title: Differences in gene expression between very curly and straight human hair

city: Braga

first: Artur

last: Cavaco-Paulo

address: Campus de Gualtar

department: CEB

country: Portugal

institute: University of Minho

summary: Hair shape is defined in the follicle: large hair follicles produce ‘terminal’ hairs, small follicles produce fine ‘vellus’ hairs, curved follicles produce curly hair in all ethnicities, according to the available literature. In order to understand better how shape is determined in the follicle and complement the publically available knowledge on hair shape genetics, our research group undertook a global high-throughput approach to compare the levels of gene expression among straight and very curly hair.  The microarray was the methodology chosen.  A list of the transcripts differently expressed that pass the statistical two independent groups test including correction for multiple testing (Bonferroni-Hochberg with 0.05 cut-off) was obtained. From 85 genes that were significantly different 68 genes were more expressed in very curly hair follicles and 17 genes were more expressed in straight hair follicles.

overall_design: The team collected 50 hair follicles from each volunteer: 6 donors with extremely curly hair and 5 donors with straight hair, all non-bald adult males with ages between 19-40 years old. The isolated RNA was processed and used on Affymetrix GeneChip HuGene 1.0 ST Arrays (Affymetrix Core Facility at Instituto Gulbenkian de Ciencia, Oeiras, Portugal)

first: Andreia

last: Gomes

first: Teresa

last: Matamá

first: Rita

last: Araújo

first: Célia

last: Cruz

first: Jörg

last: Becker


title: Gene expression data from NCI-H295R cell line treated with rottlerin samples.

status: Public on Feb 18 2024

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

type: Expression profiling by high throughput sequencing

summary: Pediatric adrenocortical tumor (ACT) is a rare neoplasm with high heterogeneity, exhibiting an incidence 10 to 15 times higher in the south and southeast regions of Brazil when compared to the global incidence.In this context, our aim was to analyze the gene expression profile in the adrenocortical carcinoma cell line (NCI-H295R) after treatment with the compound rottlerin.

overall_design: Gene expression profiles from adrenocortical tumor cells line  after tratament of rottlerin using high throughput sequencing.

first: C

middle: A

first: L

middle: G

last: Tone

first: E

middle: T

last: Valera


title: Effect of depletion of Igf2bp3 on gene expression during VSV infection in RAW 264.7 cells and mice PMs

city: Suzhou

first: Siying

last: Liu

state: Jiangsu

address: 111 Ren’ai Road

country: China

institute: Xi'an Jiaotong-Liverpool University

summary: N6-methyladenosine (m6A) modification is the most abundant RNA modification in both host mRNA and viral RNA transcripts. Dynamic regulation and recognition of m6A modification widely participate in post-transcriptional regulation of many biological processes. This project aims to define the regulation role of IGF2BP3, a m6A recognition protein, in viral infection, especially in RNA viral infection. In this study, the transcriptomes of Vesicular stomatitis virus (VSV)-infected WT/Igf2bp3-KO RAW264.7 cells and mouse peritoneal macrophages (PMs) were analyzed, suggesting the role of IGF2BP3 in the host's innate immune responses during viral infection and enhancement.

overall_design: WT/Igf2bp3-KO RAW264.7 cells and PMs were infected VSV-GFP (MOI=1) for 8 hours. Total RNAs from the cells were then extracted using the Trizol reagent, following manufacturer' s instructions. Subsequently, the cDNA libraries were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (No. NR605, Vazyme) and sequenced on Novaseq 6000 (Illumina).

first: Shiyou

last: Wang

first: Feng

last: Ma


title: RNA sequencing analysis of busulfan-treated initial segment-caput epididymis.

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

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 busulfan intraperitoneal injection.
Methods: 8-week-old wild-type mice were treated with single intraperitoneal injection of dimethyl sulfoxide (DMSO) or busulfan (40mg/kg body weight) disolved in DMSO and mice were left for 4 weeks until tissue sampling at 12 weeks 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 busulfan injection.

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


title: Effect of Ginsenoside Rb1 on inflammatory reaction and odontogenic differentiation of human dental pulp cell

city: Seoul

first: Yong Kwon

last: Chae

address: Kyungheedaero 26

country: South Korea

institute: Kyung Hee University Dental Hospital

summary: Ginsenoside Rb1 (G-Rb1) has been reported to diminish inflammation associated with diseases. We investigated the effect of G-Rb1 on the inflammatory reactions and the odontogenic differentiation of human dental pulp cells (hDPCs). G-Rb1 affected the levels of TNF-α, IL-6, and IL-8, as these showed reduced levels with exposure to lipopolysaccharide (LPS). Additionally, less mRNA and protein expressions of vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1) were shown. G-Rb1 suppressed the LPS-induced increase of cell adhesion molecules and inflammatory cytokines, while also inhibiting PI3K/Akt, phosphorylation of NF-κB transcription factors, ERK and JNK of MAPK signaling in hDPCs.

overall_design: Human dental pulp cells (hDPCs) treated with 10 μg/mL of G-Rb1 for 5 days, hDPCs cultivated in alpha minimum essential medium (α-MEM) for 5 days, and untreated hDPCs were analyzed using RNA-seq.

first: Ok-Hyung

last: Nam

first: Jae-Hwan

last: Kim

first: Si-Won

last: Kang

first: Yong-Kwon

first: Myeong-Kwan

last: Jih

first: Hyekyoung

middle: H

last: You

first: Jeong-Tae

last: Koh

first: Young


title: Bone morphogenetic protein-9 is a prognostic biomarker in outcome prediction and host_x0002_directed therapy target for sepsis

city: Chongqing

first: Haobo

last: Bai

address: No.1 Friendship Road, Yuzhong District

department: Department of Laboratory Medicine

institute: The First Affiliated Hospital of Chongqing Medical University

summary: NOT PROVIDED; REQUESTED

overall_design: male C57BL/6 mice aged 6-8 weeks were anesthetized intraperitoneally (i.p.) with a mixture of xylazine (4.5 mg/kg) and ketamine (90 mg/kg), and the cecum was exposed, ligatured at its external third, and punctured through with a 24-gauge needle (nonsevere CLP, 50~60% survival) or a 21-gauge needle (severe CLP, 0~20% survival).Murine recombinant BMP9 (catalog 5566-BP, R&D Systems) was injected intraperitoneally at 25 μg/kg after CLP, and 4 mM HCl containing 0.1% bovine serum albumin as Vehicle was delivered in a similar fashion as control solutions. The peritoneallavagefluids were obtained  at 24h after CLP,then send to Single-cell RNA sequencing.

first: Qian

last: Lu

first: Ju

last: Cao

first: Hao

last: Ding


title: A single-cell atlas of Drosophila trachea reveals glycosylation-mediated Notch signaling in cell fate specification

city: Hangzhou

first: Yue

last: Li

state: Zhejiang

address: The College of Medicine Keyan C-161, Zijingang Campus, Zhejiang University, Yuhangtang Rd. 866

department: School of medicine

institute: Zhejiang University

summary: The Drosophila tracheal system emerges as a favorable model for investigating the program of tubular morphogenesis. It is established in the embryo by post-mitotic cells, which also undergoes remodeling by modulating stem cells. Here we provide an analysis of a comprehensive cell atlas of Drosophila trachea using single-cell RNA-sequencing (scRNA-seq) and reveal cellular diversity and transcriptional profiles of tracheoblasts in Drosophila airway, which encompasses 9 major subtypes. Further evidences reveal transcription factors that are able to switch cell fate. The transcription factors, Peb, Bs, Kni, Sal and Cut are influenced by Notch signaling and determine cell identity. Moreover, Notch signaling that is responsible for the differentiation of tracheoblasts responds to protein glycosylation that is induced upon high sugar diet. Therefore, our study provides a transcriptomic atlas of tracheal development and regeneration, and suggests a glycosylation-responsive Notch signaling in cell fate determination.

overall_design:
We performed scRNA-seq to catalog the cell types and identify the transcriptional profiles of tracheal cells that constitute Drosophila airway. The fly tracheal major branches as well as associated progenitors and terminal branches were dissected and collected from 50 white pupae fed by normal diet (ND) or high sugar diet (HSD).
We performed RNA-seq to investigate the transcriptional profiles of tracheal progenitors. The tracheal progenitors were dissected and collected from white pupae.

first: Pengzhen

last: Dong

first: Tianfeng

first: Hai

last: Huang


summary: Primary peritoneal macrophages were obtained from the peritoneal exudates of mice that were pretreated with 3% thioglycolate (LA4590, Solarbio) i.p. for 5 days. The peritoneal exudate cells were collected by cold PBS and adjusted to 1 × 10^6 cells/ml in DMEM cultured at 37C and 5% CO2 in a cell incubator. At 2 hours later, after using PBS to wash out the supernatant cells, the remaining adherent cells contained more than 90% F4+/80+ macrophages by flow cytometry analysis. Peritoneal macrophages were treated with 100ng/ml of recombinant murine BMP9 or Vehicle for 6h to activate macrophages.Then, send to RNA seq,

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Primary peritoneal macrophages (vehicle and BMP9)


title: The Role of KDM2A and H3K36me2 Demethylation in Modulating MAPK Signaling during Neurodevelopment [ChIP-seq]

city: Changsha

first: Zongyao

last: Ren

address: No.88 Xiangya Road

institute: Central South University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate how KDM2A regulates downstream genes and affects NPC function and the role of KDM2A in histone methylation, we performed KDM2A and H3K36me2 ChIP-Seq. By analyzing both datasets together, we identified 2,051 overlapping peaks that were shared by both KDM2A and H3K36me2, The enriched genes were found to be associated with generating neurons, central nervous system development and cell proliferation. Furthermore, disease enrichment analysis revealed significant associations with ASD, ID and other neurodevelopmental disorders, indicating KDM2A's roles in neural development.

overall_design: We generated KDM2A knockdown H9 ESC lines using shRNA lentivirus. We designed five siRNAs and selected the two most effective ones to create shRNA, which were then packaged into shRNA lentivirus (sh1, sh4). Next, we induced these cells into NPC. We performed KDM2A ChIP-Seq in control NPC and H3K36me2 ChIP-Seq in knockdown NPC (NC, sh1, sh4). ChIP-Seq analysis revealed that KDM2A preferentially binding to TSS regions of genes that related to neurogenesis and neuron differentiation. Furthermore, knockdown of KDM2A appeared to hinder H3K36me2 binding on regulatory elements of downstream genes.

first: Chunyu

last: Liu

first: Chao

last: Chen


title: Antisense transcription of bovine leukemia virus is essential for viral replication and oncogenesis

status: Public on Feb 17 2024

city: Liège

first: Joris

last: Thomas

address: Quartier Hôpital avenue de l'Hôpital 11

country: Belgium

institute: Universite de Liege

summary: In sheep infected with bovine leukemia virus (BLV), transcription of structural, enzymatic, and accessory genes is silenced. However, the BLV provirus transcribes a series of non-coding RNAs that remain undetected by the host immune response. Specifically, three RNAs (AS1-L, AS1-S, and AS2) are consistently expressed from the antisense strand, originating from transcriptional initiation at the 3'-LTR. To investigate the role of these non-coding RNAs in viral replication and pathogenesis, a reverse genetics approach was devised, capitalizing on a mechanistic disparity in transcription initiation between the 5' and 3' promoters. A two-nucleotide mutation (GG>TA) in the TFIIB-recognition element (BRE) impaired antisense transcription originating from the 3'-LTR. In the context of the provirus, this A1 mutation significantly diminished the expression of antisense RNAs, while not notably affecting sense transcription. When inoculated to sheep, the A1 provirus was infectious but exhibited reduced replication levels, shedding light on the role of antisense transcription in vivo. In comparison to lymphoid organs in sheep infected with a wild-type (WT) provirus, the A1 mutant demonstrated alterations in both the spatial distribution and rates of cell proliferation in the lymph nodes and the spleen. Analysis through RNA sequencing and RT-qPCR unveiled an upregulation of the Hmcn1 gene in B-lymphocytes from A1-infected sheep. Further examination via confocal microscopy and immunohistochemistry revealed an increase in the amount of hemicentin-1 protein encoded by Hmcn1 in peripheral blood mononuclear cells (PBMCs) and lymphoid organs of sheep infected with the A1 mutant. RNA interference targeting Hmcn1 expression impacted the migration of ovine kidney (OVK) cells in vitro. In contrast to the WT provirus, the A1 mutant lacked oncogenic activity when inoculated into sheep.     Collectively, this study underscores the essential role of antisense transcription in BLV replication and pathogenicity. These findings may offer valuable insights into understanding the relevance of antisense transcription in the context of human T-cell leukemia virus (HTLV-1).

overall_design: To understand the role of antisense transcription, we used three groups of three sheep. One group was injected with the wild-tyde, another one with an antisense deficient virus (A1) and a third one was non infected and kept as negative control. From each sheep, we isolated PBMCs and separated into B-cells and non B-cells (NB) populations

first: Jouant

first: Jacques

last: Jean-Rock

first: Gouverneur

last: Lorian

first: Xavier

last: Saintmard

first: Lea

last: Vilano Maña

first: Majeed

last: Jamakhani

first: Michal

last: Reichert

first: Luc

last: Willems


title: Impaired bone morphogenetic protein signaling pathways perturb decidualization in patients with endometriosis

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series


title: The Role of KDM2A and H3K36me2 Demethylation in Modulating MAPK Signaling during Neurodevelopment [RNA-seq]

summary: To explore how KDM2A regulates downstream genes and impacts NPC function, we generated KDM2A knockdown H9 ESC lines using shRNA lentivirus. We designed five siRNAs and selected the two most effective ones for shRNA creation, which were then packaged into shRNA lentivirus (sh1, sh4). Subsequently, we induced these cells into NPCs and cerebral organoids. Through RNA-seq and DEG analysis, we observed that DEGs in NPCs were associated with the MAPK signaling pathway, a finding also present in cerebral organoids. We conducted a disease enrichment analysis on the obtained gene lists, revealing enrichment in neurodevelopmental disorders such as intellectual disability (ID) and autism spectrum disorder (ASD). This finding indirectly suggests that KDM2A plays a role in early neurodevelopmental processes.

overall_design: We generated KDM2A knockdown H9 ESC lines using shRNA lentivirus. We designed five siRNAs and selected the two most effective ones to create shRNA, which were then packaged into shRNA lentivirus (sh1, sh4). Next, we induced these cells into NPCs and cerebral organoids. NPCs and Day 30 cerebral organoids underwent RNA-seq (150 bp, paired-end) on the Illumina NovaSeq 6000 system. DESeq2 identified DEGs(FDR< 0.05, |log2FC| >=1) between KDM2A knockdown and control samples. DEGs were utilized for Gene Ontology, KEGG pathway analysis and PPI.


title: Impaired bone morphogenetic protein signaling pathways perturb decidualization in patients with endometriosis (SMAD1/5 siRNA studies)

summary: It is hypothesized that impaired endometrial decidualization contributes to decreased fertility in endometriosis patients. To identify the molecular defects that underpin defective decidualization in endometriosis, we subjected endometrial stromal cells from healthy individuals or with endometriosis to time course in vitro decidualization with estradiol, progesterone, and 8-bromo-cyclic-AMP (EPC) for 2, 4, 6, or 8 days. Transcriptomic profiling identified novel differences in key pathways between normal and endometriosis, including defective bone morphogenetic protein (BMP) signaling (ID1, ID2, ID3, BMP6), altered iron transport (SLC40A1, TFRC), endometrial stem cell markers (CD44, SUSD2), and retinoid signaling pathways (RORB, ALDH1L1, RARA). Genome-wide binding analyses identified an altered genomic distribution of SMAD4 in decidualized stromal cells from endometriosis patients relative to normal individuals, with an overrepresentation of gene ontologies related to signaling by transforming growth factor β (TGFβ), neurotrophic tyrosine kinase receptors (NTRK), and nerve growth factor (NGF)-stimulated transcription. We found that direct SMAD1/5/4 target genes control FOXO, PI3K/AKT, and progesterone-mediated signaling in decidualizing cells and that BMP2 supplementation of patient-derived assembloids from endometriosis patients restored decidualization. In summary, transcriptomic and genomic profiling of patient-derived endometrial cells and assembloids identified that restoring BMP/SMAD1/5/4 signaling is crucial for engaging a robust decidualization program in women with endometriosis.

overall_design: We performed RNA-sequencing analysis on endometrial stromal cells from 3 healthy donors, which were treated with either scrambled or SMAD1/5 siRNA followered by 4-day EPC treatment.

first: Diana

last: Monsivais

first: Suni

last: Tang

first: Zian

last: Liao


title: Impaired bone morphogenetic protein signaling pathways perturb decidualization in patients with endometriosis (Time-course EPC studies)

overall_design: We performed RNA-sequencing analysis on endometrial stromal cells, which were treated with EPC for 2, 4, 6, and 8 days, from 4 normal and 4 endometriosis patients.


title: Impaired bone morphogenetic protein signaling pathways perturb decidualization in patients with endometriosis (Cut&Run-Seq)

overall_design: Endometrium stromal cells from women with/without endometriosis were subjected to CUT&RUN-seq

first: Ting

last: Geng

first: Dominique

middle: I

last: Cope

first: Timothy

last: Dunn

first: Linda

last: Radilla

first: Xiaoming

last: Guan


title: Alternative splicing at a broad spectrum of target genes underlie epithelial to mesenchymal plasticity, metastatic dissemination, and resistance to chemotherapy in high-grade serous ovarian cancer.

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

summary: Phenotypic plasticity, defined as the ability of individual cells with stable genotypes to exert different phenotypes upon exposure to specific environmental cues, represent the quintessential hallmark of the cancer cell en route from the primary lesion to distant organ sites where metastatic colonization will occur. Phenotypic plasticity is driven by a broad spectrum of epigenetic mechanisms that allow for the reversibility of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions (EMT/MET). By taking advantage of the co-existence of epithelial and quasi-mesenchymal cells within immortalized cancer cell lines, we have analyzed the role of EMT-related gene isoforms in the regulation of epithelial mesenchymal plasticity (EMP) in high grade serous ovarian cancer. When compared with colon cancer, a distinct spectrum of downstream targets characterizes quasi-mesenchymal ovarian cancer cells, likely to reflect the different modalities of metastasis formation between these two types of malignancy, i.e. hematogenous in colon and transcoelomic in ovarian cancer. Moreover, upstream RNA-binding proteins differentially expressed between epithelial and quasi-mesenchymal subpopulations of ovarian cancer cells were identified that underlie differential regulation of EMT-related isoforms. In particular, the up- and down-regulation of RBM24 and ESRP1, respectively, represent a main regulator of EMT in ovarian cancer cells. To validate the functional and clinical relevance of our approach, we selected and functionally analyzed the Tropomyosin 1 gene (TPM1), encoding for a protein that specifies the functional characteristics of individual actin filaments in contractile cells, among the ovarian-specific downstream AS targets. The low-molecular weight Tpm1.8/9 isoforms are specifically expressed in patient-derived ascites and promote invasion through activation of EMT and Wnt signaling, together with a broad spectrum of inflammation-related pathways. Moreover, Tpm1.8/9 expression confers resistance to taxane- and platinum-based chemotherapy. Small molecule inhibitors that target the Tpm1 isoforms support targeting Tpm1.8/9 as therapeutic targets for the development of future tailor-made clinical interventions.

overall_design: TPM1.6/7/8/9 overexpressed RNAseq profiles of the high grade serous ovarian cancer cell line OV90

first: T

last: Xu

first: M

middle: P

first: R

last: Fodde


title: The Role of KDM2A and H3K36me2 Demethylation in Modulating MAPK Signaling during Neurodevelopment.

first: Zongyao

last: Ren


title: Gene expression signatures for auricular cartilages of microtia patients and controls

city: Shanghai

first: Run

last: Yang

address: No.83 Fenyang Rd

institute: Eye&ENT Hospital of Fudan University

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

summary: To explore the coding and non-coding gene expression in the auricular cartilage of microtia patients, we have employed RNA microarray expression profiling as a discovery platform to identify the coding and non-coding genes differentially expressed in microtia patients and controls. The discarded auricular cartilage tissue from 10 unilateral Grade III isolated microtia patients during auricular reconstruction surgery and 5 volunteers without ear malformation or other physical abnormalities during tympanoplasty surgery were collected. All fresh tissues were harvested from the tragus and cavum conchae of the auricle.

overall_design: The RNA expression in auricular cartilage tissue was measured by microarray. One independent experiment was performed on each clinical sample.

first: Jing

last: Ma


title: Identification of genes essential for the cell death induced by OSW-1 using the Genome-wide CRISPR-Cas9 knockout (GeCKO) screening

status: Public on Feb 16 2024

city: Kamigori-cho, Ako-gun

first: Kanae

last: Sasaki

state: Hyogo

address: 3-2-1 Kouto

department: Department of Molecular Biochemistry, Graduate School of Sciences

institute: University of Hyogo

summary: The Golgi stress response is an important cytoprotective system that enhances Golgi function in response to cellular demand, while cells damaged by prolonged Golgi stress undergo cell death. OSW-1, a natural compound with anticancer activity, potently inhibits OSBP that transports cholesterol and phosphatidylinositol-4-phosphate (PI4P) at contact sites between the endoplasmic reticulum and the Golgi apparatus. Previously, we reported that OSW-1 induces the Golgi stress response, resulting in Golgi stress- induced transcription and cell death. However, the underlying molecular mechanism has been unknown. To reveal the mechanism of a novel pathway of the Golgi stress response regulating transcriptional induction and cell death (the PI4P pathway), we performed a genome-wide knockout screen and found that transcriptional induction as well as cell death induced by OSW-1 was repressed by the loss of regulators of PI4P synthesis, such as PITPNB and PI4KB. Our data indicate that OSW-1 induces Golgi stress-dependent transcriptional induction and cell death through dysregulation of the PI4P metabolism in the Golgi.

overall_design: OSW-1 is a natural anticancer compound and activates the Golgi stress response. To search for genes essential for the cell death induced by OSW-1, we performed the Genome-wide CRISPR-Cas9 knockout (GeCKO) screening using OSW-1-resistant HeLa cells.

first: Hiderou

last: Yoshida

first: Yuto

last: Watanabe


title: Identification of human gene expression induced by OSW-1 treatment

overall_design: OSW-1 is a natural anticancer compound and activates the Golgi stress response. To get a comprehensive view of the transcriptome of cells treated with OSW-1, we performed RNA sequencing.

first: Takuya

last: Adachi


title: Osteogenic Differentiation Potential of Mesenchymal Stem Cells using Single Cell Multiomic Analysis

city: Indianapolis

first: Yue

last: Wang

address: 975 W. Walnut street

department: Medical Genetics

institute: Indiana University

summary: Mesenchymal stem cells (MSC) are multipotent stem cells that can differentiate into multiple cell types, including osteoblasts, chondrocytes and adipocytes. Osteoblast differentiation is reduced during osteoporosis development, resulting in reduced bone formation. Further, MSC isolated from different donors possess distinct osteogenic capacity. In this study, we used single-cell mul-tiomic analysis to profile the transcriptome and epigenome of MSC from four healthy donors. Da-ta were obtained from ~1,300 to 1,600 cells for each donor. These cells were clustered into four groups, indicating that MSC from different donors have distinct chromatin accessible regulatory elements for regulating gene expression. To investigate the mechanism by which MSC undergo os-teogenic differentiation, we used the chromatin accessibility data from the single-cell multiome data to identify individual-specific enhancer-promoter pairs and evaluated the expression levels and activities of the transcriptional regulators. The MSC from four donors showed distinct dif-ferentiation potential into osteoblasts.  MSC of donor one showed the largest average motif activi-ties, indicating that MSC from donor one was most likely to differentiate into osteoblasts. The re-sults of our validation experiments were consistent with the bioinformatics prediction. We also tested the enrichment of GWAS signals of several musculoskeletal disease traits in the patient-specific chromatin accessible regions identified in the single-cell multiome data, including osteo-porosis, osteopenia, and osteoarthritis. We found that osteoarthritis-associated variants were on-ly enriched in the regions identified from donor four. In contrast, osteoporosis and osteopenia variants were enriched in regions from donor one and least enriched in donor four. Since osteo-porosis and osteopenia are related to the density of bone cells, the enrichment of variants from these traits should be correlated with the osteogenic potential of MSC. In summary, this study provides large-scale data to link regulatory elements with their target genes to study the regula-tory relationships during the differentiation of mesenchymal stem cells and provide a deeper in-sight into the gene regulatory mechanism.

overall_design: MSC from each of the four donors were collected and combined in equal numbers to create a mixed cell preparation.  One million of the MSC mixed cells were centrifuged at 300 g for 5 minutes to remove culture media. The final single cell suspension was washed 3 times with PBS buffer without calcium and magnesium, plus 0.4% BSA. The single-cell suspension was then assessed for cell viability and quantity by using a he-mocytometer under a microscope. Cells were then lysed with 0.1X lysis buffer for 4 minutes to isolate nuclei, based on the protocol of Demonstrated Protocol Nuclei Isola-tion Complex Sample ATAC GEX Sequencing, CG000375 RevB (10X Genomics, Inc). Final nuclei concentration of 3000/ul was used for targeted cell recovery of 10000 cells. Following the Chromium NextGEM Multiome ATAC GEX User Guide, CG000338_RevB (10X Genomics, Inc), tagmentation of nuclei preparation was first per-formed. Thereafter, briefly, along with the single cell multiome gel beads and partition oil, the single nuclei master mixture containing tagmented single nuclei suspension was transferred onto a Next GEM Chip J, and the chip loaded to the Chromium Con-troller for GEM generation and barcoding, followed by pre-amplification PCR, ATAC library preparation, cDNA synthesis and cDNA library preparation. At each step, the quality of cDNA, ATAC library and cDNA library was examined by Bioanalyzer. The resulting ATAC and cDNA libraries were sequenced separately, cDNA library for 28bp and 91bp and ATAC library for 50bp paired-end sequencing on Illumina No-vaSeq 6000.


title: Effects of sEH inhibition on the eicosanoid and cytokine storms in SARS-CoV-2-infected mice

city: Durham

first: Matthew

middle: Lund

last: Edin

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: This study aimed to investigate the impact of sEH inhibition on the host response to SARS-CoV 2 infection in a mouse model with human ACE2 expression. Mice were infected with SARS-CoV-2 and treated with either vehicle or the sEH inhibitor 1-trifluoromethoxyphenyl-3-(1-propionylpiperidin-4-yl) urea (TPPU).

overall_design: Total RNA was obtained from lung and heart samples in mice engineered to express human ACE2. Ten mice were not infected, ten were infected with 1000 PFU SARS-CoV-2, and ten were infected with 1000 PFU SARS-CoV-2 alongside treatment with 3 mg/kg TPPU.

middle: L

first: Artiom

last: Gruzdev

first: Joan

last: Graves

first: Fred

middle: B

last: Lih

first: Christophe

last: Morisseau

first: James

middle: M

last: Ward

first: Bruce

middle: D

last: Hammock

first: Catherine

last: Bosio

first: Darryl

middle: C

last: Zeldin


title: Affect of maternal IgA on the developing small intestinal epithelium

city: Pittsburgh

last: Abbott

state: PA

address: 4401 Penn Ave

department: Immunology

institute: University of Pittsburgh

summary: Breast milk is associated with multiple benefits for the infant, including reduced incidence of chronic diseases such as Inflammatory Bowel Disease. We investigated the role of milk-derived maternal IgA (matIgA) on the developing small intestinal immune system. Using a model, where genotypically identical pups were fed by dams differed only in IgA production we revealed that matIgA regulates the assembly of the infant small intestinal microbiota and epithelium, supporting Lactobacillaceae and suppressing Enterobacteriaceae and the development of secretory lineage cells.  Via the microbiota, MatIgA also regulated infant immune cells and suppressed early activation of Th17 cells. We demonstrated that Enterobacteriaceae-specific CD4+ T cells, activated in the absence of matIgA, persisted long term where they may contribute to subsequent inflammatory episodes. This work suggests that maternal IgA shapes the mucosal immune response by regulating the early-life microbiota thus preventing the development of inflammatory microbiota-specific T cells with memory potential.

overall_design: small intestinal EpCAM + cells were sorted at 14, 24, and 42 day of life from IgA -/+ mice fed by either a C57BL/6 or Igha-/- dam.

first: Abbott

last: Darryl

first: Yang

last: Aaron

first: Hand

last: Timothy


title: ChIP-Seq mapping of the genome-wide distribution of FLAG-H2AK5acK9ac in genetic code expanded HeLa cells

city: TianJin

first: Kaiwen

last: Bao

institute: Tianjin Medical University

summary:
To test the deposition of FLAG-H2AK5acK9ac mark across the genome, ChIP experiments coupled high-throughput sequencing were performed using antibodies against FLAG, H2AK5ac and H2AK9ac.

Keywords: Genome binding/occupancy profiling by high throughput sequencing

overall_design: An orthogonal genetic code-expanded system developed by Dr. Tao Liu and his colleagues (ACS Synth Biol 9, 2723-2736. 10.1021/acssynbio.0c00257) was used to incorporate acetyl-lysine into H2AK5K9 in living cells by expressing AcKRS-tRNAPyl and FLAG-H2AK5UAGK9UAG. ChIP-seq experiments were performed with antibodies against FLAG using cells cultured in the absence or presence of acetyl-lysine (AcK). This genetic code expanded approach was then applied in W833R-edited HeLa cells co-depleted of TIP60 and p300. Soluble chromatins extracted from these cells followed by ChIP-seq using antibodies against H2AK5ac and H2AK9ac were then performed.

first: Can

last: Liang

first: Chunyong

last: Zhang

first: Lei

last: Shi


title: SHMT2 reduces fatty liver but is necessary for liver inflammation and fibrosis in mice

city: Detroit

first: Jian

last: Wang

state: MI

address: 6135 Woodward Ave

department: Pathology

institute: Wayne State University School of Medicine

summary: Non-alcoholic fatty liver disease is linked to disrupted serine metabolism. SHMT2 is a liver enzyme that is crucial for liver methylation and overall health. We developed a mouse strain with targeted SHMT2 knockout in hepatocytes and found that the absence of SHMT2 led to increased circulating serine and glycine levels, 1C deficiency, and depleted liver methylation potential. The study reveals the critical role of SHMT2 in maintaining hepatic 1C homeostasis and regulating the progression of non-alcoholic fatty liver disease.

overall_design:
To investigate the metabolic function of SHMT2 in intact animals, we established a mouse model with liver-specific SHMT2 deletion
We treated the animals with the AMLN diet that promotes diet-induced non-alcoholic fatty liver disease.
We conducted a comparison of liver gene expression using RNA sequencing.

first: Guohua

last: Chen


title: Defining extracellular vesicle release, uptake, and function in wound healing

city: La Jolla

first: Brian

last: Eliceiri

state: CA

address: 9500 Gilman Drive MC 8236

department: Surgery

institute: University of California San Diego Health

summary: Small extracellular vesicles (EVs) are released by cells and deliver biologically active payloads important in the intercellular signaling that coordinates the response of multiple cell types in cutaneous wound healing.  Here we focus on the use of EV reporters to address cell type specificity and central questions regarding EV source cells, target cells, heterogeneity, payload, and activity using a combination of molecular approaches to address some of the barriers to translation in the use of engineered EVs.  We identify a role for EVs released by resident macrophages present in adipose tissue and dermis to stimulate proliferation of overlying basal layer of keratinocytes.  For these studies we use an allograft model, where donor EVs are harvested from subcutaneous implants, then purified for transplantation into the wound bed of recipient mice with a defined impaired wound healing phenotype.  We demonstrate that EVs isolated from diabetic obese mice decreased keratinocyte proliferation and delayed wound closure, and that EVs loaded with specific miRNAs like miR-425-5p increased proliferation and accelerated wound closure.  Utilizing a CD9-GFP reporter system, we show that fibroblasts uptake macrophage-derived EVs.  In this work, we show that cell type-specific approaches can be used to unravel the biochemical activity of EVs in the complex microenvironment of the wound bed and form the basis for developing targeted pro-reparative EV payloads.

overall_design: To investigate the expression of different cell type markers with sequencing between wildtype and diabetic derived extracellular vesicles.

first: Dong

middle: J

last: Park

first: Sakeef

last: Sayeed


title: Microarray expression data of A375 cells at different density/culture system

city: Koto-ku

first: Hitomi

last: Shirahama

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation for Cancer Research

summary: Ferroptosis is one of the regulated cell deaths, induced by the accumulation of lipid peroxidation. Induction of ferroptosis is often influenced by the cell environment; however, much remains unknown about cellular states altering ferroptosis susceptibility. We found that melanoma cell lines become resistant to ferroptosis along with an increase in cell density. To elcidate the mechanism, we have investigated the differences in gene expression between A375 cells at different densities/culture systems.

overall_design: A375 cells were cultured at low density in two-dimensional system, high density in two-dimensional system, or in a three-dimensional system.

first: Yuri

last: Tani

first: Satomi

last: Tsukahara

first: Yuka

last: Okamoto

first: Akiko

last: Hasebe

first: Tomomiki

last: Noda

first: Akihiro

last: Tomida


title: ChIP-Seq mapping of H2AK5ac, H2AK9ac, DNTTIP1, MIDEAS, and LIG4 at AsiSI-induced DNA double-strand breaks in control or MiDAC-deficient cells

summary: To test whether MiDAC-promoted H2AK5/K9 deacetylation is implicated in DSB response, we took advantage of an improved DSB-induced via AsiSI (AiDIvA) system, in which the endonuclease restriction enzyme AsiSI is fused to the estrogen receptor (ER) hormone-binding domain and its nuclear expression in HeLa cells is controlled by doxycycline and 4-hydroxy tamoxifen (4-OHT). The precise distribution of gH2AX, H2AK5ac, H2AK9ac, FLAG-DNTTIP1, FLAG-MIDEAS, and LIG4 at AsiSI-induced DNA double-strand breaks was determined by chromatin immunoprecipitation coupled high throughput sequencing (ChIP-seq). ChIP signals from ER-AsiSI-expressing AiDIvA cells (DSB group) were normalized to ER-expressing control cells (Ctrl group).

overall_design: Chromatin immunoprecipitation DNA-sequencing for H2AK5ac, H2AK9ac, DNTTIP1, MIDEAS, and LIG4 at AsiSI-induced DNA double-strand breaks in control or MiDAC-deficient Hela cells


title: Immune suppressive effects of radiotherapy promote metastasis

city: Chicago

first: Hua

state: IL

department: Department of Radiation and Cellular Oncology

institute: University of Chicago

summary: We report the transcriptomic profile of immune cells  for lungs of tumor bearing mice of which tumor received radiation (20Gy)

overall_design: RNA-seq analyses were conducted on lung-derived CD45+ cells

first: Yuzhu

last: Hou

first: Sean

last: Pitroda

first: Jiaai

first: Xiaona

last: Huang

first: Xinshuang

last: Yu

first: Enyu

last: Rao

middle: Z

last: Luo

first: Andras

last: Piffko

first: Kaiting

last: Yang

first: Liangliang

first: Carlos

last: Martinez

first: Matthias

last: Mack

first: Everett

middle: E

last: Vokes

first: Steven

last: Chmura

first: Ralph

middle: R

last: Weichselbaum


title: Modulation of the post meal PBMC transcriptomic response of shift workers after four weeks of a dietary intervention implementing a dedicated overnight fast

city: Melbourne

first: Rochelle

last: Davis

state: VIC

address: 264 Ferntree Gully Rd, Notting Hill

country: Australia

institute: Monash University

summary: In a cross-over randomised controlled trial,19-night shift workers with abdominal obesity, completed two diet conditions separated by a two week wash out period; a) the control period = four weeks of habitual eating overnight and b) the intervention period = four weeks of avoiding food intake between 1 AM – 6 AM. At the end of each intervention period participants were given a high fat/high carbohydrate challenge meal in the morning and peripheral blood mononuclear cells were isolated from whole bood sampled at fasting, 2 and 4 hours after eating the meal.

overall_design: cross-over randomised controlled trial

first: Catherine

last: Huggins

first: Maxine

last: Bonham


title: Demonstrating the utility of the ex vivo murine mycobacterial growth inhibition assay (MGIA) for high-throughput screening of tuberculosis vaccine candidates against multiple Mycobacterium tuberculosis complex strains

city: London

first: Hannah

last: Painter

address: Keppel Street

country: United Kingdom

institute: LSHTM

relation:
SuperSeries of: GSE224467
SuperSeries of: GSE224469

overall_design: Refer to individual Series


summary: Human tuberculosis (TB) is caused by various members of the Mycobacterium tuberculosis (Mtb) complex. Differences in host response to infection have been reported, illustrative of a need to test vaccines against multiple Mtb strains in preclinical studies. We have previously shown that the murine lung and spleen mycobacterial growth inhibition assay (MGIA) can be used to assess control of ex vivo mycobacterial growth by host cells. The number of mice required for the assay is lower than in vivo Mtb challenge studies, facilitating testing of multiple strains and/or the incorporation of other cellular analyses which may inform the design of future in vivo studies. Here, we present an optimised mycobacterial growth inhibition assay (MGIA) for testing TB vaccines against multiple Mtb clinical isolates. Using an ancient and modern strain of the Mtb complex, we demonstrate that ex vivo bacillus Calmette–Guérin (BCG)-mediated mycobacterial growth inhibition recapitulates protection observed in the lung and spleen following in vivo infection of mice. Further, cellular and transcriptional correlates of growth inhibition in the lung MGIA were identified. Flow cytometric analysis revealed an increased proportion of dendritic cells and interstitial macrophages in the lung cell input from mice vaccinated parentally with BCG compared with unvaccinated mice. RNA-seq analysis of the lung cell input revealed shared and strain-specific transcriptional correlates of BCG-mediated growth inhibition. The ex vivo MGIA may represent a platform to gain early insight into vaccine performance against a collection of Mtb strains to improve preclinical evaluation of TB vaccines.

overall_design: Female C57BL/6 mice (5–7 weeks old) received 1x10^6 CFU BCG Aeras Pasteur or no treatment. Six weeks post vaccination, mice were humanely culled, and lung was removed and processed to generate single cell suspensions. Lung cells (individual mice) were uninfected/infected overnight for gene expression analysis. Specifically, 1 x 10^6 lung cells per mouse were seeded in duplicate (uninfected/infected) in 24-well plates and cultured overnight at 37°C (5% CO2) in the presence or absence of 1 x 10^6 CFU mycobacteria (N0072, N0052 or N1283). The following day, plates were centrifuged at 500 x g to pellet eukaryotic cells, supernatants were removed and 600 µL RNAprotect cell reagent was added to stabilise transcription and prevent RNA degradation. Samples were stored at –70°C until RNA extraction.

first: Helen

last: Fletcher


overall_design: Female C57BL/6 mice (5–7 weeks old) received 1x10^6 CFU BCG Aeras Pasteur via the subcutaneous route, 0.5x10^6 CFU BCG Aeras Pasteur via the intranasal route or no treatment. Six weeks post vaccination, mice were humanely culled, and lungs were removed and processed to generate single cell suspensions. RNA was extracted from 1 x 10^6 lung cells per mouse were seeded in duplicate. Specifically, cells were centrifuged at 500 x g to pellet eukaryotic cells, supernatants, removed and 600 µL RNAprotect cell reagent added to stabilise transcription and prevent RNA degradation. Samples were stored at –70°C until RNA extraction.


title: RAS-induced transformation of mammary epithelial cells relies on ZEB1-dependent cellular reprogramming through a paracrine process

city: Lyon

first: Anne-Pierre

last: Morel

state: Rhone-Alpes

address: 28, rue Laennec, Cheney D 2nd floor

country: France

institute: Cancer Research Center of Lyon

summary: The distinct frequency of activation of the RAS/MAPK signaling pathway in human cancers suggests a context-dependent cellular state of vulnerability to RAS transformation. While uncommon in breast cancers, oncogenic activation of this pathway is frequent in claudin-low (CL) tumors, a subtype of breast malignancies enriched in features of epithelial-mesenchymal transition (EMT), suggesting an interplay between RAS activation and EMT. Using inducible models of human mammary epithelial cells, we show that RAS-mediated transformation relies upon cellular reprogramming governed by the EMT-inducing transcription factor ZEB1. The path to ZEB1 induction involves a paracrine process: cells entering a senescent state following RAS induction release proinflammatory cytokines, notably IL-6 and IL1 which promote ZEB1 expression and activity in neighboring cells, thereby fostering their malignant transformation. Collectively, our findings unveil a previously unprecedented role for senescence in bridging RAS activation and EMT over the course of malignant transformation of human mammary epithelial cells.

overall_design: We performed single-cell RNA sequencing analysis in a RAS inducible cellular model, HME-RASER, generated by introducing a 4-hydroxytamoxifen (4-OHT)-inducible form of HRASG12V into human mammary epithelial (HME) cells. We analyzed induced HME-RAS ER cells at different time points (D0, D3, D7, D14 and D20). Expression profiles were obtained for 12,357 genes in 445 cells (117 cells at D0, 83 cells at D3, 74 cells at D7, 82 cells at D14 and 89 cells at D20, Samples with less than 50000 reads were excluded).

first: Alain

last: Puisieux

first: Maria

last: Ouzounova

first: Hadrien

last: De Blander


title: Effect of combination treatment of RNA polymerase I transcription inhibitor CX-5461 and histone deacetylase inhibitor panobinostat on gene expression in human multiple myeloma cell lines MM.1S and JJN3

status: Public on Feb 15 2024

first: Jian

last: Kang

state: Victoria

address: 9 Princes street, Fitzroy

department: research division

institute: St Vincent's institute of medical research

summary: The high rates of protein synthesis and processing render multiple myeloma (MM) cells vulnerable to perturbations in protein homeostasis. The induction of proteotoxic stress by targeting protein degradation with proteasome inhibitors (PI) has revolutionized the treatment of MM. However, resistance to PI is inevitable and represents an ongoing clinical challenge. Our first-in-human study of the selective inhibitor of RNA polymerase I transcription of ribosomal RNA genes, CX-5461 has demonstrated a potential signal for anti-tumor activity in three of six heavily pre-treated MM patients. Here we show that CX-5461 has potent antimyeloma activity in PI-resistant MM preclinical models in vitro and in vivo. In addition to inhibiting ribosome biogenesis, CX-5461 causes topoisomerase II trapping and replication-dependent DNA damage, leading to G2/M cell cycle arrest and apoptotic cell death. Surprisingly, the addition of PI does not enhance the therapeutic benefit of CX-5461. In contrast, CX-5461 shows synergistic interaction with the histone deacetylase inhibitor panobinostat in both the Vk*MYC and the 5T33-KaLwRij mouse models of MM by targeting ribosome biogenesis and protein synthesis through distinct mechanisms. Our findings thus provide strong evidence to facilitate the clinical development of targeting the ribosome to treat relapsed and refractory MM.

overall_design: To investigate the molecular mechanisms underlying the synergistic response to CX-5461 and panobinostat, we performed RNAseq analysis in both p53-WT MM1.S and p53-null JJN-3 cells. MM.1S cells were treated with vehicle, 500 nM CX-5461, 50 nM panobinostat or the combination for 24 hr and cellular RNA was extracted for 3’ RNA sequencing analysis (n=3).

first: Kylee

last: Maclachlan

first: Gretchen

last: Poortinga

first: Elaine

last: Sanij


title: CRISPR Activation Reverses Haploinsufficiency and Functional Deficits Caused by TTN Truncation Variants

city: Seattle

first: Chia-Lin

last: Wei

state: WA

address: 3720 15th Ave NE

department: The Northwest Genomics Center (NWGC)

institute: University of Washington

summary: TTN CRISPR activation rescued TTNtv-related functional deficits despite increasing truncated TTN levels, which provides evidence to support haploinsufficiency as a relevant genetic mechanism underlying heterozygous TTNtvs (TTN truncation variants). CRISPR activation could be developed as a therapeutic to treat a large proportion of TTNtvs.

overall_design: We adapted CRISPR activation using dCas9-VPR to functionally interrogate TTNtv pathogenicity and develop a therapeutic  in  human  cardiomyocytes  and  3-dimensional  cardiac  microtissues  engineered  from  induced  pluripotent  stem  cell models harboring a dilated cardiomyopathy–associated TTNtv. We performed guide RNA screening with custom TTN reporter assays, agarose gel electrophoresis to quantify TTN protein levels and isoforms, and RNA sequencing to identify molecular consequences of TTN activation. Cardiomyocyte epigenetic assays were also used to nominate DNA regulatory elements to enable cardiomyocyte-specific TTN activation. By obtaining sequences from chromatin immunoprecipitated DNA, we generated genome-wide maps of inter-molecular ligated DNA representing long-range interactions in chromatin with in-situ ChiIA-PET RNAPII technology.

first: Travis

last: Hinson

first: Shahnaz

last: Ghahremani

first: Yanfen

last: Zhu

first: Harianto

last: Tjong


title: Changes in cardiac miRNA transcriptome following isoproterenol infusion and coadministration of minocycline.

city: Columbia

first: Jacob

middle: Jeffrey

last: Russell

state: MO

address: 1401 Ashland Rd, Apartment E

department: Biomedical Sciences

institute: University of Missouri

type: Non-coding RNA profiling by high throughput sequencing

summary: Mice were infusion with either vehicle or isoproterenol for 21 days. Another group of mice received both isoproterenol infusion and daily minocycline administration for the duration of the experiment. After 21 days mice were assessed for cardiac function and hearts collected to isolate  miRNA.

overall_design: 12-week-old male mice received miniosmotic pumps receiving either sterile saline (vehicle control) or isoproterenol at a dose of 30 mg/kg a day. A third group of mice received both isoproterenol and coadministration of minocycline via IP injection at a dose of 50 mg/kg a day. After 21 days mice were euthanized and tissue collected for miRNA isolation and sequecing.

first: Russell

last: Jacob

first: Mummidi

last: Srinivas

first: Bender

last: Shawn

first: Bysani

last: Chandrasekar


title: Changes in the cardiac transcriptome following isoproterenol infusion and coadministration of minocycline

summary: Adverse cardiac remodeling contributes to the development and progression of heart failure (HF) driven, in part, by inappropriate sympathetic nervous system activation. While blockade of β-adrenergic receptors (β-AR) is a common therapeutic strategy in HF, not all patients respond necessitating elucidation of additional therapeutic approaches. Minocycline is an FDA-approved antibiotic with pleiotropic properties, independent of its antimicrobial action, and recent evidence suggests it may act by altering gene expression via changes in miRNA expression. Therefore, we hypothesized that minocycline would prevent adverse cardiac remodeling induced by the β-AR agonist isoproterenol involving relevant alterations in the miRNA-mRNA transcriptome. Male C57BL/6J mice received Iso (30 mg/kg/d, sc) or vehicle for 21 days via osmotic minipump and daily treatment with either minocycline (50 mg/kg, ip) or sterile saline. Isoproterenol infusion induced cardiac hypertrophy, with no change in cardiac function, that was prevented by minocycline. Total mRNA sequencing revealed that isoproterenol altered gene networks associated with inflammation and metabolism while activation of fibrosis was predicted by integrated miRNA-mRNA sequencing, involving miR-21, -30a, -34a, -92a, and -150, among others. Conversely, the cardiac miRNA-mRNA transcriptome predicted inhibition of fibrosis in hearts from mice treated with minocycline plus isoproterenol involving anti-fibrotic shifts in Atf3 and Itgb6 gene expression associated with upregulation of miR-194. Consistent with these gene signatures, picrosirius red staining confirmed isoproterenol-induced cardiac fibrosis and that this was prevented by minocycline. These results demonstrate the therapeutic potential of minocycline to attenuate adverse cardiac remodeling via miRNA-mRNA-dependent mechanisms, especially related to reduced cardiac fibrosis.

overall_design: 12 week old C57BL6J mice received isoproterenol (30 mg/kg/day body weight) or sterile saline via osmotic pump. Mice also received daily IP injections of minocycline (50 mg/kg/body) or sterile saline. After 21 days, mice were echoed and cardiac tissue collected for sequencing.

first: Srinivas

last: Mummidi

first: Vincent

last: Demarco

first: Laurel

middle: A

last: Grisanti

first: Chastidy

last: Bailey

first: Shawn

last: Bender


title: Mapk7 regulates bone-fat balance by targeting Lrp6/β-catenin axis

city: Guangzhou

first: Chuan

last: Li

address: Zhongshan 2th Road

institute: Sun yat-sen university

summary: The lineage commitment and differentiation of mesenchymal stem cells (MSCs) play a crucial role in the maintenance of bone stability. MAPK7 (Mitogen-activated protein kinase 7), a member of the MAPK family, controls cell proliferation, differentiation, and survival. However, the specific role of Mapk7 in regulating the osteogenic and adipogenic differentiation of MSCs remains to be determined. In this study, depletion of Mapk7 in MSCs (Prx1-Cre) resulted in severe low bone mass and accumulation of bone marrow fat in mice exhibiting osteoporosis. In vitro, overexpression of Mapk7 in MSCs induced an enhancement of osteogenesis in MSCs, while adipogenesis was attenuated. Mechanistically, MAPK7 availed to influence the activity of WNT/β-catenin signaling by modulating the phosphorylation of LRP6 ser1490, which ultimately impacted the osteogenic-adipogenic differentiation fate of MSCs for the first time. This is of great clinical and scientific significance for understanding the biological function of Mapk7 gene and developing new therapeutic targets for OP. Our study for the first time demonstrates that Mapk7/Lrp6/β-catenin signal axis plays a critical role in regulating the osteogenic and adipogenic differentiation of MSCs. It also suggests that modulating the function of Mapk7 may benefit the treatment of MSCs differentiation inbalance related bone diseases such as osteoporosis.

overall_design: To explore the molecular mechanism of Mapk7 in regulation of osteoblast-adipocyte lineage transition, we extracted RNA from same generation of MSCs in WT (3 week)  and CKO (3 week) mice for RNA-seq


title: Single-cell RNA sequencing analysis of E14.5 mouse skin data

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: Yale University

summary: Mouse embryo skin samples were collected around embryonic day 14.5 (E14.5). Cells from the wildtype and the Wls mutant were pooled for analyses.

overall_design: K14Cre (Dassule et al., 2000) mice were bred to Wntless fl/fl (Carpenter, 2010) mice. Chromium Single cell 3’ GEM Library and Gel Bead Kit v3.1 (PN-1000121) was used for single-cell RNA sequencing.

first: Peggy

last: Myung


title: DNA methylation-based classification of common renal tumors

city: Bethesda

first: Kenneth

last: Aldape

state: Maryland

address: Building 10, Room 2S235

department: NCI, LABORATORY OF PATHOLOGY (HNC7Z18)

institute: National Institute of Health

summary: In present work one of our main objectives was to collect enough DNA methylation profiles of diverse tumor types in renal cancer.  So, we used a collection of newly processed samples on DNA methylation data to have a variety of diverse kidney tumors from various sources. We processed a subset of samples (n=156) profiled as a part of our routine clinical methylation testing for kidney cancer at NIH. We collected one subset of samples (n =173) from our collaborators at UCSF and another subset of samples (n=82) from NYU.

overall_design: All samples were profiled in accordance with standard manufacturer’s protocol for Illumina EPIC array (http://www.illumina.com/).

first: Antonios

last: Papanicolau-Sengos

first: Omkar

last: Singh

first: Kyung

last: Park

first: Matija

last: Snuderl

first: David

last: Solomon


title: RNA-seq based in vivo transcriptomes of pine trees inoculated with pinewood nematode under Bacillus subtilis JCK-1398 treatment

city: Busan

first: Jungwook

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

department: Microbiology

institute: Pusan National University

summary: Bursaphelenchus xylophilus (pinewood nematode, PWN) is the causal agent of pine wilt disease, causing economic and environmental losses in pine forests. The establishment of systemic acquired resistance (SAR) offers positive prospects for PWN control. We chose Bacillus subtilis JCK-1398, which effectively mitigated disease symptoms in PWN-infected pine trees. To elucidate the molecular responses involved in increased SAR according to B. subtilis JCK-1398 treatment, we characterized the in vivo transcriptomes of pine trees infected by PWN with B. subtilis JCK-1398 treatment. Additionally, pine trees infected by PWN after Tween20 treatment were used as a negative control.

overall_design: To induce systemic acquired resistance (SAR), pine seedlings were treated with Bacillus subtilis JCK-1398. As a negative control, pine seedlings were treated with distilled water containing 250 μg/ml Tween 20. One week after treatment, all pine seedlings were inoculated with Bursaphelenchus xylophilus. Each sample consisted of three replicates.

first: Hyejung

last: Jung

first: Mohamed

last: Mannaa

first: Gil

last: Han

first: Young-Su

last: Seo


title: Effect of NFAT5 deficiency on gene expression in BV2 cells

city: 重庆

first: ailiyaer

last: palahati

address: 重庆市渝中区医学院路1号

institute: 重庆医科大学

summary: Tonicity-Responsive Enhancer-Binding Protein (NFAT5), also known as Tonicity-Responsive Enhancer Binding Protein (TonEBP), is a important transcription factor in the  regulation of osmoprotective and inflammatory genes. NFAT5 has been reported to regulate the pathological processes of inflammatory and autoimmune disorders. Our data provides a insight to the gene expression in NFAT5 deficiency BV2 microglia cells, which NFAT5 knocked down by sh-RNA.

overall_design: We performed comparative gene expression profiling analysis of RNA-Seq data from BV2 microglia RNA samples, which transfected with scambled sh-RNA (NC) or NFAT5 sh-RNA.

first: Hui

last: Gan

first: Jing

last: Zhao


title: Quantification of local matrix deposition during muscle stem cell activation using engineered hydrogels

city: Ann Arbor

first: Carlos

last: Aguilar

state: Michigan

address: 2800 Plymouth Rd

department: Biomedical Engineering

institute: University of Michigan

summary: Adult stem cells occupy a niche that contributes to their function but how stem cells remodel their microenvironment remains an open-ended question. Herein, biomaterials-based systems and metabolic labeling were utilized to evaluate how skeletal muscle stem cells and mesenchymal progenitors (fibro-adipogenic progenitors) deposit and remodel extracellular matrix. Differences in matrix production of muscle stem cells on substrates with different stiffness were then evaluated and linked with stem cell activation state. Reducing the ability to deposit new matrix attenuated function and mimicked impairments observed from muscle stem cells isolated in old age. Rescuing nascent protein deposition in old age stem cells with therapeutic supplementation rescued extracellular protein deposition and highlight how important this feature of niche remodeling is towards maintaining healthy stem cell function.

overall_design: To determine mechanisms related to the impaired nascent matrix, MuSCs from young and old mice were isolated via magnetic activated cell sorting and seeded on the norbornene-hyaluronic acid hydrogels at a cell density of 7500 cells/ cm2.   After 5 days on culture, cells were trypsinized and processed for bulk RNA-seq .

first: Pamela

last: Duran

first: Benjamin

last: Yang

first: Eleanor

last: Plaster

first: Madeline

last: Eiken

first: Claudia

last: Loebel

first: A


title: Nucleophosmin sustains WNT-driven cell proliferation and tumor initiation in vivo

city: Berlin

first: Chiara

last: Giacomelli

address: Robert-Rössle-Str. 10

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: Nucleophosmin (NPM1) is a nucleolar protein frequently overexpressed in many solid tumours with little known about its functional role to support carcinogenesis. Here, we identify Npm1 as a commonly upregulated gene following Apc loss in highly proliferative tissues, and high expression correlates with increased proliferation in CRC patients. We show that NPM1 is dispensable for adult epithelial tissue homeostasis, however, it has a profound effect on WNT-driven intestinal and liver tumourigenesis, leading to reduced proliferation and extension of survival. Mechanistically, NPM1 depletion triggers integrated stress response (ISR) and p53 pathway activation. P53 deletion, or inhibition of the ISR effects, rescue proliferation following NPM1 loss. Overall, our results demonstrate that NPM1 supports WNT-driven cell proliferation and tumour initiation by attenuating p53 pathway activation or induction of ISR. Being dispensable for homeostasis, NPM1 presents as a promising target for cancer therapy in WNT-driven tumours with functional p53, including difficult to treat KRAS-mutant CRC and hepatic cancers.

overall_design: To investigate the role of Nucleophosmin (Npm1) on colorectal cancer, we conditionally deleted it in an APC null/KRAS mutant cancer model. Epithelial extracts three days post-KO were harvested from mice. Ribo-seq and total cytoplasmic RNA sequencing were performed to address the effects on translation as well as transcript levels. The experiment was performed in four independent mice. Replicates are indicated by _1/_2/_3/_4. CRUK Scotland Institute Mouse IDs are indicated.

first: Georgios

last: Kanellos

first: June

last: Munro

first: Owen

last: Sansom

first: Martin

last: Bushell


title: Targeting WNT Signaling for Improved Glioma Immunotherapy [PBT]

city: Duarte

first: Yate-Ching

last: Yuan

address: 1500 East Duarte

institute: City of Hope

summary: Metabolic gene expression analysis to explore ICG-001’s impact on metabolic changes  associated with glioma differentiation after disrupting the CBP/β-Catenin interaction by treating patient-derived  GBM cell lines PBT147 and PBT030 with ICG-001 (0, 5, or 10 µM) for 24 and 72 h using Nanostring nCounter platform

overall_design: Gene expression analysis using nanostring ecounter platform Nanostring nCounter Human Metabolism Panel

first: Margarita

last: Gutova

first: Raju

last: Pillai

first: Holly

last: Yin


title: Temporal gene expression changes and affected pathways in neurodevelopment of a mouse model of Smith-Lemli-Opitz syndrome

first: Libin

last: Xu

address: 1705 NE Pacific St

department: Medicinal Chemistry

summary: Smith-Lemli-Opitz syndrome is an autosomal recessive disorder that arises from mutations in the gene DHCR7, which encodes the terminal enzyme of cholesterol biosynthesis, leading to decreased production of cholesterol and accumulation of the cholesterol precursor, 7-dehydrocholesterol, and its oxysterol metabolites. The disorder displays a wide range of neurodevelopmental defects, intellectual disability and behavioral problems. However, an in-depth study on the temporal changes of gene expression in the developing brains of SLOS mice has not been done before. In this work, we carried out the transcriptomic analysis of whole brains from WT and Dhcr7-KO mice at four time points through postnatal day 0. First, we observed the expected downregulation of the Dhcr7 gene in the Dhcr7-KO mouse model, as well as gene expression changes of several other genes involved in cholesterol biosynthesis throughout all time points. Pathway and GO term enrichment analyses revealed affected signaling pathways and biological processes that were shared amongst time points and unique to individual time points. Specifically, the pathways important for embryonic development, including Hippo, Wnt, and TGF-β signaling pathways are the most significantly affected at the earliest time point, E12.5. Additionally, neurogenesis-related GO terms were enriched in earlier time points, consistent with the timing of development. Conversely, pathways related to synaptogenesis, which occurs later in development compared to neurogenesis, are significantly affected at the later time points, E16.5 and PND0, including the cholinergic, glutamatergic, and GABAergic synapses. The impact of these transcriptomic changes and enriched pathways is discussed in the context of known biological phenotypes of SLOS.

overall_design: Total RNA was sequenced for four replicates each of whole brains from WT and Dhcr7-KO mouse embryos/neonates at four different gestational time points, including three embryonic (E12.5, E14.5, and E16.5) and one postnatal time point (PND0).

first: Li

last: Amy

first: Tomita

last: Hideaki

first: Xu

last: Libin


title: Nasal cavity epithelial cells exhibit antiviral transcriptional signatures upon activation of IFN-gamma producing antigen-specific T cells

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To evaluate the differential impact of IFN-gamma secretion on nasal cavity epithelial cells, we compared the transcriptional profiles of nasal cavity epithelial cells (CD45-, CD3- CD11b-, CD31-, CD326+) from wildtype and IFN-gamma knockout mice at 30 days (d30) post intranasal infection with a live attenuated influenza virus expressing the immunodominant H-2Kd CD8 T cell epitope from Sendai virus nucleoprotein (LAIV-SenNP). Nasal cavity epithelial cells were also analyzed from LAIV-SenNP immunized wildtype and IFN-gamma knockout mice 3 days after intranasal administration of Sendai virus nucleoprotein peptide (d30+3). The results indicate that nasal cavity epithelial cells express genes associated with antigen presentation and antiviral function following antigen-specific T cell activation, and these alterations in transcriptional programming depend on IFN-gamma secretion.

overall_design: Transcriptional profiling of 4 experimental groups (n=10 WT mice at d30, n=9 Ifng-/- mice at d30, n=10 WT mice at d30+3, and n=8 Ifng-/- mice at d30+3) collected over 2 independent replicates.

first: Christopher

first: Jacob

last: Kohlmeier

first: Sarah

last: Michalets


title: Transcriptional responses of antigen-specific CD8 T cells after secondary influenza virus challenge

summary: To evaluate the transcriptional responses of effector and memory virus-specific CD8 T cell subsets after primary and secondary influenza infection, we sorted subsets of FluNP 366-374/Db+ CD8+ T cells from the BAL, lung, and spleen at the peak of primary x31 influenza infection (day 10), resting memory (day 30), or 3 days after secondary PR8 influenza challenge (Day 30+3). Cells from the circulation were excluded from BAL and lung based on intravital labeling with anti-CD45. Memory cells from the lung were further separated in TRM and TEM subsets based on expression of CD69 at the day 30 and day 30+3 timepoints. Memory cells from the BAL were separated into long-term airway resident versus recently-recruited cells based on CD11a expression at the day 30 and days 30+3 timepoints. The results show that virus-specific BAL and lung TRM cells, but not lung TEM cells or spleen TEM cells, rapidly alter their transcriptional program and increase expression of effector molecules within 3 days of a secondary influenza challenge.

overall_design: Transcriptional profiling of FluNP 366-374/Db-specific CD8 T cells at the peak of the initial effector T cell response (day 10), resting memory (day 30), or after secondary heterosubtypic influenza challenge (day 30+3). Five minutes prior to euthanasia, mice were administered anti-CD45-PECF594 intravenously to label cells in the vasculature. Cells were isolated from the BAL, lung, and slpeen and sorted on the markers listed below. 5 mice were pooled for each timepoint to obtain sufficient cells for RNA sequencing analysis and there were 3 independent replicates.

first: Ida

last: Uddbäck


title: Identifying the role of MTHFD1L in prostate cancer progression from genetic analysis and experimental validation

city: Taichung

first: Wei-Chung

last: Cheng

address: No. 91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

country: Taiwan

institute: China Medical University

summary: One-carbon metabolism plays a crucial role in tumorigenesis as it supplies the one-carbon units necessary for nucleotide synthesis, epigenetic regulation, and redox metabolism, ensuring the rapid proliferation of cancer cells. However, their roles in prostate cancer progression remain poorly understood. In this study, we investigated the association between genetic variants in the one-carbon metabolism pathway and clinical outcomes in patients receiving androgen deprivation therapy for prostate cancer. The associations of 130 single-nucleotide polymorphisms located within 14 genes involved in the one-carbon metabolism pathway with cancer-specific survival (CSS), overall survival, and progression-free survival were assessed using Cox regression in 630 patients with prostate cancer. Subsequently, functional studies were performed using prostate cancer cell lines. After adjusting for covariates and multiple testing, MTHFD1L rs2073190 was found to be significantly associated with CSS (P = 0.000184). Further pooled analysis of multiple datasets demonstrated that MTHFD1L was upregulated in prostate cancer and increased MTHFD1L expression was positively correlated with tumor aggressiveness and poor patient prognosis. Functionally, MTHFD1L knockdown suppressed prostate cancer cell proliferation and colony formation. RNA sequencing and pathway analysis revealed that differentially expressed genes were predominantly enriched in the cell cycle pathway. In conclusion, genetic variants in MTHFD1L of one-carbon metabolism may serve as promising predictors, and our findings offer valuable insights into the underlying genetic mechanisms of prostate cancer progression.

overall_design: To investigate the biological function of MTHFD1L, we employed an siRNA-based approach to reduce its expression in PC-3 and C4-2 human prostate cancer cell lines. Comparative gene expression profiling RNA-seq analysis was conducted for PC-3 and C4-2 (WT) cells and their knockdown (siRNA) derivatives.

first: Yuan-Chin

last: Tsai

first: Shu-Pin

last: Huang

first: Yu-Ching

last: Fan

first: Ya-Ching

last: Lin

first: Chao-Yuan

first: Chia-Cheng

last: Yu

first: Victor

first: Jiun-Hung

last: Geng

first: Chia-Yang

last: Li

first: Te-Ling

last: Lu

first: Bo-Ying

last: Bao


title: OCT4 is expressed in extraembryonic endoderm stem (XEN) cell progenitors during somatic cell reprogramming

city: East Lansing

first: michael

last: halbisen

address: 603 Wilson Rd

department: Biochemistry

institute: Michigan State University

summary: During development, progenitors of embryonic stem (ES) and extraembryonic endoderm stem (XEN) cells are concomitantly specified within the inner cell mass (ICM) of the mouse blastocyst. Similarly, XEN cells are induced (iXEN cells) alongside induced pluripotent stem (iPS) cells following overexpression ofOct4,Sox2,Klf4andMyc(OSKM) during somatic cell reprogramming. It is unclear how or why this cocktail produces both stem cell types, but OCT4 has been associated with non-pluripotent outcomes. In this report, we show that, during OSKM reprogramming, many individualOct4-GFP-expressing cells are fated to become iXEN cells. Interestingly, SKM alone was also sufficient to induce iXEN cell formation, likely via activation of endogenousOct4.These observations indicate that iXEN cell formation is not strictly an artifact ofOct4overexpression. Moreover, our results suggest that a pathway to XEN may be an integral feature of establishing pluripotency during reprogramming, as in early embryo development.

overall_design:
We performed RNAseq on iXEN cell lines that had been clonally derived from Oct4-EGFP-positive single cells following retroviral reprogramming of mouse embryonic fibroblasts (MEFs) using Oct4, Sox2, Klf4, and Myc overexpression. Each sample (IXEN79-IXEN83) represents a distinct, clonally derived iXEN cell line.
We compared transcriptomes of iXEN cells derived from lentiviral reprogramming of mouse embryonic fibroblasts (MEFs) using either Oct4, Sox2, Klf4, Myc overexpression (IXOSKM01-IXOSKM05) or Sox2, Klf4, Myc overexpression (IX_SKM06-IX_SKM10). Each sample represents a stable iXEN cell line, of passage >11, derived from reprogramming distinct MEF preps.

first: Alexandra

last: Moauro

first: Michael

last: Halbisen

first: Amy

last: Ralston

first: Anthony

last: Parenti

first: Stephanie

last: Hickey


title: Global repair is the primary nucleotide excision repair subpathway for the removal of pyrimidine-pyrimidone (6-4) damage from the Arabidopsis genome

city: Istanbul

first: Sezgi

last: Kaya

state: Tuzla

address: Orta Mahalle, Universite Cad, No: 27

country: Turkey

institute: Sabanci University

summary: Ultraviolet (UV) component of solar radiation impairs genome stability by inducing the formation of pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] in plant genomes. (6-4)PPs disrupt growth and development by interfering with transcription and DNA replication. To resist UV stress, plants employ nucleotide excision repair that excises oligonucleotides containing (6-4)PPs through two subpathways: global and transcription-coupled excision repair (TCR) . Here, we analyzed the genome-wide excision repair-mediated repair of (6-4)PPs in Arabidopsis thaliana and found that (6-4)PPs can be repaired by TCR; however, the main subpathway to remove (6-4)PPs from the genome is global repair. Our analysis showed that open chromatin genome regions are more rapidly repaired than heterochromatin regions, and the repair level peaks at the promoter, transcription start site (TSS) and transcription end site (TES) of genes. Our study revealed that the repair of (6-4)PP in plants showed a distinct genome-wide repair profile compared to the repair of other major UV-induced DNA lesion called cyclobutane pyrimidine dimers (CPDs).

overall_design: To capture the repair of (6-4)PP damage, Arabidopsis thaliana Columbia (Col-0) accession plants were exposed to UV. After UV-exposure, XR-seq protocol was applied.

first: Kaya

last: Sezgi

first: Erdogan

last: Dugcar Ebrar

first: Sancar

last: Aziz

first: Adebali

last: Ogun

first: Oztas

last: Onur


title: Single-Cell Transcriptomic Profiling of Human iPSC-Derived Macrophage Differentiation Under Distinct Cytokine Conditions

city: Hannover

first: Nico

last: Lachmann

address: Carl-Neuberg-Str. 1

department: Pediatric Pneumology, Allergology and Neonatology

institute: Medizinische Hochschule Hannover

summary: The differentiation of human induced pluripotent stem cells (iPSCs) into macrophages is a complex process involving the emergence of diverse cell types and progenitors. In this study, we conducted a comprehensive single-cell transcriptomic analysis to elucidate the dynamics of iPSC-to-macrophage differentiation and explore the heterogeneity of arising cell populations. Two different cytokine conditions were employed to modulate differentiation, and we hypothesized that these conditions would yield distinct cell compartments. Our results reveal a nuanced cellular trajectory from iPSCs to macrophages, uncovering key intermediates and transitional states. Notably, the emerging cell populations remain consistent, albeit with variations in their proportions, with IL-3-only condition exhibiting a lower proportion of mature cells.  This investigation advances our understanding of iPSC-to-macrophage differentiation, shedding light on the cellular heterogeneity and trajectory dynamics. The findings have implications for the development of targeted differentiation strategies and the exploration of novel therapeutic applications in regenerative medicine and immunology.

overall_design:
Sample Types:
1. Dissociated Embryoid Bodies/Myeloid-Cell-Forming Complexes: These samples map the progenitor populations at different stages of differentiation.
Experimental Conditions and Variables:
1. Embryoid Body (EB):  after 5 days of Undirected Differentiation
2. Cytokine Conditions: Two distinct cytokine conditions were employed to modulate the differentiation process:
• Condition 1: EBs were differentiated into macrophages in the presence of 50 ng/ml interleukin-3 (IL-3).
• Condition 2: EBs were differentiated into macrophages with a combination of 25 ng/ml IL-3 and 50 ng/ml macrophage colony-stimulating factor (M-CSF).
3. Time Points: For the cytokine conditions, two time points were investigated:
• Day 8 of Hematopoietic Specification: This time point provides insights into the early stages of differentiation.
• Day 16 of Hematopoietic Specification: This time point represents a more advanced stage in the differentiation process.

first: Mi-Sun

last: Jang

first: Mania

last: Ackermann


title: Canonical Wnt signaling directs the generation of functional human PSC-derived atrioventricular canal cardiomyocytes in bioprinted cardiac tissues

city: Xiamen

first: Jie

last: Ren

state: Fujian Province

address: 2999 Jinshan Road

department: Institute of Cardiovascular Diseases

institute: Xiamen Cardiovascular Hospital of Xiamen University

summary: To investigate how stage-specific activation of canonical Wnt signaling can induce the differentiation of atrioventricular canal cardiomyocytes，We employed single-cell RNA sequencing and ChIP-seq for H3K27ac to interrogate hPSC-derived cardiac cells.

overall_design: hPSC-derived cardiac cells at day 11 and day 15 were analyzed using scRNA seq or ChIP-seq.

first: Chenxi

last: Ye

first: Yan

last: Wang


title: Targeting mitochondrial apoptotic priming state to personalize therapy for relapsed acute myeloid leukemia

city: Singapore

first: Shruti

last: Bhatt

state: Singapore

address: Blk S7 level 2,  Science Drive 3, Room 02-05

department: Pharmacy

country: Singapore

institute: National University of Singapore

summary: The majority of relapsed acute myeloid leukemia (AML) patients still succumb to disease despite improvements in therapy. We present landscapes of pharmacologic sensitivity for 22 AML patient-derived xenograft (PDX) models together with genomic and transcriptomic profiles. First, we used ex vivo dynamic BH3 profiling (DBP) to segregate PDXs according to prior treatment status and accurately predicted in vivo efficacy of drugs with varying mechanisms of action. We next selected in vivo acquired resistance to single agents of distinct mechanisms, which caused broad chemoresistance across all models associated with a reduction in mitochondrial apoptotic priming. DBP could identify drugs with persistent in vivo activity even in these resistant models. Using RNA-seq, we found conserved gene expression signatures defining relapsed phenotypes common to mechanistically distinct agents targeting FLT-3, BCL2, IAPs, and BRD-4. We replicated drug-response patterns from PDX models in primary and relapsed AML patients, demonstrating the clinical feasibility of such approach

overall_design: To investigate the mechanism of acquired drug resistance, an unbiased whole transcriptomic analysis on a total of 78 resistant samples from three PDX models (DFAM-61786, DFAM-15354, and DFAM-61345) and 16 matched-control samples was conducted.


title: Tricarboxylic Acid Cycle Metabolite-Coordinated Biohydrogels Augment Cranial Bone Regeneration Through Neutrophil-Stimulated MSCs Recruitment and Histone Acetylation-Mediated Osteogenesis

city: Chendu

first: Fangyuan

last: Shen

state: --- Select a state ---

address: No.29 Jiuyanqiao Wangjiang Road, Chengdu, 610064

institute: Sichuan University

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Tricarboxylic Acid Cycle Metabolite-Coordinated Biohydrogels Augment Cranial Bone Regeneration Through Neutrophil-Stimulated MSCs Recruitment and Histone Acetylation-Mediated Osteogenesis [RNA-Seq]

summary: Cranial bone defect is a major clinical challenge that increases the life burden of patients. Tricarboxylic acid (TCA) cycle metabolites have recently drawn considerable attention in the field of bone tissue regeneration due to their bio-safety, low cost, structural stability, and effectiveness. However, the development of TCA cycle metabolite-modified biomimetic grafts for skull bone regeneration via a facile and general approach remains lacking. Moreover, the mechanism underlying the release of TCA cycle metabolites from biomaterials in immune responses and mesenchymal stem cells (MSCs) fate (migration and differentiation) remain unknown. Herein, inspired by the Hofmeister effects, we developed a series of TCA metabolite (in the form of sodium salt)-coordinated biomimetic hydrogels (CGG) with strong mechanical and anti-swelling performances. Importantly, the sodium citrate (Na3Cit)-treated CGG hydrogels (CGG-Cit) with the highest mechanical modulus and strength significantly promoted skull bone regeneration in rats and mice. Mechanistically, using a transgenic mouse model, bulk RNA sequencing, and single-cell RNA sequencing, we demonstrated that CGG-Cit promotes Gli1+ MSCs migration via neutrophil-secreted OSM. Our results also indicate that CGG-Cit improved osteogenesis via enhanced H3K9ac modification on osteogenic master genes. Taken together, the immune microenvironments and MSCs fate-regulated biomimetic hydrogels developed herein represent a highly efficient and facile approach toward skull bone tissue regeneration with great potential for bench-to-bedside translation.

overall_design: To assess the molecular responses to CGG-Cit hydrogels and CGG hydrogels in calvarial bone defects, rats were sacrificed at week 4 post-surgery. The bone defect areas were carefully trimmed and minced to pieces, and total RNA was extracted using Trizol Reagent (Invitrogen, Thermo Fisher Scientific, USA) and subjected to RNA sequencing.

first: Tingjun

last: Liu

first: Ziying

last: You

first: Zhenming

first: Yu

last: Shi

first: Ling


title: Tricarboxylic Acid Cycle Metabolite-Coordinated Biohydrogels Augment Cranial Bone Regeneration Through Neutrophil-Stimulated MSCs Recruitment and Histone Acetylation-Mediated Osteogenesis [scRNA-Seq]

overall_design: To test whether distinct cell populations exist and affect progenitor cell recruitment, we dissected calvaria defects on day 14 post-surgery for enzymatic digestion before conducting droplet-based scRNA-seq. Briefly, we created 2 mm calvarial bone defects on the parietal bones and implanted CGG hydrogels or CGG-Cit hydrogels. At 2 weeks post-surgery, the defect regions were carefully trimmed, and tissues were digested in 0.3% collagenase in α-MEM. Cell suspensions were filtered through 70 μm strainers, and single cells were subjected to RNA sequencing.


title: Inhibition of epigenetic and cell cycle-related targets in glioblastoma cell lines: onametostat reduces proliferation and viability in both normoxic and hypoxic conditions

city: Tartu

first: Vijayachitra

last: Modhukur

address: L. Puusepa 8

country: Estonia

institute: University of Tartu

summary: The objective of the study was to compare the transcriptome of the glioblastoma cell line T98-G following the 48-h treatment with 1 microM onametostat or 0.1% DMSO (negative control) under normoxic or hypoxic conditions. It was found that treatment with onametostat lead to dramatic changes in the transcriptome profile by inducing the cell cycle arrest, suppressing RNA splicing, and down-regulating several major glioblastoma cell survival pathways. The effect of hypoxia was less pronounced.

overall_design: Compare the expression of mRNAs in lysates of differently treated T98-G cells

first: Darja

last: Lavogina

first: Mattias

last: Kaspar Krõlov

first: Hans

last: Vellama

first: Valentina

last: Di Nisio

first: Helen

last: Lust

first: Kattri-Liis

last: Eskla

first: Andres

last: Salumets

first: Jana

last: Jaal


title: Differential impacts of DNA methylation on pH dependent i-motifs formation in rice

city: Nanjing

first: Xing

last: Ma

address: No.1 Weigang, Nanjing, Jiangsu 210095, P. R. China

institute: Nanjing Agricultural University

type: Methylation profiling by high throughput sequencing


title: Differential impacts of DNA methylation on pH dependent i-motifs formation in rice [ChIP-seq]

summary: I-motifs (iMs) are four-stranded non-B DNA structures containing C-rich DNA sequences, which can be formed under various pH conditions. DNA methylation exhibits complex impacts on iM formation in vitro. However, how DNA methylation differentially affects pH dependent iM formation on a genome wide scale is completely uncharacterized in both humans and plants. To this end, we conducted iM-IP-seq under pH 5.5 and 7.0 conditions using CK and hyper/hypomethylated DNA in combination with BS-seq in rice. We found that pH 7.0 and 5.5 biased iMs had distinct genomic features and differential DNA methylation levels, the former having higher DNA methylation levels than the latter. Moreover, DNA demethylation and hyper methylation had more impacts on a subset of iM formation under pH 7.0 and 5.5, respectively, indicating that DNA de/hyper-methylation exhibits pH dependent impacts on iM formation. Importantly, we found that CG hypo-DMRs and CHH hyper-DMRs alone or coordinated with CG/CHG hyper-DMRs may play determinant roles in the regulation of iM formation under pH 5.5 and 7.0. Thus, our study shows that intrinsic DNA sequences alone or in combination with DNA methylation play vital roles in determining pH-dependent formation of iMs. It will contribute to in-depth understanding of DNA methylation in the modulation of pH dependent dynamics of iM conformation, therefore broadening its biological implications and practical application ranges.

overall_design: iM-IP-seq under pH 7.0 condition and in M. Cvip I-(hypermethylation)/zebularine (demethylation)-treatment  under pH 5.5/7.0 condition

first: Yilong

last: Feng

first: Wenli

last: Zhang


title: Differential impacts of DNA methylation on pH dependent i-motifs formation in rice [Bisulfite-seq]

overall_design: M. Cvip I-(hypermethylation)/zebularine (demethylation)-treated genomic DNA and CK (untreatment) were used for bisulfite treatment


title: RNA-sequencing in rat ventral tegmental area (VTA) following chronic ethanol and withdrawal

city: Chicago

first: Subhash

last: Pandey

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

summary: The objective of  The Center for Alcohol Research in Epigenetics (CARE) is to identify gene regulatory pathways in ventral tegmental area (VTA) that are altered in response to chronic ethanol administration and withdrawal.

overall_design: Adult male rats (6 per group)were used for each experimental group:control diet-fed, chronicethanol diet-fedand 24h withdrawal following chronic ethanol exposure. VTAtissues were dissected out and immediately frozen.  Altogether, there was a total of 18 samples (3 groups x 6 rats).  The RNAseq libraries were quantitated by qPCR and the 18 libraries were paired-end sequenced on 11 lanes (Illumina Hiseq 4000). Fastq files  generated and demultiplexed with bcl2fastq and adaptor sequences were trimmed from the 3’-end of the reads.

first: Mark

middle: S

last: Brodie

first: Harish

last: Krishnan

first: Chang

first: Huaibo

first: Ying

last: Chen

first: Alvaro

middle: G

last: Hernandez

first: Jenny

last: Drnevich

first: Dennis

last: Grayson


title: Diet and multi-omics characterization in the Study of Urban and Rural Crohn Disease Evolution (SOURCE) cohort

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

summary: The Study Of Urban and Rural Crohn disease Evolution (SOURCE, n=380) characterized exposures, diet, and host and microbial factors in rural and urban Chinese controls and newly diagnosed Crohn Disease (CD), and in treatment-naïve Israeli CD and controls. We considered diet-omics domains simultaneously to detect complex interactions in the gut to prioritize potential beneficial and pathogenic factors.

overall_design: SOURCE cohort included terminal ileum of treatment naïve Crohn's disease and non-IBD controls from Urban and Rural Chinese subjects, as well as corresponding terminal ileum from Israel Sheba medical center, which were previously uploaded to GEO GSE199906.

first: Rui

first: Amnon

last: Amir

first: Nina

last: Levhar

first: Hila

last: Shacham

first: Ren

last: Mao

first: Rotem

last: Hadar

first: Itamar

last: Toren

first: Yadid

last: Algavi

first: Kathleen

last: Abu-Saad

first: Shuoyu

last: Zhuo

first: Gilat

last: Efroni

first: Alona

last: Malik

first: Orit

last: Picard

first: Miri

last: Yavzori

first: Bella

last: Agranovich

first: Liu

last: Ta-Chiang

first: Thaddeus

last: Stappenbeck

first: Lee

last: Denson

first: Ofra

last: Kalter-Leibovici

first: Eyal

last: Gottlieb

first: Elhanan

last: Borenstein

first: Eran

last: Elinav

first: Minhu

first: Shomron

last: Ben-Horin

first: Yael

last: Haberman


title: Jedi-1/MEGF12-mediated phagocytosis controls the pro-neurogenic properties of microglia in the ventricular-subventricular zone

city: Nashville

first: Bruce

last: Carter

state: TN

address: 2215 Garland Ave

institute: Vanderbilt University

summary:
Microglia are the primary phagocytes in the central nervous system and are responsible for clearing dead cells generated during development or disease. The phagocytic process shapes the phenotype of the microglia, which affects the local environment. A unique population of microglia reside in the ventricular-subventricular zone (V-SVZ) of neonatal mice, but how they influence this neurogenic niche is not well-understood. Here, we demonstrate that phagocytosis creates a pro-neurogenic microglial phenotype in the V-SVZ and that these microglia phagocytose apoptotic cells via the engulfment receptor Jedi-1. Deletion of Jedi-1 decreases apoptotic cell clearance, triggering the development of a neuroinflammatory phenotype, reminiscent of neurodegenerative and-age-associated microglia, that reduces neural precursor proliferation via elevated interleukin (IL)-1β signaling; inhibiton of IL-1 receptor rescues precursor proliferation in vivo. Together, these results reveal a critical role for Jedi-1 in connecting microglial phagocytic activity to a phenotype that promotes neurogenesis in the developing V-SVZ.
We performed RNAseq on MACS-sorted microglia from V-SVZ and Cortex of WT and Jedi-1 knockout P7 mice.

overall_design: Differential gene expression analysis comparing microglial transcriptome differences by region and by genotype. WT cortex microglia are considered as control.

first: Vivianne

last: Morrison

first: Matthew

last: Houpert

first: Jonathan

last: Trapani

first: Asa

last: Brockman

first: Ketaki

last: Katdare

first: Hilary

last: Layden

first: Scott

middle: W

last: Hiebert

first: Gabriela

last: Nguena-Jones

first: Alexandra

last: Trevisan

first: Kathleen

last: Maguire-Zeiss

first: Lawrence

last: Marnett

first: Gregory

last: Bix

first: Rebecca

last: Ihrie


title: IL-17 activates dermal reticular fibroblasts to promote neutrophil recruitment and host defense [scRNAseq]

city: San Diego

first: Kellen

last: Cavagnero

state: California

address: 9500 Gilman Dr

institute: Univeristy of California, San Diego

summary: The complex system by which the skin regulates immune responses to the external environment is unclear. Here, we investigated cell-cell interactions underlying cutaneous defense against S. aureus. Single-cell transcriptomics (scRNA-Seq) and unbiased network analysis revealed unexpected, dominant IL-17-mediated dermal reticular fibroblast-to-neutrophil communication. Multi-faceted in vitro omics studies demonstrated that IL-17 synergized with several factors including TNF⍺ to induce fibroblast NFKBIZ and chemokine secretion. Cultured fibroblasts drove robust neutrophil recruitment through NFKBIZ-dependent CXCR2 and CXCR4 ligands. Mice lacking IL-17R in fibroblasts (PdgfraΔIl17ra) were generated to determine the significance of fibroblast-neutrophil communication. PdgfraΔIl17ra mice exhibited drastically reduced skin neutrophilia in multiple disease models and reduced defense against S. aureus. These findings were translated to humans by comprehensive analysis of biopsies from psoriasis patients on and off anti-IL-17 treatment. Thus, dermal fibroblasts are critical for skin type 17 inflammation and represent a novel target for treatment of infection and inflammatory disease.

overall_design: scRNA-seq of fibroblasts stimulated in vitro and infected, inflamed, and control mouse skin


title: Identification of novel spatially resolved markers of malignant transformation in Intraductal Papillary Mucinous Neoplasms

city: Rome

first: Antonio

last: Agostini

address: Largo Francesco Vito, 1

country: Italy

institute: Università Cattolica del Sacro Cuore


title: Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma [m1A_pileup]

city: Bethesda

first: Pedro

last: Batista

state: MD

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

summary: Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid (TCA) cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of a highly metastatic and aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxyglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1α, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively alters the activity of demethylases acting upon N6-methyladenosine (m6A), while the demethylases acting upon N1-methyladenosine (m1A) and 5-formylcytosine (f5C) in mitochondrial RNA are unaffected. The observation that metabolites may modulate specific subsets of RNA-modifying enzymes offers new insights into their gene regulatory effects and potential strategies for therapeutic intervention.

first: Christina

last: Fitzsimmons

first: Mariana

last: Mandler

first: Judith

last: Lunger

first: Dalen

last: Chan

first: Siddhardha

last: Maligireddy

last: Schmiechen

first: Supuni

middle: T

last: Gamage

first: Courtney

last: Link

first: Lisa

last: Jenkins

first: Daniel

last: Crooks

first: Jordan

last: Meier

first: W

last: Linehand


title: Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma