Nell2 knockout initial segment-caput epididymis.

status: Public on Nov 19 2023

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

institute: Nagoya University

summary: Purpose: The purpose of this study is to characterize  genes whose expressions in the initial segment (IS)-caput epididymis were affected by unilateral orchidectomy (UOD), bilateral orchidectomy (BOD), and Nell2 gene ablation. Methods: The unilateral or bilateral orchidectomy of WT mice was performed from 8 weeks old and continued for 4 weeks until tissue sampling at 12 weeks old. Contralateral epididymis was used as a control for UOD. Sham operation was also done as a control for BOD. Nell2-/- mice and their control WT mice were used wthen they were 14-week-old. IS-caput epididymal mRNA profiles were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000. Results: RNA-seq data identified differentially expressed transcripts. Conclusions: Our results show that the expression of many genes was affected by UOD, BOD, and Nell2 ablation.

overall_design: IS-caput epididymal mRNA profiles of mice with experimental treatments were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000.


title: Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus

status: Public on Nov 16 2023

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

institute: University of Geneva, Faculty of Medicine / CMU

summary: The alpha-proteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. crescentus. Small RNAs (sRNAs) are a prominent class of regulators of bacterial gene expression, and most sRNAs characterized today engage in direct base-pairing interactions to modulate translation and/or stability of target mRNAs. In many cases, the ubiquitous RNA chaperone, Hfq, contributes to the establishment of RNA-RNA interactions. Although the deletion of the hfq gene is associated with a severe loss of fitness in C. crescentus, the RNA ligands of the chaperone have remained largely unexplored. Here we report on the identification of coding and non-coding transcripts associated with Hfq in C. crescentus, and demonstrate Hfq-dependent post-transcriptional regulation in this organism. We show that the conserved, Hfq-bound sRNA RusT is transcriptionally controlled by the conserved NtrYX two-component system and induced in response to iron starvation. By combining RusT pulse expression with whole-genome transcriptome analysis we determine 16 candidate target transcripts, more than half of which encode outer membrane transporters. We hence suggest RusT to support remodeling of the C. crescentus cell surface when iron supplies are limiting.

overall_design: Examination of NtrX-HA whole genome binding/occupancy (ChIP-Seq) in Caulobacter crescentus.

first: Laura

middle: N

last: Vogt

first: Gaël

last: Panis

first: Anna

last: Schäpers

first: Nikolai

last: Peschek

first: Michaela

last: Huber

first: Kai

last: Papenfort

first: Kathrin

last: Fröhlich


title: Heterogenous nuclear ribonucleoprotein D-like controls endothelial cell functions

status: Public on Nov 21 2023

city: Marburg

first: Julia

middle: E.

last: Weigand

address: Marbacher Weg 6

department: Pharmacy

institute: University of Marburg

summary: siRNA-mediated knockdown of the RNA-binding protein HNRNPDL was performed in HUVECs. Transcriptome changes were analyzed, to elucidate target genes important in HNRNPDL control over endothelial cell proliferation, migration and spheroid sprouting.

overall_design: 4 samples in total. 2 controls (si_ctrl), 2 HNRNPDL knockdown samples (si_DL).

first: Kathi

last: Zarnack


title: Multi-omics profiling of PcG proteins and related factors in Drosophila cell lines

status: Public on Nov 15 2023

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health


title: Nickel-induced transcriptional memory in lung epithelial cells promotes interferon signaling upon nicotine exposure

status: Public on Nov 11 2023

city: New York

first: Suresh

last: Cuddapah

address: 341 E 25th St

department: Division of Environmental Medicine, Department of Medicine

institute: New York University School of Medicine

summary: Nickel is an environmental toxicant prevalent in the atmosphere. Nickel exposure is associated with a multitude of human health hazards including chronic respiratory ailments and lung and nasal cancers. Our earlier studies on nickel exposure in lung cells showed that a majority of the gene expression changes caused by nickel exposure persisted even after termination of exposure (nickel-washed-out cells (NiW)). In this study, we wanted to examine the impact of a secondary toxicant exposure on the nickel-washed-out (NiW) cells as compared to the cells that were never exposed to nickel. To accomplish this, we exposed the untreated control cells (UT) and the nickel-washed-out cells (NiW) to multiple doses of nicotine (NTE). RNA-Seq analysis showed that the exposure of NiW cells to nicotine (NiW-NTE) caused unique gene expression changes that were markedly different from the gene expression changes caused by nicotine exposure of UT cells, which were never exposed to nickel. Analysis of the differentially expressed genes using Reactome Pathway analysis predicted interferon signaling only in the NiW-NTE cells. Upstream Regulator Analysis (URA) predicted STAT-1, a transcription factor that mediates cellular response to interferons, as the top potential upstream regulator in the NiW-NTE cells. Furthermore, chromatin immunoprecipitation (ChIP) analysis revealed increased STAT-1 binding at the promoters of genes associated with interferon signaling in NiW-NTE cells. Aberrant STAT-1 activation has been shown to promote carcinogenesis and interferon signaling promotes pathogenesis of autoimmune disease. Therefore, our results suggest that the epigenetic and transcriptional memory of the cells from the previous nickel exposure could negatively influence the outcome of secondary exposure to nicotine.

overall_design: To investigate the effects of the transcriptional memory of nickel exposure on future exposures, we exposed untreated Beas-2B cells and nickel-washed-out Beas-2B cells to nicotine. Using the differentially expressed genes for each condition from the RNA-seq results, we preformed pathway Analysis and Upstream Regulator Analysis.

first: Xiaoru

last: Zhang

first: Beatrix

last: Bradford

first: Sahdev

last: Baweja

first: Taotao

last: Tan

first: Hyun-Wook

last: Lee

first: Cynthia

last: Jose

first: Nicholas

first: Manpreet

last: Katari


title: The Unique Function of Runx1 in Skeletal Muscle Differentiation and Regeneration is Mediated by an ETS Interaction Domain (ATAC-Seq)

status: Public on Nov 17 2023

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: The conserved Runt-related (RUNX) transcription factor family are well-known master regulators of developmental and regenerative processes. Both Runx1 and Runx2 are expressed in satellite cells (SC) and skeletal myotubes. Conditional deletion of Runx1 in adult SC negatively impacted self-renewal, and skeletal muscle maintenance was impaired; Runx1-deficient SC cannot support muscle regeneration in response to injury. To determine the unique molecular functions of Runx1 that cannot be compensated by Runx2 we deleted Runx1 in C2C12 that retain Runx2 expression and established that myoblasts differentiation was blocked in vitro due in part to ectopic expression of Mef2c, a target repressed by Runx1. Structure-function analysis demonstrated that the Ets-interacting MID/EID region of Runx1 absent from Runx2 is critical to regulating myoblasts proliferation, differentiation, and fusion. Analysis of in-house and published ChIP-seq datasets from Runx1 (T-cells, muscle) versus Runx2 (preosteoblasts) dependent tissue identified enrichment for a Ets:Runx composite site in Runx1-dependent tissues. Comparing ATACseq datasets from WT and Runx1KO C2C12 cells showed that the Ets:Runx composite motif was enriched in peaks open exclusively in WT cells compared to peaks unique to Runx1KO cells. Thus, engagement of a set of targets by the RUNX1/ETS complex define the non-redundant functions of Runx1

overall_design: Control or Runx1KO C2C12 cells were grown in triplicate in growth media (20%) FBS and collected when near confluency.

first: Matthew

last: Hass

first: Meng

last: Yu

first: Xinhua

last: Lin

first: Raphael

last: Kopan


title: Study of the effects of AZA and its combination with autophagy inhibitor, spautin-1 on the transcriptome of AML cell lines [I]

status: Public on Nov 08 2023

first: Claude

last: Perreault

first: N

last: Noronha

first: G

last: Ehx

first: C


title: 5-methyl cytosine profile of Anthoceros agrestis

status: Public on Nov 10 2023

city: Ikoma

first: Tetsuya

last: Hisanaga

state: Nara

address: Takayama 8916-5

institute: Nara Institute of Science and Technology

summary: Bryophytes comprise mosses, liverworts and hornworts. The chromatin landscapes of mosses and liverworts are different, leaving open the question regarding the identity of the chromatin landscape of all bryophytes. To address this question we obtained a genome wide profile of 5-methylated cytosine from a model hornwort, Anthoceros agrestis.

overall_design: Enzymatic methyl sequencing (EM-seq) for a whole genome profile of cytosine methylation.

first: Frederic

last: Berger


title: Heat-induced cell damage induces autophagy-mediated cell expansion in Arabidopsis

city: Seoul

first: Hongoo

address: Gwan-ak ro 1

country: South Korea

institute: Seoul National University

summary: Plants have evolved sophisticated cellular and molecular mechanisms to acclimate to adverse environmental stresses. Here, we report that acute heat stress induces excessive cell expansion, reaching up to 13,000 μm2, in Arabidopsis thaliana. The heat-induced cell expansion progressed along with programmed cell death. Autophagy was responsible for excessive cell expansion, as evidenced by autophagic structures in the expanded cells as well as failure of heat-induced cell expansion in autophagy-related 5-1 (atg5-1) and atg7-2 mutants. We also reveal that the transcription factor ETHYLENE RESPONSE FACTOR115 (ERF115), which is activated upon neighboring cell death, is involved in heat-induced cell expansion. ERF115 accumulation in response to heat possibly activated the expression of several ATGs by directly binding to gene promoters. In agreement, the erf115 phytochrome a signal transduction1-2 (pat1-2) double mutant exhibited reduced cell expansion under heat stress with diminished autophagic activity. Overall, our findings indicate that heat-stress-induced cell death triggers autophagy-mediated cell expansion in plant leaves, which may compensate for the death of nearby cells.

overall_design: Total RNA was extracted with a Plant RNA extraction kit (Takara, 9769B) from 1st and 2nd rosette leaves at 1 and 48 h after wound or heat treatment. Three biological replicates were collected. Sequencing libraries were constructed with a TruSeq standard mRNA library kit followed by 100-bp paired-end sequencing using the Illumina NovaSeq platform.

first: Yunji

last: Namgung

first: Hong

middle: G

first: Hongwoo

first: Pil

last: Seo


title: Quantitative proteome dynamics across embryogenesis in a model chordate

status: Public on Nov 27 2023

city: Princeton

first: Martin

last: Wühr

state: NJ

address: 246 Carl Icahn Laboratory

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton Univeristy

summary: The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ~7k translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrate Xenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.

overall_design: We measured mRNA and protein abundance (PRIDE - PXD043619) on matching samples at eight key time points of Ciona development, spanning early embryonic development, maternal zygotic transition, gastrulation, neurulation, tail elongation, and the swimming larva.

first: Alexander

last: Frese

first: Andrea

last: Mariossi

first: Michael

last: Levine


title: ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [RNA-seq]

status: Public on Nov 07 2023

city: Shanghai

first: Mo

last: Zhang

address: 800 Dongchuan Road

institute: Shanghai Jiaotong University

summary: The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF depletion, revealed that ZNF143 and CTCF collaborate to regulate higher-order genome organization. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate TAD formation and genome compartmentalization whereas directional recognition of DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping.

overall_design: We knocked out ZNF143 in the HEC-1-B cell line using the CRISPR-Cas9 system, generating two ZNF143 knockout cell lines. We performed RNA sequencing on the cells to investigate changes in gene expression upon ZNF143 knockout.

first: Qiang

last: Wu


title: Age-dependent effects of metformin on human oligodendrocyte lineage cell ensheathment capacity.

city: Montreal

first: Alyson

last: Fournier

state: QC

address: 3801 Rue University

department: Department of Neurology and Neurosurgery

institute: McGill University

summary: Metformin restores myelination potential of aged rat A2B5+ oligodendroglia (OL) progenitor cells and may enhance recovery in children with post-radiation brain injury. Human late progenitor cells (O4+A2B5+) have superior capacity to ensheath nanofibers compared to mature OLs, with cells from pediatric sources exceeding adults. In this study we assessed effects of metformin on ensheathment capacity of human adult and pediatric progenitors and mature OLs and relate differences to transcriptional changes.  A2B5+ progenitors and mature OLs, derived from surgical tissues by immune-magnetic separation, were assessed for ensheathment capacity in nanofiber plates over 2 weeks. Metformin (10µM every other day) was added to selected cultures. RNA was extracted from treated and control cultures after 2 days. For all ages, ensheathment by progenitors exceeded mature OLs.  Metformin enhanced ensheathment by adult donor cells but reduced ensheathment by pediatric cells. Metformin marginally increased cell death in pediatric progenitors. Metformin induced changes in gene expression distinct for each cell type. Adult progenitors showed up-regulation of pathways involved in process outgrowth and promoting lipid biosynthesis. Pediatric progenitors showed a relatively greater proportion of down- versus up-regulated pathways, these involved cell morphology, development, and synaptic transmission. Metformin induced AMPK activation in all cell types; AMPK inhibitor BML-275 reduced functional metformin effects only with adult cells. Our results indicate age and differentiation stage related differences of human OL lineage cells in response to metformin. Clinical trials for demyelinating conditions will indicate how these differences translate in vivo.

overall_design: RNA was extracted from dissociated cultures of A2B5+ or A2B5- cells after two days in culture under control conditions or with addition of metformin. Bulk sequencing studies were conducted on 3 or 4 samples from each of the age groups


title: ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [Hi-C]

overall_design: Hi-C experiments in wild type, ZNF143 knock out, CTCF-AID untreated, CTCF-AID ZNF143 knock out, CTCF-AID auxin treated, and CTCF-AID ZNF143 knock out and auxin treated cells.


title: ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [ChIP-seq]

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K4me3 in HEC-1-B cells.


title: ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry


title: ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [ChIP-nexus]

overall_design: ChIP-nexus for ZNF143, CTCF, and RAD21 in wild type HEC-1-B cells, ZNF143KO cells, or in CTCF-AID cell that treated with auxin for 0h or 24h.


title: 5-methyl cytosine profile and chromatin profile of Anthoceros agrestis


title: Reanalysis of ChIP-Seq of GSE117155.

status: Public on Dec 01 2023

city: Boston

first: Parmit

middle: Kumar

last: Singh

address: 450 Brookline Avenue

department: Department of Cancer Immunology and Virology

institute: Dana-Farber Cancer Institute

summary: In this reanalysis, 20 GSM series were reanalyzed for ChIp-Seq data.

relation:
Reanalysis of: GSM3272323
Reanalysis of: GSM3272324
Reanalysis of: GSM3272325
Reanalysis of: GSM3272327
Reanalysis of: GSM3272328
Reanalysis of: GSM3272322
Reanalysis of: GSM3272326
Reanalysis of: GSM3272340
Reanalysis of: GSM3272341
Reanalysis of: GSM3272342
Reanalysis of: GSM3272343
Reanalysis of: GSM3272344
Reanalysis of: GSM3272345
Reanalysis of: GSM3272346
Reanalysis of: GSM3272347
Reanalysis of: GSM3272354
Reanalysis of: GSM3272355
Reanalysis of: GSM3272356
Reanalysis of: GSM3272357
Reanalysis of: GSM3272358

overall_design:
Reanalysis of the following ChIP-Seq samples in GSE117155:
BioProject accession: PRJNA481318
GEO Sample      SRA Runs        BioSample       Title
==========      ========        =========       =====
GSM3272322      SRR7525644      SAMN09665273    Pol II
GSM3272323      SRR7525645      SAMN09665272    Flag-LEDGF
GSM3272324      SRR7525646      SAMN09665271    Flag-HDGF2
GSM3272325      SRR7525647      SAMN09665270    H3K36me2
GSM3272326      SRR7525648      SAMN09665269    SPT16
GSM3272327      SRR7525649      SAMN09665268    H3K36me3_2
GSM3272328      SRR7525650      SAMN09665267    H3K27me3_2
GSM3272340      SRR7525662      SAMN09665253    MB_H3K27me3
GSM3272341      SRR7525663      SAMN09665314    MT_H3K27me3
GSM3272342      SRR7525664      SAMN09665313    MB_H3K36me2
GSM3272343      SRR7525665      SAMN09665310    MT_H3K36me2
GSM3272344      SRR7525666      SAMN09665309    MB_H3K36me3
GSM3272345      SRR7525667      SAMN09665308    MT_H3K36me3
GSM3272346      SRR7525668      SAMN09665307    MB_HDGF2
GSM3272347      SRR7525669      SAMN09665306    MT_HDGF2
GSM3272354      SRR7525676      SAMN09665299    MB_LEDGF
GSM3272355      SRR7525677      SAMN09665298    MT_LEDGF
GSM3272356      SRR7525678      SAMN09665297    MB_RNAPII
GSM3272357      SRR7525679      SAMN09665296    MT_RNAPII
GSM3272358      SRR7525680      SAMN09665295    MB_SPT16
*data processing step:
Raw files were downloaded from NCBI and were aligned against the UCSC hg19 human genome by bowtie with the parameter described by the original article (PMID: 31616795). Aligned files were converted to BAM with SAMtools version 1.3.1 and sorted with Picard tools. Differential peak calling was done with MACS2 version 2.1.1 with parameters --broad -g 2.7e9 --broad-cutoff 0.01 -f -B. The SRA file SRR7525652 was used as input for SRR7525645 and SRR7525646 whereas SRR7525651 was used as input for SRR7525644, SRR7525647, SRR7525648, SRR7525649, and SRR7525650. Further, file SRR7525674 was input for SRR7525662, SRR7525664, SRR7525666, SRR7525668, SRR7525678 and SRR7525680 whereas SRR7525675 was an input for SRR7525663, SRR7525665, SRR7525667, SRR7525669, SRR7525677 and SRR7525679.
wig and bed data. The SRR3538917_95P.txt contains coordinates of Speckles-associated domains or SPADs and was used in publications ( PMIDs:32665593 and 35203306).


title: ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [4C]

overall_design: 4C experiments using HS5-1, SBS and SWT1 as viewpoint in Hec1B wild type cells or CRISPR edited cells.


title: RNA-seq in human MDA-MB-231 cells with CRISPR knockout of ITGAV

status: Public on Nov 06 2023

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: This dataset examined the effect of ITGAV knockout in the gene expression profiling (RNA-seq) of human MDA-MB-231 cells.

overall_design: Cas9-expressing human MDA-MB-231 cells were transduced with sgCtrl and sgITGAV. RNAseq: The total RNA was extracted using the RNeasy Mini Kit (74104, QIAGEN) and submitted for RNA-seq at Novogene (PE150, NovoSeq6000).

first: Chun-Wei

last: Chen

first: Lu

last: Yang

first: Nicole

last: Mattson


title: The MADS-box genes SOC1 and AGL24 antagonize XAL2 functions in Arabidopsis thaliana root development

status: Public on Nov 13 2023

city: Milpa Alta

first: Claudio

middle: Augusto

last: Castañón-Suárez

state: Ciudad de México

address: Av. Sonora Norte #9, Barrio Santa Martha

department: Instituto de Ecología

country: Mexico

institute: UNAM

summary: MADS-domain transcription factors play pivotal roles in numerous developmental processes in Arabidopsis thaliana. While their involvement in flowering transition and floral development has been extensively examined, their functions in root development remain relatively unexplored. Here, we explored the function and genetic interaction of three MADS-box genes (XAL2, SOC1 and AGL24) in primary root development. Our findings revealed that SOC1 and AGL24, both critical components in flowering transition, redundantly act as repressors of primary root growth as the loss of function of either SOC1 or AGL24 partially recovers the primary root growth, meristem cell number, cell production rate, and the length of fully elongated cells of the short-root mutant xal2-2. Furthermore, we observed that the simultaneous overexpression of AGL24 and SOC1 leads to short-root phenotypes, affecting meristem cell number, cell production rate, fully elongated cell size, but only the overexpression of SOC1 affects distal root stem cell differentiation. Additionally, these genes exhibit distinct modes of transcriptional regulation in roots compared to what has been previously reported for aerial tissues. Moreover, our findings revealed that the expression of certain genes involved in cell differentiation, as well as stress responses, which are either upregulated or downregulated in the xal2-2 mutant, reverted to WT levels in the absence of SOC1 or AGL24.

overall_design: Since xal2-2 mutants exhibited the most prominent short-root phenotype and limited information was available on genes regulated by XAL2, we conducted an RNA-seq analysis to identify differentially expressed genes (DEGs) (fold change > 1.5; P<0.05) in 7-day-old roots of the loss-of-function mutant xal2-2 (Garay-Arroyo et al., 2013) and the overexpression line p35S:XAL2 (Pérez-Ruiz et al., 2015) in comparison with WT roots.

first: Adriana

last: Garay-Arroyo

middle: A

first: Carolina

last: Caballero-Cordero

first: Elena

last: Álvarez-Buylla


title: ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [HiChIP]

overall_design: HiChIP for ZNF143, CTCF, and RAD21 in wild type HEC-1-B cells, ZNF143KO cells, or in CTCF-AID cell that treated with auxin for 0h or 24h.


title: Dynamic 3'UTR changes during naïve CD4+ T cell activation and proliferation are reverted in the effector/memory state

city: Basel

first: Denis

last: Seyres

address: Hebelstrasse 20

institute: UniversitatSpital Basel

overall_design: Refer to individual Series


title: Dynamic 3'UTR changes during naïve CD4+ T cell activation and proliferation are reverted in the effector/memory state [Iso-Seq]

summary: 3’ untranslated regions (3’UTRs) are critical elements of most messenger RNAs: they contain binding sites for RNA-binding proteins (RBP) and microRNAs that affect various aspects of the RNA life cycle including transcript stability. In response to T cell receptor activation, T cells undergo massive expansion during the effector phase of the immune response and dynamically modify their 3’UTRs. Whether this serves to directly regulate the abundance of specific mRNAs or is a secondary effect of proliferation remains unclear. To study 3’UTR dynamics in T helper cells we investigated division-dependent alternative polyadenylation (APA). We generated 3’ end UTR sequencing in naïve, 48h activated (anti-CD3/CD28 cultured), memory and regulatory CD4+ Tcells. 48h activated Tcells were CTV-separated into three populations: cells not yet divided, divided once and twice. 3’UTR length changes were estimated using non-negative matrix factorization approach and partially compared with long-read PacBio sequencing. We found that, in T helper cells, APA events were transient and reverted after effector phase expansion. Using an orthogonal bulk RNAseq dataset, we found that APA genes were not significantly associated with either post-transcriptional or transcriptional regulation, differential gene expression or transcript usage, demonstrating a marginal effect of APA on transcript abundance. 3’UTR sequence analysis revealed conserved binding sites for important microRNAs and RBPs co-evolving with APA events. These results highlight the important role of polyA site usage in the control of cell fate decisions and homeostasis.

overall_design: Experimental design includes 3 samples: naive, 48h activated no division and 2 divisions

first: Oliver

last: Gorka

first: Ralf

last: Schmidt

first: Romina

last: Marone

first: Georges

last: Martin

first: Mihaela

last: Zavolan

first: Lukas

last: Jeker


title: Dynamic 3'UTR changes during naïve CD4+ T cell activation and proliferation are reverted in the effector/memory state [A-Seq]

summary: 3’ untranslated regions (3’UTRs) are critical elements of most messenger RNA species and can contain binding sites for RNA-binding proteins (RBP) and microRNAs that affect various aspects of RNA life cycles including transcript stability. Cells of the adaptive immune system undergo massive expansion during the effector phase of the immune response and dynamically modify their 3’UTRs in a response to T cell receptor activation. Whether this phenomenon is a secondary effect of proliferation or a mechanism to directly regulate the abundance of specific mRNAs remains unclear. To study 3’UTR dynamics in T helper cells we investigated division-dependent alternative polyadenylation and observed a transient character of global 3’UTR shortening/lengthening in T helper cells that return to a naïve-like polyadenylation state after effector phase expansion. We also showed that 3’UTR lengthening is associated with higher transcript abundance and post-transcriptional regulation than 3’UTR shortening. Sequence analysis of conserved microRNA and RBP binding sites located within varying 3’ UTR regions highlighted the putative involvement of several microRNAs during this process. Our study emphasizes the value of polyadenylation isoforms analysis for understanding cell behaviors, revealing new aspects of the highly complex interplay of transcriptional and post-transcriptional layers in triggering transcript abundance.

overall_design: Examination of 3'UTR polyadenylation site dynamics


title: State-transition Modeling of Blood Transcriptome Predicts Disease Evolution and Treatment Response in Chronic Myeloid Leukemia (CML)

status: Public on Nov 02 2023

city: Duarte

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

summary: Chronic myeloid leukemia (CML) is initiated and initially maintained solely by the fusion gene BCR-ABL, encoding a mutant protein targeted in the clinic with tyrosine kinase inhibitors (TKIs) While TKI treatment is effective in inducing long-term remission, frequently is not curative. For these reasons, CML is an ideal disease to test our hypothesis that that transcriptome-based state-transition models accurately predict cancer evolution and treatment response. We hypothesized that transcriptome-based state-transition models accurately predict cancer evolution and treatment response.

overall_design: To test our hypothesis, we collected time-sequential peripheral blood samples from cohorts of tetracycline-off (Tet-Off) BCR-ABL-inducible transgenic mice. Using time-series bulk RNA-seq on the whole transcriptome to capture a system-wide view of all disease states, we applied state-transition theory to mathematically model CML development. We included four experimental cohorts of mice that were sampled weekly for 18 weeks or until mice became moribund with disease: Tet-on control mice where BCR-ABL expression was suppressed (n=3); Tet-off CML mice had BCR-ABL expression that induced disease that mimics human chronic phase (CP) CML (n=6); a Tet-off, Tet-on (TOTO) cohort where BCR-ABL expression allowed disease development and was then suppressed by turning Tet-on to simulate a hypothetical best-case treatment scenario (n=4); and TKI cohort to simulate a clinical setting where BCR-ABL expression was induced (Tet-off) and remained on during and after a four week nilotinib treatment window (n=7).

first: D

last: Frankhouser

first: R

last: Rockne

first: L

last: Uechi

last: Zhao

first: S

last: Branciamore

last: O'Meally

first: J

last: Izarriy

last: Ghoda

first: H

last: Ali

middle: M

last: Trent

last: Forman

first: Y

last: Fu

last: Kuo

first: B

last: Zhang

first: G

last: Marcucci


title: Transcriptional and splicing response of two Arabidopsis thaliana natural accessions to ABA-mediated stress.

city: Oeiras

first: Alba

last: Rodríguez Díez

state: Lisboa

address: Rua da Quinta Grande, 6

country: Portugal

institute: Instituto Gulbenkian de Ciência

summary: RNA-seq experiment to study the transcriptional and splicing changes of two Arabidopsis thaliana natural accessions, Col-0 and Kn-0, grown for 4 days under normal conditions and transferred to control medium or 5 µM ABA for 3 hours.

overall_design: Four day-old seedlings from Col-0 and Kn-0 Arabidopsis thaliana natural accessions exposed to either control conditions or 5 µM ABA for 3 hours. Three biological replicates were used per accession per treatment.

middle: R

last: Díez

first: Paula

last: Duque


title: Eukaryotic cytoplasm is widely structured via mesoscale condensates

first: Martin

last: Wühr

summary: Compartmentalization is an essential feature of eukaryotic life and is achieved both via membrane-bound organelles, such as mitochondria, and membrane-less biomolecular condensates, such as the nucleolus. Known biomolecular condensates typically exhibit liquid-like properties and are visualized by microscopy on the scale of ~1µm. They have been studied mostly by microscopy, examining select individual proteins. So far, several dozen biomolecular condensates are known, serving a multitude of functions, for example, in the regulation of transcription, RNA processing or signalling and their malfunction can cause diseases. However, it remains unclear to what extent biomolecular condensates are utilized in cellular organization and at what length scale they typically form. Here we examine native cytoplasm from Xenopus egg extract on a global scale with quantitative proteomics, filtration, size exclusion and dilution experiments. These assays reveal that at least 18% of the proteome is organized into mesoscale biomolecular condensates at the scale of ~100nm and appear to be stabilized by RNA or gelation. We confirmed mesoscale sizes via imaging below the diffraction limit by investigating protein permeation into porous substrates with defined pore sizes. Our results show that eukaryotic cytoplasm organizes extensively via biomolecular condensates, but at surprisingly short length scales.

overall_design: Using RNA-seq , we performed a comparative gene expression analysis of Xenopus laevis egg extract at different time points/filtration pressures

first: Felix

last: Keber

first: Thao

last: Nguyen

first: Andrea

last: Mariossi

first: Clifford

middle: P

last: Brangwynne


title: Analysis of global gene expression using RNA-sequencing reveals new roles of Yanghe Pingchuan decoction in asthma

city: China

first: Chunxia

last: Gong

address: 117 Meishan Road, Shushan District, Hefei City, Anhui Province,

institute: The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine

summary:
Context: Yanghe Pingchuan decoction (YPD) has been used for asthma treatment for many years in China.
Objective: We sought to understand the role of YPD, and find more potential targets for YPD-based treatment of asthma.
Materials and methods: An ovalbumin-induced asthma model in rats was created. Staining (hematoxylin and eosin, Masson) was used to evaluate the treatment effect of YPD. RNA-sequencing was carried out to analyze global gene expression, and differentially expressed genes (DEGs) were identified. Analysis of the functional enrichment of genes was done using the Gene Ontology database. Analysis of signaling-pathway enrichment of genes was done using the Kyoto Encyclopedia of Genes and Genomes database. Real-time reverse transcription-quantitative polymerase chain reaction was undertaken to measure expression of DEGs.
Results: Pathology showed that YPD had an improvement effect on rats with asthma. RNA-sequencing showed that YPD led to upregulated and downregulated expression of many genes. The YPD-based control of asthma pathogenesis may be related to calcium ion (Ca2+) binding, inorganic cation transmembrane transporter activity, microtubule motor activity, and control of canonical signaling (e.g., peroxisome proliferator-activated receptor, calcium, cyclic adenosine monophosphate). Enrichment analyses suggested that asthma pathogenesis may be related to Ca2+ binding and contraction of vascular smooth muscle. A validation experiment showed that YPD could reduce the Ca2+ concentration by inhibiting the Ang-Ⅱ/PLA/CaM signaling axis.
Discussion and conclusion: Control of asthma pathogenesis by YPD may be related to inhibition of the Ang-Ⅱ/PLA/CaM signaling axis, reduction of the Ca2+ concentration, and relaxation of airway smooth muscle.

overall_design: Expression of differential genes after high-throughput sequencing in normal and model asthmatic rats

first: Lingyu

last: Pan

first: Bangfu

last: He

first: Yehong

last: Sun

first: Xianchun

last: Duan

first: Yanquan

last: Han

first: Yongzhong

last: Wang


title: Senescence-associatedmolecular signatures integrated with human gene co-expressionnetworks revealsCOL6A3 asnovelmediator

city: new york city

first: Carmen

last: Argmann

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine

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


title: Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

summary: Systematic characterization of how genetic variation modulates gene regulation in a cell type specific context is essential for understanding complex traits. To address this question, we profiled gene expression and chromatin state of cells from healthy retinae of 20 human donors with a single-cell multiomics approach, and performed genomic sequencing. sc-eQTLs, sc-caQTL, sc-ASCA and sc-ASE were mapped in major retinal cell types. By integrating these results, we identified and characterized regulatory elements and genetic variants effective on gene regulation in individual cell types. Most of the identified sc-eQTLs and sc-caQTLs exhibit cell type-specific effects. Interestingly, the cis-elements harboring genetic variants with cell type-specific effects tend to be accessible in multiple cell types. Lastly, we identified the enriched cell types, fine-mapped candidate causal variants and genes, and uncovered cell type-specific regulatory mechanism underlying GWAS loci.

overall_design: snRNA-seq and snATAC-seq of peripheral lobe region of retina tissue, macula lutea tissue from 20 human donors

first: Rui

last: Chen

first: Margaret

last: DeAngelis

first: Yumei

last: Li

first: Jun

first: Xuesen

last: Cheng

first: Qingnan

last: Liang

first: Jin


title: Deletion of Slc9a1 in Cx3cr1+ cells stimulated microglial subcluster CREB1-BDNF signaling and oligodendrocyte crosstalk

city: Pittsburgh

first: Shanshan

last: Song

state: PA

address: 3501 Fifth Ave

institute: University of Pittsburgh

summary: Microglial Na/H exchanger-1 (NHE1) protein, encoded by Slc9a1, plays a role in white matter demyelination of ischemic stroke brains. In this study, we conducted single cell RNA-seq transcriptome analysis of corpus collosum and external capsule from wild-type (WT) and conditional Slc9a1 knockout (cKO) mice at 3 days post-stroke to study microglia-oligodendrocyte interactions.

overall_design:
White matter tissues were dissected from the WT or Nhe1 cKO brains at 3 days post-tMCAO

Grant ID: 933134 (Career Development Award)
Grant title: Modulating microglia-oligodendrocyte interactions for white matter repair
Funding source: American Heart Association
Grantee: Shanshan Song

first: Chaim

last: Sneiderman

first: Gary

last: Kohanbash

first: Dandan


title: Senescence-associatedmolecular signatures integrated with human gene co-expressionnetworks revealsCOL6A3 asnovelmediator [1]

summary: We report expression profiles of various senescent cell types and modes of induction.

overall_design: 5 different non-transformed cell types from various origin were rendered senescent via ionising radiation and RNAseq was perfomed.  One strain (IMR90) was induced to senesce using various methods.  DEG Sen vs non-senescent cells were determined and compared accross all types of senescence.

first: Radoslav

last: Savić

first: Priyanka

middle: L

last: Patel

first: Eduard

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