title: Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology (Ribo-Seq)

overall_design: Ribo-seq for lung tissues of K18-hACE2 transgenic mice infected by SARS-CoV-2. For the library construction, we divided conditions as two groups, the early set (Control for the early set, 1 day post-infection, 2 days post-infection) and late set (Control for the late set, 5 days post-infection, 7 days post-infection). For each condition, we prepared quadruplets.

first: Junsoo

last: Kim

first: Daehwa

last: Youn

first: Seunghoon

last: Choi

first: Youn

last: Lee

first: Dulguun

last: Sumberzul

first: Jeongeun

last: Yoon

first: Hanju

first: Hyuna

last: Noh

first: Dain

last: On

first: Seung-Min

last: Hong

first: Se-Hee

last: An

first: Hui

last: Jang

first: Sang-Hyuk

last: Seok

first: Yu

first: Seo

first: Young

middle: B

first: Ji-Yeon

last: Hwang

first: Hyo-Jung

first: Hong

first: Jun

last: Park


title: Analysis of gene expression in the Drosophila larval central nervous system

status: Public on Dec 01 2023

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

type: Methylation profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: Recent studies have brought contrasting results concerning 6-methyl-adenosine (6mA) as an epigenetic mark in eukaryote genomes. Here we investigated the genomic characteristics of 6mA in drosophila larval central nervous system in wild type and tet mutant contexts using PacBio SMRT-seq. In parallel, we performed RNA-seq experiments to assess gene expression in these two conditions.

overall_design: Drosophila melanogaster w1118 and tet null third instar larvae were raised on standard medium and their central nervous system was dissected at the third instar larval stage. High molecular weight genomic DNA was prepared and analyzed by SMRT sequencing using PacBio sequencing platform. Total RNA was extracted and  analyzed by deep sequencing using Illumina HiSeq sequencing platform.

first: Lucas

last: Waltzer

first: Yoan

last: Renaud


title: Nlrc3 signaling is required for hematopoietic stem cell emergence by activating Notch signaling in vertebrates

status: Public on Nov 30 2023

city: Hangzhou

first: shuyang

last: Cai

address: 866     Yuhangtang Road

country: China

institute: Zhejiang university

summary:
Purpose: Since Nlrc3 signaling is imperative for HSPCs production in zebrafish, to further determine the regulatory mechanism by which nlrc3 signaling regulates HSPCs. Bulk RNA sequencing analysis is performed to dissect the function and molecular mechanism between the control groups and the nlrc3 morphants groups.
Methods: The GFP+ cells in Tg(fli1a:eGFP) zebrafish embryos at 28 hpf were sorted, which is the stage that EHT occurs in the VDA and the site of hemogenic endothelial cells onset. The mRNA profiles of these cells in wild-type (WT) and Nlrc3 knockdown were deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 35 million sequence reads per sample and identified 4153 transcripts showing differential expression between the of WT and  Nlrc3 morphants, with a fold change ≥1.5 and p value <0.05. Based on the results of RNA seq, some signaling pathways essential for  the the Nlrc3 regulates the onset of HSPCs in vertebrate are dissected. Including Notch, WNT, NF-kB.
Conclusions: Hemogenic endothelial cells mRNA profiles of WT groups and Nlrc3 knockdown groups were deep sequenced and anlysis. Based on the results of RNA seq, we performed  experiments to validate the up and downstream pathway involved in the the Nlrc3 regulates the onset of HSCPs in vertebrate.

overall_design: mRNA profiling by high throughput sequencing to dissect the function and molecular mechanism by which nlrc3 signaling regulates the HSPCs in vertebrate.

first: Shuyang

first: He

last: Huang


title: BRD3 regulates the inflammatory and stress response in rheu-matoid arthritis synovial fibroblasts

city: Bern

first: Kerstin

last: Klein

state: Bern

address: Murtenstrasse 28

department: Department of Rheumatology and Immunology

country: Switzerland

institute: University Hospital Bern

summary: Individual functions of members of the bromodomain (BRD) and extra-terminal (BET) protein family underlying the anti-inflammatory effects of BET inhibitors in rheumatoid arthritis (RA) are incompletely understood. Here we aimed to analyze regulatory functions of BRD3, an under-studied member of the BET protein family, in RA synovial fibroblasts (FLS). BRD3 was silenced in FLS prior to stimulation with TNF. Alternatively, FLS were treated with I-BET. Transcriptomes were analyzed by RNA sequencing (RNAseq), followed by pathway enrichment analysis. We confirmed results for selective target genes by Real-time PCR, ELISA and Western blotting. BRD3 regulates the expression of several cytokines and chemokines in FLS, and positively correlates with inflammatory scores in the RA synovium. In addition, RNAseq pointed to a profound role of BRD3 in regulating FLS proliferation, metabolic adaption, and response to stress, including oxidative stress, and autophagy. BRD3 acts as an upstream regu-latory factor that integrates the response to inflammatory stimuli and stress conditions in FLS and executes many functions of BET proteins that have previously identified using pan-BET inhibitors.

overall_design: To study the function of BRD3 in RA synovial fibroblasts, we silenced BRD3 expression in synovial fibroblasts using lentiviral particles. Cells were stimulated with TNF or left untreated and harvested 24h after stimulation.


title: RPB1 ChIP-Seq of NSC from Wild Type (WT) and Armc5 knockout mice

city: Montreal

first: Jiangping

last: Wu

address: 900 Rue Saint Denis

country: Canada

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ARMC5 is a protein containing an armadillo domain (ARM) and a BTB domain. Its gene knockout caused many phenotypes, including dwarfism, compromise T-cell immunity, and adrenal gland hypertrophy. ARMC5 mutation in humans is associated with bilateral macronodular adrenal gland hypertrophy. We found that AMC5 KO mice suffered from an increased incidence of neural tube defects (NTDs). We revealed that ARMC5 complexed with CUL3 and POLR2A and was part of a novel POLR2A-specific ubiquitin ligase (E3). This E3 was the dominant DNA damage-independent POLR2A-specific E3 in developing neural tubes and neural precursor cells under a physiological condition. ARMC5 gene knockout (KO) caused diminished POLR2A ubiquitination and compromised POLR2A degradation via proteasomes. Surprisingly, the absence of this E3 did not lead to generalized Pol II stalling and the subsequent generalized decrease of mRNA transcription but caused an enlarged Pol II pool size, which dysregulated 108 genes in NPCs, including some known to neural development. ARMC5 KO in the intestine downregulated FOHL1 expression, which was essential in folate absorption. Whole-exome sequencing of 511 myelomeningocele (MM) patients revealed nine highly deleterious mutations in the ARMC5 coding sequence. A significant deleterious mutation Arg429Cys found in MM patients drastically weakened the interaction between ARMC5 and POLR2A, supporting our hypothesis that such mutations in ARMC5 increased the NTD risks by compromising the POLR2A-specific E3 activity. Our results indicated that this novel ARMC5-CUL3-RBX1 E3 played a critical role in Pol II pool homeostasis, and ARMC5 mutation was a modifier of NTD risks in mice and humans.

overall_design: RPB1 ChIP-Seq profiles of Neural stem cell from WT and Armc5(-/-) mice

first: Linjiang

last: Lao

first: Hongyu

last: Luo


title: Distinct mesenchymal cell states mediate prostate cancer progression [Spatial Transcriptomics]

city: New York

first: Mohamed

last: Omar

state: New York

address: 413 East 69th Street

department: Department of Pathology and Laboratory Medicine

country: USA

institute: Weill Cornell Medicine

summary: We sought to determine whether molecular alterations in tumor stroma influence prostate cancer progression and metastatic potential. To accomplish this, we compared mesenchymal cells from four genetically engineered mouse models (GEMMs) of prostate cancer representing different stages of the disease to their wild-type (WT) counterparts by single-cell RNA sequencing (scRNA-seq) and, ultimately, to human tumors with comparable genotypes. We identified 8 transcriptionally and functionally distinct stromal populations responsible for both common and GEMM-specific transcriptional programs. These are conserved between mouse models and human prostate cancers with the same genomic drivers. The transcriptional profiles of the stroma of murine models of advanced disease were similar to those of human prostate cancer bone metastases, with periostin expression by stromal cells influencing invasion and neuroendocrine differentiation. These profiles were then used to build a robust gene signature that can predict metastatic progression in localized disease independent of Gleason score. Taken together, this offers new evidence that the stromal microenvironment mediates prostate cancer progression.

overall_design: We conducted spatial transcriptomics analysis of murine tumors from the PRN mouse model (Pb-Cre4 +/-;Pten f/f; LSL-MYCN +/+; Rb1 f/f) and corresponding tissue from it wildtype using 10X Genomics CytAssist Visium platform (10x Genomics, Pleasanton, CA).

first: Hubert

last: Pakula

first: Ryan

last: Carelli

first: Filippo

last: Pederzoli

first: Giuseppe

last: Nicolò Fanelli

first: Tania

last: Pannellini

first: Fabio

last: Socciarelli

first: Lucie

last: Van Emmenis

first: Silvia

last: Rodrigues

first: Caroline

last: Fidalgo-Ribeiro

first: Pier

middle: V

last: Nuzzo

first: Nicholas

middle: J

last: Brady

first: Wikum

last: Dinalankara

first: Madhavi

last: Jere

first: Itzel

last: Valencia

first: Christopher

last: Saladino

first: Jason

last: Stone

first: Caitlin

last: Unkenholz

first: Richard

last: Garner

first: Mohammad

middle: K

last: Alexanderani

first: Francesca

last: Khani

first: Francisca

middle: N

last: de Almeida

first: Cory

last: Abate-Shen

first: Matthew

last: Greenblatt

first: David

middle: S

last: Rickman

middle: E

last: Barbieri

first: Brian

middle: D

last: Robinson

first: Luigi

last: Marchionni

first: Massimo

last: Loda


title: Integrative functional genomic analyses identify  genetic variants influencing skin pigmentation in  Africans [HiChIP & Hi-C]

city: Philadelphia

first: Yuanqing

last: Feng

state: Pennsylvania

address: 430 Clinical Research Building, 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

summary:
Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. We identified 1,157 candidate variants influencing skin pigmentation in indigenous Africans by genome-wide association studies and scans of natural selection based on differentiation in allele frequencies between lightly pigmented southern African Khoesan populations and other darkly pigmented African populations. We applied massively parallel reporter and chromosome conformation capture assays to identify novel regulatory variants and their target genes related to skin pigmentation in melanocytic cells. We identified 165 SNPs showing strong differential regulatory activities between alleles. Combining CRISPR-mediated genome editing, transcriptome profiling and melanin assays, we identified causal regulatory variants impacting pigmentation near MFSD12/HMG20B, MITF, OCA2, and DDB1/CYB561A3/TMEM138. We identified CYB561A3 as a novel gene regulating pigmentation by impacting genes involved in oxidative phosphorylation and melanogenesis. Our results broaden our understanding of the genetic basis of human skin color diversity and human adaptation.
To decipher the target genes of the MFVs, we performed Hi-C and H3K27ac HiChIP assays in MNT1 cells. Hi-C is a high-throughput method for detecting chromatin interactions at whole genome scale and is often used to identify topologically associating domains (TADs) in the nucleus. H3K27ac HiChIP can identify chromatin interactions enriched for H3K27ac, a histone modification associated with active promoters and enhancers. We performed bridge linker mediated Hi-C  and H3K27ac HiChIP using double (Hae3_Alu1) as well as single (Hae3) enzyme digestion in MNT-1 cells.

overall_design: Hi-C and H3K27ac HiChIP in MNT-1 cells

first: Sarah

last: Tishkoff


title: Late-rising CD4 T cells resolve cytomegalovirus persistent replication

city: La Jolla

first: Simon

last: Brunel

state: California

address: 9420 Athena Cir

institute: LJI

summary: Conventional antiviral memory CD4 T cells typically arise during the first two weeks of acute infection. Unlike most viruses, cytomegalovirus (CMV) exhibits an extended persistent replication phase followed by lifelong latency accompanied with some gene expression, suggesting the development of protective memory CD4 T cells may be altered. We show that during mouse CMV (MCMV) infection, CD4 T cells recognizing an epitope derived from the viral M09 protein only develop after conventional memory T cells have already peaked and contracted. Ablating these CD4 T cells by mutating the M09 genomic epitope in the MCMV Smith strain, or inducing them by introducing the epitope into the K181 strain, resulted in delayed or enhanced control of viral persistence, respectively. These cells were shown to be unique compared to their conventional memory counterparts; producing higher IFNg and IL-2 and lower IL-10 levels. RNAseq analyses revealed them to express distinct subsets of effector genes as compared to classical CD4 T cells. Additionally, when M09 cells were induced by epitope vaccination they significantly enhanced protection when compared to conventional CD4 T cells alone.  These data show that late-rising CD4 T cells are a unique memory subset with excellent protective capacities that display a development program strongly differing from the majority of memory T cells.

overall_design: Phenotypic and transcriptomic analyses of M09 T cells, from MCMV infected spleen compare to MCMV conventional M25 CD4 T cells

first: Ankan

last: Gupta

middle: A

last: Greenbaum

first: Gregory

last: Seumois

first: Pandurangan

last: Vijayanand

first: Chris


title: Glomerular podocyte RNA-seq data of the podocyte-specific Profilin1 deficient mice

city: New Haven

first: Xuefei

last: Tian

state: CT

address: 300 Cedar Street

department: Nephrology/Internal Medicine

institute: Yale University School of Medicine

summary: The progression of proteinuric kidney disease is associated with podocyte loss but the mechanisms remain unclear. Podocytes reenter the cell cycle to repair damaged ds DNA breaks. However, unsuccessful repair results in podocytes crossing the G1/S checkpoint and undergoes abortive cytokinesis. In this study, we identified Pfn1 as a major contributor in maintaining glomerular integrity and its loss in mice results in severe proteinuria, and kidney failure due to podocyte mitotic catastrophe, characterized by abundant multinucleated cells. Reentry of podocytes were identified by using FUCCI-2aR mice, accompanying the alteration of cell-cycle associated proteins, such as P21, P53, Cyclin B, and Cyclin D. Podocyte-specific translating ribosome affinity purification (TRAP) and RNAseq revealed a reduction of Ribosomal RNA-processing protein 8 (Rrp8) and re-expression of Rrp8 partially rescued the in-vitro phenotype. Clinical analysis of patients with proteinuric kidney disease demonstrated multinucleated podocytes and reduced podocyte profilin1 in kidney tissue. These results suggest that profilin is indispensible in regulating podocyte cell cycle and its disruption contributes to podocyte loss through mitotic catastrophe.

overall_design: The freshly podocytes samples were isolated from the Control mice and Pfn1 C KO mice at 3 weeks of age for the RNAseq analysis. Each sample contained 3 mice in order to get the sufficient podocytes samples, and 2 control samples and 3 Pfn1 KO samples were analyzed and summarized.

first: Shuta

last: Ishibe

first: Jianlei

last: Gu

first: Yan

last: Zhang


title: IL-12 Reprograms CAR-Expressing Natural Killer T cells to Long-Lived TH1-Polarized Cells with Potent Antitumor Activity

city: Chapel Hill

first: Mark

last: Woodcock

state: NC

address: 170 Manning Drive

institute: University of North Carolina at Chapel Hill

summary: Human natural killer T cells (NKTs) are innate-like T lymphocytes that are increasingly used for cancer immunotherapy. Here we show that human NKTs expressing the pro-inflammatory cytokine interleukin-12 (IL-12) undergo extensive and sustained molecular and functional reprogramming. Specifically, IL-12 instructs and maintain a Th1-polarization program in NKTs in vivo without causing their functional exhaustion. Furthermore, using CD62L as a marker of memory cells in human NKTs, we observed that IL-12 maintains long-term CD62L-expressing memory NKTs in vivo. Notably, IL-12 initiates de novo programming of memory NKTs in CD62L negative NKTs indicating that human NKTs circulating in the peripheral blood possess an intrinsic differentiation hierarchy and that IL-12 plays a role in promoting their differentiation to long-lived Th1-polarized memory cells. Human NKTs engineered to co-express a Chimeric Antigen Receptor (CAR) coupled with the expression of IL-12 showed enhanced antitumor activity in tumor models, persisted long-term in vivo and conserved the molecular signature driven by the IL-12 expression. Thus IL-12 reveals an intrinsic and unappreciated plasticity of peripheral human NKTs that may play a crucial role in the development of cell therapeutics.

overall_design: Human peripheral blood mononuclear cells isolated from healthy donors were obtained from a commercial vendor and NKT cells were isolated.  In the first experiment, human NKT cells were transduced with either GFP or GFP plus IL12 p40 and p35 subunits.  These were maintained in culture and expanded with IL-2 prior to RNA isolation and library preparation.  In the second experiment, human NKT cells were transduced with either GFP plus IL12 p40 and p35 subunits, or with IL12 p40 and p35 subunits plus a GD2-directed CAR construct.  Both were injected into NSG mice engrafted with tumors from the neuroblastoma cell line CHLA-255.  Tumor growth was monitored and mice were sacrificed at times according to institutional guidelines and at the termination of the experiment.  Peripheral blood collected from the heart, spleen, and liver were strained and washed.  The presence of NKTs and CAR constructs was verified by flow cytometry prior to RNA isolation and library preparation.

first: Elisa

last: Landoni

middle: G

first: Gabriel

last: Barragan

first: Gabriele

last: Casirati

first: Vincenzo

last: Cinella

first: Simone

last: Stucchi

first: Leah

middle: M

last: Flick

first: Tracy

last: Withers

first: Giulia

last: Casorati

first: Paolo

last: Dellabona

first: Pietro

last: Genovese

first: Barbara

last: Savoldo

first: Leonid

last: Metelitsa

first: Gianpietro

last: Dotti


title: Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and  chlorophyll homeostasis in Arabidopsis

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: Light regulates chlorophyll homeostasis and photosynthesis via various molecular mechanisms in plants. The light regulation of transcription and protein stability of nuclear-encoded chloroplast proteins have been extensively studied, but how light regulation of mRNA metabolism affects abundance of nuclear-encoded chloroplast proteins and chlorophyll homeostasis remains poorly understood. Here we show that the blue light receptor cryptochrome 2 (CRY2) and the METTL16-type m6A writer FIONA1 (FIO1) regulate chlorophyll homeostasis in response to blue light. In contrast to the CRY2-mediated photo-condensation of the mRNA adenosine methylase (MTA), photoexcited CRY2 co-condenses FIO1 only in the presence of the CRY2-signalling protein SUPPRESSOR of PHYTOCHROME A (SPA1). CRY2 and SPA1 synergistically or additively activate the RNA methyltransferase activity of FIO1 in vitro, whereas CRY2 and FIO1, but not MTA, are required for the light-induced methylation and translation of the mRNAs encoding multiple chlorophyll homeostasis regulators in vivo. Our study demonstrates that the light-induced liquid-liquid phase separation of the photoreceptor/writer complexes is commonly involved in the regulation of photoresponsive changes of mRNA methylation, whereas the different photo-condensation mechanisms of the CRY/FIO1 and CRY/MTA complexes explain, at least partially, the writer-specific functions in plant photomorphogenesis.

overall_design: meRIP and ribotag data to reveal roles of CRY2/SPA1/FIO1 trimolecular condensation in regulating mRNA and chlorophyll metabolism in Arabidopsis.

first: Bochen

last: Jiang

first: Lianfeng


title: Leukemia inhibitory factor suppresses hepatic de novo lipogenesis and induces cachexia in mice

status: Public on Nov 29 2023

city: New Brunswick

first: Xue

last: Yang

state: New Jersey

address: 195 Little Albany St

institute: Rutgers cancer institute of new jersey

summary: To investigate the role of LIF in cachexia, we performed gene expression profiling analysis using data obtained from RNA-seq of liver tissues from TgLC mice with Tamoxifen injection and TgL mice with Tamoxifen  injection

overall_design: Comparative gene expression profiling analysis of RNA-seq data of liver tissues from TgLC mice with Tamoxifen injection and TgL mice with Tamoxifen injection

first: Jianming

last: Wang

first: Chun-Yuan

last: Chang

first: Fan

last: Zhou

first: Juan

last: Liu

first: Huiting

last: Xu

first: Maria

last: Ibrahim

last: Gomez

first: Grace

middle: L

last: Guo

first: Hao

first: Wei-Xing

last: Zong

first: Fredric

last: Wondisford

first: Xiaoyang

last: Su

first: Eileen

last: White

first: Zhaohui

last: Feng

first: Wenwei

last: Hu


title: Autophagy of OTUD5 Destabilizes GPX4 to Confer Ferroptosis-Dependent Kidney Injury

city: Su Zhou

first: Jun

address: No.92, Zhongnan Street, Industrial Park District

institute: Children’s Hospital of Soochow University

summary: Ferroptosis is an iron-dependent programmed cell death associated with severe kidney diseases, linked to decreased glutathione peroxidase 4 (GPX4). However, the spatial distribution of renal GPX4-mediated ferroptosis and the molecular events causing GPX4 reduction during ischemia-reperfusion (I/R) remain largely unknown. Using spatial transcriptomics, we identify that GPX4 is situated at the interface of the inner cortex and outer medulla, a hyperactive ferroptosis site post-I/R injury. We show that OTU deubiquitinase 5 (OTUD5) is a GPX4-binding protein that confers ferroptosis resistance by stabilizing GPX4. During I/R, ferroptosis is induced by mTORC1-mediated autophagy, causing OTUD5 degradation and subsequent GPX4 decay. Functionally, OTUD5 deletion intensifies renal tubular cell ferroptosis and exacerbates acute kidney injury, while AAV-mediated OTUD5 delivery mitigates ferroptosis and promotes renal function recovery from I/R injury. In this work, our study highlights a new autophagy-dependent ferroptosis module: hypoxia/ischemia-induced OTUD5 autophagy triggers GPX4 degradation, offering a potential therapeutic avenue for I/R-related kidney diseases.

overall_design: To elucidate the comprehensive molecular alterations in kidneys exposed to ischemia-reperfusion (I/R), we generated a mouse model of bilateral I/R-induced acute kidney injury (AKI). Subsequently, we performed single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (stRNA-seq) on the mouse kidneys of sham and I/R-treated ones.

first: Li-Kai

last: Chu

first: Xu

last: Cao

first: Lin

last: Wan

first: Qiang

last: Diao

first: Yu

last: Zhu

last: Kan

first: Li-Li

last: Ye

first: Yi-Ming

last: Mao

first: Xing-Qiang

last: Dong

first: Qian-Wei

last: Xiong

first: Ming-Cui

last: Fu

first: Ting

last: Zhang

first: Hui-Ting

first: Shi-Zhong

last: Cai

first: Zhou-Rui

last: Ma

first: Ssu-Wei

last: Hsu

first: Reen

last: Wu

first: Ching-Hsien

last: Chen

first: Xiang-Ming

last: Yan


title: Aerobic Exercise Improves Molecular and Functional Deficits in A Murine Model of Facioscapulohumeral Muscular Dystrophy

city: Washington

first: Adam

last: Bittel

state: DC

address: 111 Michigan Ave, NW

institute: CHildren's National Hospital

summary: We investigated the effects of six weeks of voluntary wheel running in heterozygous B6(Cg)-Gt(ROSA)26Sortm1.1(DUX4*)Plj/J (FLExDUX4) mouse model of Facioscapulohumeral Muscular Dystrophy (FSHD) and their wild type (WT) littermates to characterize the structural/functional adaptations to voluntary wheel running and their molecular foundations using RNA sequencing

overall_design: Comparative gene expression profiling analysis of RNA-seq data from the triceps of male FLExDUX4 and WT littermates that underwent 6 weeks of voluntary wheel running, or a no-running control condition. Samples were collected from n=4 FLExDUX4 exercise, n= 3 FLExDUX4 control, n=4 WT Exercise, and n=3 WT control mice.

first: Daniel

middle: C

first: Heather

last: Gordish-Dressman

first: Yi-Wen


title: Decoding the gene regulatory network of endosperm differentiation in maize [DAP-seq]

city: Beijing

first: Qiang

last: Huo

address: Yuanmingyuan West Road

institute: China Agricultural University

summary: The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. We delineate the temporal gene expression pattern from 6 to 7 days after pollination. We profile the genomic DNA binding sites of 161 transcription factors differentially expressed between cell clusters and constructed a gene regulatory network by combining the single-cell transcriptomic data with the direct DNA-binding profiles, identifying 181 regulons containing genes encoding transcription factors along with their high-confidence targets, Furthermore, we map the regulons to endosperm cell clusters, identify cell-cluster-specific essential regulators, and experimentally validated three predicted key regulators. This study provides a framework for understanding cereal endosperm development and function at single-cell resolution.

overall_design: Construction of gene regulatory networks in maize endosperm using scRNA-seq and DAP-seq


title: Coloration differences in three Camellia reticulata Lindl. varieties: ‘Tongzimian’, ‘Shizitou’ and ‘Manao’

city: Kunming

first: Yan

last: Qu

address: Kunming

institute: Southwest Forestry University

summary: Our results revealed that the initial flowering stage plays a critical role in the color change of MN. Metabolome analysis demonstrated that cyanidin was the primary anthocyanin in SZT and MN’s red region, while its content was low in TZM and MN’s white region. According to the transcriptome analysis, the anthocyanins biosynthesis pathway was reconstructed in Yunnan Camellia, and the low expression of CHS was detected in TZM and MN’s white region, while ANR maintained a high expression level, which may lead to the low content of cyanidin in them. Transcription factors MYBs, bHLH, and bZIP may play a key role in regulating anthocyanin-structural genes. The co-expression analysis showed that the meristem tissue may play a crucial role in the formation of the mixed white-red color in MN.

overall_design: We conducted metabolic and transcriptomic comparison analysis to investigate the coloration differences in three Yunnan Camellia species: C. reticulata ‘Shizitou’ (SZT), C. reticulata ‘Manao’ (MN), and C. reticulata ‘Tongzimian’ (TZM).


title: Wheat stem rust interaction

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Stem rust of wheat is a deleterious fungal disease across the globe causing severe yield losses. Although, many stem rust resistance genes (Sr) are being used in wheat breeding programs, new emerging stem rust pathotypes are a challenge to important Sr genes. In recent years, multiple studies on leaf and yellow rust molecular mechanism have been done, however, for stem rust such studies are lacking. Current study investigated stem rust induced response in the susceptible wheat genotype C306 and its Near Isogenic Line (NIL) for Sr24 gene, HW2004, using microarray analysis to understand the transcriptomic differences at different stages of infection. Results showed that HW2004 has higher basal levels of several important genes involved in pathogen detection, defence, and display early activation of multiple defence mechanisms. Further Gene Ontology (GO) and pathway analysis identified important genes responsible for pathogen detection, downstream signalling cascades and transcription factors (TFs) involved in activation and mediation of defence responses. Results suggest that generation of Reactive Oxygen Species (ROS), cytoskeletal rearrangement, activation of multiple hydrolases, and lipid metabolism mediated biosynthesis of certain secondary metabolites are collectively involved in Sr24-mediated defence in HW2004, in response to stem rust infection. Novel and unannotated, but highly responsive genes were also identified, which may also contribute towards resistance phenotype. Furthermore, certain DEGs also mapped close to the Sr24-linked marker on Thinopyrum elongatum translocated fragment on wheat 3E chromosome, which advocate further investigations for better insights of the Sr24-mediated stem rust resistance.

overall_design:
Microarray data of NIL (near-isogenic line) for resistance gene Sr24 in wheat upon infection with stem rust race at three time points
Agilent Wheat 4x44k Microarray: AMADID: 022297

first: B

last: Das


title: RNA-Seq of neural stem cells from Wild Type (WT) and Armc5 knockout mice

first: Jiangping

overall_design: Neural stem cell mRNA profiles from WT and Armc5(-/-) mice

first: Hongyu

last: Luo

first: Linjiang

last: Lao


title: The SENSE (Simple prEservatioN of Single cElls) method for cryopreservation enables the generation of single-cell immune profiles from whole blood.

status: Public on Nov 28 2023

city: Atlanta

first: Manoj

last: Bhasin

state: GA

address: 615 Michael Street, Whitehead Biomedical Research Building

department: Department of Pediatrics

institute: Emory University

summary: We developed and validated a simple method for viable cryopreservation of whole blood, without any preprocessing, Simple prEservatioN of Single cElls (SENSE), with granulocyte depletion for generating high-quality single-cell profiles. We performed rigorous in-depth characterization of the SENSE method on clinical blood samples and compared it to the conventional multistep density-gradient isolation of peripheral blood mononuclear cells (PBMCs) method. The SENSE method is an effective and simple solution for the cryopreservation of blood samples in clinics/labs and single cell profiles generation.

overall_design:
To validate and assess suitability of the novel Simple prEservatioN of Single cElls (SENSE) method for cryopreserving whole blood cells, we processed the same patient sample using both traditional density gradient isolation of PBMC method and SENSE method of one-step cryopreservation of whole blood along with granulocyte depletion on the day of single cell assay. Comparative analysis of the single cell RNA sequencing (scRNA-seq) data form both methods was carried out to assess single cell quality metrics to compare quality of cells and to perform single cell profiling.
*** Submitter declares that raw data are not available due to patient privacy concerns. ***

first: Sampath

last: Prahalad


title: Transcriptomic analysis of head and neck cancer stable cell lines [RNA-seq_HU]

city: Houston

first: Wencai

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: Gain-of-function mutant p53 can function through a mutp53-MCM5-Sting-noncanonical NFkB siganling axis. We will analyze the transcriptional profils of head and neck cancer stable cell lines UM-SCC-1 and MDA1586 with overexpression or downregulation of mutant p53  in the presence or absence of Sting or RelB knockdown under the treatment with or without hydroxyurea.

overall_design: Total RNA extraction from UM-SCC-1 stable cell lines treated with hydroxyurea were used for RNA-seq.

first: Ge

last: Zhou

first: Mei

last: Zhao

first: Li

last: Shen


title: Transcriptomic analysis of head and neck cancer stable cell lines [RNA-seq]

last: Ma

summary: Gain-of-function mutant p53 can function through a mutp53-MCM5-Sting-noncanonical NFkB signaling axis. We will analyze the transcriptional profiles of head and neck cancer stable cell lines UM-SCC-1 and MDA1586 with overexpression or downregulation of mutant p53  in the presence or absence of Sting or RelB knockdown under the normal culture condition

overall_design: Total RNA extraction from UM-SCC-1 and MDA1586 stable cell lines were used for RNA-seq.


title: Role of NTRK2 on ReNcelVM differentiation

status: Public on Nov 27 2023

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

summary: The tropomyosin receptor kinase B (TrkB) is encoded by the NTRK2 gene. It belongs to the family of transmembrane tyrosine kinases, which have key roles in the development and maintenance of the nervous system. Brain-derived neurotrophic factor (BDNF) and the neurotrophins NT3 and NT4/5 have high affinity for TrkB. Dysregulation of TrkB is associated to a large spectrum of diseases including neurodegeneration, psychiatric diseases and some cancers. The function of TrkB and its role in neural development have mainly been decrypted using transgenic mouse models, pharmacological modulators and human neuronal cell lines overexpressing NTRK2. In this study, we identified high expression and robust activity of TrkB in ReNcell VM, an immortalized human neural progenitor stem cell line and generated NTRK2-deficient (NTRK2-/-) ReNcell VM using the CRISPR/Cas9 gene editing technology. Global transcriptomic analysis revealed major changes in expression of specific genes responsible for neurogenesis, neuronal development and glial differentiation. In particular, key neurogenic transcription factors were massively down-regulated in NTRK2-/- cells, while early glial progenitor markers were enriched in NTRK2-/- cells. This indicates a previously undescribed inhibitory role of TrkB on glial differentiation in addition to its well described pro-neurogenesis role. Altogether, we have generated for the first time a human neural cell line with a loss-of-function mutation of NTRK2, which represents a reproducible and readily available cell culture system to study the role of TrkB during human neural differentiation, analyse the role of TrkB isoforms as well as validate TrkB antibodies and pharmacological agents targeting the TrkB pathway.

overall_design: WT and NOX4 KO primary mouse skin fibroblasts were stimulated with 10ng/ml TGF-beta 2 in three biological replicates, total 12 samples were analyzed

first: Audrey

last: Roussel-Gervais

first: Vincent

last: Jaquet

first: Stéphanie

last: Sgroi

first: Karl-Heinz

last: Krause


title: DNA methylation changes at major histocompatibility complex in multiple sclerosis

city: San Francisco

first: Qin

state: CA

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

summary: The major histocompatibility complex (MHC) region represents by far the strongest multiple sclerosis (MS) susceptibility loci. DNA methylation changes have been consistently detected at the MHC region in MS. However, understanding the full picture of epigenetic regulations of MHC in MS remains challenging, due in part to the limited coverage in the region by standard whole genome bisulfite sequencing or array-based methods. To fill this gap, we utilized a novel but validated MHC capture protocol with bisulfite sequencing and conducted a comprehensive analysis of MHC methylation landscapes in blood samples from 147 treatment naïve MS participants and 129 healthy controls. We identified 132 differentially methylated region (DMRs) within MHC regions and found they are significantly overlapped with MS risk variants. Integration of the MHC methylome to human leukocyte antigen (HLA) genetic data further indicate that the methylation changes are significantly associated with HLA genotypes. Using DNA methylation quantitative trait loci (mQTL) mapping and the causal inference test (CIT), we identified 643 cis-mQTL-DMRs paired associations including 71 DMRs possibly mediating causal relationships between 55 SNPs and MS risk.

overall_design: Peripheral blood was sampled by venipuncture from 147 multiple sclerosis (MS) patients and 129 healthy controls. Bloods cells were then used for DNA extraction and major histocompatibility complex (MHC) targeted bisulfite sequencing.


title: HELIOS identifies an HLA-E-restricted CD8 T cell population and is associated with low effector functions.

city: Woluwé-Saint-Lambert

first: Damien

last: Neyens

state: Bruxelles

address: Avenue Hippocrate 74

country: Belgium

institute: De Duve Institute

summary: The transcription factor HELIOS is primarily known for its expression in CD4 regulatory T cells. In mice, HELIOS is also found in exhausted CD8 T cells. However, information on human HELIOS+ CD8 T cells is limited and conflicting. In this study, we characterized human HELIOS+ CD8 T cells, and found that these cells comprise approximately 21% of blood CD8 T cells. The majority of HELIOS+ CD8 T cells are memory cells, and some of them recognize peptides presented by the MHC class Ib molecule HLA-E. Memory HELIOS- T-BEThigh CD8 T cells displayed robust effector functions, while HELIOS+ T-BEThigh CD8 T cells produce low amounts of IFN- and TNF- and have a lower cytotoxic potential. Additionally, a portion of HELIOS+ CD8 T cells express TH17/TC17-related genes RORt, ROR, PLZF, CD161 and CCL20. Thus, HELIOS is expressed in various CD8 T cell populations, including T-BEThigh cells with lower effector functions, and TC17 cells. It remains to be understood why so many individuals maintain in their blood high amounts of HELIOS+ T-BEThigh CD8 T cells that produce low amounts of cytokines upon activation and what the connection between HELIOS and HLA-E restriction means.

overall_design: PBMCs from donors activated or not in vitro for 5h with coated anti-CD3 and then FACS sorted before RNA sequencing to compare HELIOS+ vs HELIOS- CD8 T cells.

first: Thibault

last: Hirsch

first: Achraqat

last: Abdel Aziz Issa Abdel Hadi

first: Nicolas

last: Dauguet

first: Christophe

last: Vanhaver

first: Alexandre

last: Bayard

first: Claude

last: Wildmann

first: Mathieu

last: Luyckx

first: Jean-Luc

last: Squifflet

first: Quentin

last: D'Hondt

first: Céline

last: Duhamel

first: Antoine

last: Huaux

first: Virginie

last: Montiel

first: Mélanie

last: Dechamps

first: Pierre

last: van der Bruggen


title: Transcriptomic analysis of head and neck cancer stable cell lines

first: Wencai

last: Ma

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

overall_design: Refer to individual Series


title: Molecular signatures of HIV latency established in different conditions revealed by single-cell RNA sequencing

first: Nadejda

middle: S.

last: Beliakova-Bethell

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary: Because HIV provirus in many cells during latency is not entirely silent, it became possible to use single-cell RNA sequencing (scRNA-seq) to determine gene expression patterns in a subset of latently infected cells. In this study, we aimed to identify molecular signatures, or biomarkers, of latency established in different conditions. We have used two in vitro models of HIV latency. The first model involved infection, activation of CD4+ T cells using anti-CD3/anti-CD28 antibodies and allowing the cells to return to quiescence (the 14-day model). The second model involved direct infection of the resting CD4+ T cells via co-culture with autologous productively infected cells to allow cell-to-cell virus transmission (the 10-day model). Furthermore, we utilized an isogenic pair of CXCR4- and CCR5-tropic viruses for direct infection of resting cells. Finally, CD4+ T cells from people with HIV were also profiled. We show common and unique molecular signatures of latency established in different conditions; a subset of genes identified in vitro was validated using cells from people with HIV.

overall_design: For the in vitro studies, primary CD4+ T cells were isolated from peripheral blood of HIV-seronegative blood donors. For the ex vivo studies, biobanked CD4+ T cell samples from people with HIV were used. Two separate gene expression profiling experiments were conducted using the in vitro models of HIV latency and scRNA-seq. In experiment #1, molecular signatures of latency were compared between the two conditions in which latency was established: following the exposure of cells to T cell receptor stimulus (the 14-day model), or directly in resting cells (the 10-day model). Cells with differential proliferative responses to the T cell receptor stimulus in the 14-day model were tracked using a viable dye carboxyfluorescein succinimidylester (CFSE) to enable comparison of signatures of HIV latency dependent on cell proliferative responses. In experiment #2, gene expression in cells latently infected with viruses of different tropism, CXCR4 and CCR5, were compared. In experiment #3, biobanked samples of CD4+ T cells from people with HIV were used to validate selected biomarkers identified in vitro. These samples were also used to more accurately define a cell as latently infected in vitro, based on HIV read distribution throughout the genome in samples from people with HIV.

first: Xinlian

last: Zhang


title: Eif4enif1 haploinsufficiency disrupts oocyte mitochondrial dynamics and leads to subfertility

first: Yuxi

last: Ding

address: D110, Medical Building, 30 Shuangqing Road

institute: Tsinghua University

summary: Premature ovarian insufficiency (POI) refers to the loss of ovarian function before the age of 40, which is among the various contributing factors towards infertility issues. Several studies have previously reported dominantly inherited POI symptoms in families carrying likely contributing heterozygous EIF4ENIF1 mutations. However, this impact of EIF4ENIF1 haploinsufficiency was barely studied in animal models to reveal the underlying molecular changes that relate to infertility. In this study, we demonstrated that haploinsufficiency of Eif4enif1 caused mouse subfertility, impaired oocyte maturation and partial early embryo developmental arrest. By dual-omic sequencing, we revealed that Eif4enif1-deficiency led to significantly altered transcriptome and translatome in mouse oocytes, which led to the further discovery of abnormal mitochondrial hyperfusion with altered mitochondria-associated ribonucleoprotein domain (MARDO) distribution in Eif4enif1-dificient oocytes. This study provided new insight into the molecular mechanism underlying clinical fertility failures, and added new evidences to discovering new therapeutic targets towards infertility.

overall_design: T&T-seq was adopted to evaluate the gene expression states of WT and Eif4enif1+/- GV oocytes. RNA-seq was adopted to examine the gene expression profile of WT and Eif4enif1+/- 1-cell and 2-cell embryos, as well as Eif4enif1+/- embryos arrested at 1-cell stage.

first: Lin

last: Li

first: Kehkooi

last: Kee


title: Short-term consumption of ultra-processed diets impairs the sense of smell and brain physiology

city: Ar-Rayyan, Doha,

first: Melanie

last: Makhlouf

address: Al Gharrafa Street,

country: Qatar

institute: Sidra Medicine


title: Decoding the gene regulatory network of endosperm differentiation in maize [MP3RNA-seq]

first: Qiang

last: Huo


title: Anopheles gambiae mosGILT regulates innate immune genes and zpg expression

status: Public on Nov 26 2023

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

institute: Zhejiang University

summary: Gene edited mosquitoes lacking a gamma-interferon-inducible lysosomal thiol reductase-like protein, namely  (mosGILTnull) have decreased Plasmodium infection, which is linked to impaired ovarian development and immune activation. The transcriptome of A. gambiae mosGILTnull was therefore compared to wild type (WT) by RNA-sequencing to delineate mosGILT-dependent pathways. Compared to WT mosquitoes, mosGILTnull A. gambiae demonstrated altered expression of genes related to oogenesis and 20-hydroxyecdysone synthesis, as well as immune-related genes. In the serendipitous discovery zpg, an essential regulator of germ cell development was found to be one of the most downregulated genes in mosGILTnull mosquitoes. These results provide the crucial missing link between two previous studies on role of zpg and mosGILT in mosquito development. This study further demonstrates that mosGILT has the potential to serve as a target for the biological control of mosquito vectors and to influence the Plasmodium life cycle within the vector.

overall_design: We utilized RNA-seq to compare the transcriptome of mosGILT wildtype and knockout mosquitoes after a blood meal

first: Gunjan

last: Arora

first: Erol

last: Fikrig


title: Decoding the gene regulatory network of endosperm differentiation in maize [RNA-seq]


title: Prostaglandin E2 controls the metabolic adaptation of T cells to the intestinal microenvironment [RNA-seq]

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Immune cells must adapt to different environments during an immune response. We studied the adaptation of CD8+ T cells to the intestinal microenvironment and how this process shapes tissue resident CD8+ T cells (TRM) in the gut. CD8+ T cells progressively remodel their transcriptome and surface phenotype as they acquire gut residency, and downregulate mitochondrial gene expression. Human and mouse gut-resident CD8+ T cells have reduced mitochondrial mass, but maintain a viable energy balance to sustain function. We found that the intestinal microenvironment is rich in prostaglandin E2 (PGE2), which drives mitochondrial depolarization in CD8+ T cells. Consequently, they engage autophagy to clear depolarized mitochondria, and enhance glutathione synthesis to scavenge reactive oxygen species (ROS). Impairing PGE2 sensing promotes TRM accumulation, while tampering with autophagy and glutathione negatively impacts the TRM pool. Thus, a PGE2-autophagy-glutathione axis defines the metabolic adaptation of CD8+ T cells to the intestinal microenvironment, to ultimately influence the TRM pool.

overall_design: We targeted 7 groups of CD8 T cells: mesenteric lymph node Naive (1),  central memory (2), effector memory (3) and resident memory (4); Small instestine Lamina propria effector memory (5) and resident memory (6);  Small intestine intraepithelial lymphocytes effector memory (7). 10^5 cells per target population from each of 3 biological replicates were isolated, processed and analyzed.

first: Matteo

last: Villa

first: David

last: Sanin

first: Erika

last: Pearce


title: Transcriptomic analysis of head and neck cancer stable cell lines [RNA-seq, p53 R273H, MCM5]

summary: Gain-of-function mutant p53 can function through a mutp53-MCM5-Sting-noncanonical NFkB signaling axis. We will analyze the transcriptional profiles of head and neck cancer stable cell lines UM-SCC-1 with overexpression of R273H mutant p53 and/or MCM5 under the normal culture condition.

overall_design: Total RNA extraction from UM-SCC-1 stable cell lines were used for RNA-seq.

first: Ge

last: Zhou

first: Mei

last: Zhao

first: Li

last: Shen


title: Short-term consumption of ultra-processed diets impairs the sense of smell and brain physiology [WOM]

summary: Considering the present scenario of fast-paced life, the major shifts in eating culture in the last five decades, and the crucial role of smell in food intake, it is thus crucial to map and better understand the effects of ultra-processed diets - especially under short-term regimens - on our brain metabolism and sense of smell. To address this question, we used mice to investigate the effects of the short-term consumption of three diets varying in macronutrient composition and origin (one whole-grain-based and two ultra-processed synthetic diets) on the transcriptional profiles of the olfactory mucosa and different brain regions.

overall_design: Comparative gene expression profiling analysis of mRNA-seq data from organs/tissues of mice submitted to High Fat Diet (HFD), Normal Chow Diet (NCD) or Synthetic Chow Diet (SCD).

first: Mélanie

first: Smija

last: Kurian

first: Luis

last: Saraiva


title: Transcriptional determinants of lipid mobilization in human adipocytes [CUT&Tag]

status: Public on Nov 24 2023

city: Huddinge

first: Niklas

last: Mejhert

address: Blickagången 16

country: Sweden

institute: Karolinska Institute

summary: Defects in white adipose tissue lipolysis drive multiple aspects of cardiometabolic disease but the transcriptional framework controlling this process has not been established. To address this, we performed a targeted perturbation screen in primary human adipocytes. Our analyses identified 37 transcriptional regulators of lipid mobilization, which we classified as: i) transcription factors, ii) histone variant chaperones, and iii) mRNA processing proteins. Based on its strong relationship with multiple readouts of lipolysis in patient samples, we performed mechanistic studies on ZNF189, which encodes the Zinc Finger Protein 189. Using mass-spectrometry and chromatin profiling techniques, we show that ZNF189 interacts with the tripartite motif family member TRIM28 and represses the transcription of an adipocyte-specific isoform of Phosphodiesterase 1B (PDE1B2). The regulation of lipid mobilization by ZNF189 requires PDE1B2 and overexpression of PDE1B2 is sufficient to attenuate hormone-stimulated lipolysis. Thus, our work identifies the ZNF189-PDE1B2 axis as a determinant of human adipocyte lipolysis and highlights a link between chromatin architecture and lipid mobilization.

overall_design: CUT&TAG DNA-sequencing following depletion of transcription factor ZNF189

first: Alison

last: Ludzki

first: Zhiqiang

last: Huang

first: Rongrong

last: Fan

first: Eckardt

last: Treuter


title: Transcriptional determinants of lipid mobilization in human adipocytes [ATAC-seq]

overall_design: ATAC-seq analysis of adipcytes following transcription factor ZNF189 depletion

first: Mattias

last: Hansen

first: Anastasios

last: Damdimopoulos


title: Transcriptional determinants of lipid mobilization in human adipocytes [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing for the transcription factor ZNF189

first: Hui

last: Gao


title: Longitudinal single-cell transcriptional dynamics throughout neurodegeneration in SCA1

city: New Haven

first: Changwoo

last: Lee

address: 295 Congress

department: Neuroscience

institute: Yale University

summary: Neurodegeneration is a protracted process involving progressive changes in myriad cell types that ultimately result in the death of vulnerable neuronal populations. To dissect how individual cell types within a heterogeneous tissue contribute to the pathogenesis and progression of a neurodegenerative disorder, we performed longitudinal single-nucleus RNA sequencing of mouse and human spinocerebellar ataxia type 1 (SCA1) cerebellar tissue, establishing continuous dynamic trajectories of each cell population. Importantly, we defined the precise transcriptional changes that precede loss of Purkinje cells and, for the first time, identified robust early transcriptional dysregulation in unipolar brush cells and oligodendroglia. Finally, we applied a deep learning method to predict disease state accurately and identified specific features that enable accurate distinction of wild-type and SCA1 cells. Together, this work reveals new roles for diverse cerebellar cell types in SCA1 and provides a generalizable analysis framework for studying neurodegeneration.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-nucleus RNA-sequencing was performed of control and SCA1 human post-mortem cerebellar cortex tissues and SCA1 knock-in (KI; Atxn1 154Q/2Q) and wild-type (WT) littermate control mice to examine the complex and dynamic interplay between diverse cell populations in the SCA1 cerebellum over time.

first: Leon

last: Tejwani

first: Neal

last: Ravindra

last: van Dijk

first: Janghoo

last: Lim


title: Transcriptional determinants of lipid mobilization in human adipocytes [Microarray]

summary:
Defects in white adipose tissue lipolysis drive multiple aspects of cardiometabolic disease but the transcriptional framework controlling this process has not been established. To address this, we performed a targeted perturbation screen in primary human adipocytes. Our analyses identified 37 transcriptional regulators of lipid mobilization, which we classified as: i) transcription factors, ii) histone variant chaperones, and iii) mRNA processing proteins. Based on its strong relationship with multiple readouts of lipolysis in patient samples, we performed mechanistic studies on ZNF189, which encodes the Zinc Finger Protein 189. Using mass-spectrometry and chromatin profiling techniques, we show that ZNF189 interacts with the tripartite motif family member TRIM28 and represses the transcription of an adipocyte-specific isoform of Phosphodiesterase 1B (PDE1B2). The regulation of lipid mobilization by ZNF189 requires PDE1B2 and overexpression of PDE1B2 is sufficient to attenuate hormone-stimulated lipolysis. Thus, our work identifies the ZNF189-PDE1B2 axis as a determinant of human adipocyte lipolysis and highlights a link between chromatin architecture and lipid mobilization.
We performed Clariom S microarray on human adipocytes to identify genes regulated by ZNF189 depletion.

overall_design: We analyzed the transcriptome of 4 replicates of siControl and siZNF189 human adipocytes.


title: ANP32B promotes colorectal cancer cell progression and reduces cell sensitivity to PRAP1 inhibitor through up-regulating HPF1

city: Shijiazhuang

first: Yinghao

last: Hao

state: Hebei

address: 215 Heping West Road

institute: The Second Hospital of Hebei Medical University

summary: The aim of this work is to explore the role of ANP32B on CRC development

overall_design: RNA-sequencing analysis was performed on RKO cells with ANP32B knockdown or ANP32B WT, then signaling pathway were identified.

first: Li-Li

last: Yang

first: Meng

last: Li

first: Wei

first: Ying-Hao


title: Death Induced by Survival gene Elimination (DISE) is correlated with neurotoxicity in Alzheimer's disease and aging

status: Public on Dec 07 2023

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Analysis of RISC bound short (s)RNAs in various cell lines and mouse models of Alzheimer's disease and in human AD patients reveals a contribution of 6mer seed toxicity to the neurotoxicity associated with AD

overall_design: Ago protein associated short RNAs were pulled down using a GW182 peptide and subjected to smRNA Seq

first: Elizabeth

last: Bartom


title: Increased DNA replication length offsets developmental defects induced by hypomorphic DNA methylcytosine methyltransferase activity [RNA-Seq]

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

summary: Dnmt1 is a key methyltransferase involved in the maintenance of DNA methylation. To determine whether developmental defects induced by hypomorphic DNA 5-methylcytosine methyltransferase activity can be offset by increasing DNA replication time, we produced fish that were mutant for both dnmt1 and DNA polymerase epsilon (pole1) and compared their whole genome bisultite sequencing and gene expression profiles to WT ones. We further determine that the observed rescue effect by pole1 is specific to dnmt1 by comparing whole-genome bisulfite sequencing and gene expression profiles of mutants for the Methionine Adenosyltransferase 2A (mat2aa) and microchromosome 10 (mcm10)

overall_design: Characterisation of gene expression profiles of dnmt1/pole1 single or double mutant fish, mat2a/pole1 single or double mutant fish or mcm10 single mutant fish via RNA-Seq

first: Divine-Fondzenyuy

last: Lawir

first: Norimasa

last: Iwanami

first: Katarzyna

last: Sikora

first: Thomas

last: Boehm


title: Prostaglandin E2 controls the metabolic adaptation of T cells to the intestinal microenvironment.

first: Immunometabolism

last: Department


title: CD163+ macrophages monitor enhanced permeability at the blood–dorsal root ganglion barrier

status: Public on Nov 23 2023

city: Solna

first: Zerina

last: Kurtović

address: Kungshamra 47, lgh 1203

department: Physiology and Pharmacology

institute: Karolinska Institutet

summary:
In dorsal root ganglia (DRG), macrophages reside in close proximity to sensory neurons, and their functions have largely been explored in the context of pain, nerve injury and repair. In this study, however, we discovered that the majority of macrophages in DRGs are in direct contact with the vasculature where they constantly monitor the circulation, efficiently phagocytosing proteins and macromolecules from the blood. Characterization of the DRG endothelium revealed a specialized vascular network spanning the arteriovenous axis, which gradually transformed from a barrier type endothelium in arteries to a highly permeable endothelium in veins. Macrophage phagocytosis spatially aligned with peak endothelial permeability and we identified caveolar transcytosis as a mechanism regulating endothelial permeability. Profiling of the DRG immune landscape revealed two subsets of perivascular macrophages with distinct transcriptome, turnover and function. CD163 expressing macrophages self-maintained locally, specifically participated in vasculature monitoring, displayed distinct responses during peripheral inflammation and were conserved in mouse and Man. Our work provides a molecular explanation for the permeability of the blood-DRG barrier and identifies an unappreciated role of macrophages as integral components of the DRG-neurovascular unit.

DOI: 10.1084/jem.20230675

overall_design: Mice were perfused with ice- cold PBS and neural tissues dissected into cold PBS. On average 40 pooled cervical, thoracic and lumbar DRGs were used. The tissues were digested in 2mg/ml Collagenase I (Gibco 17100-017), 5mg/ml Dispase II (Sigma, D4693) and 0.5mg/ml DNAse I (Roche, 11284932001) at 37C for 30min (Brain) or 40min DRGs. Myelin was removed using 38% Percoll (Sigma, GE17-0891-02). Single cell suspensions of DRG cells from 3 male and 3 female BALB/cAnNRj mice were blocked with FcR blocking solution (Miltenyi Biotec l No.130-092-575) and stained with anti-CD45:PE (BioLegend 103105). Additionally, TotalSeq™ anti-mouse Hashtag antibodies were used to label individual samples The samples were strained  through a 35-micron filter. DAPI was added to the cell solution in order to exclude dead cells. CD45+DAPI− cells were sorted on a BD Influx sorter. The sorted cells were pooled into a single lane on the 10x Genomics Chromium Single Cell 3 ′ v3 system. Library preparation and sequencing were performed at the SciLifeLab sequencing facility, Solna using an Illumina HiSeq  at 61,006 reads/cell.

first: Harald

last: Lund

first: Matthew

last: Hunt

first: Katalin

last: Sandor

first: Noah

last: Fereydouni

first: Anais

last: Julien

first: Christian

last: Göritz

first: Jinming

last: Han

first: Keying

last: Zhu

first: Robert

last: Harris

first: Jon

last: Lampa

first: Lisbet

last: Haglund

first: Tony

last: Yaksh

first: Camilla

middle: I

last: Svensson


title: Prostaglandin E2 controls the metabolic adaptation of T cells to the intestinal microenvironment [scRNA-seq]

overall_design: 4 groups of samples have been prepared for TotalSeqTM-A antibody staining and the following single cell RNA sequencing (scRNAseq), in biological triplicate: 1. naive and central memory CD8+ T cells (CD62L+) isolated from mLN (mLN TN and TCM); 2. effector memory CD8+ T cells (CD62L- CD44+) isolated from mLN (mLN TEM); 3. total CD8+ T cells isolated from LP (LP CD8); 4. total CD8+ T cells isolated from IEL (IEL CD8). This strategy was designed to focus the analysis on CD8+ T cells (hence the cell sorting approach), to monitor the entire course of the response (from mLN to IEL) and to enhance the resolution of the analysis to the stages involving the T cell adaptation to the intestinal tissue (hence the higher number of cells analyzed from LP).

first: Matteo

last: Villa

first: David

last: Sanin

first: Erika

last: Pearce


title: Transcriptional determinants of lipid mobilization in human adipocytes

first: Niklas

last: Mejhert

overall_design: Refer to individual Series


title: Increased DNA replication length offsets developmental defects induced by hypomorphic DNA methylcytosine methyltransferase activity

first: Pierre

last: Cauchy


title: Increased DNA replication length offsets developmental defects induced by hypomorphic DNA methylcytosine methyltransferase activity [Bisulfite-Seq]

overall_design: Characterisation of DNA 5-methylcytosine profiles of dnmt1/pole1 single or double mutant fish, mat2a/pole1 single or double mutant fish or mcm10 single mutant fish via bisulfite sequencing

first: Divine-Fondzenyuy

last: Lawir

first: Norimasa

last: Iwanami

first: Katarzyna

last: Sikora

first: Thomas

last: Boehm


title: Osteocalcin of maternal and embryonic origins synergize to establish homeostasis in offspring

city: Gifu

first: Kazuya

last: Tokumura

address: 1-25-4 Daigakunishi

department: Bioactive Molecules

country: Japan

institute: Gifu Pharmaceutical University

summary: Many physiological functions regulated by osteocalcin are affected in adult offspring of mothers experiencing an unhealthy pregnancy. Furthermore, osteocalcin signaling during gestation influences cognition and adrenal steroidogenesis in adult mice. Together these observations suggest that osteocalcin functions during pregnancy may be a broader determinant of organismal homeostasis in adult mammals than previously thought. To test this hypothesis, we analyzed in unchallenged wildtype and Osteocalcin-deficient, newborn, and adult mice of various genotypes and origin, and that were maintained on different genetic backgrounds, the functions of osteocalcin in the pancreas, liver and testes and their molecular underpinnings. This analysis revealed that providing mothers are themselves Osteocalcin-deficient, Osteocalcin haploinsufficiency in embryos hampers insulin secretion, liver gluconeogenesis, glucose homeostasis, testes steroidogenesis in adult offspring; inhibits cell proliferation in developing pancreatic islets and testes; and disrupts distinct programs of gene expression in these organs and in the brain. This study indicates that provided mothers lack an allele, osteocalcin exerts dominant functions. Furthermore, through their synergistic regulation of multiple physiological functions, osteocalcin of maternal and embryonic origins contributes to the establishment and maintenance of organismal homeostasis in newborn and adult offspring.

overall_design: To investigate the influence of maternal osteocalcin during gestation in the physiology of the offspring postnatally

first: Danilo

last: Correa Pinto Jr

first: Isabella

last: Canal Delgado

first: Haiyang

last: Yang

first: Alisson

last: Clemenceau

first: Andre

last: Corvelo

last: Narzisi

first: Rajeeva

last: Musunuri

first: Julian

last: Meyer Berger

first: Lauren

last: Hendricks

last: Luo

first: Hongchao

last: Li

first: Franck

last: Oury

first: Patricia

last: Ducy

first: Vijay

last: Yadav

first: Xiang

first: Gerard

last: Karsenty


title: Single-cell transcriptomics and in vitro lineage tracing reveals differential susceptibility of human iPSC-derived midbrain dopaminergic neurons in a cellular model of Parkinson’s disease

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

country: United Kingdom

institute: UK Dementia Research Institute at Cardiff University

summary: Advances in stem cell technologies open up new avenues for modelling development and diseases. The success of these pursuits however rely on the use of cells most relevant to those targeted by the disease of interest, for example, midbrain dopaminergic neurons for Parkinson’s disease. In the present study, we report the generation of a human induced pluripotent stem cell (iPSC) line capable of purifying and tracing nascent midbrain dopaminergic progenitors and their differentiated progeny via the expression of a Blue Fluorescent Protein (BFP).  This was achieved by CRISPR/Cas9 assisted knock-in of BFP and Cre into the safe harbour locus AAVS1 and an early midbrain dopaminergic lineage marker gene LMX1A, respectively. Immunocytochemical analysis and single cell RNA sequencing of iPSC-derived neural cultures confirms developmental recapitulation of the human fetal midbrain and high quality midbrain cells. By modelling Parkinson’s disease-related drug toxicity using 1-Methyl-4-phenylpyridinium (MPP+), we showed preferential reduction of BFP+ cells, a finding demonstrated independently by cell death assays and single cell transcriptomic analysis of MPP+ treated neural cultures. Together, these results highlight the importance of disease relevant cell type in stem cell modelling.

overall_design: single cell RNA sequencing data of a time course differentiation of human induced Pluripotent Stem Cells (iPSC) into dopaminergic (DA) neurons (LMX1A Cre AAVS1 BFP line). The dataset consists of 8 samples, including 4 differentiation days (D21, D30, D45 and D65). For D21, D30 and D65,  two different clones were sequenced (HET1/L25, HET2/L35). For D45, both samples are from the same clone (HET1/L25) but in one of the samples a nuclear isolation protocol was followed.

first: Lucia

last: F Cardo

first: Zongze

first: Caleb

last: Webber

first: Meng


title: Effect of iRhom1(RHBDF1) KO in cancer cells

city: Pittsburgh

first: Zhangyi

state: PA

address: 4041 Bigelow Blvd, Apt 112

institute: University of Pittsburgh

summary: To investigate the function iRhom1 in the cancer development, we established CT26 cell lines in which iRhom1 has been knocked down by CRISPR system.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Control CT26 cell and its KO derivatives iRhom1 KO

first: Song


title: C/EBPβ-induced lymphoid-to-myeloid transdifferentiation emulates granulocyte-monocyte progenitor (GMP) biology

city: Berlin

first: Achim

last: Leutz

address: Robert-Rössle-Straße 10

department: Cell Differentiation and Tumorigenesis

institute: Max Delbrück Center

summary: The CCAAT/enhancer-binding-protein beta (C/EBPβ) induces primary v-Abl immortalized mouse B cell transdifferentiation (BT) into granulocyte-macrophage-progenitor-like cells (GMPBT). GMPBT maintain cytokine independent self-renewal, lineage choice, and multi-lineage differentiation. Single cell transcriptomics now shows that GMPBT comprise a continuum of myelomonopoietic differentiation states that seamlessly fit into state-to-fate maps of normal GMP. Inactivation of the v-Abl kinase unveiled dependence on activated CSF2-Jak2-Stat5 signaling. Deletion of IRF8 diminished monopoiesis and enhanced granulopoiesis while removal of C/EBPβ abrogated self-renewal and granulopoiesis yet permitted macrophage differentiation. The GMPBT cell culture system is easily scalable to explore the basics of GMP biology and lineage commitment and largely reduces ethically and legislatively arguable, labor-intensive, and costly animal experiments.

overall_design: v-Abl-transformed mouse pre-B cells were retrovirally infected with rat Cebpb LAP* to induce transdifferentiation. Infected cells were isolated by Fluoresence-activated cell sorting based on EGFP signal on day 6 post-infection and subjected to scRNA-seq analysis.

first: Linh

last: Nguyen

first: Karin

last: Zimmermann

first: Elisabeth

last: Kowenz-Leutz

first: Ramonique

last: Lim

first: Maria

last: Hofstätter

first: Alexander

last: Mildner


title: Identifying immune signatures of sepsis in very preterm babies

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

summary: Bacterial infections are a major cause of mortality in preterm babies, yet our understanding of early-life disease-associated immune dysregulation remains limited. Here, we combined multi-parameter flow cytometry, single-cell RNA sequencing (scRNAseq) and targeted plasma analysis to prospectively and longitudinally profile blood from very preterm babies (<32 weeks gestation) across episodes of invasive bacterial infection (sepsis). We identified a dynamically changing peripheral blood immune signature of sepsis, including lymphopenia, reduced dendritic cell frequencies and monocyte HLA-DR expression, which characterized sepsis even when the common clinical marker of inflammation, C-reactive protein (CRP) was not elevated. Furthermore, scRNAseq showed upregulation of amphiregulin in different leukocyte populations during sepsis, which we validated as a plasma analyte that correlated with clinical signs of disease, even when CRP was normal. This study provides new insights into immune pathways associated with early-life sepsis and identifies potential immune analytes as diagnostic adjuncts for sepsis to guide targeted antibiotic prescribing.

overall_design: Paired blood samples were drawn from five preterm babies on the intensive care unit (n=10 samples). For each pair, one sample was taken contemporaneous with onset (or close to onset) of bacterial sepsis or necrotising enterocolitis, whereas the second sample was taken approximately one week either side of the clinical event. We then applied single cell RNA sequencing to determine gene expression changes within peripheral blood mononuclear cells (PBMC), between the paired timepoints. PBMC were stained with Cite-seq antibodies, and in some cases, anti-human Hashtag reagents, to allow better differentiation of key immune subsets, and multiplexing of multiple samples together respectively. In 4/5 babies we performed scRNAseq on total PBMC, whilst in 1 baby, we first sorted CD3+ T cells, prior to scRNA-seq.

first: Abhishek

last: Das

first: Gaayathri

last: Ariyakumar

first: Neelam

last: Gupta

first: Shraddha

last: Kamdar

first: Adele

last: Barugahare

first: Deanna

last: Deveson

first: Sarah

last: Gee

first: Kate

last: Costeloe

first: Martin

last: Davey

first: Paul

last: Fleming

first: Deena

last: Gibbons


title: miRNA-seq  of lungs tissue of swine supplemented with cholecalciferol and calcidiol

city: Kraków

first: Alicja

last: Wierzbicka

address: ul. Sarego 2

country: Poland

institute: National Research Institute of Animal Produstion

summary: Results indicate that both increasing the dose of cholcalciferol and the use of calcidiol in the diet have a significant effect on lung tissue miRNAs compared to using the standard dose of cholecalciferol. The greatest changes in the transcriptome were induced by supplementation with the increased dose of the combination of cholecalciferol and calcidiol.

overall_design: Effect of different doses of cholecalciferol and calcidiol on miRNA profiles of lungs tissue of swine. The vitamin D dosage of the groups was as follows : 1 group (control group) 2000 IU cholecalciferol (grower) and 1500 IU cholecalciferol/ kg feed (finisher)- 12 individuals, 2 group 3000IU cholecalciferol (grower) and 2500 IU cholecalciferol/ kg feed (finisher)- 7 individuals, 3 group 2000 IU cholecalciferol + 1000 IU 25(OH)D3 (grower) and 1500 IU cholecalciferol + 1000 IU 25(OH)D3/kg feed (finisher)-8 individuals, 4 group 2000 IU 25(OH)D3 (grower) and 1500 IU 25(OH)D3/kg feed (finisher)- 12 individuals

first: Kaludia

last: Pawlina-Tyszko

last: Oczkowicz

first: Tomasz

last: Szmatoła


title: Exploring Epigenetic Drift and Rare Epivariations in Amyotrophic Lateral Sclerosis by an Epigenome-Wide Association Study

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

type: Methylation profiling by genome tiling array

summary:
During the last decades, our knowledge about the genetic architecture of sporadic ALS has significantly increased. However, besides the recognized genetic risk factors, also the environment is supposed to have a role in disease pathogenesis. Epigenetic modifications reflect the results of the interaction between environmental factors and genes and may play a role in the development and progression of ALS. A recent large epigenome-wide association study (EWAS) in blood identified differentially methylated positions mapping to 42 different genes involved in cholesterol biosynthesis and immune-related pathways.
Here we performed a genome-wide DNA methylation analysis in peripheral blood cells on an Italian cohort of 61 sporadic ALS patients and 61 healthy controls. Initially, a conventional genome-wide association analysis was performed, and results were subsequently integrated with the findings from the previous EWAS using a meta-analytical approach. To delve deeper into the significant outcomes, over-representation analysis (ORA) was employed. Moreover, the epigenetic signature obtained from the meta-analysis was examined to determine potential associations with chemical compounds, utilizing the Toxicogenomic Database.
Expanding the scope of the epigenetic analysis, we explored both epigenetic drift and rare epivariations. Notably, we observed an elevated epigenetic drift in individuals with ALS compared to the control group, both at a global and single gene level. Interestingly, epigenetic drift at a single gene level revealed an enrichment of genes related to the neurotrophin signaling pathway. Moreover, for the first time rare we identified epivariations exclusively enriched in ALS cases associated with 153 genes, 88 of whom with a strong expression in cerebral areas.
Overall, our study reinforces the evidence that epigenetics may contribute to the pathogenesis of ALS and that epigenetic drift may be a useful diagnostic marker. Further research is needed to determine the role of epivariations in the identified candidate genes.

overall_design: Genome-wide DNA methylation analysis on peripheral whole blood from 61 sporadic ALS patients using Illumina Human Methylation 450K Beadchip.

first: Alberto

last: Brusati

first: Antonia

last: Ratti

first: Davide

last: Gentilini


title: Quisinostat is a brain-penetrant radiosensitizer in glioblastoma

city: Phoenix

first: Shwetal

last: Mehta

state: AZ

address: 350 W Thomas Rd

department: Ivy Brain Tumor Center

institute: Barrow Neurological Institute

summary: In recent years, histone deacetylase inhibitors (HDACi) have garnered considerable interest for the treatment of adult and pediatric malignant brain tumors. However, owing to their broad-spectrum nature and inability to effectively penetrate the blood-brain barrier, HDACi have failed to provide significant clinical benefit to glioblastoma (GBM) patients to date. Moreover, global inhibition of HDACs results in widespread toxicity, highlighting the need for selective isoform targeting. While no isoform-specific HDACi are currently available, the second-generation hydroxamic acid-based HDACi quisinostat possesses sub-nanomolar specificity for class I HDAC isoforms, particularly HDAC1 and 2. Recently, we demonstrated that HDAC1 is the essential HDAC in GBM. Here, we panalyzed the neuro-pharmacokinetic, pharmacodynamic and radiation-sensitizing properties of quisinostat in preclinical models of GBM. We found that quisinostat is a well-tolerated and brain-penetrant molecule that significantly extended survival when administered in combination with radiation in vivo. The pharmacokinetic-pharmacodynamic-efficacy relationship was established by correlating free drug concentrations and evidence of target modulation in the brain with survival benefit. Together, these data provide a strong rationale for clinical development of quisinostat as a radiosensitizer for the treatment of GBM.

overall_design: For acute treatment , mice bearing intracranial tumors were treated with either vehicle, radiation (2Gy x 3 MWF), Quisinostat (10mg/kg MWF), or combination of quisinostat + IR for one week. Three hours post last treatment, mice were sacrificed, brains harvested and processed for RNA isolation. For survival studies, mice bearing intracranial tumors were randomized into four cohorts. Cohort one was treated with vehicle (continously), cohort two with radiation (2Gy x 3; one week) alone, Quisinostat (10mg/kg MWF; continously), or combination of quisinostat (10mg/kg MWF; continously) + IR (2gy x 3; one week). Radiation was administered only for the first week when treatment was initiated. Quisinostat was administered continously on a Monday, Wednesday, Friday schedule until the animals were moribund. Mice were sacrificed and tumor samples were collected for RNA isolation once animals demonstarted neurological symptoms. RNA samples were processed for RNA-seq analysis and dIfferential gene expression analyses was performed for acute and survival conditions.

first: Costanza

last: Lo Cascio


title: Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network [PRO-seq]

city: Stockholm

first: Mattias

last: Mannervik

address: Svante Arrhenius väg 20C

department: Dept. of Molecular Biosciences

institute: Stockholm University

summary:
Background
Formation of tissue-specific transcriptional programs underlies multicellular development, including dorsoventral (DV) patterning of the Drosophila embryo. This involves interactions between transcriptional enhancers and promoters in a chromatin context, but how the chromatin landscape influences transcription is not fully understood.

Results
Here we comprehensively resolve differential transcriptional and chromatin states during Drosophila DV patterning. We find that RNA Polymerase II pausing is established at DV promoters prior to zygotic genome activation (ZGA), that pausing persists irrespective of cell fate, but that release into productive elongation is tightly regulated and accompanied by tissue-specific P-TEFb recruitment. DV enhancers acquire distinct tissue-specific chromatin states through CBP-mediated histone acetylation that predict the transcriptional output of target genes, whereas promoter states are more tissue-invariant. Transcriptome-wide inference of burst kinetics in different cell types revealed that while DV genes are generally characterized by a high burst size, either burst size or frequency can differ between tissues.

Conclusions
The data suggest that pausing is established by pioneer transcription factors prior to ZGA and that release from pausing is imparted by enhancer chromatin state to regulate bursting in a tissue-specific manner in the early embryo. Our results uncover how developmental patterning is orchestrated by tissue-specific bursts of transcription from Pol II primed promoters in response to enhancer regulatory cues.

overall_design: Examination of gene regulation during the establishment and maintenance of tissue-specific gene expression using the dorso-ventral (DV) patterning paradigm in early Drosophila embryogenesis.

first: George

last: Hunt

first: Roshan

last: Vaid

first: Sergei

last: Pirogov

first: Alexander

last: Pfab

first: Christoph

last: Ziegenhain

first: Rickard

last: Sandberg

first: Johan

last: Reimegård


title: Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network


title: Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network [CUT&TAG]

overall_design: Examination gene regulation during the establishment and maintenance of tissue-specific gene expression using the dorso-ventral (DV) patterning paradigm in early Drosophila embryogenesis.


title: Short-term consumption of ultra-processed diets impairs the sense of smell and brain physiology [Brain]

city: Ar-Rayyan, Doha,

first: Melanie

last: Makhlouf

address: Al Gharrafa Street,

institute: Sidra Medicine

summary: Considering the present scenario of fast-paced life, the major shifts in eating culture in the last five decades, and the crucial role of smell in food intake, it is thus crucial to map and better understand the effects of ultra-processed diets - especially under short-term regimens - on our brain metabolism and sense of smell. To address this question, we used mice to investigate the effects of the short-term consumption of three diets varying in macronutrient composition and origin (one whole-grain-based and two ultra-processed synthetic diets) on the transcriptional profiles of the olfactory mucosa and different brain regions.

overall_design: Comparative gene expression profiling analysis of mRNA-seq data from organs/tissues of mice submitted to High Fat Diet (HFD), Normal Chow Diet (NCD) or Synthetic Chow Diet (SCD).

first: Mélanie

first: Smija

last: Kurian

first: Luis

last: Saraiva


title: Chromatin accessibility by ATAC in wild type versus MCT1-knockout B cells

status: Public on Nov 22 2023

city: Beijing

first: Ligong

last: Chen

address: Shuangqing Road No.30

institute: tsinghua university

summary: Using ATAC-seq, we identified differential chromatin accessibility comparing MCT1-knockout B cells versus WT.

overall_design: To understand how loss of MCT1 alters chromatin accessibility in B cells, we performed ATAC-seq in primary B cells from Mb1Cre and Mct1f/fMb1Cre mice 3 days after LPS and IL4 treatment.


title: Transcriptional changes in B cells induced by MCT1 depletion

summary: Using RNA-seq we identified the gene expression changes in MCT1-deficient B cells.

overall_design: RNA seq was performed in B cells from Mb1Cre and Mct1f/fMb1Cre mice treated with LPS and IL-4 for 3 days.


title: Reassessing endothelial-to-mesenchymal transition in postnatal mouse bone marrow using single-cell RNA sequencing

city: changsha

first: Hui

last: Xie

state: hunan

address: #87 Xiangya Road

department: Orthopedics

institute: Central South University

summary: Conflicting reports exist on whether endothelial cells (ECs) serve as a source of bone marrow stromal cells (BMSCs). In studies concerning the endothelial-to-mesenchymal transition (EndoMT), ECs expressing mesenchymal markers, as well as BMSCs expressing endothelial markers, are typically considered intermediates of EndoMT. To understand the lineage relationship between ECs and BMSCs in postnatal mouse bone marrow, we performed single-cell RNA sequencing (scRNA-seq) on ECs and BMSCs obtained from 5-week-old wild-type C57BL/6J mice, and analyzed the potential intermediates of EndoMT. Subsequently, BMSC and EC lineage tracing models, flow cytometry, and immunostaining techniques were used to validate the findings from scRNA-seq analysis.

overall_design: We profiled bone marrow cells from mouse tibiae and femurs using scRNA-seq. Overall, bone marrow cells and bone fragments from tibiae and femurs of 5-week-old wild-type C57BL/6J mice were collected and digested with a mixture of collagenase, dispase and DNase. Subsequently, samples were subjected to lineage positive cell depletion by magnetic- and fluorescence-activated cell sorting (MACS/FACS). Cells positive for B220, Ter119, Gr-1, CD11b, CD3e, CD45, CD71, CD3, CD19 were depleted. Finally, we analyzed ECs expressing mesenchymal markers Prrx1, Lepr, Pdgfra, and Col1a1, as well as BMSCs expressing endothelial markers Pecam1, Cdh5, Tek, and Emcn in the scRNA-seq analysis.


title: Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network [ChIP-Seq]


title: MCT1-governed pyruvate metabolism is essential for antibody class-switch recombination through the acetylation of H3K27

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


title: Calprotectin blockade inhibits long-term vascular pathology following peritoneal dialysis-associated bacterial infection. [2]

first: Anne-Catherine

last: Raby

state: Cardiff

address: Heath Park, Academic Avenue

institute: Cardiff University

summary: Bacterial infections and the concurrent inflammation have been associated with increased long-term cardiovascular (CV) risk. In patients receiving peritoneal dialysis (PD), bacterial peritonitis is a common occurrence, and each episode further increases late CV mortality risk.  However, the underlying mechanism(s) remains to be elucidated before safe and efficient anti-inflammatory interventions can be developed. Damage-Associated Molecular Patterns (DAMPs) have been shown to contribute to the acute inflammatory response to infections, but a potential role for DAMPs in mediating long-term vascular inflammation and CV risk following infection resolution in PD, has not been investigated. We found that bacterial peritonitis in mice that resolved within 24h led to CV disease-promoting systemic and vascular immune-mediated inflammatory responses that were maintained up to 28 days. These included higher blood proportions of inflammatory leukocytes displaying increased adhesion molecule expression, higher plasma cytokines levels, and increased aortic inflammatory and atherosclerosis-associated gene expression. These effects were also observed in infected nephropathic mice and amplified in mice routinely exposed to PD fluids. A peritonitis episode resulted in elevated plasma levels of the DAMP Calprotectin, both in PD patients and mice, here the increase was maintained up to 28 days. In vitro, the ability of culture supernatants from infected cells to promote key inflammatory and atherosclerosis-associated cellular responses, such as monocyte chemotaxis, and foam cell formation, was Calprotectin-dependent. In vivo, Calprotectin blockade robustly inhibited the short and long-term peripheral and vascular consequences of peritonitis, thereby demonstrating that targeting of the DAMP Calprotectin is a promising therapeutic strategy to reduce the long-lasting vascular inflammatory aftermath of an infection, notably PD-associated peritonitis, ultimately lowering CV risk.

overall_design: Peritonitis was induced in mice by administration of live Staphyloccocus epidermidis i.p. In addition, mice did or did not (PBS administered) receive daily i.p. Peritoneal Dialysis Fluid (PDF) exposure, staring 14 days before and lasting 28 days after peritonitis induction. At Day 28, aortas from at least n=3 mice / group were collected and analysed by RT2 profiler array

first: Esra

last: Cetin

first: Morgane

last: Mazzarino


title: Investigating the role of Wnt/β-catenin signaling during embryonic mammary gland development

city: Bristol

first: Qiang

last: Lan

address: Biomedical Sciences Building, University Walk

department: School of Cellular and Molecular Medicine

institute: University of Bristol

summary: The Wnt/β-catenin signaling pathway is crucial for the development of variety of organs including the mammary gland. However, the precise role of Wnt/β-catenin signaling during embryonic mammary gland morphogenesis is still poorly understood. Here, we used an epithelial gain-of-function β-catenin mouse model to study the role of Wnt/β-catenin signaling in embryonic mammary gland development and profiled the transcriptomes of E13.5 and E16.5 control and mutant mammary epithelia.

overall_design: Ctnn1bflox3/flox3  female mice (Harada et al., 1999) were crossed with Krt14Cre/wt male mice (Huelsken et al., 2001) to delete exon 3 of Ctnn1b (encoding ß-catenin) in epithelial cells. The resulting Krt14Cre/wt; Ctnn1bflox3/wt embryos express one allele encoding wild type and one allele stabilized-β-catenin, respectively . The Krt14wt/wt; Ctnn1bflox3/wt littermate embryos were used as controls. To obtain the mammary epithelial samples, the ventral skin of E13.5 and E16.5 embryos were isolated followed by treatment with Dispase II and Pancreatin-Trypsin. Mammary epithelia from mammary buds 1-3 were manually microdissected under a dissecting microscope with fine needles. Tissues from 2-3 embryos from the same litter and same genotype were pooled for one sample before RNA extraction; for E13.5 both male and female embryos were used, whereas for E16.5 samples, only female embryos were used. Four (E13.5) or five (E16.5) biological replicates were collected from minimum three different litters.

first: Jyoti

last: Satta

first: Marja

last: Mikkola


title: FOXP3+ regulatory T Cell perturbation mediated by the IFNγ-STAT1-IFITM3 feedback loop is essential for anti-tumor immunity

status: Public on Nov 21 2023

city: Shanghai

first: Liu

last: Xinnan

address: South Chongqing Road

institute: Shanghai institute of immunology

summary: Targeting tumor-infiltrating Treg cells is an efficient way to evoke an anti-tumor immune response. How Treg cells fragility and stability are regulated remains largely unknown. IFITM3 and STAT1 are interferon-induced genes that play a positive role in the progression of tumors. Here, we showed that IFITM3-deficient Tregs blunted tumor growth by strengthening the tumor-killing response and displayed the Th1-like Treg phenotype with higher secretion of IFNγ. Mechanistically, depletion of IFITM3 enhances the translation and phosphorylation of STAT1. Conversely, the decreased IFITM3 protein and mRNA levels present in STAT1-deficient Treg cells indicate that STAT1 conversely regulates the expression of IFITM3 to form a feedback loop. Blocking the inflammatory cytokine IFNγ or directly depleting STAT1-IFITM3 axis phenocopies the restored suppressive function of TI-Tregs in the tumor model. Overall, our study demonstrates that the perturbation of TI-Tregs through IFNγ-IFITM3-STAT1 feedback is essential for anti-tumor immunity and constitutes a targetable vulnerability of cancer immunotherapy.

overall_design: To investigate the role of Ifitm3 in regulating tumor-infiltrating Treg cells of MC38 mice tumor model, we isolated tumor-infiltrating WT and IFITM3-deficient Treg cells for for RNA extraction and mRNA sequencing. Each sample includes tumor-infiltrating Treg cells from 7 tumor bearing mice.

first: Xinnan

last: Liu

first: Weiqi

last: Zhang

first: Yichao

last: Han

first: Hao

last: Cheng

first: Qi


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [HC]

city: New York

first: Ellie

last: Ivanova

state: NY

address: 550 First Ave

department: Pathology

institute: NYU Langone

summary: SARS-CoV-2 infection and vaccination elicit potent immune responses. Our study presents a comprehensive multimodal single-cell dataset of peripheral blood of patients with acute COVID-19 and of healthy volunteers before and after receiving the SARS-CoV-2 mRNA vaccine and booster. We compared host immune responses to the virus and vaccine using transcriptional profiling, coupled with B/T cell receptor repertoire reconstruction. COVID-19 patients displayed an enhanced interferon signature and cytotoxic gene upregulation, absent in vaccine recipients. These findings were validated in an independent dataset. Analysis of B and T cell repertoires revealed that, while the majority of clonal lymphocytes in COVID-19 patients were effector cells, clonal expansion was more evident among circulating memory cells in vaccine recipients. Furthermore, while clonal αβ T cell responses were observed in both COVID-19 patients and vaccine recipients, dramatic expansion of clonal gdT cells was found only in infected individuals. Our dataset enables comparative analyses of immune responses to infection versus vaccination, including clonal B and T cell responses. Taken together, our comparative analysis shows that vaccination induces a robust adaptive immune response, including a durable clonal B and T cell response, without the severe inflammation associated with infection.

overall_design: We profiled crculating immune cells from five adults with acute COVID-19 infection and nine healthy adults, seven of whom received theBNT162b2 vaccine. For three of the vaccine recipients, samples were also collected before and after receiving a booster. Samples were taken at multiple time points, resulting in a total of 42 post-vaccination and 9 post-infection samples

first: Jasmine

last: Shwetar

first: Joseph

last: Devlin

first: Terkild

middle: B

last: Buus

first: Sophie

last: Gray-Gillard

first: Akiko

last: Koide

first: Amber

last: Cornelius

first: Marie

last: Samanovic

first: Alberto

last: Herrera

first: Eleni

middle: P

last: Mimitou

first: Chenzhen

first: Trishala

last: Karmacharya

first: Ludovic

last: Desvignes

first: Niels

last: Ødum

first: Peter

last: Smibert

first: Robert

last: Ulrich

first: Mark

last: Mulligan

first: Shohei

first: Kelly

last: Ruggles

first: Ramin

last: Herati

first: Sergei

last: Koralov


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV15]

first: Ellie

last: Ivanova

first: Jasmine

last: Shwetar

first: Joseph

last: Devlin

first: Terkild

first: Sophie

last: Zhang

middle: J

middle: V


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV13]

middle: N

last: Buus

last: Gray-Gillard

first: Akiko

last: Koide

first: Amber

last: Cornelius

first: Marie

first: Alberto

first: Eleni


title: Suppression of ANGPTL4 Reprograms Endothelial Cell Metabolism and Inhibits Angiogenesis

city: New Haven

first: Bal Krishna

last: Chaube

state: CT

address: Amistad Research Building, Amistad St

department: Comparative Medicine

institute: Yale University

summary: Angiopoietin-like 4 (ANGPTL4) is known to regulate various cellular and systemic functions. However, its cell-specific role in endothelial cells (ECs) function and metabolic homeostasis remains to be elucidated. Here, using endothelial-specific Angptl4 knock-out mice (Angptl4iEC), and transcriptomics and metabolic flux analysis, we demonstrate that ANGPTL4 is required for maintaining EC metabolic function vital for vascular permeability and angiogenesis. Knockdown of ANGPTL4 in ECs promotes lipase-mediated lipoprotein lipolysis, which results in increased fatty acid (FA) uptake and oxidation. This is also paralleled by a decrease in proper glucose utilization for angiogenic activation of ECs. Mice with endothelial-specific deletion of Angptl4 showed decreased pathological neovascularization with stable vessel structures characterized by increased pericyte coverage and reduced permeability. Together, our study denotes the role of endothelial-ANGPTL4 in regulating cellular metabolism and angiogenic functions of EC.

overall_design: Comparative gene expression of early passage HUVECs treated with either siRNA to Non-silensing control (NS) or ANGPTL4 and or treated with Cobalt chloride (CoCl2) or XEN445 for 24 hours.

first: Balkrishna

first: Kathryn

last: Citrin

first: Mahnaz

last: Sahraei

first: Abhishek

middle: K

last: Singh

first: Diego

last: Saenz de Urturi

first: Wen

last: Ding

first: Richard

middle: W

last: Pierce

first: Raaisa

last: Raaisa

first: Rebecca

last: Cardone

last: Kibbey

first: Carlos

last: Fernandez-Hernando

first: Yajaira

last: Suarez


title: Calprotectin blockade inhibits long-term vascular pathology following peritoneal dialysis-associated bacterial infection. [1]

first: Anne-Catherine

last: Raby

overall_design: Peritonitis was induced in mice by  administration of live Staphyloccocus epidermidis i.p.,. Mice did or did not received Paquinimod treatment (1 mg/kg), given i.p. at the time of bacterial administration and weekly thereafter. At Day 28 following peritonits induction, aortas from at least n=3 mice / group were collected and analysed by RT2 profiler array

first: Esra

last: Cetin

first: Morgane

last: Mazzarino


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV12]

first: Ellie

last: Ivanova

first: Jasmine

last: Shwetar

first: Joseph

last: Devlin

first: Terkild

last: Buus

first: Sophie

last: Gray-Gillard

first: Akiko

last: Koide

first: Amber

first: Marie

last: Samanovic

first: Alberto

last: Herrera

last: Mimitou

first: Chenzhen

last: Zhang

first: Trishala

last: Karmacharya

first: Ludovic

last: Desvignes

first: Niels

last: Ødum

first: Peter

last: Smibert

first: Robert

last: Ulrich

first: Mark

last: Mulligan

first: Shohei

first: Kelly

last: Ruggles

first: Ramin

middle: S

last: Herati

first: Sergei

last: Koralov


title: mRNA COVID-19 vaccine elicits potent adaptive immune response without the acute inflammation of SARS-CoV-2 infection [CV11]

first: Ellie

last: Ivanova

first: Jasmine

last: Shwetar

first: Joseph

last: Devlin

first: Terkild

last: Cornelius

first: Eleni