title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and PS micro-/nanoplastics stressed E. coli K-12 LE392, P. putida KT2440, and RP4 plasmid Transcriptomes

city: Shenzhen

first: Yuanyuan

last: Kang

address: No. 6 Pingshan 1st Road, Taoyuan Street, Nanshan District

department: School of Civil and Environmental Engineering

institute: Harbin Institue of Technology

summary: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type E. coli K-12 LE392, E. coli BL21 (DE3), P. putida KT2440 and IncPα RP4 plasmid, and their mRNA response under the exposure of different sizes of Polystyrene (PS), including 20 nm, 120 nm and 1 μm. The concentrations were 0.1, 10 mg/L for every size of PS. The group without adding PS was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these 3 sizes of PS on transcriptional levels can be revealed. Illumina HiSeq PE150 was applied. NEBNextő Ultra II Directional RNA Library Prep Kit for Illumina was used for library construction. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913), P.putida reference genome (NC_002947), and IncPα plasmid reference genome (L27758) using Bowtie2. RSeQC was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

sample_organism:
Pseudomonas putida
Escherichia coli

platform_organism:
Pseudomonas putida
Escherichia coli

overall_design: Bacterial mRNA profiles of wild-type E. coli K-12 LE392, E. coli BL21 (DE3), P. putida KT2440, and IncPα RP4 plasmid in response to 0.1 mg/L 20 nm PS, 10 mg/L 20 nm PS, 0.1 mg/L 120 nm PS, 10 mg/L 120 nm PS, 0.1 mg/L 1 μm PS, and 10 mg/L 1 μm PS for 2 hours, bacteria and plasmid without adding PS are the control group, in triplicate, using Illumina HiSeq PE150.

first: Yue

first: Jianhua

last: Guo

first: Jianqiang

last: Su

first: Aijie

first: Shu-Hong

last: Gao


title: The Daily timetable of gene expression rhythms undergoes programmed warping toward the nighttime pattern in aged Arabidopsis

status: Public on Dec 05 2023

city: daegu

first: myeonghoon

last: kang

state: Daegu

country: South Korea

institute: Daegu Gyeongbuk Institute of Science and Technology (DGIST)

type: Expression profiling by high throughput sequencing

summary: The daily pattern of temporal gene expression is regulated by the circadian clock system. Under constant environmental conditions, aging is associated with a shortening of the endogenous period of circadian rhythms in Arabidopsis. This study investigated to investigate how aging influences the waveforms of rhythmic patterns of gene expression under light/dark cycles. The waveforms of the daily cycling circadian clock showed significant warping in aged leaves, which shifted their expression pattern. Transcriptomic analysis revealed that the number of daily cycling genes in aged leaves was reduced by more than half. Furthermore, in aged plants, the expression schedule of cycling genes in both young and old leaves warped. Circadian clock mutants, including toc1, which did not exhibit age-dependent warping, had significantly altered warping patterns.

overall_design: To investigate d age-dependent changes in the daily rhythm at the level of the transcriptome in arabidopsis leaves, we collected third leaves at 21 and 35DAS in 6 different time-points over a 24h period ,and performed expression profiling analysis using 3 biological replicates samples.

first: Sukjoon

last: Jung

first: Hyunmin

last: Kim

first: Juhyeon

last: Lee

first: Myeong

middle: H

first: Jung

middle: Y

first: Jong

middle: K

first: Pyung

middle: O

last: Lim

first: Hong

middle: G

last: Nam


title: Single cell-seq identify discoid lateral meniscus

status: Public on Dec 06 2023

city: Guangzhou

first: Hao

last: Sun

state: Guangdong

address: Zhongshan 2nd Road

department: Joint surgery

country: China

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

summary: Discoid lateral meniscus (DLM) is more prone to injury than a normally shaped meniscus. Our previous study successfully identified the different cell types and their corresponding marker genes in meniscus tissues, but there was no study comparing the gene expression and cell heterogenicity of discoid meniscus with normal meniscus.

overall_design: scRNA-seq was used to identify cell subsets and their gene signatures in DLM and osteoarthritis lateral meniscus (OAM) cells to determine their differentiation relationships and identify specific cell types. Pseudotime analysis and immunohistochemical staining were used to investigate temporal and spatial distribution of DLM specific clusters

first: Ruofan

last: Ma


title: The lipid Gb3 promotes germinal center B cell responses and anti-viral immunity

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

country: USA

institute: Boston Children's Hospital / Harvard Medical School

summary: Influenza viruses escape immunity due to rapid antigenic evolution, which requires vaccination strategies that allow for broadly protective antibody responses. Here, we demonstrate that the lipid globotriaosylceramide (Gb3) expressed on germinal center (GC) B cells is essential for the production of high-affinity antibodies. Mechanistically, Gb3 binds and disengages CD19 from its chaperone CD81 for subsequent translocation to the B cell receptor (BCR) complex to trigger signaling. Moreover, this lipid regulates MHC-II expression to increase diversity of T follicular helper (Tfh) and GC B cells reactive with subdominant epitopes. In influenza infection, Gb3 promotes broadly reactive antibody responses and cross-protection. Thus, we show that Gb3 determines affinity as well as breadth in B cell immunity and propose this lipid as potential vaccine adjuvant against viral infection.

overall_design:
WT mouse germinal-center B cells (3 replicates)
Gla KO mouse germinal-center B cells (3 replicates)
A4galt KO mouse germinal-center B cells (3 replicates)
WT mouse naive B cells (3 replicates)
Gla KO mouse naive B cells (3 replicates)
A4galt KO mouse naive B cells (3 replicates)

first: Pankaj

last: Sharma

first: Xiaolong

last: Zhang

first: Kevin

last: Ly

first: Yuxiang

first: Yu

last: Hu

first: Adam

last: Ye

first: Jianqiao

first: JiHyung

first: Mumeng

last: Lou

first: Chong

last: Wang

first: Quinton

last: Celuzza

first: Yuji

last: Kondo

first: Keiko

last: Furukawa

first: David

middle: R

last: Bundle

first: Koichi

middle: W

first: Florian

last: Winau


title: AMPK directly regulate a subset of genes expression in ALL cells

city: MIAMI

first: Julio

middle: C

last: Barredo

state: Florida

address: 1580 NW 10th ave room

institute: University of Miami

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To identify genome-wide genes regulated by direct association of AMPK to chromatin in response to energy/metabolic stress, we constructed CCRF-CEM (T-ALL) stable cell lines expressing HA-AMPKα2 and performed ChIP-seq and RNA-seq assays in control or glucose deprivation conditions. ChIP-seq and RNA-seq analysis identified the histone genes as a subset of genes regulated by AMPK with direct AMPKα2 occupancy at their TSS region.

overall_design:
ChIP-seq (using HA and RNA pol II antibody) in CCRF-CEM/HA-AMPKa2 cells treated with vehicle or Glucose deprivation condition.
RNA-seq in CCRF-CEM/HA-AMPKa2 cells treated with vehicle or Glucose deprivation condition.


title: Sesamin alleviates lipid accumulation induced by oleic acid in HepG2 cells

city: Weifang

first: mengyun

last: dong

state: Shandong Province

address: No. 7166, West Baotong Street

department: Public health

institute: Weifang Medical University

summary: Sesamin, a special compound present in sesame and sesame oil, has been reported the role in regulating blood lipids and improving liver function, while the underlying mechanisms remain unclear. This study aims to explore its potential mechanisms in regulating lipid metabolism. HepG2 cells were treated with oleic acid to establish an in vitro high-fat cell model to simulate impaired hepatocytes under lipid metabolism disorders.Differentially expressed genes during the sesame intervention were screened by RNA sequencing (RNA seq) and validated using real-time quantitative PCR and Western blot.The data showed that sesamin significantly upregulated the mRNA levels of genes involved in fatty acid metabolism processes such as ETFB, ACAT2, FADS2, FABP1, ACOT1, and those involved in cholesterol metabolism processes such as FDPS, PCSK9, and DHCR7, and downregulated the mRNA levels of CYP24A1 and GGT5 involved in fatty acid metabolism, as well as MVK involved in cholesterol synthesis. Sesamin significantly down-regulated the protein levels of NOTCH1, CD36, SOX4, and FABP1. In summary, sesamin alleviates lipid accumulation in HepG2 by regulating lipid metabolism, with potential mechanisms involving steroid biosynthesis, unsaturated fatty acid biosynthesis, fat digestion and absorption, fatty acid metabolism, Notch signaling pathway, and PPAR signaling pathway.

overall_design: In order to study the effect of sesamin on lipid accumulation in HepG2 cell model, HepG2 cells were treated with oleic acid, and a high-fat cell model was established in vitro to simulate the damaged liver cells in the state of lipid metabolism disorder, and the lipid-lowering effect and intervention ability of sesamin on high-fat cell model were studied.

first: Mengyun

last: Dong

first: Tianliang

first: Xueli

last: Liang


title: Somatic mutations of MLL4/COMPASS induce cytoplasmic localization providing insight into cancer prognosis and treatment

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Cancer genome sequencing consortiums have recently catalogued an abundance of somatic mutations in the chromatin-modifying enzymes that regulate enhancer chromatin function across a wide range of human cancers. Defining the molecular mechanisms underlying the potential oncogenic function for these epigenetic mutations could serve as the basis for precision medicine approaches for cancer treatment. MLL4 (KMT2D) is a key histone lysine mono-methyltransferase within the COMplex of Proteins ASsociated with Set1 (COMPASS) family that regulates chromatin at enhancers, potentially functions as a tumor suppressor and is highly mutated in a large number of human cancers. We report that the mutations which cause MLL4 protein truncation also alter its subcellular localization, resulting in loss-of-function in the nucleus and gain-of-function in the cytoplasm. We demonstrate that isogenic correction of MLL4 truncation mutation rescues the aberrant localization phenotype and restores multiple MLL4 regulatory functions, including COMPASS integrity and stabilization, histone H3K4 mono-methylation, enhancer activation, and gene regulation. Moreover, isogenic correction diminishes the sensitivity of MLL4-mutated cancer cells to targeted metabolic inhibition. Using immunohistochemistry (IHC), we identified cytoplasmic MLL4 unique to the tissue of bladder cancer patients with MLL4 mutations. Using a preclinical carcinogen bladder cancer mouse model, we demonstrate that truncated, cytoplasmic MLL4 can be a biomarker for MLL4-mutated bladder cancers and predicts response to targeted metabolic inhibition therapy. We propose using the cytoplasmic MLL4 truncation phenotype as a prognostic marker in bladder cancer. We also highlight the broader potential for patient stratification based on MLL4 mutation status in MLL4 truncation diseases, including human cancers and Kabuki Syndrome.

overall_design: We generated multiple isogenic HCT116 cell lines with allelic knockout, complete knockout, or knockin mutation correction. Then, we conducted RNA-seq, ChIP-seq and PRO-seq experiments. To study the gene expression regulation, we performed PC analysis in different clones versus parental cell line, and determined the specific MLL4 effects. To understand how mutation correction impacts enhancer function, we integrate ChIP-seq, PRO-seq with RNA-seq to determine the enhancer functions directed regulated by MLL4/COMPASS.

first: Zibo

last: Zhao

first: Yuki

last: Aoi


title: Metabolic stress induces gene reprograming in ALL cells [RNA-seq]

summary: To identify genes transcriptionally regulated under energy/metabolic stress, we treated CCRF-CEM/HA-AMPKa2 cells with Glucose deprivation condition for 24 hours, and examined their RNA profile using RNA-Seq. More than 3000 genes was altered (Fold Change > 1.5 or < -1.5, q value < 0.05) under energy/metabolic stress (glucose deprivation) vs. control, with approximately 60-70% genes exhibiting downregulation, whereas the remainder show upregulation.  Note: sample headers in data_matrix_ctrl_no_glucose.txt, CTRL_7: Ctrl rep1 sample count number; CTRL_8: Ctrl rep2 count number; ONG_9: No glucose rep1 count number; ONG_10: No glucose rep2 count number;

overall_design: RNA-seq in CCRF-CEM/HA-AMPKa2 cells treated with vehicle or Glucose deprivation condition.

first: Guangyan

last: Sun

first: Guy

middle: J

last: Leclerc


title: Modeling Transient Changes in Circadian Rhythms I

city: Evanston

first: William

last: Kath

address: 2145 Sheridan Rd

department: Engineering Sciences and Applied Mathematics

institute: Northwestern University

summary: The circadian clock can adapt itself to external cues, but the molecular mechanisms and regulatory networks governing circadian oscillations' transient adjustments are still largely unknown. Here we consider the specific case of circadian oscillations transiently responding to a temperature change. Using a framework motivated by Floquet theory, we model the mRNA expression level of the fat body from Drosophila melanogaster following a step change from 25C to 18C. Using the method we infer the adaptation rates of individual genes as they adapt to the new temperature. To deal with heteroskedastic noise and outliers present in the expression data we employ quantile regression and wild bootstrap for significance testing. Model selection with finite-sample corrected Akaike Information Criterion (AICc) is performed additionally for robust inference. We identify several genes with fast transition rates as potential sources of temperature-mediated responses in the circadian system of fruit flies, and the constructed network suggests that the proteasome may play important roles in governing these responses.

overall_design: We use high-throughput RNA-seq data to identify key molecular elements involved in the transient response of the fly's circadian system to temperature changes.

first: Ziyu

first: Dae-Sung

last: Hwangbo

first: Sumit

last: Saurabh

first: Clark

last: Rosensweig

first: Ravi

last: Allada

middle: L

first: Rosemary

last: Braun


title: The m6A reader HNRNPC promotes non-small cell lung cancer progression by enhancing E2F2 mRNA stability

city: Guiyang

first: Chuyu

last: Li

state: Guizhou

address: 28 Guiyi Street, Yunyan District

department: Department of Respiratory and Critical Care Medicine

institute: Affiliated Hospital of Guizhou Medical University

summary: HNRNPC, as one of the m6A reading proteins, has been confirmed to be highly expressed in a variety of tumors and promote the occurrence and progression of tumors. Previous studies have confirmed that HNRNPC significantly promoted the proliferation, migration and invasion of NSCLC cells, and its high expression was related to the clinical stage, lymph node and distant metastasis of patients, and could be used as an indicator of poor prognosis of NSCLC. However, the role of HNRNPC in regulating gene expression through m6A methylation modification in the occurance and progression of NSCLC remains largely unexplored. To investigate the target genes bound by HNRNPC, samples from A549 cells were harvested by RIP lysis buffer, and then the lysates were immunoprecipitated by 5μg anti-HNRNPC antibody. finally, the potential target genes were identified by RIP-seq.

overall_design: A549 cells were harvested by RIP lysis buffer, and then the lysates were immunoprecipitated by 5μg anti-HNRNPC antibody. The purified input and HNRNPC-IP RNA samples were then subjected to RNA-seq analysis.

first: Chunyu

first: Minghua

last: Liao

first: Xianming

last: Zhang


title: AMPKα2 binds to chromatin to regulate gene expression in ALL cells [ChIP-seq]

first: Julio

last: Barredo

summary: To identify genome-wide genes regulated by direct association of AMPKα2 to chromatin, ChIP-Seq assays were performed using HA (HA-AMPKα2) and RPB1 (RNA Pol II) antibodies in CCRF-CEM/HA-AMPKα2 (CN2) cells treated with glucose deprivation or no treatment controls. ChIP-seq analysis identified around 600 genes to which loci AMPKα2 was directly bound; many of these genes with HA-AMPKα2 recruitment overlapped with genes exhibiting RNA Pol II enrichment.

overall_design: ChIP-seq (using HA and RNA pol II antibody) in CCRF-CEM/HA-AMPKa2 cells treated with vehicle or Glucose deprivation condition.


title: Glucocorticoid and Mineralocorticoid Receptor Signaling have Sex-dependent and Independent Effects in Mouse Hippocampus

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Many stress-related neuropsychiatric disorders display pronounced sex differences in their frequency and clinical symptoms. Glucocorticoids are primary stress hormones that have been implicated in the development of these disorders but whether they contribute to the observed sex bias is poorly understood. Glucocorticoids signal through two closely related nuclear receptors, the glucocorticoid (GR) and mineralocorticoid receptor (MR), that are both expressed at high levels in the hippocampus. To investigate the sex-dependent and independent actions of glucocorticoids in the hippocampus, we developed knockout mice lacking hippocampal GR (GREmx1-cre), MR (MREmx1-cre), or both GR and MR (GRMREmx1-cre).  Genome-wide microarrays were performed on RNA isolated from the hippocampus of male and female flox control and knockout mice in order to 1) identify genes dysregulated in a sex-dependent and independent manner by a deficiency in GR, MR, or both GR and MR signaling and 2) identify the genes responsible for the sex-dependent and independent phenotypes observed in these mice.

overall_design: Mice harboring a floxed GR allele and MR allele (dflox) and mice with conditional knockout of the glucocorticoid receptor (GR) (GREmx1-cre), mineralocorticoid receptor (MR) (MREmx1-cre), or both GR and MR (GRMREmx1-cre) in the hippocampus have been previously described (Oakley et al, Neurobiol Stress.2021 Jul 21;15:100369.doi: 10.1016/j.ynstr.2021.100369). For this microarray, total RNA was isolated from the whole hippocampus of adult male and female dflox control, GREmx1-cre, MREmx1-cre, and GRMREmx1-cre mice (n = 3-4 mice per genotype).

first: Robert

last: Oakley

first: John

middle: A

last: Cidlowski


title: Gene expression profile of NK cells from Wilde type C57BL/6 (B6) and Irf4-/- injected with B16-F10 post 20 days or not [bulk RNA-seq]

city: HOUSTON

first: Xiaolong

state: Texas

address: 6670 Bertner Avenue, R7-211

department: Immunobiology & Transplant Research Center

institute: Houston Methodist Research Institute

summary: IRF4 deficient NK cells displayed more resistant to exhaustion during B16-F10 metastasis, to investigate how IRF4 deletion enhances the resistance of NK cells to exhaustion, we sorted NK cells from WT and Irf4-/- mice ingected with B16-F10 or not for RNA-seq

overall_design: we i.v. injected B16-F10 cells into WT C57BL/6 (B6) and Irf4–/– mice, harvesting their splenic NK cells on day 20 for mRNA sequencing. As control groups, we also included splenic NK cells from WT and Irf4–/– mice that had not received B16-F10 injections. Then we sorted NK cells for RNA-seq.

first: Dawei

last: Zou

first: Wenhao

last: Chen


title: XTX301, a tumor-activated Interleukin-12 has the potential to widen the therapeutic index of IL-12 treatment for solid tumors as evidenced by pre-clinical studies.

city: Waltham

first: Damiano

last: Fantini

address: 828 Winter Street, Suite 300

institute: Xilio Therapeutics

summary:
Interleukin-12 (IL-12) is a proinflammatory cytokine, that has shown promising anti-tumor activity in mice and humans by promoting the recruitment and activation of immune cells in tumors. However, the systemic intravenous administration of IL-12 has been accompanied by considerable toxicity, prompting interest in researching alternatives to have preferential IL-12 bioactivity in the tumor. We have generated XTX301, a half-life extended IL-12 molecule fused to the human Fc protein via a protease cleavable linker and pharmacologically inactivated by an interleukin-12 receptor subunit beta 2 (IL-12Rβ2) masking domain. Intravenous administration of a mouse surrogate molecule (mXTX301) demonstrated significant tumor growth inhibition in mouse models of colorectal cancer and melanoma without causing systemic toxicities.
Here, we performed gene expression analysis of tumor samples to characterize the mechanism of action of mXTX301. MC38 tumor-bearing mice were treated with vehicle, mXTX301, or an unmasked positive control. A comprehensive examination of global gene expression revealed a similar pattern of molecular changes for mXTX301 and unmasked control on Day 4 and Day 7 compared to vehicle, with both molecules inducing the upregulation of several immune-related genes such as Stat1, Il12rb1, Irf1 and Cxcl9 . Thus, mXTX301 demonstrated pharmacodynamic effects in mouse tumors that are consistent with known IL-12 biology.

overall_design: MC38 tumor-bearing mice were randomized in 3 treatment groups. The first group received a masked IL-12 mouse surrogate molecule (mXTX301) at the concentration of 0.39mg/kg. The second group received an unmasked positive control molecule at a concentration of 0.03mg/kg. The third group was treated with vehicle. Mice were sacrificed on day 4 or day 7 after the drug injection. Each group (treatment and duration) included n=5 mice.

first: Ekta

last: Patel

first: Sallyann

last: Vu

first: Susan

last: Cantin

first: Natalia

middle: V

last: Malkova

first: Jennifer

last: O’Neil

first: Uli

last: Bialucha


title: A dicer-related helicase opposes the age-related pathology from SKN-1 activation in ASI neurons.

city: Los Angeles

first: Chris

last: Turner

state: CA

address: 3715 McClintock Ave

institute: University of Southern California

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

overall_design: Refer to individual Series


title: Gene expression changes in different clones of SAMHD1 knock-out (KO) cells grown in 3D structures (spheroids)

city: Badalona

first: Lucia

last: Gutierrez-Chamorro

address: Ctra/ del Canyet

country: Spain

institute: IrsiCaixa

summary: To explore the mechanisms underlying SAMHD1 effect on breast cancer prognosis whole transciptome profiling was performed in WT and in different clones of SAMHD1-KO breast cancer cell line (T47D cells) grown in spheroids. Spheroids represents better the tumor microenvironment.

overall_design: Gene expression changes in SAMHD1 knock-out cell line grown in spheroids. 2 different clones of SAMHD1-KO cells were analysed; for WT and KO-clone A1, 4 different replicates and for KO-clone A2, two replicates.

first: Lucía

last: Chamorro

first: Eva

last: Riveira-Muñoz

first: Eudald

last: Felip

first: Bruna

last: Oriol-Tordera

first: Ifeanyi

last: Ezeonwumelu

first: Mireia

last: Margelí

first: Ester

last: Ballana


title: Gene expression in TAZ knockout and control hearts in different strain backgrounds.

first: William

middle: T

last: Pu

address: 300 Longwood Ave

institute: Children's Hospital Boston

summary: TAZ knockout (KO/Y) and littermate control (WT/Y) mice were generated by crossing TAZ(KO/X) females in the C57BL6J background to male mice from C57BL6J, CAST/EiJ or A/J backgrounds. F1 mutant males in C57 and CAST-F1 backgrounds had cardiomyopathy and low heart function, whereas A/J F1 mutant males had normal heart function.

overall_design: Within each genetic background (C57/J, CAST-F1, AJ-F1), we compared KO/Y to WT/Y littermates at 2 months of age. Ventricular tissue was used for RNA isolation.

first: Suya

last: Wang


title: Transcriptomic profile of Traf6-deficient CD8+ TILs

city: Wuhan

first: shuan

last: ran

state: Hubei

address: Jiefang Road 1277

department: Department of Cardiovascular Surgery

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Transcriptomic profile of sorted CD8+ TILs from Rag1-/- mice 4 days after transferred. Each group has two replicates.

overall_design: Naive CD8+ T cells from Traf6cKO(CD45.2) or Control(CD45.1) mice were isolated and mix in 1:1, 2 M T cells were transferred in B16 bearing mice on day 10 and harvest on day 14. Each group has two replicates.


title: The mechanism of oncogenomic function of androgen receptor induced UGT2B15 in esophageal squamous cell carcinoma

city: Beijing

first: Jiahui

last: Cai

address: Cancer Hospital Chinese Academy of Medical Sciences

summary: Identification of genes whose expression is altered with UGT2B15 overexpression RNA-Seq in KYSE410 cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KYSE410 cells and its overexpression derivatives (UGT2B15).

first: Furong

last: Huang

first: Hongyan

last: Chen

first: Zhihua

last: Liu


title: IL-15-DEPENDENT IMMUNE CROSS-TALK BETWEEN NK CELLS AND DENDRITIC CELLS IN HIV-1 ELITE CONTROLLERS

city: Cambridge

first: Ce

last: Gao

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard


title: Modeling Transient Changes in Circadian Rhythms II

last: Kath

first: Ziyu

last: Zhao

first: Dae-Sung

last: Hwangbo

first: Sumit

last: Saurabh

first: Clark

last: Rosenzweig

first: Ravi

last: Allada

first: Rosemary

last: Braun


title: DSP-MNase-DNA-seq

city: Tianjin

first: kangjing

last: Li

address: 24-B3, Weijin Road Campus, Tianjin University

institute: Tianjin University

summary: Chromatin is the highly complex structure consisting of DNA, histone, and trans-acting factors (TAFs). Binding of TAF proteins to specific chromosomal loci regulates gene expression. Therefore, profiling chromatin is essential to understand gene expression mechanism. Although various chromatin profiling techniques using genome sequencing are available, high-throughput proteomics of TAFs on the chromatin is still challenging and their relationship with DNA sequences needs deeper understanding. Here, we develop a new method to extract the open-chromatin region and elucidate the DNA which is mainly regulated by TAFs in low and high density cell by DNA-seq.

overall_design: Genome wide examination of TAF binding region in human skeleton muscle cell

first: Fumihiko

last: Nakamura

first: Kangjing


title: Dll4 inhibition promotes angiogenesis and graft volume retention in cell-assisted lipotransfer

city: Daegu

first: Taehee

last: Jo

address: 1035 Dalgubeol daero

department: Department of Plastic and Reconstructive Surgery

institute: Keimyung University Dongsan Hospital

summary:
Purpose: Autologous fat grafting is one of the most effective and safest treatment for soft tissue restoration and augmentation, and many efforts has been done to improve its efficiency including adipose tissue derived stem cell (ASC) supplementation. Here, we evaluated the role of Notch ligand Delta-like ligand 4 (Dll4) in angiogenesis in grafted fat and the effect on graft survival using the murine fat graft model, and its impact on the ASC supplementation.
Methods: We performed RNA-seq analysis of 3 mouse fat graft groups: 1) control fat grafts, 2) ASC added fat graft, and 3) ASC added fat graft with Dll4 inhibition. The fat grafts were harvested 8 weeks after grafting (n=4), and generated mRNA profiles by deep sequencing using Illumina NovaSeq 6000.
Results: We found that when we treated Dll4 blocking antibody to inhibit Dll4, which was highly expressed in endothelial cells (ECs) of grafted fat, angiogenesis in the grafted fat was significantly induced, promoting fat graft retention. In addition, this effect was shown to synergistically improve the fat graft retention when ASCs were concomitantly supplemented. Transcriptome analysis further identified that the expression of the junctional proteins was increased in the ECs and inflammatory processes were downregulated in the grafted fat with ASC supplementation and Dll4 inhibition.
Conclusions: This study serves as a basis for developing new potential therapeutic approaches to improve graft retention after cell-assisted transfer by Dll4 inhibition.

overall_design: Adipose mRNA profiles of 8 week fat graft: 1) control fat grafts, 2) ASC added fat graft, and 3) ASC added fat graft with Dll4 inhibition.

first: Il-Kug

last: Kim


title: CBFB-DSP-ChIPseq and YAP-DSP-ChIPseq

summary: We developed a new method to extract  open-chromatins  that contain trans-acting factors (TAFs)-DNA complex crosslinked with dithiobis(succinimidyl propionate) (DSP). Using this method we identified CBFB as a cell density-sensitive TAF, which translocates between the cytoplasm and the nucleus in cell density-dependent manner.  Here, we demonstrate that the extracted TAF/DNA complex is also amenable to ChIP-seq analysis.

overall_design: Genome wide examination of CBFB binding region in human skeleton muscle cells.


title: Neuronal extracellular vesicles mediate BDNF-dependent dendritogenesis and synapse maturation via microRNAs

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular vesicles (EVs) are emerging as novel mediators of cellular communication, in part via the delivery of their contents including microRNAs; small non-coding RNAs that regulate gene expression and are crucial for neuronal circuit formation and function. Whether microRNAs are transferred between differentiated neurons is so far unknown. Moreover, the physiological role of EVs in inter-neuronal signaling is largely elusive. We observed that EVs derived from brain-derived neurotrophic factor (BDNF)-treated neurons induced dendrite complexity, synapse maturation and neuronal firing in recipient hippocampal neurons. This was dependent on the activity of three microRNAs, miR-132-5p, miR-218-5p and miR-690, that were specifically up-regulated in BDNF-induced EVs. Transcriptomic analysis further showed the differential expression of genes related to synaptogenesis in BDNF-EV-treated neurons, many of which are conserved targets of these miRNAs. Overall, this work demonstrates a novel mechanism of inter-neuronal communication, which may be highly relevant in neurological disorders characterized by aberrant BDNF signaling.

overall_design: Mouse primary cortical neurons were treated with BDNF (50ng/ml, 20min), prior to isolating small extracellular vesicles (EV) from cell culture media and cell lysates, 16 hours later. Donor cell lysates and corresponding EVs were subjected to small RNA sequencing (Ctrl or BDNF treated). In another set of experiments, EVs derived from Ctrl- or BDNF-treated neurons (Ctrl-EV or BDNF-EV, respectively) were added to primary hippocampal neurons for 24 hours. Hippocampal cell lysates treated with Ctrl, BDNF (50ng/ml, 20min), Ctrl-EV, BDNF-EV were subjected to RNA sequencing

first: Anna

last: Antoniou

first: Anja

last: Schneider

first: Lalit

last: Kaurani


title: Exploring the Effects of Experimental Parameters and Data Modeling Approaches on In Vitro Transcriptomic Point-of-Departure Estimates

first: Logan

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

summary: Multiple new approach methods (NAMs) are being developed to rapidly screen large numbers of chemicals to aid in hazard evaluation and risk assessments. High-throughput transcriptomics (HTTr) in human cell lines has been proposed as a first-tier screening approach for determining the types of bioactivity a chemical can cause (activation of specific targets vs. generalized cell stress) and for calculating transcriptional points of departure (tPODs) based on changes in gene expression. In the present study, we examine a range of computational methods to calculate tPODs from HTTr data, using six data sets in which MCF7 cells cultured in two different media formulations were treated with a panel of 44 chemicals for 3 different exposure durations (6, 12, 24 hr).

overall_design: Multiple computational approaches for determining tPODs are compared using six HTTr datasets, all generated from a single cell type (MCF7, a breast cancer cell line), but using three different exposure durations and with two different media formulations. Each dataset included 44 chemicals in an eight-point concentration-response.  We previously published a subset of these data (GSE162855) corresponding to one exposure time (6 hrs) and media formulation (DMEM + 10% HI-FBS). In the current study we incorporate additional data for all 5 additional combinations of exposure times (6, 12, and 24 hrs) and media formulations (DMEM + either 10% HI-FBS or 10% charcoal-stripped FBS), and compare results across a broader set of computational approaches for determining an overall transcriptomic point of departure (tPOD) for each chemical.

first: Joshua

last: Harrill

first: Derik

middle: E

last: Haggard

first: Joseph

last: Bundy

first: Clinton

middle: M

last: Willis

first: Imran

last: Shah

first: Katie

last: Paul Friedman

first: Danilo

last: Basili

first: Alistair

last: Middleton

first: Richard

middle: S

last: Judson


title: Gene expression profile at single cell level of NKP cells from Wilde type C57BL/6 (B6) and Irf4-/- mice bone marrow [scRNA-seq]

status: Public on Dec 04 2023

first: Xiaolong

last: Zhang

summary: IRF4 deficiency affect the development of mature NK cells, we used single cell RNA sequencing(scRNA-seq) to investigate the changes in NKP cells resulting from the deletion of IRF4.

overall_design: We sorted Lin−Sca-1−c-kit−CD122+NK1.1−Ncr1− NKP cells from the bone marrow of Wilde type C57BL/6 (B6) and Irf4–/– mice. These sorted NKP cells were subjected to single-cell RNA sequencing

first: Dawei

last: Zou

first: Yin

last: Zheng

first: Wenhao

last: Chen


title: MicroRNAs in Nasal Lavage Extracellular Vesicles as Potential Therapeutic Targets for Mucus Hypersecretion

city: Seoul

first: Daeun

last: Jeong

address: 50-1, Yonsei-ro, Seodaemun-gu

institute: Yonsei university

summary: Small RNA sequencing was conducted to identify the miRNAs responsible for AR using exosomes isolated from the nasal lavage (NAL) fluid of the control (n=9) and AR patient groups (n=8).

overall_design: To identify the miRNAs responsible for AR, we conducted small RNA sequencing using exosomal RNAs isolated from the NAL fluid of control subjects (n = 9) or patients with AR (n = 8).

first: Ji-Hwan

last: Ryu

first: Youn-Wook

last: Chung

first: Da-Eun


title: Methylation analysis of STAT3 targets in gastric cancer patient samples

city: Chiayi County

first: Jie Ting

last: Low

state: Minxiong Township

address: No. 168, Daxue Road, Section 1

country: Taiwan

institute: National Chung Cheng University

type: Methylation profiling by genome tiling array

summary: To investigate the differences of STAT3-mediated DNA methylation in gastric cancer patient samples, genome wide DNA methylation profiling for STAT3-positive/negative patient samples

overall_design: Bisulphite converted DNA from the patient samples were hybridized to the Illumina Infinium MethylationEPIC BeadChips

first: Michael

last: Chan

first: Jian-Liang

last: Chou

first: Yu-Ming

last: Chuang

first: Jie-Ting


title: RNA Sequencing of Perirenal Adipose Tissue from Intrauterine Growth Restricted and Normally-Grown Near Term Sheep Fetuses with and without intact adrenal medulla.

city: Tucson

first: Sean

last: Limesand

state: AZ

address: 4101 N Campbell Ave

department: Animal & Comparative Biomedical Sciences

institute: University of Ariziona

summary: The study objective was to determine differentially expressed mRNA transcripts in perirenal adipose tissue from fetal sheep that underwent sham or adrenal demedullation prior to fetal growth restriction to determine the role of catecholamines on gene expression following placental insufficiency-induced intrauterine growth restriction.

overall_design: Adipose tissue was collected from the perirenal space above the left kidney and RNA was isolated for high-throughput sequencing frod sheep fetuses with placental insufficiency-induced IUGR and controls as well as fetuses that underwent bilateral adrenal demedullation..


title: A novel method to efficiently differentiate human osteoclasts from blood-derived monocytes

city: Goettingen

first: Linh

last: Dang

address: Robert Koch 40

institute: UMG

summary: Osteoclasts are the tissue-specific macrophage population of the bone and unique in their bone-resorbing activity. Hence, they are fundamental for bone physiology in health and disease. However, efficient protocols for the isolation and study of primary human osteoclasts are scarce. In this study, we aimed to establish a protocol, which enables the efficient differentiation of functional human osteoclasts from monocytes. To this end, human monocytes were isolated through a double-density gradient from healthy donor blood. The differentiation to macrophages was performed either in cell culture dishes or in Teflon-coated bags. The impact of these two distinct differentiation protocols on the gene expression profile of macrophages was assessed via RNA-Sequencing. The macrophages were then further differentiated to terminal osteoclasts through the addition of Receptor Activator of NF-κB Ligand (RANKL). The yield and function of multinuclear osteoclasts was significantly increased upon initial differentiation of monocytes to macrophages in Teflon-coated bags. Our study has established a novel protocol for the isolation of primary human osteoclasts that improves osteoclastogenesis in comparison to the conventionally used cultivation approach.

overall_design: Monocytes from 5 healthy donors were differentiated to macrophages in the presence of M-CSF. Two differentiation protocols were compared for matched samples of the same donor: 1. Macrophages derived from monocytes cultured in regular cell culture plates; 2. Macrophages derived from monocytes cultured in Teflon-coated bags

first: Suganja

last: Chandrabalan

first: Melanie

last: Timmen

first: Corinna

last: Wehmeyer

last: Stange

first: Tim

last: Beißbarth

first: Claudia

last: Binder

first: Annalen

last: Bleckmann

first: Kerstin

last: Menck


title: The effect of depletion of VPAC2 on gene expression in Panc02 Pancreatic Ductal Adenocarcinoma cell line

city: Atlanta

first: Tenzin

last: Passang

state: Georgia

address: 1365 Clifton Road NE

department: Hematology and Medical Oncology

institute: Emory University

summary: Identifying mechanisms underlying tumor growth and immune resistance is needed to treat pancreatic ductal adenocarcinoma (PDAC) effectively. The complexity of the tumor microenvironment (TME) suggests that the crosstalk between cells in the TME could drive drug resistance and relapse in PDAC. We have previously determined that vasoactive intestinal peptide (VIP) is overexpressed in PDAC and that VIP receptors expressed on T cells are a targetable pathway that sensitizes PDAC to anti-PD1 therapy. In this study, we show that pancreatic cancer cells engage in autocrine signaling of VIP through VIP-receptor 2 (VPAC2), and that high co-expression of VIP with VPAC2 leads to reduced relapse-free survival in PDAC patients. Mechanistically, we identified piwi-like RNA-mediated gene silencing2 (Piwil2) as a tumor-cell intrinsic protein downstream of VPAC2 that regulates cancer cell growth. In addition, we discovered TGFβ-1 as a potential tumor-extrinsic inhibitor of T cell function induced by VPAC2 signaling. In vivo, knock out and knockdown of VPAC2 on PDAC cells led to reduced tumor growth rate and increased sensitivity to anti-PD-1 therapy in various mouse models of PDAC that were T- cell dependent. Overall, these findings emphasize the implications of VIP/VPAC2 signaling in the PDAC tumor microenvironment and further support the rationale for developing VPAC2-specific antagonists.

overall_design:
To investigate the role of VPAC2 in pancreatic cancer growth, we established Panc02 cell lines in which VPAC2 was deleted using CRISPR-Cas9 editing system.
We then performed bulk RNA-Seq on the parental and the 2 single clones from CRISPR-KO Panc02 cells.
Differential genes analysis on data obtained from RNA-Seq was performed using DESeq2 comparing  parental to VPAC2KO cells.

first: Edmund

last: Waller


title: Fusobacterium nucleatum intraoral infection and periodontitis in C57BL/6J mice

city: gainesville

first: Kesavalu

middle: Lakshmyya

last: Naidu

address: 1600 SW Archer Road

department: Dentistry

institute: University of Florida

summary: Individual miRNA analyzed were successfully constructed through NanoString technology of a total of 577 mouse miRNAs in 20 number of SHAM mice and 20 number of Fusobacterium nucleatum infected mice, which have been euthanized on the end of 16 weeks infection study.

overall_design: The study depicted here, is a 16 weeks of total, 10 mice/group, Sham infected and Fusobacterium nucleatum infected groups both in 8 weeks and 16 weeks, followed 16 weeks, euthanized and extracted left mandibles for miRNA expression profiles, of a total of 577 unique Nanostring miRNA panels. This leading to successful construction of supervised.

first: Aravindraja

last: Chairmandurai

first: Lakshmyya

last: Kesavalu


title: Effect of targeted degradation of androgen receptor full-length and variant-7 on gene expression in castration-resistant prostate cancer cells

first: TaeHyun

last: Bae

address: Yongeon 103 Daehangno, Jongno-gu

institute: Seoul National University

summary: The androgen receptor demonstrates transcriptional activity and, through the induction of related genes, contributes to the proliferation of prostate cancer cells. Despite the development of anti-prostate cancer therapies, resistance to current treatments persists in some patients. The expression of mutants or variants of androgen receptors is a significant factor in the emergence of resistance. Consequently, the targeted degradation of these mutants or variants of androgen receptors paves the way for the development of novel therapeutics for patients with castration-resistant prostate cancer. Our data provides the potential of the our novel TPD platform to target previously considered “undruggable” proteins and overcome certain drug resistance mechanisms

overall_design: To investigate alterations in gene expression levels, we treated 22Rv1, an androgen-independent prostate cancer cell line, with a novel androgen receptor-targeting degrader. For the comparison of mRNA expression levels, we included control groups of 22Rv1 treated with the vehicle, enzalutamide, and an autophagy-activating ligand. Cells were treated with the indicated compounds for 24 hours and lysed with Trizol. We conducted gene expression profiling analysis using data from RNA-sequencing, with each group consisting of biologically independent triplicates.

first: Tae

middle: H


title: A nasal cell atlas reveals heterogeneity of tuft cells and their role in directing olfactory stem cell proliferation

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

summary: The olfactory neuroepithelium serves as a sensory organ for odors and forms part of the nasal mucosal barrier. Olfactory sensory neurons are surrounded and supported by epithelial cells. Among them, microvillous cells (MVCs) are strategically positioned at the apical surface, but their specific functions are enigmatic and their relationship to the other specialized epithelial cells, particularly the solitary chemosensory cell family, is unclear. Here, we establish that the family of MVCs comprises tuft cells and ionocytes in both mice and humans. Integrating analysis of the respiratory and olfactory epithelia, we define the unique receptor expression of TRPM5+ tuft-MVCs compared to Gɑ-gustducinhigh respiratory tuft cells and characterize a new population of glandular DCLK1+ tuft cells. To establish how allergen sensing by tuft-MVCs might direct olfactory mucosal responses, we employed an integrated single-cell transcriptional and protein analysis. Inhalation of Alternaria induced mucosal epithelial effector molecules including Chil4, and a distinct pathway leading to proliferation of the quiescent olfactory horizontal basal stem cell (HBC) pool, both triggered in the absence of olfactory apoptosis. While the Chil4 pathway was dependent on STAT6 signaling and innate lymphocytes, neither were required for HBC proliferation. Alternaria- and ATP- elicited HBC proliferation was dependent on tuft-MVCs, establishing these specialized epithelial cells as regulators of olfactory stem cell responses. Together our data provide high resolution characterization of nasal tuft cell heterogeneity and uncover a novel  function for TRPM5+ tuft-MVCs in directing the olfactory mucosal response to allergens.

overall_design: Saltanat, Ualiyeva

first: Evan

last: Lemire

first: Caitlin

last: Wong

first: Alexander

last: Perniss

first: Amelia

last: Boyd

first: Evelyn

last: Avilés

first: Dante

last: Minichetti

first: Alice

last: Maxfield

first: Rachel

last: Roditi

first: Ichiro

last: Matsumoto

first: Xin

last: Wang

first: Wenjiang

last: Deng

first: Nora

last: Barrett

first: Kathleen

last: Buchheit

first: Tanya

last: Laidlaw

first: Joshua

last: Boyce

first: Lora

last: Bankova


title: Clonal proliferation of smooth muscle cell in human atherosclerosis

city: GAITHERSBURG

first: Kenji

last: Kawai

state: MARYLAND

address: 19 FIRSTFIELD ROAD

institute: CVPath institute

summary: Two different coronary artery samples with erosion plaques were selected from female heterozygous for the deletion BGN. Hybridization of target RNA-specific probes was used to visualize the spatial distribution of mutants. After determine the leison with clonality and non-clonal SMC proliferation, spatial transcriptomics was used to identify differentially expressed transcripts within clonal and non-clonal regions.

overall_design:
Spatial transcriptomics analysis. Sample selection for 10X Genomics Visium V1 FFPE assay was based on the erosion plaque phenotypes selected for the detection of BGN using BaseScope (ACD). Adjacent section was selected from two of the coronary artery FFPE blocks corresponding to the erosion phenotypes. Total RNA was isolated from ten 5 µm sections from the FFPE blocks using RNeasy FFPE kit (Qiagen). RNA was analyzed using TapeStation (Agilent) and DV200 of ≥50% was observed for generating successful Visium spatial gene expression libraries. Next, the FFPE blocks for two erosion plaque phenotypes were sectioned at 5-8 µm thickness and mounted within a single 6.5 × 6.5 mm capture area on the Visium v1 spatial gene expression slide. Spatial transcriptomics assay using Visium V1 spatial gene expression slide and reagent kits were used according to instructions outlined by 10X Genomics (Pleasanton, CA). Visium Spatial Gene Expression was performed for FFPE sectioned tissues that produce spatially barcoded, Illumina® sequencer-ready libraries that are dual indexed. The generated libraries were loaded on a NovaSeq 6000 System (Illumina) and sequencing was performed using the following read protocol: read 1, 28 cycles (spatial barcode, UMI); i7 index read, 10 cycles (sample index); i5 index read, 10 cycles (sample index); read 2, 91 cycles (insert). Visium v1 raw data processing: Raw FASTQ files for a given capture area and corresponding capture area histology images were processed with Space Ranger software version 1.3.0 (10X Genomics, Pleasanton CA). Space Ranger Pipeline was used to align Fastq reads to human hg38 reference genome, and the probe set reference file specific only to human FFPE tissues because the synthetic probe DNA was sequenced rather than cDNA of a captured transcript. For FFPE samples, Space Ranger counts oligo ligation events to build the feature-barcode matrix.
Gene expression analysis. The data files of raw transcriptomics were posted at NCBI’s Gene Expression Omnibus public database. Sequencing data was then imported into Partek Flow Enterprise Edition software (Partek Inc., Louis, MO). The data was filtered to exclude features where value <= 1.0 in at least 99.0 % of the cells and further normalized to CPM (counts per million) at Add: 1.0, Log: 2.0. A subset of SMCs was selected from the normalized counts by selecting for ACTA2 positive cells. Principle Component analysis (PCA) was then performed on these SMCs and for visualization, dimensionality reduction was performed using Uniform Manifold Approximation and Projection (UMAP) for the top 20 principal components from the graph-based clustering for ACTA2 positive cells. The data was further classified as with attributes for ACTA2 positive cells expressing BGN. We selected two regions each of WT-Clonal, Del-Clonal and non-clonal ROIs from two erosion sections as described in Supplemental Figure S5 (total 6 ROIs/section x2 = 12 ROIs). FDR (false discovery rate) < 0.05 and fold change < -1 or > 1. Marker genes identified were differentially expressed genes (DEGs) identified by one-to-one comparison of each cluster with all other clusters with P-values < 0.05 for regions of no clonality to clonality (Clonal WT + Del) to generate hierarchical cluster mapping (dot plot).

first: Saikat

last: Gosh

first: Palak

last: Shah

first: Aloke

last: Finn


title: Pan-cancer analysis of pyrimidine metabolism using pathway-based approach unravels complex signaling pathways connections with a role in chemoresistance

city: Odense

first: Paolo

last: Ceppi

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: To investigate the effect of DHODH inhibitor, Brequinar (BRQ), in inhibiting the pyrimidine metabolism and its associated signaling pathways, lung cancer cell line (A549) was treated with BRQ for 72 hours and performed gene expression profiling using RNA-seq.

overall_design: Differential gene expression analysis for A549 cells treated with BRQ and control cells at 72 hours in replicates.

first: Vignesh

last: Ramesh

first: Luisa

last: Pinna


title: Integrated physiological, whole transcriptomic and functional analysis reveals the regulatory mechanisms of rainbow trout (Oncorhynchus mykiss) in response to short-term and chronic hypoxia stress

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

summary: The frequency of fish encountering hypoxia has risen dramatically as global warming and water pollution intensify, posing a serious threat to survival. Rainbow trout (Oncorhynchus mykiss), which is an economically important fish worldwide, belongs to a typical hypoxia-sensitive fish. However, little is known about the response mechanisms employed by rainbow trout to hypoxia stress. In this study, we systematically analyzed the changes of liver biochemical parameters in rainbow trout exposed to moderate hypoxic conditions (DO: 4.5 ± 0.1 mg/L) for different durations (4, 8, 12, 24 h and 1 month) and 12 h and 24 h reoxygenation, and histologic and transcriptome (lncRNA, miRNA and mRNA) under hypoxia stress for 12 h (Tm12L) and 1 month (TmlL) compared with control, and the interaction between LOC110520201, miR-2188-y and sod1 was verified by dual-luciferase reporter, overexpression and silencing assays. Histological observations revealed that liver suffered severe damage in Tm12L but not in TmlL. Integrating biochemical parameters and mRNA expression profiles, we found that exposure to short-term hypoxia stress resulted in enhanced immune response, aerobic and anaerobic glycolysis, gluconeogenesis and lipid metabolism. In TmlL, increased anaerobic glycolysis and decreased aerobic glycolysis were observed, and antioxidant and immune capacity has returned to normal. Additionally, several key hypoxia-related genes (epo, vegfc, epor, sod1, ppara, foxo1a, gk, dusp1, nlrc3 and nlrp3) and ceRNA regulatory networks were identified from 2711 differentially expressed (DE) mRNAs, 575 DElncRNAs and 395 DEmiRNAs, including LOC110520201-miR-2188-y-sod1, LOC110533332-miR-144-y-vegfc, LOC110526066-miR-465-x-ppara and LOC110535032-miR-743-y-nlrp3. The analysis of expression patterns in liver and rainbow trout liver cells treated with hypoxia suggested that changes in LOC110520201, miR-2188-y and sod1 showed a ceRNA regulatory relationship. Further experiments demonstrated that sod1 is a target of miR-2188-y, and LOC110520201 silencing increased the expression of miR-2188-y and inhibited sod1 expression. These results facilitated our understanding of the molecular mechanisms of hypoxia response in rainbow trout and provided genetic resources for breeding hypoxia-tolerant varieties.

first: Jinqiang

last: Huang

first: Shenji

last: Wu


title: BCG vaccination stimulates Integrated Organ Immunity by feedback of the adaptive immune response to imprint prolonged innate antiviral resistance

city: Palo Alto

first: Audrey

last: Lee

address: 240 Pasteur Dr. 1500 BMI

institute: Stanford University

summary: Bacille Calmette-Guérin (BCG) vaccination can confer non-specific protection against heterologous pathogens. However, the underlying mechanisms remain mysterious. We used scRNA-seq in this study to identify transcriptional changes in the immune and epithelial cells in the lungs following BCG vaccination in mice

overall_design: Lung immune and epithelial cells were enriched by Fluorescence-activated cell sorting using respective cell markers and mixed with non-enriched fraction for scRNA-seq

first: Zhuoqing

last: Fang


title: Structural basis of nucleosomal H4K20 recognition and methylation by SUV420H1 methyltransferase

city: Shenzhen

first: Zengqi

last: Wen

state: Guangdong

address: No 66, Gongchang Road, Guangming District

department: School of Medicine

institute: Sun Yat-sen University

summary: Here we report the cryo-electron microscopy (cryo-EM) structures of SUV420H1 associated with canonical nucleosome core particles (NCPs) or H2AZ containing NCPs. We find that SUV420H1 shows conformational change after bound to a nucleosome and make extensive site-specific contacts with histone and DNA regions, thus enabling H4K20 insertion for catalysis specifically. Through in vivo functional analysis, we validated special residues of SUV420H1 that are critical for its catalytic activity and function in chromatin state regulation.Thus, our study provides molecular insights into the nucleosome-based recognition and histone- methylation mechanisms of SUV420H1.

overall_design:
We ectopically expressed SUV420H1(Aa1-550) or SUV420H1(Aa1-550) with a single K258E, S255F, S283L, Y349A, R352A or R357H mutation in a HeLa SUV420H1-/- cell line, and performed ATAC-seq under each condition.
Please note that each processed data file was generated from both replicates and is linked to the corresponding rep1 sample records


title: Transcriptome analysis PIM kinase inhibition vs degradation

first: Marcas

last: Agostinelli

state: Arizona

address: 2690 W Avenida Azahar

department: Bioinformatics

institute: Novogene

summary: PIM kinases have important pro-tumorigenic roles and mediate several oncogenic traits, including cell proliferation, survival, and chemotherapeutic resistance. As a result, multiple PIM inhibitors have been pursued as investigational new drugs in cancer; however, response to PIM inhibitors in solid tumors has fallen short of expectations. We found that inhibition of PIM kinase activity stabilizes protein levels of all three PIM isoforms (PIM1/2/3), and this can promote resistance to PIM inhibitors and chemotherapy. To overcome this effect, we designed PIM proteolysis targeting chimeras (PROTACs) to target PIM for degradation. PIM PROTACs effectively downmodulated PIM levels through the ubiquitin-proteasome pathway. Importantly, degradation of PIM kinases was more potent than inhibition of catalytic activity in inducing apoptosis in prostate cancer cell line models. In conclusion, we provide evidence of the advantages of degrading PIM kinases versus inhibiting their catalytic activity to target the oncogenic functions of PIM kinases.

overall_design: To investigate the effects of inhibiting vs degrading PIM kinases on the transcriptome, PC3 cells were treated with a PIM kinase inhibitor (SGI-1776) or a PROTAC (SGI-1776-VHL-02) at two different concentrations for 48 hours.

first: John

last: Brognard

first: Pedro

last: Torres-Ayuso

first: Meghri

last: Katerji

first: Noel

last: Warfel


title: BCG vaccination stimulates Integrated Organ Immunity by feedback of the adaptive immune response to imprint prolonged innate antiviral resistance [GeoMx]

summary: GeoMx Whole Transcriptome Atlas (WTA) of mouse lungs with CD4, PanCK, DAPI staining

overall_design: Formalin-fixed paraffin-embedded mouse lung tissue sections were stained with CD4, PanCK, DAPI antibodies. ROIs were selected based on marker staining and AOIs were collected from each ROIs.

first: David

last: Scoville

first: Yan

last: Liang

first: Alistaire

last: Ruggiero


title: Phase Separation of FOXA1 Unpacks the Condensed Chromatin to Function as a Pioneer Factor [RNA-seq]

city: Beijing

first: ji

last: yiliang

address: No. 10 right outside the Western headlines

department: Department of Immunology

institute: Capital Medical University

summary: Eukaryotic DNA is packaged into chromatin in the nucleus, which restricts the binding of transcription factors (TFs) to the target DNA sites. FOXA1 functions as a pioneer TF to bind condensed chromatin and initiates the opening of local chromatin for gene expression. However, the principles of how FOXA1 recruits to and unpacks the condensed chromatin remain elusive. Here, we revealed that FOXA1 intrinsically undergoes phase separation through its N-PrLD and C-IDR regions, identified as phase separation region (PSR). Notably, the phase separation property confers FOXA1 the ability to dissolve the chromatin condensates. In addition, the DNA-binding capacity of FOXA1 contributes to its phase separation property. Further genome-wide investigation showed that FOXA1 is recruited to and unpacks the condensed chromatin by its PSR to regulate the function of breast cancer cells. This work provides a principal example of how pioneer TFs function to initiate competent chromatin states by phase separation.

overall_design: ChIP-seq,ATAC-seq and RNA-seq for vector,overexpress FH and FOXA1 in MDA-MB-231 cells

first: Ping

last: Chen

first: Liang

last: Wan


title: Phase Separation of FOXA1 Unpacks the Condensed Chromatin to Function as a Pioneer Factor [ATAC-seq]


title: Controlled Nutrient Delivery to Pancreatic Islets Using Polydopamine-Coated Mesoporous Silica Nanoparticles

first: Avnesh

last: Thakor

state: California

address: 3155 Porter Drive

department: Radiology

summary: In the present study, we designed a nanoscale platform for the sustained and controlled delivery of nutrients to pancreatic islets-upon transplantation.  Our platform consists of a mesoporous silica nanoparticle (MSNP), loaded with glutamine (G), an essential amino acid required for islet survival and function, and capped with polydopamine (PD). To control the release of glutamine, various concentrations (0.5 - 2 mg/mL) of PD and incubation times (0.5 – 2 h) with MSNPs were investigated in terms of pharmacological properties and biological functions. After extensive testing, PD-G-MSNPs made using PD coating of 0.5 mg/mL incubated for 0.5 h resulted in the optimal platform to maintain the islet viability and functionality in vitro. Following syngeneic renal sub-capsule islet transplantation in STZ-diabetic mice, PD-G-MSNPs improved the engraftment of pancreatic islets as well as their function, resulting in re-establishment of glycemic control. Collectively, our data shows that PD-G-MSNPs can support transplanted islets by providing them with a controlled and sustained supply of nutrients.

overall_design: Aim of this study: investigate the protective effect of PD-G-MSNPs on mouse pancreatic islets following exposure to inflammatory cytokines. The work will include the relevant significant pathways (specifically, function and immune-realted pathways) up- and down-regulated in mouse pancreatic islets w/ and w/o PD-G-MSNPs following exposure to inflammatory cytokines (IL-1beta, TNF-alfa and IL6) for 48h. The experimental groups are three: healthy islets (control), islets inflammed, islets inflammed treated with PD-G-MSNPs. The experiment has been performed in triplicate.

first: Rosita

last: Primavera

first: Abantika

last: Ganguly


title: Space microgravity increases expression of genes associated with proliferation and differentiation in human cardiac spheres

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Previously, we reported upregulation of cardiac proliferation in cardiac progenitors derived from human induced pluripotent stem cells (hiPSC-CPCs) that were exposed to space microgravity for 3 days. The overall objective of this investigation was to understand how long-term exposure to microgravity affects the expansion and differentiation of hiPSC-CPCs.  Cryopreserved cardiomyocytes derived from human-induced pluripotent stem cells (hiPSC-CMs) were exposed to space microgravity for 3 weeks in the International Space Station (ISS) and retrieved for transcriptomic profiling.  RNA-seq analysis and gene ontology analysis revealed upregulation of cardiac tissue function and morphological terms while downregulating inflammation and ECM regulation terms. Upregulation of genes associated with cell cycle regulation and proliferation were notable as well.  Combined with previous work, these results suggest that space microgravity improved cardiac differentiation and structure formation and potentially, proliferation.

overall_design: On the ISS, the astronauts thawed the cryopreserved cardiac progenitor spheres, and cultured the cells using the MVP system from Techshot, Inc.33 The MVP system allows loading of multiple samples under both ISS µG and ISS 1G conditions (the 1G condition on the ISS was achieved by centrifugation). Each condition was run in triplicates.The cells were cultured at 37°C in the MVP system for 22 days on the ISS with medium exchange every other day. At the end of the mission, live cultures were returned to ground via warm storage after having been cultured aboard the ISS. Upon arrival at Emory University, cardiac spheres were transferred immediately into an incubator and let recover overnight. The following day cardiac spheres were transferred from the collection bags into low adhesion dishes. Medium was changed from CO2-independent medium to standard cardiomyocyte culture medium (RPMI 1640 with 2% B27 supplement), and cardiac spheres were then maintained overnight, followed by RNA isolation.

first: Hyun

last: Hwang

first: Antonio

last: Rampoldi

first: Parvin

last: Forghani

first: Dong

last: Li

first: Jordan

last: Fite

first: Gene

last: Boland

first: Kevin

last: Maher

first: Chunhui

last: Xu


title: Collagen type VI regulates TGFβ bioavailability in skeletal muscle

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Collagen VI-related disorders (COL6-RDs) are a group of rare muscular dystrophies caused by pathogenic variants in collagen VI genes. ¬¬Collagen type VI is a heterotrimeric, microfibrillar component of the muscle extracellular matrix (ECM), predominantly secreted by resident fibroadipogenic precursor cells in skeletal muscle. Collagen VI absence or mislocalization in the skeletal muscle ECM underlies the non-cell autonomous dystrophic changes and dysfunction in skeletal muscle in COL6-RDs with an as of yet elusive direct mechanistic link between the ECM and myofiber dysfunction. Here, we derive a novel mouse model of COL6-RD, Col6a2-/- mice, and conduct a comprehensive natural history study in male and female animals aged to 60 weeks of age. Col6a2-/- mice have a normal lifespan but develop muscle weakness based on standardized behavioral tests (grip and hanging wire test), muscle atrophy with histologic hallmarks of muscular dystrophy, and reduced muscle force prodcution on physiologic parameters. We also report a robust dysregulation of TGFβ pathway early in the disease process and thus propose a new mechanism for pathogenesis of the disease that links the ECM regulation of TGFβ with downstream skeletal muscle abnormalities, paving the way for developing therapeutics that target this pathway.

overall_design: Thirty-two samples representing quadricep muscle from male and female mice representing wildtype (WT) and Col6a2 -/- at two different age groups (5 weeks and 25 weeks old).

first: Payam

last: Mohassel

first: Jachinta

last: Rooney

first: Yaqun

last: Zou

first: Gina

last: Norato

first: Hailey

last: Hearn

first: Matthew

last: Nalls

first: Pomi

last: Yun

first: Tracy

last: Ogata

first: Sarah

last: Silverstein

first: David

last: Sleboda

first: Thomas

last: Roberts

first: Daniel

middle: B

last: Rifkin

first: Carsten

last: Bönnemann


title: Single institution study of the immune context for canine oral melanoma cased on transcriptome analysis of the primary malignant tumor

city: west lafayette

first: Isabelle

middle: F

last: Vanhaezebrouck

state: IN

address: 625 harisson

department: College of veterinary

institute: Purdue University

summary:
Abstract
Introduction
Understanding a tumor's immune context is paramount in the fight against cancer. Oral melanoma in dogs serves as an excellent translational model for human immunotherapy. However, additional study is necessary to comprehend the immune landscape of dog oral melanomas, including their similarity to human melanomas in this context.

Methods
This retrospective study utilizes formalin-fixed paraffin-embedded (FFPE) tissue samples to analyze RNA sequences associated with oral melanoma in dogs. Nanostring Technologies was used for conducting RNA sequencing. The focus is on understanding the differences between melanoma tumors restricted to the oral cavity (OL) and the same primary oral tumors with a history of metastasis to the lymph nodes or other organs (OM). Normal buccal mucosa samples are also included as a normal tissue reference.

Results
In the OM patient group, gene signatures exhibit significant changes relative to the OL patient group, including significantly decreased expression of S100, BRAF, CEACAM1, BCL2, ANXA1, and tumor suppressor genes (TP63). Relative to the OL tumors, the OM tumors had significantly increased expression of hypoxia-related genes (VEGFA expression), cell mobility genes (MCAM), and PTGS2 (COX2).  The analysis of the immune landscape in the OM group indicates a shift from a possible "hot" tumor suppressed by immune checkpoints (PDL1) to significantly heightened expression not only of those checkpoints but also the inclusion of other immune blockades such as PD1 and IDO2. In addition, the OM group had significantly reduced expression of Toll-like receptors (TLR4) and IL-18 relative to the OL group, contributing to the tumor's immune escape.   Additionally, signs of immune cell exhaustion are evident in both the OM and OL groups through significantly increased expression of TIGIT relative to normal tissue. Both the OM and OL groups had significantly increased expression of the immune cell marker CD4 expression relative to normal tissue. Further, CD4 expression significantly decreased in OM relative to OL; however, this study cannot determine the specific cell types expressing CD4 in OM and OL tumors.

Discussion
This preliminary study reports significant changes in gene expression for oral melanoma between canine patients with localized disease relative to those with metastatic disease. In the future, a more in-depth investigation involving immunohistochemistry analysis and single-cell RNA expression is necessary to confirm our findings.

overall_design: Local malignant (OL) cavity samples were compared to oral malignant (OM) samples. Genetic analyses were also performed for normal samples as baseline.

first: Vanhaezebrouck

last: Isabelle F

first: Bakhle

last: Kimaya M.

first: Lyle

last: Tiffany L.

first: Konradt

last: Christoph

first: Scarpelli

last: Matthew L

first: Knapp

last: Deborah. W


title: Time of day and genotype sensitivity adjust molecular responses to temperature stress in Sorghum

city: Riverside

first: Dawn

last: Nagel

address: 900 University Avenue

institute: UC Riverside Department of Botany and Plant Sciences

summary: Sorghum is one of the four major C4 crops that are considered to be tolerant to environmental extremes. Sorghum shows distinct growth responses to temperature stress depending on the sensitivity of the genetic background. About half of the transcripts in sorghum exhibit diurnal rhythmic expressions emphasizing significant coordination with the environment. However, an understanding of how molecular dynamics contribute to genotype-specific stress responses in the context of the time of day is not known. We examined whether temperature stress and the time of day impact the gene expression dynamics in cold-sensitive and tolerant and heat-sensitive and tolerant sorghum genotypes. We found that time of day is highly influencing the temperature stress responses, which can be explained by the rhythmic expression of most thermo-responsive genes. This effect is more pronounced in thermo-tolerant genotypes, suggesting a stronger regulation of gene expression by the time of day and/or by the circadian clock. Genotypic differences were mostly observed on average gene expression levels, but we identified groups of genes regulated by temperature stress in a time-of-day and genotype-specific manner. These include transcriptional regulators and several members of the Ca2+-binding EF-hand protein family. We speculate that expression variation of these genes between genotypes may be responsible for contrasting sensitivities to temperature stress in tolerant vs susceptible sorghum varieties. These findings offer a new opportunity to selectively target specific genes in efforts to develop climate-resilient crops based on their time of day and genotype variation responses to temperature stress.

overall_design: We performed a transcriptomic analysis from leaves that were collected in control conditions or after 1 h temperature stress (either cold or heat stress), applied at four different times of day (ZT1, ZT6, ZT9 and ZT15), in the thermo-sensitive genotype RTX430 and in tolerant genotypes (SC224 and Macia for the cold stress and heat stress experiments, respectively).

first: Titouan

last: Bonnot

first: Krishna

last: Jagadish


title: Phase Separation of FOXA1 Unpacks the Condensed Chromatin to Function as a Pioneer Factor [ChIP-seq]

first: ji

last: yiliang

first: Ping

last: Chen

first: Liang

last: Wan


title: GNL3 ChIP-seq

city: Montpellier

first: Cyril

last: Ribeyre

address: 141 rue de la cardonille

country: France

institute: CNRS

summary: Analysis of GNL3 binding sites in HeLa S3 cells

overall_design: Marine Canut and Cyril Ribeyre


title: Unlocking Molecular mechanisms and identifying druggable targets in matched-paired brain metastasis of Breast and Lung cancers

status: Public on Dec 03 2023

city: Rotterdam

first: Shiva

last: Najjary

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

summary: Introduction: The incidence of brain metastases in cancer patients is increasing, with lung and breast cancer being the most common sources. Despite advancements in targeted therapies, the prognosis remains poor, highlighting the importance to investigate the underlying mechanisms in brain metastases. The aim of this study was to investigate the differences in the molecular mechanisms involved in brain metastasis of breast and lung cancers. In addition, we aimed to identify cancer lineage-specific druggable targets in the brain metastasis. Methods: To that aim, a cohort of 44 FFPE tissue samples, including 22 breast cancer and 22 lung adenocarcinoma (LUAD) and their matched-paired brain metastases were collected. Targeted gene expression profiles of primary tumors were compared to their matched-paired brain metastases samples using nCounter PanCancer IO 360™ Panel of NanoString technologies. Pathway analysis was performed using gene set analysis (GSA) and gene set enrichment analysis (GSEA). The validation was performed by using Immunohistochemistry (IHC) to confirm the expression of immune checkpoint inhibitors. Results: Our results revealed the significant upregulation of cancer-related genes in primary tumors compared to their matched-paired brain metastases (adj. p ≤ 0.05). We found that upregulated differentially expressed genes in breast cancer brain metastasis (BM-BC) and brain metastasis from lung adenocarcinoma (BM-LUAD) were associated with the metabolic stress pathway, particularly related to the glycolysis. Additionally, we found that the upregulated genes in BM-BC and BM-LUAD played roles in immune response regulation, tumor growth, and proliferation. Importantly, we identified high expression of the immune checkpoint VTCN1 in BM-BC, and VISTA, IDO1, NT5E, and HDAC3 in BM-LUAD. Validation using immunohistochemistry further supported these findings. Conclusion: In conclusion, the findings highlight the significance of using matched-paired samples to identify cancer lineage-specific therapies that may improve brain metastasis patients outcomes.

overall_design: RNA was extracted from FFPE samples of (primary LUAD and their matched paired brain metastasis n=22, primary BC and their matched paired brain metastasis n=22)

first: Willem

last: de Koning

first: Johan

last: Kros

first: Dana

last: Mustafa


title: Phase Separation of FOXA1 Unpacks the Condensed Chromatin to Function as a Pioneer Factor (NIH-3T3 cells)

overall_design: ChIP-seq and ATAC-seq for vector,overexpress FH and FOXA1 in NIH-3T3 cells.


title: Extracellular vesicle small RNA cargo discriminates non-cancer donors from pediatric B-cell acute lymphoblastic leukemia patients

city: St. John's

first: Sherri

middle: Lynn

last: Christian

state: Newfoundland and Labrador

address: 45 Arctic Avenue

department: Biochemistry

country: Canada

institute: Memorial University of Newfoundland and Labrador

summary: Pediatric B-cell acute lymphoblastic leukemia (B-ALL) is a disease of abnormally growing B lymphoblasts. Here we hypothesized that extracellular vesicles (EVs), which are nanosized particles released by all cells (including cancer cells), could be used to monitor B-ALL by sampling plasma instead of bone marrow. EVs are especially attractive as they are present throughout the circulation regardless of the location of the originating cell.  First, we used nanoparticle tracking analysis to compare EVs between non-cancer donor (NCD) and B-ALL blood plasma; we found that B-ALL plasma contains more EVs than NCD plasma. We then isolated EVs from NCD and pediatric B-ALL peripheral blood plasma using a synthetic peptide-based isolation technique (Vn96), which is clinically amenable and isolates a broad spectrum of EVs. RNA-seq analysis of small RNAs contained within the isolated EVs revealed a signature of differentially packaged and exclusively packaged RNAs that distinguish NCD from B-ALL. The plasma EVs contain a heterogenous mixture of miRNAs and fragments of long non-coding RNA (lncRNA) and messenger RNA (mRNA). Transcripts packaged in B-ALL EVs include those involved in negative regulation of the cell cycle, suggesting that B-ALL cells may use EVs to discard gene sequences that control growth. In contrast, NCD EVs carry sequences representative of multiple organs, including brain, muscle, and epithelial cells. Overall, this signature could potentially be used to monitor B-ALL disease burden in pediatric B-ALL patients via blood draws instead of invasive bone marrow aspirates.

overall_design: To determine if there is a small RNA signature of extracellular vesicles that distinguishes pediatric B-ALL from non-cancer donors, we isolated extracellular vesicles from both cohorts and performed small RNA Seq on EV RNA cargo.

first: Modeline

middle: N

last: Longjohn


title: Phase Separation of FOXA1 Unpacks the Condensed Chromatin to Function as a Pioneer Factor

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

overall_design: Refer to individual Series


title: Androgen receptor signalling driving cancer stem cells (CSCs) state in triple-negative breast cancer

city: Darlinghurst

first: Heloisa

middle: Helena

last: Milioli

state: NSW

address: 384, Victoria St

department: Cancer

country: Australia

institute: Garvan Institute of Medical Research

summary: Therapeutic strategies that improve survival outcomes for advanced-stage breast cancers have proven a major clinical challenge. Here, we define an androgen receptor signalling network that governs the maintenance and de novo formation of cancer stem cells in triple-negative breast cancer. In response to chemotherapy, androgen receptor activation switches cells into a cancer stem cell state, while androgen receptor antagonism suppresses cancer stem cell formation and function. In vivo, we validate that the androgen receptor antagonist, seviteronel, significantly improves chemotherapy-mediated inhibition of primary and metastatic tumour growth.

overall_design:
MCF7 cells (Michigan Cancer Foundation) and ZR75-1 cells (American Type Culture Collection) lines were verified through short tandem repeat profiling and tested negative for mycoplasma contamination. Parental cell lines were cultured in RPMI 1640 media (Thermo Fisher) supplemented with 10% fetal bovine serum (GE Healthcare) and 20 mM HEPES (Thermo Fisher). HMEC cells were purchased from ATCC and transformed into HMLER cells by the sequential addition of hTERT, SV40-ER and RAS as previously described21. Cells were cultured in serum-free mammary epithelial growth medium (MEGM) and MEGM Single Quots (Lonza, cat no. CC-4136: 1 ml bovine pituitary extract (BPE), 0.5 ml GA-1000 (30 mg/ml Gentamicin and 15 µg/ml Amphotericin), 0.5 ml insulin, 0.5 ml hydrocortisone and 0.5 ml hEGF). Cells were maintained at 37oC with 5% CO2. HCC38 cells were purchased from ATCC and cultured in RPMI containing 10% FBS containing penicillin/streptomycin (PS; 5.000 units penicillin and 5 mg streptomycin/ml in H2O, Sigma Aldrich, cat no. P4333). All cell lines were routinely tested to confirm the absence of mycoplasma contamination.
Cells were grown in P150 plates for 48h-72h, depending on growth kinetics, till plates reached 80% confluence. At harvest time, cells were washed twice with cold PBS1x (Invitrogen), scraped and collected in eppendorfs. Cells were spun down, washed once more with cold PBS1x, removing the supernatant, followed by snap freezing in liquid nitrogen. Frozen cell pellets (1 x 10^6 cells) were used for RNA extraction of RNA using the commercial RNeasy Kit (Qiagen). Quality of RNA was assessed using a bioanalyzer Eukaryote Total RNA Nano chip. Samples that scored above RIN:9 were used to generate the mRNA library, using a  TruSeq Stranded mRNA LT - Set A kit (Illumina:   RS-122-2101). CD44-low versus CD44-high cell lines: MCF-7, ZR75-1, HMLER and HCC38. Samples were submitted for depth pair-end sequencing (Illumina HiSeq 2500 v4.0) at the Garvan Molecular Genetics.

first: Beatriz

middle: P

last: San Juan

first: Soroor

last: Hediyeh-Zadeh

first: Christine

last: Chaffer


title: Insulin-like growth factor I reduces coronary atherosclerosis in pigs with familial hypercholesterolemia

city: New Orleans

first: Sergiy

last: Sukhanov

state: Louisiana

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University School of Medicine

summary: To investigate effects of IGF-1 on human-like coronary atherosclerosis we used high fat diet-fed Rapacz pigs with familial hypercholesterolemia (FH pigs). We used spatial transcriptomics (ST) analysis to identify global transcriptome changes in advanced plaque compartments and to obtain mechanistic insights into IGF-1 effects.  IGF-1-injected FH pigs had 1.8-fold increase in total circulating IGF-1 levels compared to control. IGF-1 decreased relative coronary atheroma (data obtained by serial intravascular ultrasound) and lesion cross-sectional area (post-mortem histology). IGF-1 increased fibrous cap thickness, and reduced necrotic core size, macrophage content, and cell apoptosis, changes consistent with promotion of a stable plaque phenotype. ST analysis revealed that IGF-1 suppressed FOS/FOSB factors and gene expression of MMP9 and CXCL14 suggesting possible involvement of these molecules in IGF-1’s effect on atherosclerosis.

overall_design: FH pigs were fed with high-fat diet and received daily injections of IGF-1 or saline (control) for 6 months. A total 4 cryosections of right coronary artery (RCA) were obtained from female FH pigs (N=2, IGF-1-treated pigs, N=2, saline-treated pigs, control) and used for spatial transcriptomics (ST). Section imaging, RNA extraction, cDNA library preparation and sequencing were performed in according to the ST’s  manufacturer (Visium/10X genomics) recommendations.

first: Tadashi

last: Yoshida

first: Yusuke

last: Higashi

first: Patrice

last: Delafontaine


title: TLR2 promotes tumour proliferation in KRAS-dependant PDAC in the absence of ARF6

status: Public on Dec 02 2023

city: Barcelona

first: Ritobrata

last: Ghose

address: Carrer del Doctor Aiguader, 88, CRG 5th Floor Reception

institute: Center for Genomic Regulation

summary: Metastasis is responsible for nearly 90% of all cancer-related deaths. Despite global efforts to prevent aggressive tumours, cancers such as pancreatic ductal adenocarcinoma (PDAC) are poorly diagnosed in the primary stage, resulting in lethal metastatic disease. RAS mutations are known to promote tumour spread, with mutant KRAS present in almost 90% of cases. Until recently, mutant KRAS remained untargeted and, despite the recent development of inhibitors, results show that tumour cells develop resistance. Another strategy for targeting mutant KRAS-dependent PDAC metastasis may come from targeting the downstream effectors of KRAS. One such axis, which controls tumour proliferation, invasiveness and immune evasion, is represented by ARF6-ASAP1. Here we show that targeting ARF6 results in adaptive rewiring that can restore proliferation and invasion potential over time. Using time-series RNA and ATAC sequencing approaches, we identified TLR-dependent NFκB, TNFα and hypoxia signalling as key drivers of adaptation in ARF6-depleted KRAS-dependent PDAC. Using in vitro and in vivo assays, we show that knocking down TLR2 with ARF6 significantly reduces proliferation, migration and invasion. Taken together, our data shed light on a novel co-targeting strategy with the therapeutic potential to counteract PDAC proliferation and metastasis.

overall_design: To understand the adaptive landscape of PDAC when KRAS-downstream signalling nodes at different hierarchical levels are perturbed, we treated MIA PaCa-2 cells with shRNAs targeting either ARF6 or ASAP1, and monitored them for a prolonged period of up to 21 days. We performed time-resolved RNA sequencing (RNA-seq) for cells treated with shNT, shARF6 or shASAP1 at time points Day 3, 7, 14 and 21

first: Shubhamay

last: Das

first: Julia

last: Urgel-Solas

first: Fabio

last: Pezzano

first: Debayan

last: Datta

first: Upamanyu

first: Antoni

last: Ganez Zapater

first: Natalia

last: Pardo Lorente

first: Lorena

last: Espinar Calvo

first: Laura

last: Garcia

first: Chiara

last: Cannata

first: Verena

last: Ruprecht

first: Ana

last: Janic

first: Sara

last: Sdelci


title: Seviteronel plus chemotherapy is a new targeted combination therapy to treat triple-negative breast cancer

first: Heloisa

last: Milioli

overall_design: HCC38 cells were purchased from ATCC and cultured in RPMI containing 10% FBS containing penicillin/streptomycin (PS; 5.000 units penicillin and 5 mg streptomycin/ml in H2O, Sigma Aldrich, cat no. P4333). All cell lines were routinely tested to confirm the absence of mycoplasma contamination. HCC38 CD44Hi cells treated with control siRNA or two different siRNAs targeting AR (AR ex1, AR ex7). HCC38 CD44Hi cells also followed treatment with AR antagonists vehicle (DMSO), Seviteronel, Abiraterone or Enzalutamide.

first: Beatriz

last: San Juan

first: Christine

last: Chaffer


title: The effect of Epigallocatechin-3-Gallate (EGCG), a main active ingredient in tea residues, on improving fruit quality and prolonging postharvest storage in apple

city: Tai-an

first: Yuan Yuan

last: Li

address: No. 61 Dai Zong Street

institute: College of Horticultural Science and Engineering, Shandong Agricultural University

summary: EGCG, as an active oxygen scavenger, has a significant effect on inhibiting the greasiness of apples. However, the impact of greasiness on fruit storage and how EGCG eliminates this effect, as well as its influence on apple quality formation, have not been clarified. In this study, we found that exogenous application of EGCG effectively improved a series of nutritional growth indicators, including seedling growth status and photosynthetic activity. Additionally, it significantly increased indicators of reproductive growth, such as fruit diameter, soluble solids content, surface wax, and surface smoothness. Through our experiments, we further discovered that greasiness primarily affects fruit respiration, accelerating fruit decay and causing harm during storage, while EGCG mitigates this process. We also found that the application of tea residue had similar effects to exogenous EGCG. Collectively, these studies suggest that EGCG could be used as a novel foliar fertilizer to enhance overall fruit quality. Moreover, the application of tea residue has similar effects to EGCG, providing a cost-effective solution for apple production.

overall_design: Fuji apples were evacuated in 5 μmol L-1 aqueous EGCG solution for 5 min, and then 30 apples each were treated in the same way using ddH2O as a control. Three apples from each treatment and control were selected for transcriptome analysis.

first: Yating

last: Wu

first: Han

last: Jiang

first: Yuan-Yuan

first: Yanhui

last: Lv


title: Single-cell resolution of longitudinal blood transcriptome profiles in rheumatoid arthritis, systemic lupus erythematosus and healthy control pregnancies

city: Trondheim

first: Pål

last: Sætrom

address: Erling Skjalgsons gate 1

department: Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology, NTNU

summary: Rheumatoid arthritis (RA), Systemic Lupus Erythematosus (SLE) are genetically the most closely related of the major rheumatic diseases as they share components of the type I IFN signalling pathway linked to treatment response and disease activity. One difference between the two is how they respond to pregnancy; while RA often improves, SLE is prone to flare. Multiple mechanisms contribute to immunological tolerance of the foetus during pregnancy. More research involving comparative analyses is needed, however, as understanding how pregnancy-related immune-modulation differs in RA and SLE can potentially lead to better treatment options. We provide data from a cohort of women with universal accessibility to health care that have been followed closely throughout their pregnancies, are well regulated and have low disease activity. We analysed samples both by bulk- and scRNA-seq, and ran a cell-type estimation, validated by flow cytometry, before combining this in a cell-type adjusted analysis. This novel comparative approach gives an improved resolution of expression profiles in RA and SLE pregnancies.

overall_design:
335 whole blood samples from 84 RA, SLE, and healthy controls before pregnancy, at each trimester, 6 weeks, 6 months, and 12 months postpartum were analysed. We ran bulk and single cell RNA analyses and then combined these for cell-type estimation, validated by flow cytometry. These results were then used in a cell-type adjusted analysis for an improved resolution of unrecognized gene expression changes associated with RA and SLE pregnancies.
---------------------
Authors state:
The raw data are personal sensitive data and cannot be submitted due to Norwegian legal constraints.

first: Hilde

last: Lien

first: Tina

last: Pedersen

first: Bente

last: Jakobsen

first: Arnar

last: Flatberg

first: Konika

last: Chawla

last: Særtom

first: Mona

last: Fenstad


title: RNA-seq analysis of hilar and peripheral biliary organoids from a mouse model of Alagille syndrome

city: Solna

first: Emma

middle: R

last: Andersson

state: Not required for this country

address: Solnav. 9, BioMedicum

country: Sweden

institute: Karolinska Institutet

summary: To study molecular differences in wild-type and regenrated bile ducts in a mouse model of Alagille syndrome (Andersson, Chivukula, Hankeova, et al. Gastroenterology, 2018;154(4):1080-1095), we derived intrahepatic cholangiocyte organoids from hilar (pICOs) and peripheral (pICOs) regions of adult livers following a published protocol for organoids derivation and culture (Broutier et al., Nat Protoc. 2016;11:1724–1743). At passage 5, we isolated total RNA and performed bulk RNA-sequencing on 3 biological replicates from each region and genotype.

overall_design: Organoids were grown in Matrigel domes. At passage 5, RNA was collected using RNeasy Plus micro kit (Qiagen, 74034), sequencing library was prepared using TruSeq RNA SMP prep Kit-v2 SetA from Illumina (RS-122-2001) and it was sequenced on Illumina NextSeq 550 platform.


title: Single cell RNA sequencing of embryonic day 14.5 testes isolated from wild-type and mutant mice lacking Nr5a1 in Sertoli cells from embryonic day E13.5

city: ILLKIRCH Cedex

first: Norbert

last: GHYSELINCK

state: CU STRASBOURG

address: 1 rue Laurent Fries BP10144

department: Functional Genomics & Cancer

institute: Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)

summary: To investigate the role of the nuclear receptor NR5A1 in testis after sex determination, we have analyzed mice lacking NR5A1 in Sertoli cells (SC) from embryonic day (E) 13.5 onwards. Ablation of Nr5a1 impairs the expression of genes characteristic of the SC identity (e.g., Sox9, Amh), causes SC death from E14.5 through a Trp53-independent mechanism related to anoikis, and induces disorganization of the testis cords. Together, these effects cause germ cells to enter meiosis and die. Single-cell RNA-sequencing experiments revealed that NR5A1-deficient SC change their molecular identity: some acquire a “pre-granulosa-like” identity, while other revert to a “supporting progenitor-like” cell identity, most of them being “intersex” because they express both testicular and ovarian genes. Fetal Leydig cells (LC) do not display significant changes, indicating that SC are not required beyond E14.5 for their emergence or maintenance. In contrast, adult LC were absent from the postnatal testes. In addition, adult mutant males display persistence of Müllerian duct derivatives, decreased anogenital distance and reduced penis length, which can be explained by the loss of AMH and testosterone synthesis due to SC failure.

overall_design: Testes from E13.5 and E14.5 control and mutant fetuses were dissected out in PBS and cell suspensions were prepared as described above. Cell number and viability were determined by a Trypan Blue exclusion assay on a Neubauer Chamber. Samples consisting of > 90% viable cells were processed on the Chromium Controller from 10X Genomics (Leiden, The Netherlands). Ten thousand cells were loaded per well to yield approximately 5000 to 6000 captured cells into nanoliter-scale Gel Beads-in-Emulsion (GEMs). GEMs were generated by combining barcoded gel beads, a reverse transcription master mix containing cells, and partitioning oil onto Chromium Chip B. Following full length cDNA synthesis and barcoding from poly-adenylated mRNA, GEM were broken and pooled before cDNA amplification by PCR using 11 cycles. After enzymatic fragmentation and size selection, sequencing libraries were constructed by adding Illumina P5 and P7 primers (Illumina, Evry, France), as well as sample index via end repair, A tailing, adaptor ligation and PCR with 10 cycles. Library quantifications and quality controls were determined using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Libraries were then sequenced on Illumina HiSeq 4000TM as 100 bases paired-end reads, using standard protocols.

first: Sirine

last: SOUALI-CRESPO

first: Diana

last: CONDREA

first: Nadège

last: VERNET

first: Betty

last: FÉRET

first: Muriel

last: KLOPFENSTEIN

first: Violaine

last: ALUNNI

first: Marie

last: CERCIAT

first: Matthieu

last: JUNG

first: Manuel

last: MARK

first: Frédéric

last: CHALMEL


title: Laser microdissection coupled with RNA-seq profiling of the E11.5 mouse mandibular epithelium along the dorsoventral axis

status: Public on Dec 01 2023

city: Iowa City

first: HUOJUN

last: CAO

state: IA

address: 801 Newton Road

institute: University of Iowa

summary: How the dorsal-ventral axis of the vertebrate jaw, particularly the position of tooth initiation site, is established remains a critical and unresolved question. Tooth development starts with the formation of the dental lamina, a localized thickened strip within the maxillary and mandibular epithelium. To identify transcriptional regulatory networks (TRN) controlling the specification of dental lamina from the naïve mandibular epithelium, we utilized Laser Microdissection coupled low-input RNA-seq (LMD-RNA-seq) to profile gene expression of different domains of the mandibular epithelium along the dorsal-ventral axis in wild type mouse and two loss-of-function mouse models of domain specific transcription factors.

overall_design: To identify genes that are critical for mandibular epithelial patterning, we applied Laser Microdissection (LMD) coupled Smart-Seq2 RNA-seq to generate transcriptome profiles of four domains along the dorsal-ventral axis of the E11.5 mouse mandibular epithelium (also known as the oral-aboral axis). The four domains, from dorsal to ventral, included: 1) a posterior/dorsal domain; 2) a Dental Lamina (DL) domain; 3) an anterior domain; and, 4) an aboral/ventral domain. To determine the role of domain specific TFs in mandibular epithelium patterning and DL formation, we also generated transcriptome profiles of two loss-of-function mouse models: 1) DL specific transcription factor: Pitx2; 2) Aboral domain specific transcription factor: Tfap2a and Tfap2b.

first: Fan

last: Shao

first: Eric

last: Van Otterloo

first: Huojun

last: Cao


title: Total RNA-seq in Calu3 cells upon SARS-CoV2 infection

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: This study addresses the question how host cells transcriptionally respond to SARS-CoV2 infection.

overall_design: Calu3 cells were infected with Influenza or SARS CoV-2 virus for various time points before harvesting them for RNA and chromatin profiling.

first: Sebastian

last: Weigang

first: Georg

last: Kochs

first: Martin

last: Schwemmle

first: Prashant

last: Rawat

first: Ritwick

last: Sawarkar


title: ChIP-seq in Calu3 cells upon SARS-CoV2 infection


title: Slam-seq in Calu3 cells upon SARS-CoV2 infection


title: SARS-CoV2 causes host transcriptional attenuation through an epigenetic pathway.