title: Passive shaping of intra- and intercellular m6A dynamics via mRNA metabolism

status: Public on Jul 25 2024

city: Rehovot

last: Dierks

state: Central District

address: Herzl St 234, Weizmann Institute of Science to the Department of Biomolecular Sciences, Laboratory of Dr. Scherz-Shouval

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: m6A is the most widespread mRNA modification and is primarily implicated in controlling mRNA stability. Fundamental questions pertaining to m6A are the extent to which it is dynamically modulated within cells and across stimuli, and the forces underlying such modulation. Prior work has focused on investigating active mechanisms governing m6A levels, such as recruitment of m6A writers or erasers leading to either ‘global’ or ‘site-specific’ modulation. Here, we propose that changes in m6A levels across subcellular compartments and biological trajectories may result from passive changes in gene-level mRNA metabolism. To predict the intricate interdependencies between m6A levels, mRNA localization, and mRNA decay, we establish a differential model ‘m6ADyn’ encompassing mRNA transcription, methylation, export, and m6A-dependent and independent degradation. We validate the predictions of m6ADyn in the context of intracellular m6A dynamics, where m6ADyn predicts associations between relative mRNA localization and m6A levels, which we experimentally confirm. We further explore m6ADyn predictions pertaining to changes in m6A levels upon controlled perturbations of mRNA metabolism, which we also experimentally confirm. Finally, we demonstrate the relevance of m6ADyn in the context of cellular heat stress response, where genes subjected to altered mRNA product and export also display predictable changes in m6A levels, consistent with m6ADyn predictions. Our findings establish a framework for dissecting m6A dynamics and suggest the role of passive dynamics in shaping m6A levels in mammalian systems.

overall_design: These sereies comprises different experimental series with varying treatments. There is: WT and Mettl3 KO cytoplasmic and nucelar fraction followed by RNA-seq. Cytoplasmic and nucelar fractionation experiment of NIH3T3 cells followed  by m6A-seq2. Cytoplasmic and nucelar fraction of pMEFs cells followed by m6A-seq2. CPT treatement followed by m6A-seq2 in MCF7 cells. Actinomycin D timecourse followed by m6A-seq2 in A9 cells. YTHDF1-3 triple knock-down experiment via siRNA followed by m6A-seq2 in NIH3T3 cells. YTHDF1-3 triple knock-down experiment via siRNA followed cytoplasmic and nucelar fraction followed by RNA-seq in NIH3T3 cells. Heat stress timecourse followed by m6A-seq2 in WT primary MEFs. Heat stress timecourse followed by m6A-seq2 in HSF1 KO primary MEFs. Cytoplasmic and nucelar fractionation experiment followed by RNA-seq after heat stress in WT primary MEFs. Cytoplasmic and nucelar fractionation experiment followed by RNA-seq after heat stress in HSF1 KO primary MEFs.

first: Schraga

last: Schwartz

first: Ran

last: Shachar

first: Ronit

last: Nir

first: Miguel

last: Garcia-Campos

first: Anna

last: Uzonyi

first: Ursula

last: Toth

first: Walter

last: Rossmanith

first: Lior

last: Lasman

first: Boris

last: Slobodin

first: Jacob

middle: H

last: Hanna

first: Yaron

last: Antebi

first: Ruth

last: Scherz-Shouval

last: Wiener


title: Cross-talk between ILC2 and Gata3high Treg locally constrains adaptive type 2 immunity

status: Public on Jul 19 2024

city: Brussels

first: Julie

last: Stockis

address: Avenue Hippocrate 74

department: de Duve Institute

country: Belgium

institute: UCLouvain

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Exploiting functional regions in the viral RNA genome as druggable entities

status: Public on Aug 12 2024

city: Hubei

first: Dehua

last: Luo

address: shizishan 1st

country: China

institute: HZAU

summary: The design of RNA-targeting antivirals offers a potent means in controlling viral infections. An essential prerequisite to this design depends on identifying functional RNA structures in the viral genome, as well as those that are readily accessible to drugs in cells. Techniques that probe RNA structures in situ have been developed recently including SHAPE-MaP. In this study, we report on the application of SHAPE-MaP to the Porcine Epidemic Diarrhea Virus (PEDV) RNA genome to categorize RNAs that are well folded, dynamic, or in the single strands by the combination of two parameters, SHAPE reactivity and Shannon entropy. Dynamic RNAs have the potential to fold into specific structures, and stabilizing their structures with compounds could be a new idea for drug design, which is demonstrated by the example of the G-quadruplex forming sequence. siRNAs targeting stable single-stranded RNA regions presented higher antiviral success rates. Our results show that the RNAs in the single strands could be efficient antiviral targets, and that SHAPE-MaP is an effective method to identify targetable structures in the viral RNA genomes through analysis of folding features.

overall_design: The whole genome structure of PEDV (ID: MK584552.1) were probed by SHAPE-MaP.

first: Yingge

last: Zheng

first: Zhiyuan

last: Huang

first: Dengguo

last: wei

first: Yingxiang

last: Deng


title: Therapy of allergic rhinitis using ribavirin spray to clear nasal commensal viruses

status: Public on Aug 21 2024

city: Shanghai City

first: Yue

last: Dong

address: 800 Xiangyin Road

institute: Naval Medical University

summary: To explore the impact of nasal commensal viruses on the onset and progression of allergic rhinitis, We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of CD45+ cells in the nasal mucosa of mice  treated with Vehicle, Ribavirin, Vehicle-OVA, or Ribavirin-OVA.

overall_design: CD45+ cells in the nasal mucosa of mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Ye

last: Zhou

first: Jin

last: Hou


title: The Prostacyclin Receptor is a Nrf2-regulated Immune Checkpoint in CD8+ T cells

status: Public on Jul 17 2024

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Department of Metabolism and Nutritional Programming

country: USA

institute: Van Andel Insitute

summary: Understanding how circulating metabolites enforce pathways in dysfunctional immune cells may illuminate modes of intervention directed at reviving immune function. The NRF2 pathway is the most widely documented cytoprotective axis in land-dwelling eukaryotes. However, the role of this pathway in CD8+ T cells—which seek and destroy tumors and pathogen infected cells—has yet to be elucidated. Our lab has conducted a RNAseq meta-analysis of CD8+ T cells upon tumor, viral and bacterial inoculation. Curiously, the NRF2 pathway was robustly upregulated in dysfunctional CD8+T cells. To further investigate the role of NRF2 in these contexts we developed a mouse model whereby the NRF2 axis is permanently hyperactivated in CD8+ T cells, hereafter referred to as NRF2Hi. Our in vivo data demonstrate that NRF2Hi CD8+ T cells offer little overall cytoprotection and poorly control tumors and pathogens versus wildtype (WT) control CD8+ T cells. To understand why upregulation of the NRF2 axis could be unfavorable to CD8+ T cell function we conducted RNAseq on NRF2Hi versus WT cells upon viral infection of mice. We found that NRF2Hi cells massively upregulate the prostacyclin receptor (PTGIR), which binds to prostacyclin—a circulating metabolite of arachidonic acid that has only been investigated in vasodilation and is seemingly benign to CD8+ T cells. To decipher the role of PTGIR in CD8+ T cells, we silenced its expression and observed a revival of CD8+ T cell function, significantly reducing tumor and pathogen burden. Collectively, our data illuminate a NRF2-regulated immune checkpoint, PTGIR. Interventions that suppress the interaction between PTGIR and prostacyclin may serve therapeutic benefit in clinical contexts such as cancer and chronic pathogen infections.

overall_design: We adoptively transferred WT and KEAP1 KO (NRF2Hi) CD8 LCMV-specific (P14) CD90.1 cells into congenic CD90.2 hosts prior to infection with the acute, Armstrong strain of LCMV. On day 7 post infection, cells were isolated and RNAseq was performed. Data represent 5 mice total per condition, from 2 separate biological runs

first: Michael

last: Dahabieh

first: Lisa

last: DeCamp

first: Zhen

last: Fu


title: 3D brain vascular niche model captures invasive behavior and gene signatures of glioblastoma

status: Public on Jul 18 2024

city: Boston

first: Vivian

middle: K

last: Lee

state: Massachusetts

address: 60 Fenwood rd, 5016E

institute: Brigham and Womens Hospital, Harvard Medical School

summary: Glioblastoma (GBM) is a highly lethal brain cancer with no effective treatments; understanding how GBM cells respond to tumor microenvironment remain challenging as conventional cell cultures lack cytoarchitecture while in vivo models present complexity all at once. Developing a culture system to bridge the gap is thus crucial. Here, we employed a multicellular approach using human glia and vascular cells to optimize a 3-dimensional (3D) brain vascular niche model that enabled not only long-term culture of patient derived GBM cells but also recapitulation of key features of GBM heterogeneity and gene reprogramming in accordance with invasion behaviors and vascular association. Remarkably, vascular contact of GBM cells induced genes concerning neuronal, synaptic, and glia interaction, as well as immune suppression. This gene signature also displayed regional enrichment particularly in leading edge and microvascular proliferation zones and predicted worse prognosis for GBM patients. Furthermore, gene variance analysis uncovered histone demethylation and xylosyltransfererase activity as the main themes for the top induced genes in vivo, signifying the importance of chromatin remodeling and posttranslational modification proteoglygan such as CSPG in GBM adaption. Finally, our model also demonstrated a capacity to maintain GBM quiescence state and a protective niche against chemotherapy. In summary, our 3D model recapitulated key features of GBM heterogeneity and unveiled a previously unappreciated influence of brain glia-vascular unit for transcriptional adaption for neural/synaptic interaction and immunosuppression. The brain vascular niche model may serve as an effective bridge between 2D cultures and in vivo models for GBM modeling and therapeutic development.

overall_design: To investigate how GBM cells respond to different tumor microenvironment, we establisehd various in vitro and in vivo models with patient-derived GBM cells. Then, we performed gene expression profiling analysis using data obtained from RNA-seq of 2 different patient-derived cell lines cultured in 4 different conditions.

first: Rut

last: Tejero

first: Nathaniel

last: Silvia

first: Anirudh

last: Sattiraju

first: Aarthi

last: Ramakrishnan

first: Li

last: Shen

first: Alexandre

last: Wojcinski

first: Santosh

last: Kesari

first: Roland

last: Friedel

first: Hongyan

last: Zou

first: Guohao

last: Dai


title: Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.

status: Public on Jul 09 2024

city: Salt Lake City

first: Rodney

last: Stewart

state: UT

address: 2000 Circle of Hope Dr

department: Oncological Sciences

institute: University of Utah

summary: Zebrafish SHH MB tumors were generated by CRISPR-Cas9-mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA-seq.

overall_design: Whole brains were collected from 3 individual tp53 mutant control animals, 3 individual tp53 mutant and ptch1 crispant animals, and 3 individual tp53 heterozygous and ptch1 crispant animals.

first: Mattie

middle: J

last: Casey

middle: A


title: Identification of differential expression circRNAs profile in Gynecological cancer associated cell lines

status: Public on Jul 13 2024

city: Dalian

first: lingxi

last: tian

state: liaoning

address: lingshui street

institute: Dalian University of Technology

summary: Developing a classification model based on differential expression circRNAs profile in cancer cells to improive diagnosis of Gynecological cancer (Cervical cancer:Hela, ovarian cancer: NIHOVCAR3 SKOV3, breast cancer: MCF7, endometrial cancer:RL95-2, normal cell:A293T).

overall_design: Total RNA was extracted from the above cells after culture (Cervical cancer:Hela, ovarian cancer: NIHOVCAR3 SKOV3, breast cancer: MCF7, endometrial cancer:RL95-2, normal cell:A293T). lncRNA sequencing was performed using Illumina PE150 platform, and all cell samples included 3 replicates. To identify up-regulated or down-regulated genes and circRNAs, cancer cell samples (Hela, NIHOVCAR3, SKOV3, MCF7, RL95-2) were compared with normal cells (A293T) as controls.

first: Lingxi

last: Tian

first: Jun

last: Yang

first: Yan

last: Gao


title: Alizarin Red perturbs skeletal patterning and biomineralization via Catalase inhibition

status: Public on Jul 01 2024

first: Cynthia

last: Bradham

address: 24 Cummington Mall

institute: Boston University

summary: Alizarin Red (AZ) is an anthraquinone dye that is commonly used in histological studies and textiles. Exposure to AZ results in morphological perturbations in several species, including rats, frogs, and dogs; however, the mechanisms by which AZ has these effects is largely unexplored, and little is known about its effect on development. We have previously shown that AZ is teratogenic to sea urchin larvae, and that AZ was the only calcium-binding mineralization marker among five tested that perturbed skeletal patterning. Here, we characterize these defects further and demonstrate that embryos exposed to AZ have abnormal skeletal element rotation, branching, and bending. Immunostains and polychrome labeling revealdelayed migration of primary mesenchyme cells and initiation of biomineralization. Although gross ectodermal dorsal-ventral specification, ciliary band restriction, and neuronal specification occur normally in most AZ-treated embryos, we find abnormal patterning and connectivity of the serotonergic neurons. Temporal transcriptomics comparisons confirm delayed development and implicate changes neuron-related GO terms with AZ treatment. Particle velocity imaging experiments show that ciliary beating normally directs fluid flow into the larval mouth, while AZ treatment perturbs the normal pattern of vortices and redirects flow away from the mouth. Finally, we show that the effects of AZ on skeletal patterning are largely due to the inhibition of catalase and subsequent elevation of reactive oxygen species. Specifically, catalase knockdown and transient hydrogen peroxide treatment are each sufficient to phenocopy the hallmark AZ skeletal patterning defects. This study is the first to define the consequences of AZ and its effects on neuronal function and catalase activity, with consequent impacts on development, skeletal patterning, and biomineralization.

overall_design: Control and alizarin-treated sea urchin embryos at 12, 18, 24 and 30 hpf

first: Abigail

middle: E

last: Descoteaux

first: Marko

last: Radulovic

first: Mayank

middle: M

last: Ghogale

first: Santhan

last: Chandragiri

first: N

middle: D

last: Abayawardena

first: Bikram

last: Shrestha

first: Athula

last: Wikramanayake

first: Vivek

middle: N

last: Prakash


title: DOGMA-seq of opioid addiction treatment in HIV-1 infected individuals

city: New Haven

first: Ya-Chi

last: Ho

state: Connecticut

address: 295 Congress Avenue,BCMM 354E

institute: Yale University

summary: Opioid use and HIV-1 infection a impact immune function independently, but their impact on the immune system together is unknown. To understand the impact of opioids on immune function in HIV-1 infected individuals we used DOGMA-seq to examine the transcriptome, chromatin accessibility, and surface protein expression in HIV-1-infected individuals undergoing opioid addiction treatment.

overall_design: 12 individuals were sampled at time 0 and after 3 months of treatment with an opioid replacement therapy consisting of either methadone,  bueprenoropine with naloxone, or naltrexone. Both PBMC and negative selection  isolated CD4 + T cells were profiled using DOMGA-seq with the Biolegend TotalSeq™-A Human Universal Cocktail, V1.0.

first: Jack

last: Collora


title: The TLR8 agonist Selgantolimod regulates Kupffer cell differentiation status and indirectly impairs HBV entry into hepatocytes via an IL-6-dependent mechanism (PHH)

status: Public on Aug 10 2024

city: Lyon

first: Xavier

last: Grand

address: 46 allée d'Italie

country: France

institute: INSERM U1052, UCBL1, ENS de Lyon


title: Cortical stimulation-based transcriptome shifts on Parkinson's disease animal model

status: Public on Jul 11 2024

city: Yeonsu-gu, Incheon

first: Johyeon

last: Nam

address: 265, Harmony-ro

department: Division of Life Sciences

country: South Korea

institute: Incheon National University

summary: Parkinson's disease is the second most prevalent neurodegenerative disorder, characterized by the degeneration of dopaminergic neurons. Significant improvements in gait balance, particularly step length and velocity, were revealed by less-invasive wireless cortical stimulation. Transcriptome sequencing was performed to demonstrate the cellular mechanism, specifically targeting the primary motor cortex where the stimulation was applied. Our findings indicated that the differentially expressed genes (DEGs), initially down-regulated following Parkinson's disease induction, were subsequently restored to normal levels after cortical stimulation. We propose these DEGs as a potential target for motor disorder treatment in Parkinson's disease. These genes are implicated in crucial processes such as astrocyte-mediated blood vessel development and microglia-mediated phagocytosis of damaged motor neurons, suggesting their significant roles in improvement of behavior disorder. Moreover, these biomarkers not only facilitate rapid and accurate diagnosis of Parkinson's disease but also assist precision medicine approaches.

overall_design: This study evaluated the efficacy of cortical stimulation using a cutting-edge graphene-based electrode array and wireless technology to mitigate the symptoms in a rat model of PD induced by 6-OHDA. Specifically, the graphene array was surgically placed in the primary motor cortex of the rats, followed by daily wireless stimulation at 130 Hz for one hour, over two weeks. The participants were divided into three groups: control (Ctrl), PD, and Stimulation (Stim). This study aimed to explore the biological mechanisms that facilitate the observed behavioral improvements in patients with PD following stimulation through comprehensive transcriptome analysis using NGS techniques.

first: Hongseong

last: Shin

first: Chaeyeon

last: You

first: Eunha

last: Baeg

first: Jae

middle: G

last: Kim

first: Sunggu

first: Mi-Ryung

last: Han


title: PRC2-mediated apoptosis evasion is a therapeutic target of MDS/AML harboring inv(3)/t(3;3) and monosomy 7 (CUT&Tag)

status: Public on Jun 29 2024

city: Yokohama

first: Hiroyoshi

last: Kunimoto

address: 3-9 Fukuura, Kanazawa

department: Department of Stem Cell and Immune Regulation

country: Japan

institute: Yokohama City University Graduate School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) harboring both inv(3)/t(3;3) and monosomy 7 (-7) are highly aggressive myeloid cancers whose molecular pathogenesis and therapeutic vulnerability remain elusive. High throughput drug screens, CUT&Tag/RNA sequence and functional assays using human MDS/AML cells revealed that EZH2 inhibitors efficiently induce apoptosis preferentially in MDS/AML with inv(3)/t(3;3) and -7 through activation of GADD45γ-p38-p53 axis. EVI1 activated in 3q-rearranged MDS/AML was responsible for GADD45γ silencing by direct binding to its consensus sequence within GADD45γ promoter and recruitment of PRC2 complex via interaction with EZH2, which can be therapeutically targeted by EZH2 inhibition. MDS/AML with inv(3)/t(3;3) and -7 showed preferential sensitivity to EZH2 inhibition in both mouse model and patient samples. Thus, MDS/AML cells with inv(3)/t(3;3) and -7 possess apoptosis evasion mechanism through EVI1-PRC2-mediated repression of GADD45γ-p38-p53 axis, which is a potential therapeutic vulnerability in MDS/AML patients with these high-risk cytogenetic lesions.

overall_design: To explore the downstream target of EZH2 inhibition relevant to apoptosis induction in YCU-AML1 and OCI-AML20 cells, we performed CUT&Tag sequence (CUT&Tag-seq) for H3K27me3 using OCI-AML20, YCU-AML1, FKH-1 and Kasumi-3 cells treated with either vehicle or valemetostat 300nM for 7 days.


title: Stimulation of tumor infiltrating B-cells improves ex-vivo TIL expansion for melanoma sample immunotherapy I

status: Public on Jun 30 2024

city: Tampa

first: Daniel

last: Abate-Daga

state: Florida

address: 12902 Magnolia Dr.

department: Immunology

institute: H. Lee Moffitt Cancer Center and Research Institute

summary: Many studies have shown association of tumor infiltrating B-cells and presence of tertiary lymphoid structure with improved clinical responses to immune checkpoint inhibitors therapy. We hypothesized that their presence could also have an impact on TIL therapy response. To address this, we performed RNA-seq of FFPE samples from a cohort of patients that received TIL therapy. Melanoma tumors collected prior to TIL infusion were evaluated for immune content in 9 responders and 11 non-responders to TIL therapy.  Our data demonstrate an increase in class-switched memory B-cells in responders compared with non-responders to TIL therapy. In the myeloid compartment, increased presence of dendritic cell populations (pDC, aDC, and iDC) and basophils was observed in responders to TIL therapy, as well as higher content of γδ T cells and effector memory CD8+ T cells (CD8+ Tem) in the T-cell compartment. Next, we assessed the TLS presence in the same cohort by a gene expression signature of 12 chemokines using principal component analysis. The responders showed a higher TLS score compared with the non-responder patients, suggesting that patients responding to TIL therapy had more TLS in their tumors than the non-responder patients. These observations indicate that, same as in the immune checkpoint inhibitors therapy response, presence of B-cells and TLS might have a positive impact in the clinical outcome to TIL therapy.

overall_design: RNA sequencing was performed on formalin-fixed paraffin-embedded (FFPE) melanoma samples from patients enrolled in Moffitt Cancer Center’s TIL clinical trials. The data was analyzed acocordantly to the response to TIL therapy.

first: Renata

middle: R

last: Rossetti

first: Sean

last: Yoder

first: Yian

last: Chen

first: Dongliang

last: Dun

first: Anders

last: Berglung


title: Setd2 overexpression rescues bivalent gene expression during SCNT-mediated ZGA by enhancing H3K36me3 at gene bodies and excluding H3K27me3 from promoters [RNA-seq]

city: Shanghai

first: Xiaolei

last: Zhang

address: N0.1239 of Siping Road, Shanghai, China

institute: Tongji University

summary: Successful cloning through somatic cell nuclear transfer (SCNT) face significant challenges due to epigenetic obstacles. Recent studies have highlighted the roles of H3K4me3 and H3K27me3 as potential epigenetic barriers. However, the underlying mechanisms remain largely unclear. In this study, we generated genome-wide maps of H3K4me3 and H3K27me3 from mouse pre-implantation NT embryos. Our analysis revealed aberrant over-representation of H3K4me3 and H3K27me3 bivalent in 2-cell stage NT embryos, potentially linked to the deficiency of H3K36me3. Notably, the overexpression of Setd2, a H3K36me3 methyltransferase, successfully restored multiple epigenetic marks, including H3K36me3, H3K4me3 and H3K27me3. Additionally, it reinstated the expression levels of ZGA-related genes by re-establishing H3K36me3 at gene body regions to exclude H3K27me3 from bivalent regions, and ultimately improved cloning efficiency. These findings highlight the excessive bivalent state as a potent barrier and emphasize the removal of these barriers as a promising approach to achieving higher cloning efficiency.

overall_design:
To investigate the function of small molecule inhibitor WDR5-0103 during SCNT-mediated reprogramming, we added WDR5-0103 into the culture medium of SCNT embryos.
To investigate the function of Setd2 during SCNT-mediated reprogramming, the SCNT embryos were injected with Setd2 mRNA after activation.
We then performed gene expression profiling analysis using data obtained from Smart-seq2 of 2-cell stage and/or 4-cell stage SCNT embryos after WDR5-0103 addition and Setd2 mRNA injection.

first: Ruimin

last: Xu

first: Yuyan

last: Zhao

first: Yijia

last: Yang

first: Hong

last: Wang

first: Xiaoyu

last: Liu

first: Chong

last: Li

first: Shaorong

last: Gao


title: Cell-type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures

status: Public on Jul 15 2024

city: Baltimore

first: Joshua

last: Popp

state: Maryland

address: 3100 Wyman Park Drive South Wing, Room S249

department: Biomedical Engineering

institute: Johns Hopkins University

summary: Identifying the molecular effects of human genetic variation across cellular contexts is crucial for understanding the mechanisms underlying disease-associated loci, yet many cell-types and developmental stages remain underexplored. Here we harnessed the potential of heterogeneous differentiating cultures (HDCs), anin vitrosystem in which pluripotent cells asynchronously differentiate into a broad spectrum of cell-types. We generated HDCs for 53 human donors and collected single-cell RNA-sequencing data from over 900,000 cells. We identified expression quantitative trait loci in 29 cell-types and characterized regulatory dynamics across diverse differentiation trajectories.This revealed novel regulatory variants for genes involved in key developmental and disease-related processes while replicating known effects from primary tissues, and dynamic regulatory effects associated with a range of complex traits.

overall_design: We differentiated two replicates of 51 iPSC lines across 17 batches consisting of 4 to 8 lines per batch. Each batch contained at least one line of each sex. In each batch, lines were formed and maintained in parallel. Each replicate represents a separate instance of HDC differentiation and will capture technical effects introduced during formation, maintenance, dissociation, and collection.

first: Popp

last: Joshua M

first: Rhodes

last: Katherine

first: Jangi

last: Radhika

first: Li

last: Mingyuan

first: Barr

last: Kenneth

first: Tayeb

last: Karl

first: Battle

last: Alexis

first: Gilad

last: Yoav


title: MeRIP-seq data of MACO/R model mice at 0, 6 and 24 hours in the brain

city: Shenyang

first: li

last: bingwu

address: shenhe

institute: Shenyang Pharmaceutical University

type: Methylation profiling by high throughput sequencing

summary: We performed brain MCAO/R modeling in mice, and extracted tissues at 0, 6, and 24 hours after modeling for MeRIP-seq analysis to explore the biological function of m6A in the ischemia-reperfusion process.


title: Neuronal DNA repair reveals strategies to influence CRISPR editing outcomes

status: Public on Jul 30 2024

city: San Francisco

first: Gokul

middle: Nathan

last: Ramadoss

state: California

address: 1200 Mariposa St

institute: UCSF

summary: Genome editing is poised to revolutionize treatment of genetic diseases, but poor understanding and control of DNA repair outcomes hinders its therapeutic potential. DNA repair is especially understudied in nondividing cells like neurons, which must withstand decades of DNA damage without replicating. This lack of knowledge limits the efficiency and precision of genome editing in clinically relevant cells. To address this, we used induced pluripotent stem cells (iPSCs) and iPSC-derived neurons to examine how postmitotic human neurons repair Cas9-induced DNA damage. We discovered that neurons can take weeks to fully resolve this damage, compared to just days in isogenic iPSCs. Furthermore, Cas9-treated neurons upregulated unexpected DNA repair genes, including factors canonically associated with replication. Manipulating this response with chemical or genetic perturbations allowed us to direct neuronal repair toward desired editing outcomes. By studying DNA repair in postmitotic human cells, we uncovered unforeseen challenges and opportunities for precise therapeutic editing.

overall_design: To determine how dividing and nondividing cells respond to Cas9-VLP treatment, we conducted bulk RNAseq on WTC-NGN2 human iPSCs and iPSC-derived neurons, before and after treatment with Cas9-VLP.

first: Julianne

last: Jin

first: Martin

last: Kampmann

first: Bruce

last: Conklin


title: Bulk RNAseq REX-1 RFP mESC 2019

city: Detroit

first: Daniel

last: Rappolee

address: 275 E Hancock St

department: OBGYN

institute: Wayne State University

summary:
This experiment examines how increasing stress (sorbitol) can override normal stemness (NS) conditions, which LIF maintains, causing lineage imbalance and otherwise affecting cells in the early embryo.
It also compares NS to normal differentiation (ND) (without LIF).
D3 are from 8 blastocysts of 129/Sv+/+ strain mice germ line competent 1. No sex is given as these may actually be a product of different sexes of the 8 blastocysts. The D3 cells were obtained for ATCC (American Type Culture Collection).
1. Doetschman TC, Eistetter H, Katz M, Schmidt W, Kemler R. The in vitro development of blastocyst-derived embryonic stem cell lines: formation of visceral yolk sac, blood islands and myocardium. J Embryol Exp Morphol 1985;87:27-45.
Rex1 promoter- Red fluorescence protein (RFP) transgenic viable reporter ESC were created and validated previously2.
2. Li Q, Gomez-Lopez N, Drewlo S, et al. Development and Validation of a Rex1-RFP Potency Activity Reporter Assay That Quantifies Stress-Forced Potency Loss in Mouse Embryonic Stem Cells. Stem Cells Dev 2016;25:320-8.

overall_design: Bulk RNAseq of Rex1 promoter- Red Fluorescent Protein (RFP) mESC cultured for 72hr with different stimuli. Triplicate biological experiments.

first: Ximena

middle: L

last: Ruden

first: Mohammed

last: Abdulhasan

first: Katherine

last: Gurdziel


title: Huntingtin loss-of-function contributes to transcriptional deregulation in Huntington’s disease (miRNA-Seq)

status: Public on Jun 27 2024

city: Poznań

first: Emilia

last: Kozłowska

address: Noskowskiego 12/14

country: Poland

institute: IBCH PAS

type: Non-coding RNA profiling by high throughput sequencing

summary: Huntington’s disease (HD) is a fatal neurodegenerative disorder that is caused by the expansion of CAG repeats in the HTT gene, which results in a long polyglutamine (polyQ) tract in the huntingtin protein (HTT). In this study, we searched for networks of deregulated RNAs that contribute to initial transcriptional changes in HD neuronal cells and HTT-deficient cells. We used RNA-seq (including small RNA sequencing) to analyze a set of isogenic, human induced pluripotent stem cell (iPSC)-derived neural stem cells (NSCs); and we observed numerous changes in gene expression and substantial dysregulation of miRNA expression in HD and HTT-knockout (HTT-KO) cell lines. The gene set that was upregulated in both HD and HTT-KO cells was enriched in genes that are associated with DNA binding and regulation of transcription. For both of these models, we confirmed the substantial upregulation of the transcription factors (TFs) TWIST1, SIX1, TBX1, TBX15, MSX2, MEOX2 and FOXD1 in NSCs and medium spiny neuron (MSN)-like cells. Moreover, we identified miRNAs that were consistently deregulated in HD and HTT-KO NSCs and MSN-like cells, including miR-214, miR-199, and miR-9. We suggest that these miRNAs function in the network that regulates TWIST1 and HTT expression via regulatory feed-forward loop (FFL) in HD. Additionally, we reported that the expression of selected TFs and miRNAs tended to progressively change during the neural differentiation of HD cells, what was not observed in HTT-KO model. Based on comparing the HD and HTT-KO cell lines, we propose that early transcriptional deregulation in HD is largely caused by loss of HTT function.

overall_design: In this study, we aimed to reveal and compare networks of deregulated RNAs during the neural differentiation of a set of isogenic human cell lines in the context of HTT function and dysfunction. We differentiated a set of isogenic iPSC lines (control IC1, HD and HTT-KO) into NSCs. Then we performed RNA-seq experiments using RNA isolated from 3 biological replicates of cotrol NSC line (IC1) and 4 biological replicates of HD and HTT-KO NSC lines.

last: Kozlowska

first: Agata

last: Ciolak

first: Grazyna

last: Adamek

first: Julia

last: Szczesniak

first: Agnieszka

last: Fiszer


title: Single-Cell Analysis Reveals Novel Immune Perturbations in Fibrotic Hypersensitivity Pneumonitis

first: Xiting

last: Yan

address: 300 Cedar Street, Ste S441D

department: Internal Medicine

institute: Yale School of Medicine

summary: Rationale: Fibrotic hypersensitivity pneumonitis is a debilitating interstitial lung disease driven by incompletely understood immune mechanisms. Objectives: To elucidate immune aberrations in fibrotic hypersensitivity pneumonitis in single-cell resolution. Methods: Single-cell 5’ RNA sequencing was conducted on peripheral blood mononuclear cells and bronchoalveolar lavage cells obtained from 45 patients with fibrotic hypersensitivity pneumonitis, 63 idiopathic pulmonary fibrosis, 4 non-fibrotic hypersensitivity pneumonitis, and 36 healthy controls in the United States and Mexico. Analyses included differential gene expression (Seurat), transcription factor activity imputation (DoRothEA-VIPER), and trajectory analyses (Monocle3/Velocyto-scVelo-CellRank). Measurements and Main Results: Overall, 501,534 peripheral blood mononuclear cells from 110 patients and controls and 88,336 bronchoalveolar lavage cells from 19 patients were profiled. Compared to controls, fibrotic hypersensitivity pneumonitis has elevated classical monocytes (adjusted-p=2.5e-3) and are enriched in CCL3hi/CCL4hi and S100Ahi classical monocytes (adjusted-p<2.2e-16). Trajectory analyses demonstrate that S100Ahi classical monocytes differentiate into SPP1hi lung macrophages associated with fibrosis. Compared to both controls and idiopathic pulmonary fibrosis, fibrotic hypersensitivity pneumonitis patient cells are significantly enriched in GZMhi cytotoxic T cells. These cells exhibit transcription factor activities indicative of TGFb and TNFa/NFkB pathways. These results are publicly available at https://ildimmunecellatlas.org. Conclusions:  Single-cell transcriptomics of fibrotic hypersensitivity pneumonitis patients uncovered novel immune perturbations, including previously undescribed increases in GZMhi cytotoxic CD4+ and CD8+ T cells – reflecting this disease’s unique inflammatory T-cell driven nature – as well as increased S100Ahi and CCL3hi/CCL4hi classical monocytes also observed in idiopathic pulmonary fibrosis. Both cell populations may guide the development of new biomarkers and therapeutic interventions.

overall_design: To delineate shared fibrosis and disease-specific immune cell aberrations in fibrotic hypersensitivity pneumonitis, individual or multiplexed patient samples underwent 10X 5' v2 single-cell RNA sequencing. Samples from human patients were either bronchoalveolar lavage or peripheral blood mononuclear cells, from 3 cohort sites (Chicago, Mexico City, and New Haven).

first: Amy

middle: Y

last: Zhao

first: Avraham

last: Unterman

first: Nebal

middle: S

last: Abu Hussein

first: Prapti

last: Sharma

first: Fadi

last: Nekola

first: Jasper

last: Flint

first: Yan

last: Xiting

first: Taylor

last: Adams

first: Aurelien

last: Justet

first: Tomokazu

last: Sumida

first: Jiayi

first: Jonas

middle: C

last: Schupp

first: Micha

last: Raredon

first: Farida

last: Ahangari

first: Giuseppe

last: Deluliis

first: Yingze

last: Zhang

first: Ivette

last: Buendia-Roldan

first: Ayodeji

last: Adegunsoye

first: Anne

middle: I

last: Spering

first: Antje

last: Prasse

first: Changwan

last: Ryu

first: Erica

last: Herzog

first: Moises

last: Selman

first: Annie

last: Pardo

first: Naftali

last: Kaminski


title: Transcriptional characterization of reproductive driven liver remodeling

status: Public on Jun 26 2024

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 2720 S. Moody Avenue

institute: OREGON HEALTH & SCIENCE UNIVERSITY

summary: The liver undergoes tissue remodeling throughout the course of a reproductive cycle. During pregnancy/lactation the liver expands in size. Post-weaning, the liver goes through involution, returning to a pre-pregnant state. Here, we deeply, and unbiasedly, characterize the transcriptional profiles in the murine liver across a lactation/wean cycle to reveal the underlying molecular changes associated with these distinct reproductive states.

overall_design:
To investigate changes to the liver over a reproductive cycle we conducted bulk RNAseq on livers of wildtype BALB/C mice over the course a reproductive cycle. Mice were bred at 10-12 weeks of age, and litter size was normalized for even lactation burden. Pups were weaned between 10-14 days of lactation to generate synchronized involution groups. Whole livers were isolated from age matached animals at the following time points: non-pregnant (nulliparous), lactation day 10, post-wean days 2, 4, 6, 8 (involution days 2, 4, 6, 8), and 4-weeks post-wean (regressed). Livers were flash frozen and pulverized prior to RNA extraction.

Please note that samples were sequenced across multiple lanes or sequencers, resulting in multiple SRR accessions per GSM sample.
For proper analysis, all FASTQ files belonging to the same GSM should be combined before processing. Please see more details in the readme.txt.

first: Michelle

last: Ozaki

first: Yi

first: Pepper

last: Schedin


title: CUT&Tag and BioCUT&Tag enables investigation of the AT-rich epigenome of Plasmodium falciparum from low input samples

city: Nijmegen

first: Jonas

last: Gockel

email: jonas-gockel@web.de, jonas.gockel@ru.nl

address: Geert Grooteplein-Zuid 8

country: Netherlands

institute: Radboud University

summary: This study aimed to adapt CUT&Tag to Plasmodium falciparum samples as an efficient and sensitive alternative to classical ChIP-sequencing. We compare H3K9me3 and HP1 CUT&Tag with ChIP-seq datasets, showing successful establishment of CUT&Tag in P. falciparum. Next we aimed to scale down required input material for our CUT&Tag reactions and generated high-quality HP1 tracks with as little as 10.000 nuclei. To minimise potential sample loss we tested feasibility of utilising (frozen) saponin parasite isolates as input material instead of nuclei, which proved to be viable. Lastly, we deployed our new technique Dimerisation-induced Biotinylation-CUT&Tag (DiBioCUT&Tag) to catch transient interactions by biotinylation of strongly associated proteins such as histones. We tested this technique on HP1 and compared standart CUT&Tag with DiBioCUT&Tag. Furthermore, we explored interactions of the transcription factor BDP5, which we were previously unable to succesfully ChIP.

overall_design: We sequenced (DiBio)CUT&Tag libraries generated from different Plasmodium falciparum strains. We used different epitope targets (Anti-HP1, Anti-H3K9me3, Anti-IgG, Anti-Biotin), varied the input material amount (1M, 100K, 10K) and Input material type (isolated Nuclei, fresh parasite isolates, frozen parasite Isolates)

first: Gala

last: Ramón-Zamorano

first: Jessica

last: Kimmel

first: Tobias

last: Spielmann

first: Richárd

last: Bártfai


title: DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [CUT&Tag]

status: Public on Jun 20 2024

city: Guangzhou

first: Lijun

last: Xiang

state: Guangdong

address: No.55, West of Zhongshan Avenue

department: Guangzhou Key Laboratory of Insect Development Regulation and Application Research

institute: South China Normal University

summary: G-quadruplex structures (G4s) have been identified in genomes of multiple organisms and proven to play important epigenetic regulatory roles in various cellular functions. However, the G4 formation mechanism remains largely unknown. Here, we found a negative correlation between DNA 5mC methylation and G4 abundance. The abundance of genomic G4s significantly increased when the whole-genome methylation level was reduced in DNMT1-knockout cells. This increase was then suppressed by DNMT1 over-expression. And more G4s were detected in the hypomethylated cancer cell line HepG2 and rectal cancer tissues. Besides, 5mC modification significantly inhibited G4 formation of the potential G-quadruplex sequences (PQSs). The transcription of genes with 5mC modification sites in their promoter PQSs was affected after treatment with G4 stabilizer pyridostatin or methylation inhibitor 5-aza-dC. The global reduction of genomic methylation elevates gene transcription levels through increased G4s. Taken together, DNA 5mC methylation prevents PQSs from folding into G4s in genomes.

overall_design: ATAC for 293T cells and DNMT1-KO 293T cells

first: Kangkang

last: Niu

first: Hui


title: Direct Inhibition of Tumor Hypoxia Response with Synthetic Transcriptional Repressors

status: Public on Jun 22 2024

city: Chicago

first: Dongbo

last: Yang

state: IL

address: 929 E 57th St

institute: University of Chicago

summary: Many oncogenic transcription factors (TFs) are considered to be undruggable due to their reliance on large protein-protein and protein-DNA interfaces. TFs like hypoxia-inducible factors (HIFs) and X-box binding protein 1 (XBP1) are induced by hypoxia and other stressors in solid tumors and bind to UPRE/HRE motifs to control oncogenic gene programs. Here, we report a strategy to create synthetic transcriptional repressors (STRs) that mimic the bZIP domain of XBP1 and recognize the UPRE/HRE motif. A lead molecule, STR22, binds UPRE/HRE DNA sequences with high fidelity and competes with both TFs in cells. Under hypoxia, STR22 globally suppresses HIF1a binding to HRE-containing promoters/enhancers, inhibits hypoxia-induced gene expression and blocks pro-tumorigenic phenotypes in TNBC cells. In vivo, intratumoral and systemic STR22 treatment inhibited hypoxia-dependent gene expression, primary tumor growth and metastasis of TNBC tumors. These data validate a novel strategy to target the tumor hypoxia response through coordinated inhibition of TF-DNA binding.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq: For the in vitro HeLa cell experiment, total RNA was extracted from cell culture samples treated as described in the main text using the RNeasy Plus Mini Kit (Qiagen). Three independent biological replicates were performed per experimental condition for a total of 9 RNA samples. For the in vivo 4T1 tumor experiment, five PBS and five STR22-treated tumors were collected from ten BALB/c mice. Fresh tumors were placed inside M Tubes (Miltenyi Biotec, 130-093-236), then homogenized with TRI Reagent (Zymo Research, R2050-1) by a gentleMACS Dissociator (Miltenyi Biotec 130-093-235). Total RNA extraction with genomic DNA removal was performed using the Direct-zol RNA MiniPrep Plus kit (Zymo Research, R2072). RNA sample quality check, library construction, and sequencing were performed by the University of Chicago Genomics Facility following standard protocols. Samples from each experiment were sequenced in two runs on a NovaSeq 6000 sequencer to generate paired-end 100bp reads. For each sample, raw FASTQ files from two flow cells were combined before downstream processing. RNA-seq data were analyzed as previously reported and briefly described below. A local Galaxy 20.05 instance was used for the following steps. Quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3. The reads were mapped to the human genome (UCSC hg19 with GENCODE annotation) or the mouse genome (UCSC mm10 with GENCODE annotation) using RNA STAR 2.7.5b. The resulting mapped reads from each sample were counted by featureCounts 1.6.4 for per-gene read counts. The raw counts were analyzed for differential expression between experimental conditions using DESeq2 1.22.1, which also generated a normalized gene expression matrix. The Morpheus software (Broad Institute) was used to draw gene expression heatmaps using the DESeq2-normalized gene expression data. For each gene, the normalized expression values of all samples were transformed by subtracting the mean and dividing by the standard deviation. The transformed gene expression values were used to generate heatmaps. Significant genes and their expression fold change results were analyzed by Ingenuity Pathway Analysis (IPA) software (Qiagen) to predict changes in Canonical Pathways and Diseases and Biological Functions. ChIP-seq: DNA sample quality check, library construction, and sequencing were performed by the University of Chicago Genomics Facility following standard protocols. Samples were sequenced on a NovaSeq 6000 sequencer to generate paired-end 100bp reads. RNA-seq data were analyzed using a local Galaxy 20.05 instance using the following steps: quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3. IP and input reads for each sample were mapped to the human genome (UCSC hg19 with GENCODE annotation) using BWA-MEM 0.7.17.1. To visualize ChIP-seq results, the mapped reads files were counted and the resulting TDF files graphed using Integrative Genomics Viewer 2.9.4. The mapped reads were converted to a SAM file format using samtools 1.2. Peak calling, motif analysis, and annotations were performed by Homer 4.11.1 using the IP and input SAM files for each sample. Settings for peak calling were included in the submitted peak files.

first: Zeyu

last: Qiao

first: Long

last: Nguyen

first: Marsha

last: Rosner

first: Raymond

last: Moellering


title: A Vago-like gene enhances dengue and Zika virus dissemination in Aedes aegypti

status: Public on Jun 24 2024

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

institute: Institut Pasteur

summary: Arthropod-borne viruses (arboviruses) such as dengue virus (DENV) and Zika virus (ZIKV) pose a significant threat to global health. Novel approaches to control arbovirus spread are focused on harnessing the antiviral immune system of their main vector, the Aedes aegypti mosquito. In arthropods, genes of the Vago family are often presented as analogs of mammalian cytokines with potential antiviral functions, but the role of Vago genes upon virus infection in Ae. aegypti is largely unknown. We performed a phylogenetic analysis of the Vago gene family in Diptera that prompted us to focus on a Vago-like gene that we named VLG-1. Using CRISPR/Cas9-mediated gene editing, we generated a VLG-1 mutant line of Ae. aegypti that revealed a proviral effect of this gene upon DENV and ZIKV infection. In the absence of VLG-1, virus dissemination throughout the mosquito’s body was impaired, albeit not altering virus transmission rates. A tissue-specific transcriptome analysis revealed that the loss of VLG-1 impacted numerous biological processes potentially linked to viral replication, such as the oxidative stress response. Our results challenge the conventional understanding of Vago-like genes as antiviral factors and underscores the need for further research to elucidate the molecular mechanisms underlying mosquito-arbovirus interactions.

overall_design: To investigate the global impact of VLG-1 loss and its link with virus infection in Ae. aegypti, we analyzed the midgut and body (carcass + head) transcriptomes of VLG-1Δ mutant and control lines on days 2, 5, and 9 after a DENV-1 or mock bloodmeal. Each RNA-Seq library is a pool of 10 individual tissues.

first: Elodie

last: Couderc

first: Anna

middle: B

last: Crist

first: Josquin

last: Daron

first: Femke

last: van Hout

first: Artem

last: Baidaliuk

first: Umberto

last: Palatini

first: Stéphanie

last: Dabo

first: Thomas

last: Vial

first: Louis

last: Lambrechts

first: Sarah

last: Merkling


title: DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [ATAC-seq]

first: Lijun

last: Xiang

overall_design: Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC) for 293T cells and DNMT1-KO 293T cells

first: Kangkang

last: Niu

first: Hui


title: Epigenetic changes play a role in regulating the epithelial-mesenchymal transition in human trophoblast differentiation [Methylation array]

status: Public on Jul 03 2024

city: Nutley

first: Benjamin

last: Tycko

state: New Jersey

address: 111 Ideation Way

department: Epigenetics

institute: Hackensack Meridian Health Center for Discovery and Innovation (HMH-CDI)

type: Methylation profiling by genome tiling array

summary: The phenotype of term, human placental extravillous trophoblast (EVT) reflects both the first trimester differentiation from villous cytotrophoblast (CTB) and later gestational changes, including the loss of proliferative and invasive capacity. Invasion abnormalities, as observed in preeclampsia and placenta accreta spectrum, are not usually diagnosed until the second or even third trimester of pregnancy. Characterization of the normal processes at term, including arrest of  invasion is therefore crucial. In this report gene expression analysis demonstrates definitively the epithelial-mesenchymal transition (EMT) mechanism which underlies differentiation and provides a trophoblast-specific EMT signature. Methylation profiling shows that CTB, already hypomethylated relative to other somatic cells, show a further degree of hypomethylation in their transition to EVT. A small fraction of genes show both gain of methylation and changes in gene expression. Prominent are genes involved in the EMT such as the transcription factor RUNX1, loss of which leads to reduced migratory capacity in JEG3 trophoblast cells. Examination of these EMT genes leads us to suggest that the gains of methylation may assist in maintaining term EVT in a mesenchymal but non-invasive state.

overall_design:
Cytotrophoblast (CTB) and extravillous trophoblast (EVT) were isolated from placenta samples and analyzed with the Illumina Infinium Methylation EPIC array.
Please note that this dataset accompanies the GSE256412 records.

first: Mauricio

last: Rigo

first: William

last: Ackerman IV

first: Sonia

last: DaSilva-Arnold

first: Catherine

last: Do

first: Mariam

last: Tariq

first: Angelica

last: Castano

first: Stacy

last: Zamudio

first: Nicholas

middle: P

last: Illsley


title: DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [WGBS]

overall_design: Whole Genome Bisulfite Sequencing (WGBS ) for 293T cells and DNMT1-KO 293T cells


title: Epigenetic changes regulating the epithelial-mesenchymal transition in human trophoblast differentiation

city: Maplewood

first: Nick

state: NJ

address: Richmond Ave

institute: Placental Research Group LLC

overall_design:
To examine differences between term cytotrophoblast (CTB) and extravillous trophoblast (EVT), we isolated these cells in a paired manner from the basal plate of the human placenta and extracted total RNA
RNA extracted from 9 paired samples of cytotrophoblast and extravillous trophoblast and 4 sets of villous core cytotrophoblast (vCTB) was used to generate a cDNA library. RNA-sequencing was followed by gene expression analysis.

first: Martha

last: Salas


title: The role of EZH2 in sepsis-induced acute lung injury [RNA-Seq]

status: Public on Jun 18 2024

city: Beijing

first: Ziyi

last: Wang

address: Litang Road 168, Changping District, Beijing

institute: Beijing Tsinghua Changgung Hospital

summary: To investigate the role of EZH2 in sepsis-induced acute lung injury, we established a mouse model of sepsis in which macrophages specifically knocked out EZH2.We then used RNA-seq data from lung tissues of four groups of mice for gene expression profiling.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from lung tissue in mice groups (sham、CLP、EZH2KO sham、EZH2KO CLP).

first: Zhong


title: Setd2 overexpression rescues bivalent gene expression during SCNT-mediated ZGA by enhancing H3K36me3 at gene bodies and excluding H3K27me3 from promoters [ChIP-seq]

first: Xiaolei

last: Zhang

overall_design: Ultra-low-input chromatin immunoprecipitation followed by sequencing (ULI-NChIP-seq) for histone moifications H3K4me3, H3K27me3 and H3K36me3 in mouse somatic cell nuclear transfer embryos.

first: Ruimin

last: Xu

first: Yuyan

last: Zhao

first: Yijia

last: Yang

first: Hong

first: Xiaoyu

last: Liu

first: Chong

last: Li

first: Shaorong

last: Gao


title: PARP1 inhibition counteracts EBV+ lymphoma progression through EBNA2/MYC axe

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Our group has previously identified how PARP1 can control EBV latency by: (1) altering the 3D virus chromatin structure [28]; (2) regulating CTCF binding on EBV promoters and supporting the latency expression program [29-32]; (3) repressing the lytic gene expression by binding BZLF1 promoter [33, 34]. To date, the therapeutic effect of PARP1 inhibitors on EBV+ lymphomagenesis has been poorly explored. Therefore, we aimed to investigate whether PARP1i was able to counteract EBV-driven tumors in a LCL xenograft model and identify, and confirm, possible mechanisms underlying its therapeutic effect. In the present study we demonstrate that PARP1 inhibition restricts EBV-driven lymphoma in vivo, pointing out the oncogene MYC as its functional target. Specifically, PARP1 inhibition reverts the tumor growth and the metastatic potential of EBV+ LCL, inducing a dramatic transcriptional reprogramming. Interestingly, the absence of PARP1 activity causes a decrease in MYC expression, subsequently leading to a dysregulation of MYC-associated co-factors and targets, both in vivo and in vitro. Our findings also corroborate the link between PARP1 and EBNA2 expression, that we previously demonstrated in vitro. Overall, our study strengthens the central role of PARP1 in EBV malignant transformation and outlines the EBNA2/MYC pathway as an additional target of PARP1 regulation in LCL

overall_design: RNA-seq for untreated and BMN (Talazoparib) treated samples

first: Giorgia

last: Napoletani

first: Italo

last: Tempera


title: Setd2 overexpression rescues bivalent gene expression during SCNT-mediated ZGA by enhancing H3K36me3 at gene bodies and excluding H3K27me3 from promoters

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

overall_design: Refer to individual Series


title: The target gene investigation in osteoblats (OBs) treated with mmu-miR-1963 enriched in EVs from OCs with prostate cancer (PCa) cells [target_EV-miR-1963]

status: Public on Jun 06 2024

city: Tokyo

first: Takaaki

last: Tamura

address: 6-7-1 Nishishinjuku, Shinjyuku-ku

institute: Tokyo Medical University

summary: Bone metastatic lesions of PCa contain areas of bone destruction and formation that are directed by OCs and osteoblasts (OBs), respectively. OC-derived EVs are reported to maintain normal bone homeostasis; however, there is no study investigating the role of EVs from OCs in the presence of PCa. We identified mmu-miR-1963 enriched in EVs from OCs co-cultured with several PCa cell lines. NGS analyses were performed to investigate predicted target genes of EV-miR-1963 in OBs.

overall_design: To investigate the role of EVs derived from OCs with PCa cells, we cultured murine monocytic cell line RAW 264.7, which has potential to differentiate into OC-like cells, with metastatic PCa cell lines and controls. We prepared different types of OCs and EVs from these cells ; OCs normally differentiated from RAW264.7 cells (OC cells), OC cells co-cultured with normal prostate epithelial cells: PNT2 cells (OCN cells), osteolytic PCa cells: PC3M cells (OCP cells), and osteoblastic PCa cells; C4-2B cells (OCC cells). OC differentiation was induced in the presence of RANKL. EVs were isolated from culture supernatant using ultracentrifugation. As a result, we identified mmu-miR-1963 as an enriched microRNA (miRNA) in OCP and OCC EVs. We prepared total RNAs extracted from OCP/OCC/OCN EV treated OBs and mmu-miR-1963/NC mimic transfected OBs and then NGS analyses were performed to investigate predicted target genes of EV-miR-1963 enriched in OCP and OCC EVs in mineralizing OBs (mOBs). Total RNAs are extracted 24h after the treatment in the presence of ascorbic acid and β-glycerophosphate.

first: Tomofumi

last: Yamamoto

first: Yusuke

last: Yoshioka

first: Takahiro

last: Ochiya


title: Huntingtin loss-of-function contributes to transcriptional deregulation in Huntington’s disease (RNA-Seq)

first: Emilia

last: Kozłowska

last: Kozlowska

first: Agata

last: Ciolak

first: Grazyna

last: Adamek

first: Julia

last: Szczesniak

first: Agnieszka

last: Fiszer


title: Gene expression data for 637 human primary breast tumors with recurrence, ER/PR/HER2 status, and overall survival

status: Public on Jun 07 2024

city: Tampa

first: Eric

last: Welsh

state: FL

address: 12902 Magnolia Dr

department: Biostatistics and Bioinformatics

institute: H Lee Moffitt Cancer Center

summary:
We performed gene set enrichment and differential expression analysis to identify biological pathways associated with locoregional recurrence in primary breast tumors.
A custom Affymetrix microarray genechip was used to assess the gene expression of each tumor sample.

overall_design: From a prospective tissue collection protocol representing one academic and two community hospitals, we identified 637 consecutively-treated women with primary breast tumors of invasive ductal or invasive lobular histology. Profiling of RNA extracted from tumor samples was performed with Affymetrix microarrays. Clinical variables include patient age, race, staging information, receptor status, primary surgery type, radiotherapy, and chemotherapy, while outcomes include time to locoregional recurrence and overall survival.

first: Du

last: Dongliang

first: Nicholas

last: Figura

first: Matthew

last: Mills

first: Jacob

last: Purcell

first: George

last: Grass

first: Kamran

last: Ahmed

first: Peter

middle: W

last: Blumencranz

first: Kathleen

last: Allen

first: Christine

last: Laronga

first: Javier

middle: F

last: Torres-Roca

first: Ram

last: Thapa

first: Brooke

last: Fridley

first: Chrisopher

last: Wilson

first: Steven

last: Eschrich

first: Louis

last: Harrison

first: Timothy

last: Robinson

first: Roberto

last: Diaz


title: The gene expression profiles of maturing osteoclasts (OCs) co-cultured with prostate cancer (PCa) cell lines.

first: Takaaki

last: Tamura

summary: Bone metastatic lesions of PCa contain areas of bone destruction and formation that are directed by OCs and osteoblasts (OBs), respectively. Bone resorption induced by OCs is a necessary priming event for tumor progression in PCa bone metastasis.; however,  the characteristics of OCs affected by PCa have not been fully elucidated. Here, we performed NGS analysis to investigate the characteristics of OCs in the presence of PCa.

overall_design: To investigate the impact of secretome derived from PCa cells on the molecular characteristics of OCs, we cultured murine monocytic cell line RAW 264.7, which has potential to differentiate into OC-like cells, with metastatic PCa cell lines and controls. We prepared different types of OCs ; OCs normally differentiated from RAW264.7 cells (OC cells), OC cells co-cultured with normal prostate epithelial cells: PNT2 cells (OCN cells), osteolytic PCa cells: PC3M cells (OCP cells), and osteoblastic PCa cells; C4-2B cells (OCC cells). OC differentiation was induced in the presence of RANKL.

first: Yusuke

last: Yoshioka

first: Takahiro

last: Ochiya


title: The microRNA profiles of extracellular vesicles (EVs) from  osteoclasts (OCs) co-cultured with prostate cancer (PCa) cell lines [OCEVmiRNA-seq]

summary: Bone metastatic lesions of PCa contain areas of bone destruction and formation that are directed by OCs and osteoblasts (OBs), respectively. OC-derived EVs are reported to maintain normal bone homeostasis; however, there is no study investigating the role of EVs from OCs in the presence of PCa.

overall_design: To investigate the EV contents derived from OCs with PCa cells , we cultured murine monocytic cell line RAW 264.7, which has potential to differentiate into OC-like cells, with metastatic PCa cell lines and controls. We prepared different types of OCs and EVs from these cells ; OCs normally differentiated from RAW264.7 cells (OC cells), OC cells co-cultured with normal prostate epithelial cells: PNT2 cells (OCN cells), osteolytic PCa cells: PC3M cells (OCP cells), and osteoblastic PCa cells; C4-2B cells (OCC cells). OC differentiation was induced in the presence of RANKL. EVs were isolated from culture supernatant using ultracentrifugation.


title: Gut microbiota depletion delays peripheral nerve development and impairs neuromuscular junction maturation

status: Public on Jun 10 2024

city: Turin

first: Chiara

last: Cicconetti

state: (TO)

address: Via Nizza, 52

department: Dept. of Life Sciences and Systems Biol

country: Italy

institute: University of Turin

summary: Perturbance of gut microbiota (GM) composition has implications in onset and progression of an emerging number of diseases.   Here we demonstrate a regulatory impact on proper development of the peripheral nervous system (PNS) and its functional connection to skeletal muscles (SM). We analysed peripheral nerves, dorsal root ganglia (DRG) and SM of neonatal and adult mice that were raised as a) germ free (GF) mice, b) gnotobiotic mice, i.e. selectively colonised with 12 known gut bacteria (OMM12), or c) colonised with complex GM (CGM). Stereological and morphometrical analysis mainly revealed that absence of GM impairs the development of median nerves, resulting in smaller diameter hypermyelinated axons. Accordingly, transcriptomic analysis on DRG and sciatic nerves highlighted a panel of differentially expressed developmental and myelination genes. Moreover, GF mice demonstrated histologically atrophic SM, impaired formation of neuromuscular junctions, and deregulated expression of related genes. Our results, for the first time, imply the existence of a “GM-PNS-axis”.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for neonatal and young adult CGM, GF and OMM12 mice on dorsal root ganglia (DRG) and sciatic nerves.

first: Matilde

last: Cescon

first: Giovanna

last: Gambarotta

first: Sonia

last: Calabrò

first: Francesca

last: Anselmi

first: Svenja

last: Kankowski

first: Liosa

last: Lang

first: Marijana

last: Basic

first: Andre

last: Bleich

first: Silvia

last: Bolsega

first: Salvatore

last: Oliviero

first: Stefania

last: Raimondo

first: Dario

last: Bizzotto

first: Kirsten

last: Haastert-Talini

first: Giulia

last: Ronchi


title: PanethcellTNF-signalinginducesbacterialsepsis: PC transcriptome 15h ater TNF

status: Public on Jun 03 2024

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

institute: VIB-UGent

summary: Paneth Cells (PCs) are secretory cells located in the crypts of Lieberkühn of the small intestine. They produce antimicrobial peptides (AMPs) and are thought to keep the microbiome under control. The cytokine TNF, which functions mainly via its TNF receptor 1 (TNFR1 or P55), is a driving force in many inflammatory bowel disease (IBD) patients, but its impact on PCs is poorly known. We have generated PC-specific P55 knockout mice (P55Paneth KO) and found that these mice are protected against lethal TNF-induced systemic inflammatory response syndrome (SIRS). The impact of TNF on PCs is characterized by morphological changes and by intestinal bacterial translocation into organs, such as liver, in which these bacteria induce expression of numerous genes, associated with typical sepsis signatures. The presence of these bacteria cause lethality of the mice. Based on bulk RNA-SEQ on pure PCs, P55 signaling stimulated mainly a type-I IFN response in the PCs, which drives the bacterial translocation and lethality via IFNAR1. Interestingly, based on ER stress reporter mice, PCs constitutively have high amounts of spliced XBP1 (XBP1s) protein, presumably to support their secretion of AMPs, and TNF eradicates this XBP1s production, leading to failure of the unfolded protein response (UPR). This causes reduced antimicrobial activity in PCs, in a P55 and IFNAR1-dependent way. Our data suggest a novel axis induced by TNF in PCs, leading to interferon-induced UPR failure causing lethal bacterial translocation to the liver (and other organs)

overall_design: To investigate the effect of TNF on the paneth cell (PC) transcriptome, PCs were isolated 15h after TNF or PBS (control) injection in mice using cell sorting. 3 PBS and 4 TNF samples were taken (biological replicates; each from a different mice) for RNA isolation and sequencing

first: Charlotte

last: Wallaeys

first: Natalia

last: Garcia-Gonzalez

first: Jolien

last: Vandewalle

first: Tineke

last: Vanderhaeghen

first: Hester

last: Dufoor

first: Melanie

last: Eggermont

first: Riet

last: De Rycke

first: Serge

last: Verbanck

first: George

last: Kollias

first: Richard

last: Blumberg

first: Takao

last: Iwawaki

first: Claude

last: Libert


title: Pioneer neurons are molecularly distinct, and their axon targeting is regulated by retinoic acid signaling (WT 30 h)

status: Public on Jun 01 2024

first: Alex

last: Nechiporuk

state: OR

address: 3181 SW Sam Jackson Park Road

institute: Oregon Health and Science Univ

summary: During nervous system development, pioneer neurons are the first to extend their axons into target tissues, creating a scaffold for follower neurons. Despite years of study, whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line (pLL) sensory neurons during axon growth using single-cell RNA sequencing (scRNA-seq) revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state, whereas “pioneer” is a later developmental state. The scRNA-seq data revealed active retinoic acid (RA) signaling in followers, but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret, which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development.

overall_design: Thirty hour old TgBAC(neurod1:EGFP)nl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube.

first: Benjamin

last: Woodruff

first: Lauren

last: Miller

first: Lindsey

last: Royer

first: Nicholas

last: Calistri

first: Laura

last: Heiser

middle: V


title: Inorganic Biomaterials Shape the Transcriptome Profile to Induce Endochondral Differentiation

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy Medical Research and Education Building II

institute: Texas A&M Health Science Center

summary: We investigate cellular responses to traditional bioactive mineral-based nanomaterials, such as hydroxyapatite (nHA), whitlockite (nWH), silicon-dioxide (nSiO2), and the emerging synthetic 2D nanosilicates (nSi), on human mesenchymal stem cells (hMSCs). Specifically, using next-generation transcriptome sequencing (RNA-seq), we uncover key signaling pathways and transcriptome dynamics due to exposure to these inorganic nanomaterials. Whole-transcriptome sequencing identified a stabilized skeletal progenitor state in stem cells treated with nanosilicates that suggests endochondral differentiation of hMSCs, resulting in increased deposition of matrix mineralization compared with control or other treatment groups.

overall_design: Examination of effect of inorganic nanomaterials nSi, nWH, nHA, and nSiO2 on hMSC fate

first: Anna

last: Brokesh

last: Cross

last: Kersey

first: Manish

middle: K

last: Jaiswal

first: Akhilesh

last: Gaharwar


title: EphB2-mediated ephrin-B reverse signaling on microglia drives an antiviral but also inflammatory response in HIV

city: Riverside

first: Marcus

last: Kaul

address: 900 University Ave, SOM RB Room 311

department: Biomedical Sciences

institute: University of California, Riverside

summary: HIV Associated Neurocognitive Disorder (HAND) is a condition behaviorally characterized by cognitive and neurological impairments, and pathologically characterized by neuroinflammation and a loss of synaptic integrity and function. Although therapeutics exist to increase the lifespan of people living with HIV, they are not effective at preventing HIV induced neuronal damage and the prevalence of HAND remains virtually unchanged. We observed an increase in expression of ephrin-B/EphB in post-mortem CNS specimen of people who lived with HIV and brain pathology. Given the previously recognized impact of EphB2 on inflammation in the periphery, the functional role of EphB2-mediated ephrin-B reverse signaling on microglia was assessed. A a pro-inflammatory and antiviral mRNA expression profile was observed. The stimulation produced condirioned media, including secreted inflammatory factors, that were sufficient to induce non-cell contact-dependent neurotoxicity. Finally, knockdown of microglial ephrin-B1, EphB2 binding partner, resulted in a partial alleviation of the microglial pro-inflammatory signature and subsequent neurotoxicity. In this study, we show that elevated EphB2, and its reverse signaling through ephrin-B1 in microglia, can drive neuroinflammation and toxicity suggesting this pathway can mediate neurotoxicity in neuroHIV. Furthermore, we propose that this neuroinflammatory mechanism may play a role in promoting other neurodegenerative diseases.

overall_design: HMC3 cells were transfected with ephrin-B1 siRNA or non-targeting, negative control siRNA for 48 hours prior to treatment with pre-clustered EphB2-Fc or Control-Fc for 24 hours. Pre-clustering was accomplished by incubation for 1 hour on ice, mixing every 15 minutes. Following 24 hour EphB2-Fc or Control-Fc treatment, HMC3 cells were lysed for RNA isolation using Qiagen's RLT Buffer with 1% beta-mercaptoethanol. Isolated RNA was quality-controlled and sequenced.

first: Jeffrey

last: Koury

first: Hina

first: Samantha

last: Sutley-Koury

first: Dominic

last: Fok

first: Xinru

last: Qiu

first: Ricky

last: Maung

last: Gelman

first: Iryna

last: Ethell


title: Pioneer neurons are molecularly distinct, and their axon targeting is regulated by retinoic acid signaling

first: Alex

last: Nechiporuk

overall_design: Fourteen-hour old, eighteen-hour old, twenty-two hour old, forty-eight hour old TgBAC(neurod1:EGFP)nl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube.

first: Benjamin

middle: M

last: Woodruff

last: Miller

last: Royer

first: Jacqueline

last: McVay


title: transcriptome of purified PC and non-PC fractions: GR-WT & GR-KO

status: Public on Jun 17 2024

first: Steven

last: Timmermans

summary: Paneth Cells (PCs) are secretory cells located in the crypts of Lieberkühn of the small intestine. They produce antimicrobial peptides (AMPs) and are thought to keep the microbiome under control. The cytokine TNF, which functions mainly via its TNF receptor 1 (TNFR1 or P55), is a driving force in many inflammatory bowel disease (IBD) patients, but its impact on PCs is poorly known. We have generated intestinal glucocorticoid receptor knockout mice (GR villin KO) and investigated the diffrences between WT and KO paneth and non-paneth cell fractionf from the cell sorting.

overall_design: cells were isolated form naive mice that were either GRKO or GR WT. Both the PC and non-PC crypt cells were used for sequencing for a total of 4 conditons with 3 replicates each

first: Charlotte

last: Wallaeys

first: Natalia

last: Garcia-Gonzalez

first: Jolien

last: Vandewalle

first: Tineke

last: Vanderhaeghen

first: Hester

last: Dufoor

first: Melanie

last: Eggermont

first: Riet

last: De Rycke

first: Serge

last: Verbanck

first: George

last: Kollias

last: Souffriau

first: Richard

last: Blumberg

first: Takao

last: Iwawaki

first: Claude

last: Libert


title: A murine model lacking Lyst recapitulates Chediak-Higashi syndrome with an earlier-onset neurodegenerative phenotype

city: Rockville

first: May Christine

last: Malicdan

state: MD

address: 5625 Fisher's Ln

department: National Human Genome Research Institute

institute: National Institutes of Health

summary: Chediak-Higashi Syndrome (CHS) is a rare autosomal recessive disorder caused by mutations in the lysosomal trafficking regulator (LYST) gene, characterized by partial oculocutaneous albinism, bleeding diathesis, immune deficiency, and progressive neurodegeneration. We generated a Lyst knockout model (ΔLYST-B6) in which to accurately study pathophysiology seen in patients. Here we show the ΔLYST-B6 model faithfully recapitulates characteristic features of CHS, including neurological manifestations at 6 months of age with associated progressive loss of Purkinje cells. Transcriptomic and lipidomic analyses of ΔLYST-B6 brain tissue reveals numerous differentially expressed genes and lipids in the cerebellum of 18-month-old ΔLYST-B6 mice suggesting progressive cerebellar decline and microglial involvement. Immunofluorescence studies implicate a plausible role of Bergmann glia in the pathology of CHS. Our findings demonstrate that the ΔLYST-B6 model recapitulates key features of the human CHS phenotype, including CHS-associated neurodegeneration, and provides a reliable model in which to study the function of LYST and explore future therapies for CHS.

overall_design: A knockout mouse model (ΔLYST-B6) lacking a functional murine Lyst homologue was generated by deleting exons 4-53 using CRISPR/Cas9 gene editing on the C57BL/6J genetic background. To characterize the neurological phenotype of ΔLYST-B6 mice, brain tissues (cerebellum and cortex) were collected from 3- and 18-month-old wildtype and ΔLYST-B6 mice.


title: Single-cell analysis reveals clonal expansions of pro-inflammatory tissue-resident memory Th17 cells in Crohn's disease

status: Public on May 31 2024

city: Seoul

first: Yoonho

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea

department: Department of Biochemistry and Molecular Biology

institute: University of Ulsan College of Medicine

summary: To investigate the transcriptional profiles and functional characteristics of Trm cells in the small bowel of Crohn's disease (CD) and their interactions with immune cells, we performed single-cell RNA sequencing on CD3+ T cells and CD45+ immune cells.

overall_design:
Intestinal immune cells were isolated by CD3+ or CD45+ in lamina propria (LP) and submucosa/muscularis propria-enriched fractions (SM/MP) from small bowel tissue samples in each patient.
***Submitter states that raw data is not provided due to hospital policy***


title: Transcriptome analysis after CCCP and/or DHA treatment in uveal melanoma cells

city: Shanghai

first: Minyue

last: Xie

state: China

address: No. 227, South Chongqing Road

institute: School of Medicine, Shanghai Jiao Tong University

summary: In order to study the mechanism of CCCP combined with DHA treatment in uveal melanoma, we applied RNA-seq to identify its target genes in ocular melanoma.

overall_design: Examination the different expressed genes after treated by CCCP and DHA in uveal melanoma cells.

first: Shengfang

last: Ge


title: Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [ATAC-seq]

status: Public on May 22 2024

city: Villejuif

first: Clémence

last: Henon

address: 114 rue Edouard Vaillant

institute: Gustave Roussy

summary: Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, aggressive sarcoma driven by the EWSR1-WT1 chimeric transcription factor. Despite this unique oncogenic driver, DSRCT displays a polyphenotypic differentiation of unknown causality. Using single-cell multi-omics on samples from patients, we find that DSRCT tumor cells cluster into consistant subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs.

overall_design: ATAC-seq was performed in the JN-DSRCT-1 cell line after a 48-hour siRNA-mediated silencing using a control non-targeting siRNA, a CCND1-targeting siRNA, a EWSR1::WT1 siRNA, or in a control condition without transfection.

first: Julien

last: Vibert

first: Léo

last: Colmet-Daage

first: Sophie

last: Postel-Vinay


title: CUT&Tag sequencing of large intestinal ILC2s from mice

status: Public on May 28 2024

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

summary: To investigate the transcriptional regulation of Xbp1s in ILC2s, sorted large intestinal ILC2s from mice were used for CUT&Tag sequencing to analyze the target of Xbp1s.

overall_design: Sorted ILC2s from the large intestine were cultured with IL-2, IL-7, IL-25 and IL-33. CUT&Tag experiments were performed using the antibody against Xbp1s.

first: Yanyan

last: Cui

first: Yatai

last: Chen

first: Detian

last: Yuan

first: Shiyang

last: Li


title: Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [Visium: Spatial transcriptomics]

overall_design:
Spatial transcritomics analyses were performed using Visium assays on scRNA-seq-matched FFPE samples (n=6 patients)

***************************************************************
Submitter states that missing raw files are due to patient privacy concerns.
***************************************************************


title: Determine which gene promoter EZH2 binds to in macrophages in the state of sepsis [ChIP-seq]

first: Ziyi

last: Wang

summary: In order to explore the role of EZH2 in the occurrence and development of sepsis in macrophages, we stimulated RAW264.7 cells with LPS to construct a sepsis cell model, and explored the binding site of EZH2 by co-immunoprecipitation combined with high-throughput sequencing.

overall_design: We stimulated RAW264.7 cells with LPS to simulate the macrophage status in sepsis, and identified the binding site of EZH2 protein on the whole genome by chromatin immunoprecipitation (ChIP) combined with high-throughput sequencing technology.

first: Zhong


title: Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [Cell_line_RNA-seq]

overall_design: RNA-seq was performed on JN-DSRCT-1 cell line after a 48-hour siRNA-mediated silencing using a control non-targeting siRNA or a EWSR1::WT1 siRNA.


title: Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [Patient_bulkRNA-seq]


title: Chromatin-focused genetic and chemical screens identify BRPF1 as a targetable vulnerability in Taxol-resistant triple-negative breast cancer [RNA-seq]

status: Public on May 14 2024

city: İstanbul

first: Tugba

last: Bagci-Onder

address: Rumelifeneri Yolu, Sarıyer

department: Koç University Research Center for Translational Medicine

country: Turkey

institute: Koç University

summary: Triple-negative breast cancer (TNBC) stands out as a particularly aggressive and frequently recurring form of breast cancer. Due to the absence of hormone receptors, the available treatment avenues are constrained, making chemotherapy the primary approach. Unfortunately, the development of resistance to chemotherapy poses a significant challenge, further restricting the already limited therapeutic alternatives for recurrent cases. Understanding the molecular basis of chemotherapy resistance in TNBC is pivotal for improving treatment outcomes. Here, we generated two different Taxol-resistant TNBC cell lines with dose-escalation method to mimic chemotherapy resistance in vitro. These cells exhibited hallmark features of resistance, including reduced cell growth, altered morphology, and resistance to apoptosis. Transcriptome analysis uncovered elevated ABCB1 expression and multidrug-resistant phenotype in the resistant cells. To comprehensively investigate the key epigenetic regulators of Taxol resistance, we conducted epigenome-wide CRISPR/Cas9 and chemical probe library screens. Both screens pinpointed Bromodomain and PHD Finger Containing 1 (BRPF1) which is the reader protein in MOZ/MORF histone acetyl-transferase complex, as the regulator of Taxol resistance in TNBC cells. Knockout of BRPF1, but not the other members of the MOZ/MORF complex, sensitized resistant cells to Taxol. Additionally, BRPF1 inhibitors, PFI-4 and OF-1, in combination with Taxol significantly reduced cell viability. Transcriptome analysis upon BRPF1 loss or inhibition revealed a negative impact on ribosome biogenesis-related gene sets, resulting in a global decrease in protein translation in Taxol-resistant cells. Our ChIP-qPCR analysis further demonstrated that active BRPF1 directly interacts with the ABCB1 promoter, enhancing its expression and inducing a multidrug-resistant phenotype. Conversely, knockout or inhibition of BRPF1 leads to decreased ABCB1 expression. This dual mechanism critically sensitizes Taxol-resistant TNBC cells to chemotherapy. Our findings uncover a comprehensive molecular framework, highlighting the pivotal role of epigenetic reader protein BRPF1 in Taxol resistance and providing potential avenues for therapeutic intervention in TNBC.

overall_design: To mimic chemotherapy resistance in vitro, we generated two different Taxol-resistant SUM159PT cell lines, namely T1-160 and T2-450. We first performed RNA-seq to uncover the differentially expressed genes in resistant cells when compared to parental cells. Later, we identified BRPF1 as a regulator of taxol resistance in T1-160 cells through epigenome-wide CRISPR/Cas9 screening. Next, we either knocked out BRPF1 by two different sgRNAs or inhibited via BRPF1 inhibitors (PFI-4 and OF-1) and performed RNA-seq to understand the changes in the transcriptome when BRPF1 is absent or inhibited.

first: Ozlem

last: Bayram

first: Ahmet

last: Cingöz

first: Ebru

last: Yilmaz

first: Ali

last: Aksu

first: Beril

last: Esin

first: Nareg

last: Pinarbasi-Degirmenci

first: Ayse

middle: D

last: Cavga

first: Beyza

last: Dedeoglu

first: Buse

last: Cevatemre

first: Hamzah

last: Syed

first: Martin

last: Philpott

first: Adam

last: Cribbs

first: Udo

last: Oppermann

first: Nathan

middle: A

last: Lack

first: Ceyda

last: Ayhan

first: Tamer

middle: T

last: Önder


title: IL-8+ neutrophils drive inexorable inflammation in severe alcohol-associated hepatitis [scRNA-seq]

status: Public on May 13 2024

first: Yukun

last: Guan

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

summary: Patients with alcohol-associated liver cirrhosis (AC) may develop severe alcohol-associated hepatitis (sAH), but the mechanisms underlying the transition from AC to sAH still remain unclear. We performed single cell RNA (scRNA) sequencing analysis of livers and peripheral white blood cells (WBC) from sAH and AC patients. We found that the significant difference between sAH and AC was that sAH livers had a markedly higher number of neutrophil subsets than AC livers. Thus, we further focused on the neutrophil cluster and found two distinct sAH-specific liver neutrophils are notably characterized by heightened expression of CXCL8 (IL-8) defined as IL-8+ neutrophils blood. Our current study has demonstrated that sAH had self-sustaining IL-8+ neutrophil accumulation that likely drives inexorable liver inflammation and failure in sAH. Based on our study, we believe targeting IL-8+ neutrophils is a promising therapeutic strategy for sAH.

overall_design: We performed scRNA sequencing analysis of 6 liver tissues and 7 peripheral white blood cells (WBC) from sAH and AC patients, including 5 sAH livers, 4 sAH WBCs; 1 AC liver, and 3 AC WBCs.

last: GUAN

first: Brandon

last: Peiffer

first: Dechun

last: Feng

first: Zhaoli

last: Sun

first: Bin

last: GAO


title: The target gene investigation in osteoclats (OCs) treated with mmu-miR-5112 enriched in EVs from OCs with prostate cancer (PCa) cells [target_EV-miR-5112]

first: Takaaki

last: Tamura

summary: Bone metastatic lesions of PCa contain areas of bone destruction and formation that are directed by OCs and osteoblasts (OBs), respectively. OC-derived EVs are reported to maintain normal bone homeostasis; however, there is no study investigating the role of EVs from OCs in the presence of PCa. We identified mmu-miR-5112 enriched in EVs from OCs co-cultured with several PCa cell lines. NGS analyses were performed to investigate predicted target genes of EV-mmu-miR-5112 in OCs.

overall_design: To investigate the role of EVs derived from OCs with PCa cells, we cultured murine monocytic cell line RAW 264.7, which has potential to differentiate into OC-like cells, with metastatic PCa cell lines and controls. We prepared different types of OCs and EVs from these cells ; OCs normally differentiated from RAW264.7 cells (OC cells), OC cells co-cultured with normal prostate epithelial cells: PNT2 cells (OCN cells), osteolytic PCa cells: PC3M cells (OCP cells), and osteoblastic PCa cells; C4-2B cells (OCC cells). OC differentiation was induced in the presence of RANKL. EVs were isolated from culture supernatant using ultracentrifugation. As a result, we identified mmu-miR-5112 as an enriched microRNA (miRNA) in OCP and OCC EVs. We prepared total RNAs extracted from OCP/OCC/OCN EV treated OCs and mmu-miR-5112/NC mimic transfected OCs and then NGS analyses were performed to investigate predicted target genes of EV-miR-5112 enriched in OCP and OCC EVs in maturing OCs (mOCs). Total RNAs are extracted 24h after the treatment in the presence of RANKL.

first: Tomofumi

last: Yamamoto

first: Yusuke

last: Yoshioka

first: Takahiro

last: Ochiya


title: Transcriptome profiling of non-islet metabolic tissues in ~500 DO mouse liver, adipose, heart, and skeletal muscle tissue from mice fed high-fat, high-sugar diet. [Liver]

status: Public on May 10 2024

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

summary: Perform RNAseq with existing frozen mouse DO tissues from ~500 DO mice were sensitized on a HFHS diet (Keller, Gatti et al. 2018). The same mice have been extensively characterized for T2D-relevant clinical phenotypes, ex-vivo islet function, and other features including microbiome profiling.  Gene expression and proteomic profiling has already been completed in islets. We will collect and analyze the genetic architecture of gene expression in liver, adipose, heart, skeletal muscle. Tissues will be sent to JAX Bar Harbor from Alan Attie’s lab. These tissues were from the same mice used for transcriptome analysis of islets (Genetics May 1, 2018 vol. 209 no. 1 335-356)

overall_design: transcription profiling by high-throughput sequencing design

first: Candice

middle: N

last: Baker


title: Derivation of human trophoblast stem cells from placentas at birth

status: Public on May 09 2024

city: Raleigh

first: Balaji

last: Rao

state: North Carolina

address: Partners II, 840 Main Campus Drive, Room 3107, Raleigh, North Carolina 27606

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: Human trophoblast stem cells (hTSCs) have emerged as a powerful tool for modeling the placental cytotrophoblast (CTB) in vitro. hTSCs were originally derived from CTBs of the first trimester or blastocyst-stage embryos in trophoblast stem cell medium (TSCM) that contains epidermal growth factor (EGF), the glycogen synthase kinase-beta (GSK3b) inhibitor CHIR99021, the transforming growth factor-beta (TGFb) inhibitors A83-01 and SB431542, valproic acid (VPA), and the Rho-associated protein kinase (ROCK) inhibitor Y27632. Here we show that hTSCs can be derived from CTBs isolated from the term placenta, using TSCM supplemented with a low concentration of mitochondrial pyruvate uptake inhibitor UK5099 and lipid-rich albumin (TUA medium). Notably, hTSCs could not be derived from term CTBs using TSCM alone, or in the absence of either UK5099 or lipid-rich albumin. Strikingly, hTSCs cultured in TUA medium for a few passages could be transitioned into TSCM and cultured thereafter in TSCM. hTSCs from term CTBs cultured in TUA medium as well as those transitioned into and cultured in TSCM thereafter could be differentiated to the extravillous trophoblast and syncytiotrophoblast lineages, and exhibited high transcriptome similarity with hTSCs derived from first trimester CTBs. We anticipate that these results will enable facile derivation of hTSCs from normal and pathological placentas at birth with diverse genetic backgrounds, and facilitate in vitro mechanistic studies in trophoblast biology.

overall_design: RNA sequencing was conducted on the following cells/conditions: two primary hTSC lines from term placenta cultured in TUA medium, TSCM from TUA medium, and TA medium. Two term derived cell lines are T1 (also referred to as CTB21126R+) and T2 (also referred to as  CTB22131R+). Total sample #17. Two primary hTSC lines from the first trimester (CT29, CT30) were used as the control group.

first: Victoria

last: Karakis

first: Mahe

last: Jabeen

first: John

last: Britt

first: Adriana

last: San Miguel


title: Transcriptome profiling of non-islet metabolic tissues in ~500 DO mouse liver, adipose, and skeletal muscle tissue from mice fed high-fat, high-sugar diet. [Adipose]

summary: Perform RNAseq with existing frozen mouse DO tissues from ~500 DO mice were sensitized on a HFHS diet (Keller, Gatti et al. 2018). The same mice have been extensively characterized for T2D-relevant clinical phenotypes, ex-vivo islet function, and other features including microbiome profiling.  Gene expression and proteomic profiling has already been completed in islets. We will collect and analyze the genetic architecture of gene expression in liver, adipose, skeletal muscle. Tissues will be sent to JAX Bar Harbor from Alan Attie’s lab. These tissues were from the same mice used for transcriptome analysis of islets (Genetics May 1, 2018 vol. 209 no. 1 335-356)


title: Transcriptome profiling of non-islet metabolic tissues in ~500 DO mouse liver, adipose, and skeletal muscle tissue from mice fed high-fat, high-sugar diet. [skeletal muscle]


title: Stress granule assembly impairs macrophage efferocytosis [RIP-seq]

status: Public on May 01 2024

first: Ye

last: Zhou

address: Xiangyin Road

department: National Key Laboratory of Immunity & Inflammation

institute: Naval Medical University

summary: Stress granules (SGs) assembly in response to various stress, has been demonstrated in the regulation of anti-viral immune response and tumor progression. However, lack of evidence to illustrate the relation between SGs formation and allergic diseases. Applied G3BP1-RIP-seq in RAW264.7 cells, G3BP1 binding mRNAs are defined.

overall_design: To investigate the G3BP1 binding mRNA, we applied G3BP1-RIP-seq in RAW264.7 cells.

first: Zhou

last: Ye

first: Yang

last: Zixuan

first: Hou

last: Jin


title: Novel insights into immunohistochemical analysis for diagnosing serous neoplasm of the pancreas: aquaporin 1, stereocilin, and transmembrane protein 255B

status: Public on May 06 2024

first: Nobuyoshi

last: Hiraoka

address: 5-1-1 Tsukiji, Chuo-ku

department: Pathology Division

institute: National Cancer Center Research Institute

summary: Serous (cystic) neoplasm (SCN) of the pancreas is usually benign cystic neoplasm and has unique biological characteristics that are different from those found in the normal pancreatic tissue or pancreatic ductal adenocarcinoma (PDAC) tissue. In order to investigate molecular mechanisms involved in the unique biological phenotypes of, we compared gene expression profiles of SCN tissues with those of normal pancreatic tissues or those of PDAC tissues.

overall_design: Gene expression profiles of five serous cystic neoplasm of the pancreas tissues were measured using Agilent SurePrint G3 Human GE v3 8x60K Microarray.

first: Chikashi

last: Watase

first: Masanori

last: Fuse

first: Yoshinori

last: Ino

first: Chie

last: Naito


title: Stress granule assembly impairs macrophage efferocytosis [SG RNA-seq]

summary: Stress granules (SGs) assembly in response to various stress, has been demonstrated in the regulation of anti-viral immune response and tumor progression. However, lack of evidence to illustrate the relation between SGs formation and allergic diseases. Applying RNA-seq in total RNA and SGs of primary macrophages, SG-specific expressed genes were defined.

overall_design: Total RNA and SGs RNA are purified from primary macrophages. RNA-seq is undertaken to investigatethe SG-specific expressed gene.


title: Stress granule assembly impairs macrophage efferocytosis [MeRIP-seq]

summary: Stress granules (SGs) assembly in response to various stress, has been demonstrated in the regulation of anti-viral immune response and tumor progression. However, lack of evidence to illustrate the relation between SGs formation and allergic diseases. Using m7G meRIP-seq for CDS region of mRNA in macrophages, m7G modification of Lrp1 mRNA is defined.

overall_design: To investigate the m7G modification of Lrp1 mRNA, we applied meRIP-seq for CDS region of mRNA in macrophages.


title: Porcine Rotavirus VP6 Protein Wrests IPEC-J2 METTL3-Mediated M6A Modification to Fight Antiviral Immune Response

status: Public on Apr 19 2024

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: Tongwei Road

institute: Nanjing agricultural university

summary: N6-methyladenosine (m6A), the most abundant mRNA modification, can regulate various mRNA metabolism to affect numerous physiological and pathophysiological processes, including immune function. However, the regulation of m6A methylation and its role in immune defense against virus infections remain unexplored. Here, we found that Porcine rotavirus (PoRV) infection decreased global m6A levels in host cells by downregulating m6A writer METTL3. Remarkably, knockdown of Mettl3 or m6A reader Ythdf2 enhances antiviral resistance in IPEC-J2 cells. Through RNA-seq and m6A -seq, we identified interferon regulatory factor 2 (IRF2) and interferon induced protein 44-like (IFI44L) as key m6A targets during PoRV infection. Silencing Mettl3 or Ythdf2 elevated mRNA stability of Irf2 and Ifi44l to restricting viral replication. Conversely, depletion of Irf2 and Ifi44l rendered host cells more susceptible to PoRV infection. Our findings uncover a novel m6A-mediated antiviral mechanism targeting the interferon response factors IRF2 and IFI44L, shedding new light on the epitranscriptomic regulation of host-pathogen interactions.

sample_organism:
Sus scrofa
Porcine rotavirus

platform_organism:
Sus scrofa
Porcine rotavirus

overall_design: To determine alterations in m6A methylation patterns induced by virus infection and map potential m6A modification sites on mRNAs of differential expressed genes

first: Yaxu

last: Liang

first: Xuejiao

last: Zhu

first: Ning

last: Peng