title: Identification of MRG15 as barrier to somatic reprogramming

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

summary: Epigenetic reprogramming requires depletion of 4 factors ; Oct4, Sox2, Klf-4 and c-Myc. We have 4 groups of samples. 2 group is collected as fibroblasts and it is referred as Day Zero. The other groups are collected at the sixth day of epigenetic reprogramming referred as Day Six. Day 18 of epigenetic reprogramming, %5- 15 of cell population transformed into pluripotent stem cells. At day six this percentage is lower.Our previous studies have showed that inhibition of H3K36me3 mark thusleading to H3K36me2 mark on chromatin) significantly increased reprogramming efficiency. A CRISPR Knock-Out Library was built to identify which of the H3K36me3 mark reader protein can phenocopy absence of K36me3 loss in terms of reprogramming efficiency. MRG15 Knock Out has showed the most similar increase in reprogramming as loss of K36me3 mark. It has been reported that MRG15 is responsible from alternative splicing of some genes. Our hypothesis is; in the presence of H3K36me3 mark MRG15 can bind this mark on chromatin and recruit proteins related to alternative splicing ( eg. PTBP1)and regulate alternative splicing.

overall_design: We performed a gene expression profiling analysis and detection of differential alternative splicing analysis using data obtained from RNA-seq of dh1f cells expressing non targeting vector and lenticrisprv2 targeting MRG15. Both groups were collected pre and post OSKM treatment. post-OSKM group were sixth day of reprogramming.

first: Elifsu

last: Kartal

first: Tamer

last: Önder

first: Marco

last: Preussner


title: Characterization of mesenchymal support required for in vivo engraftment and development of human PSC-derived organoids

status: Public on Jan 01 2025

city: Cincinnati

first: Michael

last: Helmrath

address: 3333 Burnet Avenue

country: USA

institute: Cincinnati Children’s Hospital Medical Center

type: Expression profiling by high throughput sequencing

summary: Human gastrointestinal (GI) organoids derived from pluripotent stem cells have unique potential for studying organogenesis, physiology, and diseases. To this end, their transplantation into animal models to further their development into functional organs provides a valuable tool. However, organoids from different GI regions, for example, the esophagus or intestine, harbor different engraftment capabilities. Here, we developed a tissue-engineering approach and show that enhancing the mesenchyme-to-endoderm ratio enables reliable engraftment of GI organoids. However, endoderm/mesoderm recombinations reveal that only Human Intestinal Organoid (HIO) mesenchyme allows full development of GI epitheliums in vivo. Comparative mesenchyme analysis from esophageal, gastric, intestinal, and colonic organoids shows endothelial cell enrichment within the HIO mesenchyme, and we demonstrate by endothelial cell depletion or addition that these cells are required and sufficient for proper GI organoid development in vivo. Our findings highlight the optimal mesenchymal cellular composition needed to support GI organoid engraftment, tissue growth, and function.

overall_design: We performed a single-cell transcriptomic analysis of HEOs, HGOs, HCOs, and HIOs by profiling a total of 27 437 cells isolated from organoids at days 18 and 28 of culture, to analyze the composition of there respective mesenchymes.

first: Simon

last: Valès

first: Nambirajan

last: Sundaram

first: Théo

last: Noël

first: Nicole

middle: E

last: Brown

first: Carine

last: Bouffi

first: Garrett

middle: W

last: Fisher

first: Jennifer

last: Hawkins

first: Holly

middle: M

last: Poling

first: Alexandra

middle: K

last: Eicher

first: James

last: Wells

first: Maxime

last: Mahe

middle: A


title: ROS-Responsive Potassium Ionophore-Based Nanoplatform Potentiates Cancer Pyroptosis-Immunotherapy via ER Stress

city: ZhengZhou

first: Ming

last: Wang

address: jianshe Road

country: China

institute: ZhengZhou university

summary: Pyroptosis is an emerging programmed cell death with great potential in antitumor immunotherapy. However, the actual application of pyroptosis is hampered by its nonspecificity and inefficiency. In this study, a reactive oxygen species (ROS) responsive potassium (K+) ionophore-based nanoplatform rPPAA18C6 is constructed based on the triblock polymers PEG-PPBAEM-PAA18C6 to potentiate cancer pyroptosis and immunotherapy via the K+ metabolic disturbance mediated endoplasmic reticulum (ER) stress. The PEG (P) is used to prolong the circulation time in vivo,  PPBAEM (r) is used to target the tumor cells and responds to the higher ROS, and PAA18C6 is used to perturb of K+ homeostasis. Moreover, rPPAA18C6 can also function as a drug carrier for chemodrug (doxorubicin, Dox). We find that rPPAA18C6@Dox provokes immune responses in melanoma (B16F10) via pyroptosis-related immunogenic cell death (ICD), in which damage-associated molecular patterns (DAMPs) are released to promote maturation of dendritic cells (DCs), activate cytotoxic T lymphocytes (CTLs), and convert immunosuppressive “cold” tumor to immunogenic “hot” tumor. Moreover, the combined therapy with anti-PD-L1 exhibits apparent tumor suppression far more than expected, suggesting a powerful candidate of rPPAA18C6@Dox for high-efficient immune checkpoint blockade (ICB) therapy. This study thus provides a promising strategy to specifically initiate pyroptosis and potentiate immunotherapy by perturbation of K+ metabolism via a smart nanoplatform.

overall_design: To detect the gene expression of B16F10 cells stimulated with rPPAA18C6@Dox, RNA-Seq was performed by OE Biotech Co., Ltd. Briefly, B16F10 cells were seeded in a 6-well plate at a density of 5.0 × 105 cells/well, and cultured at 37 °C for overnight. Then, the medium was replaced with fresh medium containing PBS and rPPAA18C6@Dox (50 μg/mL). After cultured at 37 °C for 8 h, the cells were collected in RNAiso Plus reagent for RNA isolation.

first: Xiaohan

last: Yao

first: Yongjuan

last: Li


title: Robust antitumor activity of a de novo interleukin-21 mimic

city: Bethesda

first: Peng

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: A long-standing goal of cancer immunotherapy is to activate cytotoxic antitumor T cells across a broad range of affinities and dampen suppressive regulatory T (Treg) cell responses, but current approaches achieve these goals with limited success. Here, we report a de novo IL-21 mimic, 21h10, designed to have augmented stability and high signaling potency in both humans and mice. In multiple animal models, 21h10 showed robust antitumor activity, exceeding that of native IL-21 for murine melanoma, inducing a rapid regression of murine adenocarcinoma, and exhibiting potent activity in an orthotopic pancreatic cancer model that is refractory to conventional immunotherapies. In the tumor microenvironment, 21h10 induced highly cytotoxic antitumor T cells from clonotypes with a range of affinities for endogenous tumor antigens, driving high expression of interferon-𝛾 (IFN-𝛾) and granzyme B compared to native IL-21, while in the CD4+  T cell compartment, the frequency of IFN-𝛾+ Th1 cells was increased while Foxp3+ Treg cells were reduced. Thus, 21h10 is a highly active IL-21 mimic with human-mouse cross-reactivity that potentiates low-affinity antitumor responses and has considerable translational potential.

overall_design: RNA-Seq analyses using mouse CD8+ T cells that were pre-activated with anti-CD3 + anti-CD28, and cultured in complete RPMI media for 48 hours at 37°C. Cells were rested overnight, and then either without stimulation or stimulated with either mIL-21 or 21h10 for 24h.

first: Jung-Ho

last: Chun

first: Birkley

middle: S

last: Lim

first: Suyasha

last: Roy

middle: J

last: Walsh

first: Gita

middle: C

last: Abhiraman

first: Kevin

last: Zhangxu

first: Elisa

last: Clark

first: Asheema

last: Khanna

first: Tavus

last: Atajanova

first: Samantha

last: Tower

first: Rakeeb

last: Kureshi

first: Megan

middle: T

last: Hoffman

first: Tina

last: Nguyen

middle: Y

last: Liu

first: Alfredo

last: Quijano-Rubio

last: Jude

first: Umut

last: Ulge

first: Stacey

last: Gerben

first: Analisa

last: Murray

first: Piper

last: Heine

first: Michelle

last: DeWitt

first: Lauren

last: Carter

first: Neil

middle: P

last: King

first: Daniel-Adriano

last: Silva

first: Hao

last: Kueh

first: Vandana

last: Kalia

first: Surojit

last: Sarkar

first: K

last: Garcia

first: Warren

last: Leonard

first: Stephanie

last: Dougan

first: David

last: Baker


title: DNA virus infections shape transposable element activity in vitro and in vivo [HFF]

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

country: Germany

institute: institute of Virology, University Medical Center Freiburg

summary: We show strong activation of TEs in the context of DNA virus infection and investigate the molecular mechanisms of how TEs are induced. We demonstrate that herpesvirus infection leads to a robust expression of the MLT and THE1-class of LTR containing retrotransposons as well as a subset of long-interspersed nuclear elements-1 (LINEs), Alu-elements and some HERVs. Mechanistically we demonstrate that this TEs upregulation is induced by two pathways that act synergistically: de-repression of KAP1/TRIM28 mediated by phosphorylation and expression of the pioneer factor double-homeobox 4 (DUX4).

overall_design: RNA-sequencing was performed from HCMV infection and KAP1 knockdown

first: Jiang

last: Tan

first: Vedran

last: Franke

first: Eva

last: Neugebauer

first: Justine

last: Lagisquet

first: Anna

last: Katharina Kuderna

last: Walter

first: Armin

last: Ensser

first: Markus

last: Landthaler

first: Thomas

last: Stamminger

last: Gramberg

first: Altuna

last: Akalin

first: Emanuel

last: Wyler


title: DNMT1 regulates human erythropoiesis by modulating cell cycle and endoplasmic reticulum stress in a stage-specific manner

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

summary: The dynamic balance of DNA methylation and demethylation is required for erythropoiesis. Our previous transcriptomic analyses revealed that DNA methyltransferase 1 (DNMT1) is abundantly expressed in erythroid cells at all developmental stages. However, the role and molecular mechanisms of DNMT1 in human erythropoiesis remain unknown. Here we found that DNMT1 deficiency led to cell cycle arrest of erythroid progenitors which was partially rescued by treatment with a p21 inhibitor UC2288. Mechanically, this is due to decreased DNA methylation of p21 promoter, leading to upregulation of p21 expression. In contrast, DNMT1 deficiency led to increased apoptosis during terminal stage by inducing endoplasmic reticulum (ER) stress in a p21 independent manner. ER stress was attributed to the upregulation of RPL15 expression due to the decreased DNA methylation at RPL15 promoter. The upregulated RPL15 expression subsequently caused a significant upregulation of core ribosomal proteins (RPs) and thus ultimately activated all branches of unfolded protein response (UPR)leading to the excessive ER stress, suggesting a role of DNMT1 in maintaining protein homeostasis during terminal erythroid differentiation. Furthermore, the increased apoptosis was significantly rescued by the treatment of ER stress inhibitor TUDCA. Our findings demonstrate the stage-specific role of DNMT1 in regulating human erythropoiesis and provide new insights into regulation of human erythropoiesis.

overall_design: To determine the molecular mechanism of for the DNMT1 deficiency-induced apoptosis, we performed RNA-seq analysis on the purified luciferase-shRNA and DNMT1-knockdown orthochromatic erythroblasts.

first: Qianqian

last: Yang

first: Lixiang

last: Chen

first: Ting

last: Wang


title: Inflammatory milieu by crosstalk between podocytes and proximal tubular cells in type 2 diabetic kidney disease

city: Seoul

first: Yong jun

last: Kim

address: 329, Daehak-ro 103, Jongno-gu, Seoul, Republic of korea

department: biomedical science

country: South Korea

institute: Seoul National University

summary: Due to the limited availability of therapeutic agents for type 2 diabetic kidney disease (DKD), there is a need for further knowledge derived from experimental models and innovative techniques. In addressing this issue, single-cell RNA sequencing (scRNA-seq) has been exclusively applied to a genetically modified DKD model, but not an induced model representing type 2 DKD. Herein, we analyzed scRNA-seq and other experiments from an induced type 2 DKD model, and validated the results in human-derived biospecimens. The model was induced by combining a high-fat diet with streptozotocin to simulate induced type 2 DKD. scRNA-seq, histological, and flow cytometric analyses were conducted, and their results were compared with control mice. The findings were then applied to human kidneys exhibiting diabetic glomerulosclerosis associated with type 2 diabetes.

overall_design: single-cell RNAdata for induced type 2 DKD with HFD/STZ

first: Peong

middle: G

last: Park

first: Juhyeon

last: Hwang

first: Yongjun

first: Hyunje

first: Seung

last: Han


title: CD74 regulates the tumor immunosuppressive microenvironment in triple-negative brest cancer

city: Rehovot

first: Idit

last: Shachar

address: Herzl

department: Systems Immunology

country: Israel

institute: Weizmann Institute of Science

summary: CD74 is a cell-surface receptor for the cytokine macrophage migration inhibitory factor (MIF). MIF binding to CD74 induces a signaling cascade resulting in the release of its cytosolic intracellular domain (CD74-ICD), which regulates transcription in naive B and chronic lymphocytic leukemia (CLL) cells. In the current study, we investigated the role of CD74 in the regulation of the immunosuppressive tumor microenvironment (TME) in triple-negative breast cancer (TNBC). TNBC is the most aggressive breast cancer subtype, in which there is a massive infiltration of immune cells to the tumor microenvironment, making this tumor a good candidate for immunotherapy. The tumor and immune cells in TNBC express high levels of CD74, however, the function of this receptor in this environment was not fully characterized. Regulatory B cells (Bregs) and tolerogenic dendritic cells )tol-DCs( were previously shown to attenuate the antitumor immune response in TNBC. Here, we demonstrate that CD74 enhances tumor growth by inducing the expansion of tumor-infiltrating tol-DCs and Bregs. Utilizing CD74-KO mice, conditionally CD74 -/- Cre-flox mice lacking CD74 in CD23+ mature B cells and mice lacking CD74 in the CD11c+ population and a CD74 inhibitor (DRQ), revealed that MIF secreted from the tumor cells activate CD74 expressed on DCs. This activation induces the binding of CD74-ICD to the SP1 promotor, resulting in the upregulation of SP1 expression. SP1 binds the IL-1β promotor, leading to the downregulation of its transcription. The reduced levels of IL-1β lead to decreased anti-tumor activity by allowing expansion of the tol-DC, which induce the expansion of the Breg population, suggesting the cross-talk between these two populations. Taken together, these results suggest that CD74+ CD11c+ DCs are the dominant cell type involved in the regulation of the TNBC progression. These findings indicate that CD74 might serve as a novel therapeutic target in triple-negative breast cancer.

overall_design: we wanted to investigate the role of CD74 in DCs. To this purpose WT mice were injected with E0771 cancer cell line and divided in two group. One  treated with PBS and one treated with DRQ, a CD74 inhibitor, starting from day 10. 3 weeks post-injection, mice were sacrificed and DCs were sorted from the tumor microenvironment of the PBS/DRQ -treated mice and RNA-seq was performed. ֹ

first: Bianca

last: Pellegrino

first: Keren

last: David

first: Stav

last: Rabani

first: Bar

last: Lampert

first: Lin

last: Leng

first: Richard

last: Bucala

first: Arthur

last: Vanderbark

first: Shirly

last: Becker-Herman


title: Extracellular vesicles carrying significant amounts of microRNAs are present in milk powders.

city: St Genès-Champanelle

first: Christine

last: LEROUX

address: Route de Theix

country: France

institute: INRAE

type: Non-coding RNA profiling by high throughput sequencing

summary: Milk-derived extracellular vesicles (mEVs) have been proved to play a critical role in intercellular communication, mainly through the microRNAs (miRNAs) that they carry, to regulate biological functions of the target cells. Given miRNAs are evolutionarily conserved, EVs present in commercial milk may play a role in the physiology and health consumers. It is therefore essential to know the effects of technological treatments such as skimming and spray drying on the EV content of milk powders and on the cargo of bioactive molecules, in particular miRNAs, that they convey. Since goat’s milk or goat milk based formulas are considered as a healthy alternative for infants with cow’s milk sensitivities, including allergy, we undertook to analyze the EV content of skimmed and unskimmed goat's milk powders and to characterize their RNA content, in particular their miRNomes. mEVs were isolated using an optimized protocol based on Size Exclusion Chromatography (SEC) and compared regarding morphology, number and size by Transmission Electron Microscopy (TEM) and Nanoparticle Tracking Analysis (NTA). Their RNA and protein content were determined and their miRNomes established, using RNA sequencing. In this study we demonstrated that goat milk powders, skimmed or not upstream the spray drying treatment, contained many mEVs, ranging from 5.4 1011 to 2.5 1012 particles per mL of reconstituted milk, with an average size between 136.8 and 160.6 nm. We also demonstrated that mEVs carried significant amounts of RNA, including miRNAs. Using RT-qPCR, mRNAs encoding five of the major milk proteins were detected, suggesting that mEVs originated from mammary epithelial cells. We established the goat milk powder miRNome by identifying 351 miRNAs of which 233 are common to the 262 miRNAs previously profiled in raw goat milk. The 20 most abundant miRNAs (TOP 20) account for 80% of the total reads and the hierarchy of this TOP 20 miRNAs is somewhat overturned when comparing goat milk powder and raw goat milk. Surprisingly, whereas the comparison of raw from cow and goat milk confirmed the prevalence of miR-148a, miR-21-5p and miR-26a/miR-30a-5p, let-7a-5p and let-7f, which occupied ranks 1 and 2, respectively, in powders, were relegated to ranks 6 and 10 and 5 and 11 in raw goat and cow milk, respectively. Conversely to what was previously reported, we provide evidence that: i) EVs of typical morphology are present in goat milk powders; ii) mEVs survived the technological processes used to produce the powders; iii) their miRNA cargo is protected from degradation even though their miRNomes are not an exact mirror of miRNomes of EVs derived from fluid raw milk.

sample_organism:
Bos taurus
Capra hircus

platform_organism:
Bos taurus
Capra hircus

overall_design:
We analyze the EV content of skimmed and unskimmed goat's milk powders and to characterize their RNA content, in particular their miRNomes. mEVs were isolated using an optimized protocol based on Size Exclusion Chromatography (SEC) and compared regarding morphology, number and size by Transmission Electron Microscopy (TEM) and Nanoparticle Tracking Analysis (NTA). Their RNA and protein content were determined and their miRNomes established, using RNA sequencing.
milk powder EV miRNAs

first: Tao

last: Ye

first: Zuzana

last: Krupova

first: Sophie

last: Gallier

first: Patrice

last: Martin


title: ITGAV in PBMCs is identified as a hub gene in oxidative stress-related immunosuppression and delayed burn wound healing and is reversed by MnCl2

city: xi'an

first: Qingan

last: Jia

state: Shaanxi

address: No. 127, Youyi West Road, Beilin District

institute: Northwestern Polytechnical University

summary: Peripheral blood mononuclear cell (PBMC) RNA-seq datasets from burn patients with sepsis were acquired from the Gene Expression Omnibus (GEO), and OSRGs were retrieved from the GeneCards database. Weighted gene coexpression network analysis (WGCNA) was performed to validate the relationships between burns and immune cells. Machine learning and logistic regression were employed to select hub genes, which were used to construct predictive signatures. High- and low-risk groups were defined by risk scores, and the expression of integrative hub genes was confirmed, with the results validated by real-time quantitative polymerase chain reaction (PCR) in PBMCs from 30 burn patients and burn models with different levels of severity. Integrin subunit alpha V (ITGAV) was confirmed as a hub gene, and its regulatory role was explored in vivo. Finally, the therapeutic role of MnCl2 was confirmed, and RNA-seq was performed to evaluate the associated signaling mechanisms.

overall_design: Two OSRG molecular patterns exhibiting differential immune regulation were established. By WGCNA, the STRING database, and differential expression analysis, and a three-gene signature was selected by random forest (RF), least absolute shrinkage and selection operator (LASSO), and logistic regression, which included independent prognostic factors and performed well in receiver operating characteristic (ROC) and calibration curves. Finally, ITGAV was selected as an integrative hub gene, and the therapeutic role of MnCl2 in burn wound healing was determined to be associated with improved immunosuppression.

first: Zihan

last: Xu

first: Qiangbo

last: Zhang

first: Shengzhi

last: Mu


title: Single-cell 5-hydroxymethyl cytosine dynamics during remote memory formation

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

type: Methylation profiling by high throughput sequencing

summary: We introduce the Split-Pool based Epigenetic Decoding (SPEED) method, a combinatorial barcoding strategy enhancing the throughput of single-cell 5-hydroxymethyl cytosine (5hmC) or 5-methylcytosine (5mC) profiling. SPEED enables simultaneous, unbiased examination of 5hmC traits across distinct brain regions, surpassing limitations of individual cell scrutiny. Using SPEED  we unveil dynamic 5hmC patterns  linked to remote memory formation in the brain.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We isolated and crosslinked nuclei, fragmented and end-repaired DNA, performed three rounds of barcode ligation within nuclei, extracted genomic DNA, biotin-labeled 5-hydroxymethylcytosine (5hmC), and enriched 5hmC-containing fragments using Streptavidin beads. Subsequently, we eluted the 5hmC-containing fragments, and libraries were constructed for further analysis.

first: Jiang

last: Xiao

first: Peihong

first: Yongchuan

last: Zhu

first: Li

last: Yang

first: Lulu

last: Hu


title: Integration of ATAC-seq and RNA-seq identifies typing and prognosis evaluation target molecules of triple negative breast cancer

city: hefei

first: youguang

last: pu

state: 安徽

address: NO 96，Jinzhai Road

institute: University of Science and Technology of Chin

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Molecular subtyping plays a vital role in the treatment of breast cancer, however, current clinical outcomes remain unsatisfactory despite having multiple molecular subtypes available, particularly for triple-negative breast cancers. Henceforth, our research primarily focuses on traditional molecular subtyping by utilizing transcriptome sequencing and ATAC-seq sequencing techniques to classify both tumor tissues and adjacent tissues from patients with breasts cancers into distinct groups. Through this process, we aim to identify key gene expressions involved in the development of breasts cancers as well as epigenetic characteristics influenced by alterations in chromatin accessibility patterns. Subsequently, employing conventional methods used for classifying breasts cancers into different molecular types enables us to further investigate significant variations observed specifically within triple-negative breasts cancers regarding their gene expression profiles and chromatin accessibility patterns. Lastly, utilizing data from TCGA database pertaining exclusively to cases involving triple-negative breasts cancers allows us to conduct regression analyses concerning our aforementioned findings while simultaneously selecting relevant molecular models closely associated with this particular subtype of breasts malignancy. Additionally evaluating how these differentially expressed genes influence prognosis through prognostic modeling analysis tailored towards predicting outcomes solely within cases involving individuals diagnosed with triple negative-breast malignancies will enable us ultimately construct an innovative model incorporating both gene expressions along with chromatin accessibility patterns as distinguishing features providing more substantial guidance towards improving clinical treatments targeting individuals afflicted by such conditions.

overall_design:
We performed transposase-accessible chromatin sequencing (ATAC-seq) analysis of breast cancer samples, including ER-positive(+) human epidermal growth factor receptor 2 (HER2)-negative(−) and triple-negative tumors. We also reanalysed ATAC-seq data of tumors in the Cancer Genome Atlas (TCGA) BC cohort to validate our observations.
Breast cancer tissue and adjacent paracancerous tissue

first: Youguang

last: Pu


title: YAP dysregulation triggers hypertrophy by CCN2 secretion and TGFβ uptake in human pluripotent stem cell-derived cardiomyocytes

city: Santa Barbara

first: Alex

last: Chialastri

state: CA

address: 2002 BioEngineering Bldg

department: Chemical Engineering

institute: University of California Santa Barbara

summary: Our research has demonstrated the following: (1) Confirmed that MYH7 mutations D239N, H251N, G256E lead to hypercontractility in hiPSC-derived cardiomyocytes (hiPSC-CMs); (2) Increase in YAP’s nuclear localization in both hiPSC-CMs and patient tissue with MYH7 HCM mutations; (3) A correlation between YAP's nuclear localization and enhanced force generation; (4) Nuclear deformation as a mechanism enabling YAP's nuclear entry and activation; (5) Transcriptomic changes resulting from positive and negative modifications in force generation; and (6) A distinctive paracrine hypertrophic signal reliant on cardiomyocyte-cardiac fibroblast crosstalk. Our unique insights to the intricacies of hypertrophic cardiomyopathy phenotypes hold the potential to provide mechanistic clarity, informing potential therapeutic strategies.

overall_design: We performed bulk RNA-seq on D60 hiPSC-CMs from four separate conditions: 1) WT hiPSC-CMs, 2) WT hiPSC-CMs + levosimendan (300 nM) to mimic the hypercontractile phenotype, 3) MYH7-R663H hiPSC-CMs, and 4) MYH7-R663H hiPSC-CMs+ verapamil (100 nM) in an effort to reduce hypercontractility and therefore presumably restore a normal transcriptional profile (2 & 3 = high force, 1 & 4 = low force). MYH7-R663H hiPSC-CMs are iPSCs derived cardiomyocytes derived from a cliniically diagnosed Hypertrophic Cardiomyopathy patient sample.

first: Orlando

last: Chirikian

first: Mohamed

last: Faynus

first: Markus

last: Merk

first: Zachary

last: Singh

first: Christopher

last: Muray

first: Jeffrey

last: Pham

first: Alison

middle: V

last: Roest

last: Goldstein

first: Trevor

last: Pyle

first: Kerry

last: Lane

first: Brock

last: Roberts

first: Jacqueline

last: Smith

first: Ruwanthi

middle: N

last: Gunawardane

first: Nathan

last: Sniadecki

first: David

middle: L

last: Mack

first: Jennifer

last: Davis

first: Daniel

last: Bernstein

first: Sebastian

last: Streichan

first: Dennis

middle: O

last: Clegg

first: Siddharth

last: Dey

first: Maxwell

middle: Z

last: Wilson

first: Beth

last: Pruitt


title: Next Generation Sequencing Quantitative Analysis of altered expression of genes in CBX4 overexpressing gastric cancer cells

city: Nanjing

first: Yunru

last: Gu

address: Guangzhou Road 300

institute: The First Affiliated hospital of Nanjing Medical University

summary: Gastric Cancer (GC) remains a significant global cause of mortality, with projected new cases expected to rise to 1.8 million annually and deaths to 1.3 million by 2040 based on demographic projections. Previous study revealed that CBX4 was a vital oncogene that widely involved in tumor initiation and progression. Yet the biological role and underlying regulatory mechanism of CBX4 in GC progression remain unclear. Our study aims to explore the target genes or the relative signaling pathway of CBX4 and the underlying mechanism in the progression of GC.

overall_design: To investigate the regulatory mechanism of CBX4 in GC progression, the total RNA of HGC-27 cells transfected with Vector or CBX4-overexpressing plasmids was extracted and the next generation sequencing was performed to display the expressing profile difference between Vector and CBX4-overexpressing group.

first: Yuan

last: Fang

first: Tingting

last: Xu

first: Yongqian

last: Shu


title: miR214 regulates sex determination through gsdf in zebrafish

city: Mainz

first: René

last: Ketting

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: Sex determination is a variable and complex mechanism, yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non-coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it, we can provide a piece of the puzzle, which once again highlights the complexity and flexibility of sex determination.

overall_design: Danio rerio gonads extracted from miR214 knockouts in different parent backgrounds: maternal or paternal, heterozygous or homozygous. Four different biological replicates per experimental condition.

first: Nadine

last: Wittkopp

first: António

last: de Jesus Domingues


title: Rare codon recoding for selective and efficient noncanonical amino acid incorporation [RNA-seq]

city: hangzhou

first: Wenlong

last: Ding

state: zhejiang

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

department: Life Sciences Institute

institute: Zhejiang University

summary: The ability to genetically encode noncanonical amino acids (ncAAs) has empowered proteins with improved or novel properties. However, existing strategies in mammalian cells rely on the introduction of blank codon for incorporating ncAAs, which is very inefficient and limits their widespread applications. Here, we develop a rare codon recoding strategy that takes advantage of the relative rarity of the TCG codon to achieve highly selective and efficient ncAA incorporation through systematic engineering and big data model predictions. We highlight the broad utility of this strategy for the incorporation of dozens of ncAAs into various functional proteins at the wild-type protein expression levels, as well as the synthesis of proteins with up to 6-site ncAAs or 4 distinct ncAAs in mammalian cells for downstream applications.

overall_design: Given the high recoding efficiency of the engineered TCG recoding system, we wondered whether it would lead to high background incorporation in the proteome and affect cell viability. For this purpose, We perform the RNA-seq to examine the transcriptomics of cells tranfected with TCG recoding system (RTS). Three groups were setted. Sample-1 was HEK293T cells transfected with TCG recoding system dubbed as "RTS". Sample-2 was HEK293T cells transfected with TCG recoding system and EGFP-151TCG reporter named as "RTS-Rep" . Sample-3 was HEK293T cells transfected with blank plasmid vector named as "Vec". The three samples were subjected to RNA-Seq to analyze the global difference in expression level.

first: Wei

last: Yu


title: Effect of ATR inhibition on transcription after UV irradiation

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

summary: UV irradiation causes significant changes in gene expression and induces DNA damage. DNA damage is detrimental to the cell and has to be repaired in a timely manner. DNA damage checkpoints regulate progression through the cell cycle when DNA damage is detected and give time for the cell to repair the damage efficiently. We have preliminary evidence suggesting that ATR, otherwise known for its role of DNA damage checkpoint in S phase and G2/M phase, might also be involved in a yet unheeded UV-induced G1 block. To investigate this, we performed mRNA sequencing, in the hope to unravel which genes/gene families are involved in this checkpoint in response to UV, how this changes in response to ATR inhibition, and the overall changes in gene expression.

overall_design: HEK293 Flp In T-REx WT cells were UV irradiated, allowed to recover for 3h, and then treated with DMSO or ATRi (VE-821 3uM). Samples were harvested 0h, 3h, h, and 20h after UV irradiation.

first: Thierry

last: Boissière

first: Jesper

middle: Q

last: Svejstrup


title: Is one-way ocean acidification a good choice in future ocean acidification research?

city: Xiamen

first: Jichen

last: Chen

state: None Selected

address: Fujian province xiamen city

institute: Xiamen University

summary: The comparision between gradual ocean acidification (GC) and one way ocean acidification (HC) of physiological and molecular responses on diatom Skeletonema costatum

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type and GC type and HC type of diatom Skeletonema costatum

first: Jian

last: Ao

first: Guang

last: Gao


title: Single-cell transcriptome profile of mouse gallbladder cells after nanoplastics exposure

first: wentao

last: shao

address: 150, jimo road

department: Shanghai East Hospital

institute: Tongji University School of Medicine

summary: To understand molecular events of gallbladder cells during nanoplastics exposure, we performed scRNA-seq on gallbladder using 10x Genomics Chromium platform

overall_design: In order to determine the effects of nanoplastics on gallbladder, mice were treated with nanoplastics by oral gavage for 3 weeks (acute exposure) and 6 weeks (chronic exposure), respectively

first: Wentao

last: Shao

first: Zhaoyan

last: Jiang


title: Effect of alternative CXCR2 ligands on human neutrophils in vitro

city: Shanghai

first: Xiaojie

last: Shi

state: Shanghai

address: No. 393 Huaxia Road

department: SIAIS

institute: ShanghaiTech University

summary: Targeting neutrophils has emerged as a promising therapeutic strategy for various inflammatory diseases. Here, we investigate a highly specific monoclonal antibody that targets CXCR2, which is a major chemokine receptor on neutrophils. This antibody functions as an inverse agonist, binds tightly to CXCR2 in a mutually exclusive manner versus IL-8, and completely blocks CXCR2-β-arrestin signaling and subsequent neutrophil functions. Treatment with the antibody appears to result in an overall reversal of IL-8 induced gene expressions in primary human neutrophils. The antibody demonstrates remarkable efficacy in controlling dysregulated neutrophil activity in peripheral circulation and inflammatory tissues in four inflammation animal models. In addition, administration of the antibody not only ameliorates the symptoms of neutrophilia, but also mitigates tissue damage in cases of acute lung inflammation and delayed-type-hypersensitivity reactions. We also checked the effects of the antibody on human neutrophils activated by the natural ligand IL-8 or not in vitro through RNAseq.

overall_design: We used human primary neutrophils to verify the functional gene expression differences in neutrophils with and without lps stimulation and/or abN48-2-IgG1 treatment.

first: Yue

last: Wan

first: Tao

last: Wang


title: Detection and profiling of microRNAs in butter

first: Christine

last: LEROUX

summary: Milk is the body fluid richest in microRNAs (miRNAs), which are small (18-25nt) non-coding RNAs, regulating many biological processes and thus influencing human health. With the objective of determining their bioavailability in processed dairy products, we studied three commercial butters. To examine the presence or not of miRNAs in butter, we first investigated six miRNAs by RT-qPCR. Following the affirmative result, we established butter miRNomes using small-RNA-Seq, which identified 526 miRNAs, including 50% in common with a milk and milk fat miRNome. The three butters did not have exactly the same TOP 30 miRNAs and were not the exact mirror of the TOP 30 of the miRNAs already reported in Holstein milk and milk fat miRNomes, suggesting differences during the butter production process or storage. Prediction of the influence of the TOP 30 butter miRNAs showed potential effects on cell life and regulation of gene expression that could affect consumer health. In the future, the effects of miRNAs bioavailability on the health of human consuming dairy products will need to be considered. Our results highlight the importance of expanding our understanding of the bioavailability of food miRNAs, including in various processed dairy foods.

overall_design: microRNA profiles of 3 commercial butter samples, generated by deep sequencing using Illumina HISeq 4000

last: Leroux

first: Yannick

last: Faulconnier

first: Sébastien

last: Bes

first: J

middle: B

last: German

first: David

last: Mills

first: Fabienne

last: Le Provost

first: Sandrine

last: Le Guillou


title: DNA virus infections shape transposable element activity in vitro and in vivo

first: Florian

last: Full

summary: DUX4 is known to be crucial for TEs induction during zygotic genome activation in early embryonic development. In adults, DUX4 is usually silenced and we previously showed that DUX4 expression is induced by infection with various DNA viruses. We demonstrate binding of DUX4 to TEs upon herpesviral infection and analysis of genes adjacent to TEs shows pathways that are known to be crucial for tumor development. Overexpression of DUX4 significantly induced TEs expression, while its knockout (KO) diminished TEs expression upon HSV-1 infection, underscoring the essential role of DUX4 in TEs activation.

overall_design: RNA-sequencing was performed from DUX4 inducible 293T cells with and without dox treatment.

first: Jiang

last: Tan

first: Vedran

last: Franke

first: Eva

last: Neugebauer

first: Justine

last: Lagisquet

first: Stephanie

last: Walter

first: Markus

last: Landthaler

first: Thomas

last: Gramberg

first: Altuna

last: Akalin

first: Emanuel

last: Wyler


title: Identification of adipo-osteoprogenitors in murine bone marrow

city: Chengdu

first: XUEYANG

last: LIAO

state: Sichuan

address: NO.14 3rd section of Renminnan Road

institute: Sichuan university

summary: The bone marrow in mammals house both hematopoietic and mesenchymal cells that are responsible for sustaining blood and bone cell production, respectively, throughout adult life. Although the hematopoietic system is well understood, the molecular identities, hierarchy of the marrow mesenchymal cells and their respective contribution to bone homeostasis are just beginning to be unraveled. By employing single-cell RNA sequencing (scRNA-seq) technology, we have discovered a subset of bone marrow mesenchymal cells co-expressing adiponectin (Adipoq) and osterix (Osx) which are traditionally considered adipocyte or osteoblast markers, respectively. Trajectory analyses predict the Adipoq+Osx+ bi-marker cells to be common progenitors for osteoblasts and marrow adipogenic lineage cells. Lineage tracing with Osx-CreERT2 or Adipoq-CreERT2 supports that the bi-marker cells give rise to both osteoblasts and adipocytes in vivo. Imaging studies localize the bi-marker cells to the endosteal bone niche. The data therefore support the hypothesis that Adipoq+Osx+ bi-marker cells are adipo-osteoprogenitors attuned to the physiological milieu in the bone marrow. The studies have shed light on the role of the adipo- osteoprogenitors in bone physiology and pathophysiology.

overall_design: Identification and illuminating of adipo-osteoprogenitors (Osteo-CAR) in murine bone marrow

first: Xueyang

last: Liao

first: Fanxin

last: Long


title: Dietary bacteria controls C. elegans lipid metabolism through pathways converging at phosphatidylcholine

city: Taipei

first: Yi-Chun

last: Wu

address: No. 1, Sec. 4, Roosevelt Rd.,

country: Taiwan

institute: National Taiwan University

summary:
Dietary factors play a pivotal role in regulating metabolism in both health and disease. Lipid metabolism is particularly important for organismal health and longevity. However, the mechanisms by which dietary factors influence lipid metabolism remain poorly understood. Here, using the nematode C. elegans as a model system, we investigated the influence of distinct bacterial diets on fat metabolism. We found that dietary vitamin B12 activates the S-adenosyl methionine (SAM) and phosphatidylcholine (PC) biosynthetic pathways. This activation leads to elevated levels of PC, which in turn suppresses the expression of the gene fat-7 and modulates lipid droplet dynamics through the regulatory proteins SBP-1/SREBP1 and SEIP-1/SEIPIN, respectively. Additionally, we identified a feedback loop involving SBP-1-mediated regulation of acid sphingomyelinase ASM-3, which enhances the production of phospho-choline and further stimulates PC synthesis. Our localization studies further suggest that ASM-3 may act as a signaling mediator between the intestine and coelomocytes, coordinating their roles in vitamin B12-mediated fat regulation. Overall, our findings shed new light on the complex interplay between diet and metabolic regulation, with a particular emphasis on the central role of phosphatidylcholine.
To understand the mechanism underlying the regulation of host lipid content triggered by different bacteria diets, we examined the gene expression changes elicited by the two different bacterial diets in young adult animals by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNAseq data from worms feeding DA1877 or OP50 diet.

first: Hsiao-Fen

last: Han

first: Shao-Fu

last: Nien

first: Sufeng

last: Chiang


title: The biological mechanisms related to hub genes in the development of heart failure in dialysis patients were investigated through transcriptome sequencing

city: Nanchong Sichuan

first: Wenwu

last: Tang

state: Sichuan province

address: Shunqing District Zhongcheng Street Fujiang Road No.234 North Sichuan Hospital Shunqing Campus

institute: North sichuan medical college

summary: Purpose: Heart failure (HF) has a very high prevalence in patients with maintenance hemodialysis (MHD). However, there is still a lack of effective and reliable HF diagnostic markers and therapeutic targets for patients with MHD.  Patients and methods: In this study, we analyzed transcriptome profiles of 28 patients with MHD by high-throughput sequencing.

overall_design: Sample preparation and processing  Peripheral blood mononuclear cell (PBMC) samples of 15 dialysis patients without heart failure (Normal) and 15 dialysis patients with heart failure (Case) human were collected for mRNA transcriptome sequencing. RNA was isolated and purified from the total samples using TRlzol (invitrogen, CA,USA) according to the manufacturer's protocol. NanoDrop ND-1000 (Wilminton, DE, USA) was used to control the total RNA sender bulk and cleanliness. The fragmented RNA was synthesized into cDNA by reverse transcriptase, and the cDNA was amplified and purified. Building the library and prepared for sequencing on the illumina Novaseq 6000 sequencing platform. After the inferior-quality reads were deleted, the cleanreads were aligned into the human genomic reference (GRCh38_gencode_v33) by HISATI16.

first: Xiexi

last: Sheng


title: Ca2+ influx through ORAI1 and ORAI2 channels regulates chromatin accessibility in CD4+ T cells

city: New York

first: Maxwell

last: McDermott

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

summary: Activation of CD4+ T cells by T cell receptor (TCR) signaling results in altered gene expression as a result of epigenetic and transcriptional regulation. A critical TCR signaling pathway in CD4+ T cells is driven by Ca2+ influx across the plasma membrane through Ca2+ release-activated Ca2+ (CRAC) channels that are formed by ORAI1 and ORAI2 proteins. Here we analyzed the effects of suppressing Ca2+ influx in mouse CD4+ T cells on chromatin accessibility by genetically deleting the ORAI1 channel alone or both ORAI1 and ORAI2 channels. CD4+ T cells specific for ovalbumin (OVA) from TCR transgenic OT-II were activated by in vivo exposure to influenza A virus (IAV) expressing OVA neoantigen. Changes in chromatin accessibility of CD4+ T cells in response to IAV-OVA infection were determined by ATAC sequencing

overall_design: CD4+ T cells were isolated from wildtype, Orai1fl/fl Cd4Cre OTII (ORAI1 KO) or Orai1fl/fl Cd4Cre Orai2-/- OT-II (ORAI1/2 KO) mice and injected i.v. into TCRalpha-/- host mice. Host mice were left uninfected or infected intranasally with 200 VFU of the mouse-adapted influenza A virus strain PR8-OVA. 8 days post-infection, CD4+ T cells were isolated from mediastinal lymph nodes of host mice for subsequent analysis by ATAC sequencing.

first: Li

last: Zhong

first: Yinhu

last: Wang

first: Stefan

last: Feske


title: Rare codon recoding for selective and efficient noncanonical amino acid incorporation [Ribo-seq]

first: Wenlong

last: Ding

overall_design: We found that co-expession of reporter could reduce the background incorporation of ncAA in proteome, when our TCG recoding translation system was performed. To explain Given the high recoding efficiency of the engineered TCG recoding system, we wondered whether it would lead to high background incorporation in the proteome and affect cell viability. For this purpose, We perform the Ribo-seq.

first: Wei

last: Yu


title: Sex-dependent niche responses modulate steady-state and regenerative hematopoiesis

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

department: CITI

institute: CLEVELAND CLINIC LERNER COM-CWRU

summary: Hematopoietic stem cells (HSCs) adapt to organismal blood production needs. While it has been established that sexual dimorphism drives differential hematopoietic function in males vs. females, the mediators responsible for these effects remain unclear. Here, we characterize hematopoiesis in male and female mice at steady state and during regeneration following hematopoietic stem cell transplantation (HST). We found that steady-state males possessed greater bone marrow (BM) hematopoietic stem and progenitor cell (HSPC) populations and varied in frequency for stromal populations. PCR analysis from stromal CD45(-)-purified BM cells demonstrated alterations in niche genes, including Ptn, IL6, Angpt1, Vcam1, and Spp1, together suggesting the male microenvironment is primed for HSC differentiation and mobilization. RNA sequencing of BM lineage(-) cells revealed differential expression of genes, like Hif1a and Aldh1, and corresponding cellular pathways—including those involving reactive oxygen species, oxidative phosphorylation, and Tnf-a signaling via NF-κB—underscoring male lineage(-) cells as more inflammatory and proliferative. To determine the functional outcomes of steady-state transcriptional differences we performed sex-matched and mismatched transplantation studies of lineage(-) donor cells into male and female recipients. We demonstrated a role for TNF-a-driven proliferation of male donor cells and Cxcl12-mediated homing into male recipients during short-term 56-day HST recovery. Serial transplantation of lineage(-) cells suggested the male short-term proliferative advantage may precede long-term disadvantages of inflammation-induced exhaustion. We show that sex-specific cellular and molecular signaling, marked by differing expression of niche factors and inflammatory mediators, shapes normal and regenerative hematopoiesis, with implications for the fundamental and clinical understanding of hematopoietic function.

overall_design: To investigate sexual dimorphism in hematopoiesis, we separated lineage-depleted bone marrow (BM) hematopoietic stem and progenitor (HSPC) populations from male and female C57/BL6 mice at steady state, isolated their RNA, and performed bulk RNA sequencing from samples. N=5 mice/arm.

first: Rahul

last: Chaudhary

first: Julianne

last: Smith

first: Riya

last: Tiwari

first: Bailey

middle: R

last: Klein

first: Brittany

last: Cordova

first: Frederick

last: Petroze

first: Brian

last: Richardson

first: Alyssia

last: Broncano

first: Juyeun

last: Lee

first: Prerana

last: Bangalore Parthasarathy

first: Karina

last: Inacio Ladislau De Carvalho

first: Scott

last: Cameron

first: Justin

middle: D

last: Lathia

first: Wendy

last: Goodman

first: Mark

first: Amar

last: Desai


title: OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide (WGBS)

city: SAN DIEGO

first: Anjana

last: Rao

state: CALIFORNIA

address: 9420 Athena CIRCLE, LA JOLLA

institute: LA JOLLA INSTITUTE

summary: The O-GlcNAc transferase OGT interacts robustly with all three mammalian TET methylcytosine dioxygenases. We show here that deletion of theOgtgene in mouse embryonic stem cells (mESC) results in a widespread increase in the TET product 5-hydroxymethylcytosine (5hmC) in both euchromatic and heterochromatic compartments, with concomitant reduction of the TET substrate 5-methylcytosine (5mC) at the same genomic regions. mESC engineered to abolish the TET1-OGT interaction likewise displayed a genome-wide decrease of 5mC. DNA hypomethylation in OGT-deficient cells was accompanied by de-repression of transposable elements (TEs) predominantly located in heterochromatin, and this increase in TE expression was sometimes accompanied by increased cis-expression of genes and exons located 3’ of the expressed TE. Thus, the TET-OGT interaction prevents DNA demethylation and TE expression in heterochromatin by restraining TET activity genome-wide. We suggest that OGT protects the genome against DNA hypomethylation and impaired heterochromatin integrity, preventing the aberrant increase in TE expression observed in cancer, autoimmune-inflammatory diseases, cellular senescence and ageing.

overall_design: In this study, we examine the impact of Ogt-iKO and disrupted TET1-OGT interaction in mouse embryonic stem cells (mESCs). Our analysis focuses on changes in DNA methylation patterns, specifically alterations in 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) levels. We also explore the expression of transposable elements (TEs), especially in heterochromatin regions, and assess the cis-expression of neighboring genes and exons. This research aims to understand the genetic mechanisms underlying DNA methylation and TE expression in mESCs.

first: Hugo

last: Sepulveda

first: Xiang

last: Li

first: Xiaojing

last: Yue

last: Angel

first: Caitlin

last: Brown

first: Melina

last: Brunelli

first: Natasha

last: Jansz

first: Leo

last: Arteaga-Vazquez

first: Fabio

last: Puddu

first: Creed

last: Paidi

first: Jamie

last: Scotcher

first: Patrick

last: Kennedy

first: Cindy

last: Manriquez

first: Samuel

last: Myers

first: Robert

last: Crawford

first: Geoffrey

last: Faulkner


title: OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide (CMS-IP)

last: Rao


title: Neonatal Hypothyroidism Rearranges the 3D Chromatin Structure in the Liver

city: South Bend

first: Murlidharan

last: Nair

state: IN

address: 1700 Mishawaka Ave

department: Biology and CS/Informatics

institute: Indiana University South Bend

summary: Children with congenital hypothyroidism (1 in every ~2,500 live births) may develop a dramatic neurological, muscle-skeleton, and metabolic syndrome due to insufficient thyroid hormone (TH) signaling during development 1-3. While the mechanisms involved remain largely unknown, it is well established that the condition is irreversible if treatment is not initiated during the immediate post-natal period. Here we used high-throughput genomic and epigenomic techniques (Hi-C) to generate high-resolution, genome-wide 3D maps of chromatin interaction in mice with developmental liver-specific hypothyroidism (caused by Dio2 inactivation). The neonatal disruption of hepatic TH signaling only minimally affected genomic compartmentalization but caused substantial rearrangements (e.g. shifting or splitting) in thousands of topologically associating domains (TADs). The rearranged TADs contained DNA sites of hypermethylation, areas of reduced chromatin accessibility, and hundreds of repressed genes. In many instances, the enhancer-promoter (E-P) interaction in key repressed genes had been weakened, explaining the permanent change in how the liver handles excess fat or alcohol in the adult mouse 4-6.

overall_design: The Alb-D2KO mice, characterized by hepatocyte-specific Dio2 inactivation, were developed by crossbreeding floxed C57BL/6J D2 mice (dio2Flx) with mice expressing Cre-recombinase under the albumin promoter (Cre-ALB) [B6.Cg-Tg(Alb-cre)21Mgn/J; The Jackson Laboratory]. Cre-ALB mice were employed as control animals. All subjects in the study were male and 16 weeks old, and they were housed under standard conditions of room temperature (22 °C) and a 12-hour dark/light cycle.  To ensure robustness and reliability, the Hi-C data assays were performed with duplicate biological replicates. A pool of four liver samples from each experimental group was utilized in these assays, contributing to the comprehensive analysis of spatial genomic interactions in the liver tissues of the mice under investigation.

first: Tatiana

last: Fonseca

first: T

last: Murlidharan Nair

first: Antonio

last: Bianco


title: Increased chromatin accessibility drives transition to androgen receptor splice variant dependence in castration-resistant prostate cancer [RNA-Seq]

city: Boston

first: Steven

last: Balk

state: MA

address: 3 Blackfan Circle

department: Hematology/Oncology

institute: Harvard Medical School

summary: Androgen receptor (AR) splice variants, of which ARv7 is most common, are increased in prostate cancer (PC) that develops resistance to androgen signaling inhibitor drugs, but the extent to which they drive AR activity, and whether they have novel functions or dependencies, remain to be determined. We generated a subline of VCaP PC cells (VCaP16) that was resistant to the AR inhibitor enzalutamide (ENZ) and found that AR activity was independent of the full length AR (ARfl), despite its continued high level expression, and was instead driven by ARv7. The ARv7 cistrome and transcriptome in these cells mirrored that of the ARfl in VCaP cells, although ARv7 chromatin binding was weaker, and strong ARv7 binding sites correlated with higher affinity ARfl binding sites across multiple models and clinical samples. Notably, although ARv7 expression increased rapidly in response to ENZ, there was a long lag before it gained chromatin binding and transcriptional activity. This lag was associated with an increase in chromatin accessibility, with the AR and nuclear factor I (NFI) motifs being most enriched at these more accessible sites. Moreover, the transcriptional effects of combined NFIB and X knockdown versus ARv7 knockdown were highly correlated. These findings indicate that ARv7 can drive the AR program, but that its activity is dependent on adaptations that increase chromatin accessibility to enhance its intrinsically weak chromatin binding.

overall_design: To study adaptational mechanisms of ENZ-resistance in prostate cancer,  VCaP cells were cultured in medium with increasing concentrations of ENZ (up to 16 uM) over ~2 months to select for resistance. A subline resistant to ENZ was generated (VCaP16). We studied global transcriptomic effects by RNA-seq in responce to short 10uM ENZ treatment for 96hrs in VCaP and in ENZ-resistant VCaP16 cells compared to parental VCaP.  To study transcriptomic activity of ARv7 in VCaP16 cells we performed RNA-seq in responce to  ARv7 siRNA, AR Exon1 siRNA (targeting ARfl and ARv7), AR Exon7 siRNA (targeting ARfl), and non-targeting siRNA; and in responce to ARfl degrader treatment - 500nM ARCC-32 for 36hrs (or 24hrs paired with ChIP-seq) vs DMSO. To study effects of FOXA1 and NFIB and NFIX  VCaP16 cells were treated with FOXA1 or NFIs(NFIB+NFIX) and non-targeted siRNAs followed by RNA-seq.

first: Larysa

last: Poluben

first: Joshua

last: Russo

first: Mannan

last: Nouri


title: RNA changes upon glucose starvation

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

summary: The adaptation of tumor cells to metabolic stress is crucial for tumor development. We demonstrate that the translation of NRF2, a master regulator of antioxidant response, is controlled by the OGDH-METTL3 axis in melanoma for glucose starvation adaptation. To elucidate the regulatory mechanism of the OGDH-METTL3 axis during glucose starvation, we conducted co-immunoprecipitation and mass spectrometry analysis to identify the binding partner of OGDH that governs both the OGDH-METTL3 axis and tumor cell adaptation to glucose deprivation.

overall_design: Control and OGDH knockdown A375 cells were starved with glucose for 5 hours respectively, and then collected by trizol. Three parallel groups of samples were collected for each experiment.

first: Jiaxin

last: Zhou

first: Xiaoyan

last: Chen

first: Kejun

last: Xu


title: Pathobiont driven antibody sialylation through IL-10 undermines vaccination

city: San Diego

first: Nathan

middle: E.

last: Lewis

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

summary: The pathobiont S. aureus (SA) induces non-protective antibody imprints that underlie ineffective staphylococcal vaccination. However, the mechanism by which SA modify antibody activity is not clear. Herein, we show that IL-10 is the decisive factor that abrogates antibody protection.  SA-induced B10 cells drive antigen-specific vaccine suppression that affects both recalled and de novo developed B cells. Released IL-10 promotes STAT3 binding upstream of sialyltransferase ST3gal4 and increases ST3gal4 expression by B cells, leading to hyper- a2,3 sialylation of antibodies and loss of protective activity. IL-10 enhances a2,3 sialylation on cell-wall associated IsdB, IsdA and MntC antibodies along with suppression of the respective SA vaccines.  Consistent with mouse findings, human anti-SA antibodies as well as anti-pseudomonal antibodies from cystic fibrosis subjects are hyper-sialylated, compared to anti-GAS and pseudomonal antibodies from normal individuals. Overall, we demonstrate a pathobiont-centric mechanism that modulates antibody glycosylation through IL-10 leading to loss of staphylococcal vaccine efficacy.

overall_design: Single-cell immune profiling of the S.  aureus IsdB vaccine and αIL-10 treated IsdB vaccine. In this study, we conducted BCR sequencing for three different samples: LAC (LAC-infected mice given adjuvant alone), LAC/IsdB (LAC-infected mice vaccinated with IsdB) and LAC/IsdB/aIL10 (LAC-infected mice vaccinated with IsdB and treated with αIL-10).

first: George

last: Liu

first: Austin

middle: W

last: Chiang

middle: E


title: OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide

first: Anjana

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

overall_design: Refer to individual Series


title: Transcriptomic differences between Cal27 parental and sphere cells

city: Wuhan

first: Yuantong

state: Hubei

address: Luoyu road

institute: Wuhan University

summary: We compared transcriptomic differences between Cal27 parental and sphere cells.

overall_design: To further investigate the transcriptomic differences between Cal27 parental and sphere cells, we used a suspension culture assay to isolate cancer stem cells. Primary adhesion cells were characterized as "parental cells", and isolated cancer stem cells were characterized as "sphere cells".

first: Lei


title: Transcriptomic differences between SCC4 parental and sphere cells

summary: We compared transcriptomic differences between SCC4 parental and sphere cells.

overall_design: To further investigate the transcriptomic differences between SCC4 parental and sphere cells, we used a suspension culture assay to isolate cancer stem cells. Primary adhesion cells were characterized as "parental cells", and isolated cancer stem cells were characterized as "sphere cells".


title: Would reducing chlorophyll content result in a higher photosynthesis nitrogen use efficiency in crops?

city: shanghai

first: linxiong

last: mao

state: shanghai

address: NO.300 fenglin road

institute: CAS Center for Excellence in Molecular Plant Sciences / Institute of Plant Physiology and Ecology

summary: Decreasing antenna size is regarded as a potential strategy to improve photosynthesis for higher yield potential. Reducing chlorophyll content has been used as a strategy to decrease antenna size. One of the commonly cited benefits of this strategy has been its ability to improve crop nitrogen use efficiency; however, field evidence for this so far is limited. Here we used a mutant, p35s-Ami-YGL1, which has a lower chlorophyll content and also lower antenna size, to study the impacts of modifying leaf chlorophyll content on tissue nitrogen content and nitrogen use efficiency of plants. We show that the nitrogen contents for different tissues, including the seed tissue, on a weight basis were increased in p35s-Ami-YGL1, together with a decrease in C: N. Concurrently, we found that tissue carbon content decreased, while the content of chlorophyll precursors increased. These results suggest that the observed increase in tissue nitrogen content in Ami-YGL1 does not reflect an increase in plant nitrogen absorption or use efficiency, rather it is a result of stunted carbon fixation capacity of plants. The observed increase in seed nitrogen content in Ami-YGL1 suggests a potential strategy to increase seed nitrogen content in crops.

overall_design:
The p35s-Ami-YGL1 mutant plants were generated with RNAi technology as described earlier (Mao et al., 2023). We used three homozygote transgenic lines (line 1, 7 and 8) during this study.  Rice (Oryza sativa spp japonica cv Nipponbare) and p35s-Ami-YGL1 were grown in the experimental station of the Shanghai Institute of Plant Physiology and Ecology (121°8′1.33″E, 30°56′26.73″N). During the growth period in 2021 or 2022, the rice was transplanted into the well-fertilized field in a 7×7 layout (25cm ×25 cm) and for each line. To avoid boundary effects, plants belong to the boundary lines were excluded in the measurement. The experiments were done in two years at different field sites (2019, 2021).   At the same time, we also carried out relevant measurements in the plant greenhouse. The greenhouse was subjected to an alternating light/dark cycle (12 hours of light and 12 hours of darkness), with a light intensity of approximately 400 μmol m-2 s-1 and the temperature was set at around 28 oC.
Strategic Priority Research Program of the Chinese Academy of Sciences (grant number: XDB37020104)
National Research and Development Program of Ministry of Science and Technology of China (2019YFA0904600; 2020YFA0907600)
the general program of National Science Foundation of China (31870214, 31970378)


title: Remodeling the step-wise mouse placental development by using totipotent blastomere-like stem cells [scRNA-seq]

city: Beijing

first: Chunhui

last: Wang

state: Beijing

address: 5 Summer Palace Road, Haidian District, Beijing

department: School of Life Sciences

institute: Peking University

summary: During development, totipotent blastomeres initiate the first cell fate decision to generate inner cell mass and trophectoderm. The trophectoderm forms the placenta mediating fetal-maternal communications, while placental deficiencies cause infertility and pregnancy disorders in humans. However, in vitro systems remodeling the step-wise placental development, particularly encompassing the pre-implantation phase, are still unavailable. Here, using mouse totipotent blastomere-like cells (TBLCs), we successfully realize inducing and long-term maintaining trophectoderm-like stem cells (TELSCs), and further generating placental trophoblast organoids. Interestingly, an intermediate morula trophectoderm-like cells (TELCs) were transiently induced from TBLCs, and quickly converted into TELSCs assembling blastocyst trophectoderm. In 3D culturing condition, TELSCs can form rosette-like structures at peri-implantation period, to eventually generate trophoblast organoids, in which trophoblast progenitors/giant cells, spongiotrophoblasts and syncytiotrophoblasts were all identified at the single-cell level. Transcriptomic and epigenomic analyses enable tracing the step-by-step transition from TBLCs to mature trophoblast lineages. Thus, this study provides a comprehensive differentiation system to understand and investigate placental development.

overall_design: mESCs, mTBLCs, mTELCs (mixed mTELCs before FACS and FACS-purified mTELCs using different methods), mTELSCs (different passages), mTELSC-derived TOs at different time points, mTSCs and mTSC-derived TOs at different time points were used for RNA-seq. ATAC-seq were performed at mTELCs and mTELSCs. CUT&Tag for histone modifications (H3K4me3 and H3K27me3) and whole genome bisulfite sequencing were performed at mTELCs, mTELSCs, mTSCs and mTELSC-derived TOs. mTELSC-derived TOs at day 9 were used for scRNA-seq.

first: Xinyi

last: Jia

first: Peng

last: Du


title: Remodeling the step-wise mouse placental development by using totipotent blastomere-like stem cells [WGBS]


title: Remodeling the step-wise mouse placental development by using totipotent blastomere-like stem cells [CUT&Tag]


title: Remodeling the step-wise mouse placental development by using totipotent blastomere-like stem cells [RNA-seq]


title: Remodeling the step-wise mouse placental development by using totipotent blastomere-like stem cells


title: Remodeling the step-wise mouse placental development by using totipotent blastomere-like stem cells [ATAC-seq]


title: RNA N6-methyladenosine modification-mediated regulation of macrophage senescence promotes atherosclerosis by ALKBH5/CCL5 axis

city: Hangzhou

first: Rifeng

last: Gao

state: Zhejiang

address: No. 88 Jiefang Road

institute: Zhejiang University

summary: Senescent foamy macrophages are the key pathogenic drivers of atherosclerosis (AS) progression and plaque stability. The RNA N6-methyladenosine (m6A) modification plays an important role in the development of various diseases. However, its role in foamy macrophage aging during AS is still not clarified. To assess m6A methylation levels and m6A modifying enzyme profiles, the infiltrated macrophages were sorted using CD68+ magnetic beads from plaque tissues of patients with AS and high-fat diet feeding Apoe-/- mice. The ALKBH5f/f, Lyz2Cre, Apoe-/- mice were constructed to observe senescent macrophage infiltrated in plaques and AS progression. The RNA-seq, MeRIP, RIP and dual luciferase assays were performed to explore the mechanisms of ALKBH5-mediated formation of senescent macrophage. Downregulated m6A methylation levels and upregulated ALKBH5 expression were observed in aortic plaques and infiltrated macrophages from AS patients and mice. Compared with control mice, ALKBH5f/f, Lyz2Cre, Apoe-/- mice decreased AS plaques and enhanced plaque stability by suppressing senescence of foamy macrophages and senescence-associated secretory phenotypes. In addition, the data of the RNA-seq, MeRIP, RIP and dual luciferase assays showed that ALKBH5 deletion reduced the mRNA level of CC chemokine ligand 5 (CCL5) by increased m6A methylation in macrophages. Actinomycin D assay indicated ALBH5 knockout destroyed stability of Ccl5 mRNA. Mechanismly, ALKBH5 promotes senescent macrophage formation by CCL5/CC chemokine receptor 5 (CCR5)/mTORC1/autophagy signaling. And ALKBH5 induced macrophage derived CCL5 recruits increasingly CD8+IFNγ+ T cells by CCL5-CCR5 axis. Furthermore, the application of ALKBH5 inhibitor IOX-1 and CCR5 monoclonal antibody Adaptavir are potential clinical interventions for the inhibition of senescent macrophage formation and AS progress.  Myeloid ALKBH5 deletion mitigates AS progression by suppressing the formation of senescent macrophages and the recruitment of CD8+IFNγ+ T cells. These findings favour the ALKBH5/CCL5/CCR5 signaling as novel targets for atherosclerosis therapy.

overall_design: We performed RNA-seq analysis of HFD-treated ALKBH5flox/flox, APOE-/-(n=3) and ALKBH5flox/flox, Lyz2-Cre, APOE-/-(n=3) sorted macrophages.

first: Kun

last: Yang


title: MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility [scRNA-Seq]

first: Hsiang-Ying

last: Lee

address: No.5 Yiheyuan Road

summary: The Mediator complex plays a crucial role in regulating gene expression by interacting with transcription factors. In this study, we investigated the function of MED16, a core member of the tail module of the Mediator complex, in hematopoietic development. Our findings reveal that MED16 serves as a critical modulator of hematopoiesis by controlling chromatin accessibility at specific target genes. Loss of MED16 leads to a shift towards erythropoiesis and myelopoiesis in both human and mouse models. We found that MED16 deficiency increases chromatin accessibility at the RUNX1-binding promoter, promoting the expression of erythroid and innate immunity genes through cooperation with the FAcilitate Chromatin Transcription (FACT) complex. Furthermore, our study suggests that high MED16 expression may serve as a potential biomarker for myelodysplastic syndromes (MDS). Knockdown of MED16 in bone marrow mononuclear cells (BMMNCs) of MDS promotes erythroid differentiation, which may offer a potential therapeutic strategy for hematopoietic dysplasia diseases. Our findings demonstrate that MED16 acts as a negative regulator of erythroid and myeloid development and demonstrate its critical role in modulating the chromatin landscape in cooperation with RUNX1 and the FACT complex.

overall_design:
To account for the heterogeneity of cells in the primary culture system, we performed single-cell RNA-seq on erythroblasts.we  established erythroblasts in which MED16 has been been knocked down by shRNA
We then performed gene expression profiling analysis using data obtained from single-cell RNA-seq.
Comparative gene expression profiling analysis of single-cell RNA-seq data for erythroblasts and its KD derivatives

first: Si

last: Xie

first: Fan

last: Wu

first: Xin-Ying

last: Zhao

first: Qiu-Yu

last: Yue


title: MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility [RNA-Seq mouse]

overall_design:
To investigate the MED16 in the regulation of erythroid differentiation in vivo, we  established Ter119+ cells in  Med16 fl/fl and Med16 KO mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq.
Comparative gene expression profiling analysis of RNA-seq data for Ter119+ and its KO derivatives


title: MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility [RNA-Seq human]

overall_design:
To investigate the MED16 in the regulation of erythroid differentiation, we  established HSPCs/BMMNCs in which MED16 has been been knocked down by shRNA and HSPCs in which MED16 has been overexpressed.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at  different  time points.
Comparative gene expression profiling analysis of RNA-seq data for HSPCs/BMMNCs and its KD/OV derivatives


title: MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility


title: OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide (RNA-Seq)

last: Rao

first: Hugo

last: Sepulveda

first: Xiang

last: Li

first: Xiaojing

last: Angel

first: Caitlin

last: Brown

first: Melina

last: Brunelli

first: Natasha

last: Jansz

first: Leo

middle: J

last: Arteaga-Vazquez

first: Fabio

last: Puddu

first: Creed

last: Paidi

first: Jamie

last: Scotcher

first: Patrick

last: Kennedy

first: Cindy

last: Manriquez

first: Samuel

last: Myers

first: Robert

last: Crawford

first: Geoffrey

last: Faulkner


title: High-throughput exploration of single-cell transcriptional alterations associated with remote fear memory formation

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Leveraging SPEED in tandem with snRNA-Seq, we uncover molecular identities of distinct neural subtypes, concurrent 5hmC alterations at active enhancers and gene bodies, and dynamic gene expression associated with remote memory formation. This comprehensive analysis encompasses several thousand cells from the cerebral and cerebellar cortex of home-caged (HC) and fear-conditioned (FC) mice.

overall_design: The isolated and purified nuclei were subjected to single-nuclei sequencing utilizing the Chromium Next GEM Single Cell 5’ Reagent Kits v2 from 10 × Genomics.

first: Jiang

last: Xiao

first: Peihong

last: Zhang

first: Yongchuan

last: Zhu

first: Li

last: Yang

first: Lulu

last: Hu


title: MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility [ChIP-Seq mouse]

first: Hsiang-Ying

last: Lee

overall_design:
To investigate the MED16 in the regulation of erythroid differentiation, we  established HSPCs  in which MED16 has been been knocked down by shRNA.
Chromatin immunoprecipitation DNA-sequencing(Chip-seq) for MED16,RUNX1,SPT16 in HSPCs/erythroblasts
Colocalization analysis of Chip seq for MED16 and RUNX1 in HSPCs/erythroblasts. Comparative chromatin binding profiling analysis of MED16 and SPT16 in HSPCs/erythroblasts and it s KD derivatives.

first: Si

last: Xie

first: Fan

last: Wu

first: Xin-Ying

last: Zhao

first: Qiu-Yu

last: Yue


title: MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility [ChIP-Seq human]


title: MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility [ATAC-Seq mouse]

overall_design: To investigate the potential role of MED16 in regulating chromatin and the transcriptome, we performed the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) using HSPCs/erythroblast in  in which MED16 has been been knocked down by shRNA. Comparative chromatin accessibility profiling analysis of ATAC-seq data for HSPCs/erythroblasts and its KD derivatives.


title: MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility [ATAC-Seq human]


title: Enhancing Precise Genome Editing in Human Pluripotent Stem Cells through Dual Inhibition of DNA Damage Response and Repair Pathways [WES]

city: Seoul

first: Hyuk-Jin

last: Cha

address: 215-20 Gwan-ak ro Gwan-ak gu

institute: Seoul National University

summary: Precise genome editing is crucial for establishing isogenic human disease models and ex vivo stem cell therapy from the patient-derived human pluripotent stem cells (hPSCs). Unlike Cas9-mediated knock-in, cytosine base editor (CBE) and prime editor (PE) achieve the desirable gene correction without inducing DNA double strand breaks. However, hPSCs possess highly active DNA repair pathways and are particularly susceptible to p53-dependent cell death. These unique characteristics impede the efficiency of gene editing in hPSCs. Here, we demonstrate that dual inhibition of p53-mediated cell death and distinct activation of the DNA damage repair system upon DNA damage by CBE or PE additively enhanced editing efficiency in hPSCs. The BE4stem system comprised of dominant negative p53 (p53DD) and three UNG inhibitor (UGI), engineered to specifically diminish base excision repair (BER), improved CBE efficiency in hPSCs. Addition of dominant negative MLH1 to inhibit mismatch repair activity and p53DD in the conventional PE system also significantly enhanced PE efficiency in hPSCs. Thus, combined inhibition of the unique cellular cascades engaged in hPSCs upon gene editing could significantly enhance precise genome editing in these cells.

overall_design: To investigate off-target effects on exome level after gene editing, we established gDNA of EP (Electroporation only, control group) and BE4max, BEStem, PE4, PEStem treated sample.

first: Ju

middle: C

last: Park

first: Yun

last: Kim

first: Gue

middle: H

last: Hwang

first: Chan

middle: Y

last: Kang

first: Sangsu

last: Bae

first: Hyuk


title: Cellular rejuvenation protects neurons from inflammation mediated cell death (RNA-seq).

city: Montreal

first: Alyson

last: Fournier

state: QC

address: 3801 Rue University

department: Department of Neurology and Neurosurgery

country: Canada

institute: McGill University

summary: In multiple sclerosis (MS), invasion of the central nervous system by peripheral immune cells, activation of resident microglia and astrocytes, and demyelination occur as a cascade of events that trigger neuronal damage and death. The molecular signals in neurons that activate damage in response to the complex immune environment have not been fully characterized. Retinal ganglion cell neurons (RGCs) of the central nervous system (CNS) undergo axonal injury and cell death in MS and this is recapitulated in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. To profile the molecular landscape of pathologically inflamed neurons, we isolated RGCs from mice that were subjected to the EAE protocol and performed RNA-sequencing and ATAC-sequencing analysis. Pathway analysis of the RNA-sequencing data revealed that RGCs exhibited a molecular signature reminiscent of aged neurons with features of senescence. Pathway level analysis of single-nucleus RNA-sequencing analysis of human MS neurons also demonstrated a similar senescence-like phenotype. Immunofluorescence analyses confirmed alterations to various markers of senescence in RGCs in EAE mice, including alterations to the nuclear envelope, changes to chromatin marks, and accumulation of DNA damage. Transduction of RGCs with an Oct4-Sox2-Klf4 transgene to rejuvenate neurons to a younger epigenetic and transcriptomic state in the EAE model was sufficient to increase survival of RGCs. Together, this work reveals a novel senescent like phenotype in neurons in a model of pathological inflammation and in neurons from MS patients.  Rejuvenation of the aged transcriptome improves visual acuity and neuronal survival in the EAE model supporting the notion that anti-aging therapies and/or senotherapeutic agents may directly target neurons for neuroprotection in autoimmune disorders.

overall_design: EAE was induced in 7–8-week-old female subjects. RNA sequencing was conducted at various stages, including naive, presymptomatic, onset, and peak stages.


title: Cellular rejuvenation protects neurons from inflammation mediated cell death (ATAC-seq).

overall_design: EAE was induced in 7–8-week-old female subjects. ATAC sequencing was conducted at various stages, including naive, presymptomatic, onset, and peak stages.


title: Exploring the mechanism of transcutaneous auricular vagus nerve stimulation on improving post-stroke cognitive impairment in MCAO rats using RNA-seq

city: CHANGSHA

first: Zhendong

last: LI

address: Changsha, Hunan Province

institute: Hunan University of Chinese Medicine

summary: Our previous findings have shown that taVNS is effective in improving PSCI. However, its specific mechanism and the target genes, biological processes, and signaling pathways it regulates are still unclear and require more in-depth research.  We established a cognitive impairment model in MCAO rats and administered taVNS treatment. Cognitive function was assessed using Y-maze and novel object recognition (NOR) experiments. Pathological changes in hippocampal tissue were observed through HE and Nissl staining. RNA-seq was conducted on hippocampal tissue from each group, and differentially expressed genes (DEGs) were performed for GO and KEGG enrichment. Hub genes were identified using the STRING database and betweenness centrality values. taVNS treatment significantly improved cognitive function (Y-maze and NOR) and pathological morphology of hippocampal tissue (HE and Nissl staining) in the PSCI model rats. A total of 341 taVNS targeted DEGs were identified, and they may be implicated in chromosome segregation, mitotic nuclear division, cell cycle, NOD-like receptor signaling pathway, NF-kappa B signaling pathway, and Toll-like receptor signaling pathway, etc. The expression trends of TLR4, Myd88, and NF-κB mRNAs in the Hub genes were significantly inhibited by taVNS.

last: Li

first: Hangjian

last: Qiu

first: Xiaoqian

last: Wang


title: Twist2-Cre liver vs Twist2-Cre/A20fl/fl liver in mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

overall_design: Transcriptional profiling of Twist2-Cre liver and Twist2-Cre/A20fl/fl liver.Twist2-Cre mice  were purchased from The Jackson Laboratory. Twist2-Cre/A20fl/fl mice were generated by mating with A20 flox/flox mice with Twist2-Cre mice. From the liver of 24week-old mice, total RNA were extracted.

first: Keiya

last: Watakabe

first: Masato

last: Miyoshi

first: Sei

last: Kakinuma


title: Designed chimeric nanoparticle displaying viral fusion apparatus elicit potent neutralizing antibody against Epstein-Barr virus infection

city: Guangzhou

first: Cong

last: Sun

state: Guangdong

address: No.651 Dongfeng East Road

department: Cancer Center

institute: Sun Yat-sen University

summary: Epstein-Barr virus (EBV) ubiquitously infects global population and leads to a variety malignancies and autoimmune diseases. It establishes its lytic-latency life cycle relying on the tropism transition between B cell and epithelial cell, during which its critical glycoprotein gB and gHgL act as the fusion apparatus mediating viral recognition and membrane fusion in either cell type. Thus. simultaneous targeting to fusion apparatus would be ideal strategy to construct potent EBV prophylactic vaccine. In this study, we designed chimeric nanoparticle multivalently displaying gB and gHgL with even gp42 upon the nanoparticle surface, inducing significantly robust neutralizing antibody generation in both murine and non-human primate models. As we further identify the comparable immunization potency between chimeric nanoparticle and whole live virion and preponderance of gB in neutralizing antibody elicitation, we used single-B cell sequencing to dissect the B cell response to chimeric nanoparticle immunization in mouse and isolate a gB-specific neutralizing antibody Fab5 targeting novel vulnerable site. These findings offers insight to advanced vaccine design for EBV and other herpesviruses.

overall_design: The mice were immunized with gB/gHgL-chimeric nanoparticle and the total B cell were isolated by MACS. Then fluorescence labeled-gB or gHgL was used to further isolate gB or gHgL-specific B cells. These antigen-specific cells were sorted by FACS and suspended for single-B cell sequencing after constructing  whole transcriptome and VDJ library.

first: Haoyu

last: Zhang

first: Mu-Sheng

last: Zeng


title: Long-read RNA-seq(Iso-seq) analysis of HBV-KMT2B integrated HPCs in which HBV genome is integrated into KMT2B region.

city: bunkyo-ku

address: yushima

department: Gastroenterology

institute: Tokyo Medical and Dental University

summary: We identified full-length complementary DNA by long-read RNA-seq (Iso-seq) in HBV-KMT2B integrated HCC sample. To compare the data of HCC sapmle with HBV-KMT2B integrated HPCs, which reproduces the sequence of the HCC sample, we performed long-read RNA-seq in HBV-KMT2B integrated HPCs, as well.

overall_design: For Iso-seq, we extracted total RNA from HBV-KMT2B integrated HPCs after removing MEF using Feeder Removal Microbeads mouse (Miltenyi Biotec).

first: Jun

last: Tsuchiya


title: Two-dimensionally cultured functional hepatocytes generated from human induced pluripotent stem cell-derived hepatic organoids for pharmaceutical research

city: Suita

first: Jumpei

last: Inui

address: Yamadaoka 1-6

institute: Osaka University

summary: Human induced pluripotent stem (iPS) cell-derived hepatocyte-like cells (HLCs) are expected to replace primary human hepatocytes (PHHs) as a new stable source of hepatocytes for pharmaceutical researches. However, HLCs have lower hepatic functions than PHHs, take a long time to be differentiated and cannot be prepared in large quantities due to not proliferating after their terminal differentiation. To overcome these problems, we have established hepatic organoids (iHOs) from HLCs. The iHOs could proliferate approximately 10^20-fold by more than 10 passages and expressed most hepatic genes higher than HLCs. Furthermore, in order to enable the widespread use of iHOs for in vitro drug discovery research, we have developed the two-dimensional culture protcol for them. Two-dimensional cutured iHOs (2D-iHOs) expressed most of major hepatocyte marker genes and proteins much higher than HLC, iHOs, and even PHHs. The 2D-iHOs had glycogen storage capacity, the capacity to uptake and release indocyanine green (ICG), albumin and urea secretion, and the capacity of bile canaliculi formation. Importantly, the 2D-iHOs had the activity of major drug-metabolizing enzymes and responded to hepatotoxic drugs, comparable to PHHs. Thus, 2D-iHOs overcome the limitation of the current models and promise to provide robust and reproducible pharmaceutical assays.

overall_design: Human iPS cell-derived hepatocytes (HLCs), hepatic organoids established from them (iHOs), and two-dimensional cultured hepatic organoids (2D-iHOs) were dubjected to RNA-sequencing.

first: Wakana

last: Nagai

first: Chiharu

last: Imamura

first: Yukiko

last: Ueyama-Toba

last: Yokota

first: Hiroyuki

last: Mizuguchi


title: Single-cell transcriptomes of macaque seminiferous tubule under different conditions

first: Yicong

last: Xu

address: No. 135, Xingang Xi Road

summary: To understand the variations of spermatogonial stem cells among different seasons and ages in macaque, we performed scRNA-seq of seminiferous tubule in pre-pubertal, post-pubertal, and elderly rhesus monkeys in different reproductive seasons.

overall_design: The tissues of macaque testicle under different conditions was isolated and the transcriptome library of cells was built

first: Shengnan

first: Ke

first: Kai

last: Chen

first: Wei

last: Si

first: Jin


title: The regulatory RNA Ern0160 is involved in pathogenicity of Enterococcus faecium

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

institute: CHU de Rennes

summary: In this study, we aimed to further characterize Ern0160 functions and identify its targets. In silico prediction screen highlighted putative mRNA candidates. For two of them, homologous genes encoding for LysM-containing domain proteins (EFAU004_01059 and EFAU004_01150), we validated a direct and specific interaction to Ern0160. In addition, we found that Ern0160 overexpression was responsible for the repression of the target genes, emphasizing the mode of action of this sRNA. As a recent study provided the role of these genes in the virulence of E. faecium Aus0004 in a mouse model of systemic and urinary tract infections, we proposed that Ern0160 could be part of the regulatory network involved during colonization/infection by attenuating virulence. Furthermore, in vitro tests of antibiotic susceptibility profiles to vancomycin, teicoplanin, daptomycin, ciprofloxacin, and levofloxacin showed that a strain expressing Ern0160 presented lower MICs of fluoroquinolones compared to a ern0160-deleted strains. Very interestingly, we found that a gene implicated in fluoroquinolone resistance in E. faecium, Efmqnr was downregulated when Ern0160 was over-expressed, indicating a link between this sRNA and antibiotic resistance. For the first time, this study investigated throughout the identification of its cellular targets the regulation that could lead to virulence and fluoroquinolone resistance in E. faecium.

overall_design: Transcriptome analysis by RNA-seq to compare the levels of all transcripts in ern0160-deleted E. faecium Aus0004 mutant versus wild-type strain and in trans-complemented srn0160-deleted E. faecium Aus0004 mutant versus srn0160-deleted E. faecium Aus0004 mutant with empty plasmid

first: Loren

last: Dejoies

first: Valérie

last: Bordeau

first: Killian

last: Le Neindre

first: Sophie

last: Reissier

first: Brice

last: Felden

first: Svetlana

last: Chabelskaya

first: Charlotte

last: Michaux


title: Functional Characterisation of Active Enhancers in Human Astrocytes Using a High-throughput CRISPRi Screen

city: Kensington

first: Irina

last: Voineagu

state: NSW

address: UNSW Sydney, High Street

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: We used CROP-seq to perform a high-throughput, parallel screen of 979 candidate enhancer perturbations in normal human astrocytes (NHAs), a primary cell-line. We identified the target gene(s) for 145 of these candidates, which were enriched for transcription with eRNA, transcription factor footprinting, and superenhancer annotation. Most regulatory interactions were <50kb, targeting the nearest gene in ~50% of cases, but were not typically captured by eQTL or in silico predictions. These data elucidate the regulatory network of an understudied-but-crucial brain cell-type.

overall_design: Single-cell RNA-seq using 10X Chromium V3 Chemistry was performed on NHA cells stably-transduced with dCas9-KRAB, and transduced with a lentiviral library containing guide RNAs for 979 candidate enhancers, 125 positive control promoters, and 300 non-targeting negative controls

first: Nicole

middle: F

last: Green

first: Gavin

last: Sutton


title: Protective effect of Pien Tze Huang on colitis-associated colorectal cancer

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goal of this study is to compare the differentially expressed genes in colon tissue of Control and AOM/DSS induced colitis-associated cancer (CAC) mouse model  with or without Pien Tze Huang (PZH) treatment. The AOM/DSS induced CAC mouse model were randomly divided into 2 groups: Model and Model + PZH groups (n=5 for each group). Control mice (n=5) were set as control. mice in Control and Model groups were  intragastrically with double distilled water, while mice in PZH and Model + PZH groups were intragastrically with 250 mg/kg/d of PZH for 91 days.  Then the colon tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with colonic mice in 4 groups: Control, PZH, Model, Model + PZH treated (n=5 for each group) to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Liya

last: Liu


title: Selamectin increases cisplatin sensitivity by inhibiting cisplatin-resistant genes expression and autophagy in uveal melanoma

city: Shanghai

first: Jie

last: He

address: Zhi Zao Ju

institute: Shanghai Jiao Tong University School of Medicine

summary: Cisplatin resistance is the main reason for uveal melanoma (UM) treatment failure. Thus, developing strategy that increasing cisplatin sensitivity is needed. In this study, we performed drug repositioning analysis with the Connectivity Map database using a panel of previously identified cisplatin sensitivity–associated genes and cisplatin resistance–associated genes as the signature and obtained the antiparasitic drug selamectin. We demonstrated that the selamectin and cisplatin combination showed a synergistic effect on inhibiting UM cell growth. Experiments in tumor-bearing nude mice further showed that selamectin and cisplatin have synergistic effects in reducing tumor growth. Previous studies have linked increased autophagy with tumor resistance to chemotherapy. We found that selamectin inhibited the expression of the autophagy-related gene ATG9B, thus reducing autophagy. The cisplatin resistance–associated genes PDGFRB, DUSP1, MAST1 and IL11 were significantly downregulated in UM cells treated with selamectin. In summary, our study shows that selamectin enhanced the sensitivity of UM to cisplatin, through the mechanism of inhibiting cisplatin resistance–associated gene expression and autophagy. These findings may provide a new strategy for the treatment of UM.

overall_design: MUM2B cells were treated with DMSO or 1 uM selamectin for 24 hours. Total RNA was extracted and then sent for RNA sequencing.

first: Jianfeng


title: Analysis of molecular mechanism of HPV18 carcinogenesis by transcriptome sequencing

city: 湖北

first: Yiyi

last: Kang

address: Donghu road

institute: WuHan University

summary: In order to study the molecular mechanism of HPV18 carcinogenesis, we used conditional reprogramming technique to culture normal cervical epithelial cells, cervical intraepithelial Neoplasia HPV18 cells and patient-derived cervical cancer cell lines for 24 h and stimulated with estradiol for 24 h,and collected total RNA samples for mRNA sequencing (RNA-SEQ). Then, Gene expression profiling was performed using RNA-seq data from six groups of cells.

overall_design: Comparative gene expression profile analysis of RNA-seq data in normal cervical epithelial cells group, normal cervical epithelial cells - estrogen stimulated group, cervical intraepithelial Neoplasia HPV18 cells group, cervical intraepithelial Neoplasia HPV18 cells - estrogen stimulated group, patient-derived cervical cancer cell group, patient-derived cervical cancer cell - estrogen stimulated group.

first: Si

last: Chen

first: Ming

last: Wu

first: Zhaoyu

last: Su


title: Effect of different salinities on the expression of growth genes in Thalassiosira pseudonana

city: 青岛

first: 佳岷

last: 李

address: 山东省青岛市崂山区松岭路238号中国海洋大学

institute: 中国海洋大学

summary: Differential gene expression in algae under specific conditions

overall_design: A total of 18 samples with replicates were used for RNA-seq to investigate the differences in gene expression in Thalassiosira pseudonana cultured at 30PSU salinity as a control, and at 3PSU and 9PSU salinity.

first: Jiamin

last: Lee

first: Wenjie

last: Sun


title: MicroRNA-150 controls experimental autoimmune encephalomyelitis by regulating CD4 T cell differentiation and function [RNA-seq II]

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: MicroRNAs are small non-coding RNA molecules that fine-tune diverse biological processes and are often found to be dysregulated in diseases, such as multiple sclerosis (MS). MS is an immune-mediated disease of the central nervous system characterized by demyelination, axonal loss and neurodegeneration. We have previously shown microRNA-150 (miR-150) levels to be elevated in cell-free cerebrospinal fluid (CSF) of MS patients compared to controls. We aimed to investigate the physiopathological function of miR-150 in vivo by generating miR-150 knock-out (KO) and knock-in (KI) mice using CRISPR/Cas9 technology. To specifically interrogate the role of miR-150 upon inflammation of the central nervous system (CNS), we induced experimental autoimmune encephalomyelitis (EAE), a mouse model for MS, in these newly generated mice. After induction of EAE, miR-150KO mice developed milder disease compared to WT littermate controls while miR-150KI mice presented with exacerbated EAE. Disease amelioration in miR-150KO was accompanied by decreased infiltration of CD4+ T cells in the central nervous system compared to WT and KI mice, as well as increased FoxP3+ regulatory T (Treg) cells in inguinal lymph nodes at disease priming stage. We demonstrated that Treg cells were fundamental for EAE amelioration in miR-150KO mice, as their partial depletion during EAE priming stage in miR-150KO FoxP3DTR mice restored disease incidence and severity to the levels observed in WT and KI mice. Transcriptomic profiling of CD4+ T cells isolated from miR-150KO mice revealed upregulation of genes associated with Treg cell function, but also reduced gene translation and autophagy, as compared to WT and particularly KI cells. The role of miR-150 in affecting the fate of CD4+ T cells was further supported by the grater tendency of miR-150KO CD4+ T cells to differentiate into Treg cells in-vitro. In conclusion, miR-150 deficiency favored considerably milder CNS inflammation by promoting differentiation of a more anti-inflammatory CD4+ T cell repertoire.

overall_design: mRNA profiles of sorted CD4 T cells from miR-150 knock-out, wildtype and knock-in mice upon different Tcell differentiation conditions in vitro

first: Maja

last: Jagodic

first: Chiara

last: Sorini

first: Tejaswi

last: Badam


title: MicroRNA-150 controls experimental autoimmune encephalomyelitis by regulating CD4 T cell differentiation and function

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

overall_design: Refer to individual Series