title: An atlas of small non-coding RNAs in Human Preimplantation Development [RNA-seq]

city: Stockholm

first: Cheng

last: Zhao

address: Solnavägen 1, 171 77 Solna

department: Department of Clinical Science

institute: Karolinska institute

summary: Our current understanding of the molecular circuitries that govern early embryogenesis remains limited, particularly in the human. Small non-coding RNAs (sncRNAs) regulate gene expression transcriptionally and post-transcriptionally, however, the expression of specific biotypes and their dynamics during preimplantation development remains to be determined. Using Small-seq, we identified the abundance of and dynamic expression of piRNA, rRNA, snoRNA, tRNA, and miRNA in human embryos from day 3 to 7. Among the biotypes, both miRNA and snoRNA displayed distinct associations with developmental time and lineage formation, many of which were  found to target key gene expression programs in pluripotency and lineage establishment. We observed an enrichment of the chromosome 19 miRNA cluster (C19MC) in the trophectoderm (TE), and the chromosome 14 miRNA cluster (C14MC) and MEG8-related snoRNAs in the inner cell mass (ICM). Additionally, isomiR analyses suggested miRNAs are modified differentially during blastulation. Finally, six novel miRNAs and their embryo gene targets we identified. Our analyses provide the first comprehensive measure of sncRNA biotypes and their corresponding dynamics throughout human preimplantation development, providing an extensive resource. Elucidating the functional roles of sncRNAs during preimplantation development will provide insight into the establishment of the blastocyst and exit from pluripotency.  Further, better understanding the miRNA regulatory programs in human embryogenesis will inform strategies to improve embryo development and outcomes of assisted reproductive technologies. We anticipate broad usage of our data as a resource for studies aimed at understanding embryogenesis, optimising stem cell-based models, assisted reproductive technology, and stem cell biology.

overall_design: We utilized Small-seq in parallel with Co-seq on single-cells derived from human embryos spanning embryonic day (E) 3 to E7.

first: Stewart

last: Russell

first: Savana

last: Biondic

first: Karen

last: Menezes

first: Michael

last: Hagemann Jensen

first: Clifford

middle: L

last: Librach

first: Sophie

last: Petropoulos


title: LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [RNA-Seq_RSeT+DT_H9_L1KD+siRNA-KD]

status: Public on Sep 07 2024

city: Toronto

first: Juan

last: Zhang

state: Ontario

address: 25 Orde Street, Room 6-1001 MRS

country: Canada

institute: LTRI

type: Expression profiling by high throughput sequencing

summary: To study siRNA-mediated TPRX1, TP53 and H3.XY co-knockdown effected when transfected together with L1 targeting anti sense oligos (ASO-L1) in RSeT+DT naïve hES cells.

overall_design:
In this study, we investigated if co-knockdown of TPRX1, TP53 or H3.XY expression would reverse the ASO-L1 knockdown induced 8-cell (8C) stage-specific genes upregulation.
RSeT media maintained naive H9 hES cells were transfected with non-specific targeting control anti-sense oligos (ASO-Ctr) or ASO-L1, together with 6-FAM (Fluorescein) labeled siRNAs targeting non-specific sequence (NTsi), TPRX1 (TPRX1si), TP53 (TP53si) and H3.XY (H3.XYsi), respectively. Transfected cells were maintained in the RSeT media added with 10 nM DZNep and 5nM TSA (RSeT+DT). 48 hours later, FAM+ cells were FACS collected and immediately processed for RNA extraction and RNA-seq library prep.

first: Miguel

last: Ramalho-Santos


title: Label-free single-cell RNA Multiplexing leveraging genetic variability

status: Public on Sep 06 2024

city: Aachen

first: Tore

last: Bleckwehl

address: Pauwelsstrasse 30

department: Klinik fuer Nieren- und Hochdruckkrankheiten, rheumatologische und immunologische Erkrankungen (Medizinische Klinik II)

country: Germany

institute: RWTH Uniklinik

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

overall_design: Refer to individual Series


title: An atlas of small non-coding RNAs in Human Preimplantation Development [Small-Seq]

country: Sweden

type: Non-coding RNA profiling by high throughput sequencing

middle: J


title: An atlas of small non-coding RNAs in Human Preimplantation Development

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Single-nucleus single-nucleus assay for transposase-accessible chromatin with sequencing analysis of in vitro cardiac differentiations

city: La Jolla

first: Alyssa

last: Holman

state: CALIFORNIA

address: 9500 Gilman Drive Leichtag Biomedical Research Building 485

country: USA

institute: University of California San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here, we utilize single-cell gene regulatory analysis to interrogate the gene expression within CMs generated from monolayer (2D) and embryoid body (3D) hPSC cardiac differentiation systems.

overall_design: We performed differentiations into 2D and 3D CM systems, and collected cells at six distinct stages for snATAC-seq collection.

middle: R

first: Shaina

last: Tran

first: Elie

middle: N

last: Farah

first: Neil

middle: C

last: Chi


title: CRISPR/Cas9 Transcription Factor Knockout Screen for Regulators of In Vitro Cardiac Differentiation

summary: Utilizing a high-throughput functional genomic screen, we identified transcription factors that were functionally relevant in 2D and 3D stem cell-based cardiomyocyte (CM) differentiation systems by knocking out >1,600 TFs.

overall_design: We performed differentiations into 2D or 3D CM systems using a doxycycline-inducible Cas9 H9 stem cell line transduced with a comprehensive TF library. Once differentiated, CMs and non-CMs were sorted out based on TNNT2 expression and sequenced using NGS. Mageck analysis was performed to determine the guides enriched in non-CMs or CMs.

first: Eugin

last: Destici

first: Ting

last: Li


title: An atlas of small non-coding RNAs in Human Preimplantation Development (Mouse embryo RNA-seq)

overall_design: Upon reaching the desired developmental stage (8-cell stage at E2.5 or 32-cell stage at E3.5), several control and mimic-treated mouse embryos (3-5 embryos per group per timepoint) were collected and sequenced to investigate the function of miR-381-3p in mouse preimplantation embryos。


title: LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [RNA-Seq_Primed_H9_L1KD]

summary: To study L1 knockdown effect in mTeSR primed hES cells

overall_design:
In this study, we investigated LINE1 (L1), a major family of transposon elements (TEs) in the human genome, in primed hES cells for its roles in regulating 8-cell (8C) stage-specific totipotent genes.
mTeSR cultured primed H9 hES cells were transfected with 6-FAM (Fluorescein) labeled non-specific targeting ASO (ASO-Ctr), L1 targeting sense oligo (SO-L1) and anti-sense oligo (ASO-L1), respectively. Cells were maintained in the RSeT media post transfection. 48 hours later, FAM+ cells were FACS collected and immediately processed for RNA extraction and RNA-seq library prep.


title: MrgprA3 neurons drive cutaneous immunity against helminths through selective control of myeloid-derived IL-33

status: Public on Sep 10 2024

city: Philadelphia

middle: M.

last: Inclan-Rico

state: PA

address: 3800 Spruce St

department: Pathobiology

institute: University of Pennsylvania, School of Veterinary Medicine


title: RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues, cancer cells, and macrophages [RNA-Seq]

city: Singapore

first: Teodorus Theo

last: Susanto

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

summary: Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translation. Nevertheless, a lack of technologies to enrich RAPs across sample types has prevented systematic analysis of RAP identities, dynamics, and functions. We have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including DHX30 and LLPH, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development linked to the translation of genes with long coding sequences. In addition, we showed RAPIDASH can identify ribosome changes in cancer cells. Finally, we characterized ribosome composition remodeling during immune cell activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs in multiple cell types, tissues, and stimuli and is adaptable to characterize ribosome remodeling in several contexts.

overall_design: RAPIDASH characterization by short read sequencing of polyA-selected RNAs differentially enriched by the additional sulfhydryl-charged resin chromatography step compared to sucrose cushion alone. Refer to Figure S2

first: Teodorus

first: Victoria

last: Hung

first: Andrew

middle: G

last: Levine

first: Yuxiang

last: Chen

first: Craig

middle: H

last: Kerr

first: Yongjin

last: Yoo

middle: A

last: Oses-Prieto

first: Lisa

last: Fromm

first: Zijian

first: Travis

last: Lantz

first: Kotaro

last: Fujii

first: Marius

last: Wernig

first: Alma

last: Burlingame

first: Davide

last: Ruggero

first: Maria

last: Barna


title: Genome-wide expression analysis of Arabidopsis Col-0 plant and clf mutant plant under high humidity [RNA-seq]

city: Shanghai

first: Minhang

last: Yuan

address: Fenglin

department: Shanghai Institute of Plant Physiology and Ecology

country: China

institute: Chinese Academy of Sciences

summary:
Purpose: The goal of this study is to demonstrate the global expression profile of Arabidopsis wild type and clf mutant plants in response to high air humidity
Methods: Four-week-old Arabidopsis plant leaves were treated with ~95% relative humidity for 0.5 hour (0h as control)
Results and Conclusions: This study showed that many genes including ABA-responsive genes and stomotal movement-related genes were differentially expressed in the clf mutant plant.

overall_design: Investigation of genome-wide expression profiles of Arabidopsis wild type plant and clf mutant in response to high air humidity

first: Jingni

last: Wu

first: Xiu-Fang

last: Xin


title: In vivo CRISPR screens identify Mga as an immunotherapy target in triple-negative breast cancer

city: Houston

first: Chang

last: Yang

state: Texas

address: 6565 MD Anderson BLVD

department: Experimental Radiation Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: Immune evasion is not only critical for tumor initiation and progression, but also determines the efficacy of immunotherapies. Through iterative in vivo CRISPR screens with seven syngeneic tumor models, we identified core and context-dependent immune evasion pathways across cancer types. We also provided a high-confidence valuable dataset for the understanding of tumor intrinsic immunomodulators and the discovery of novel anti-cancer therapeutic targets. With a focus on triple-negative breast cancer (TNBC), we found that Mga knock-out significantly enhances anti-tumor immunity and inhibits tumor growth. Transcriptomics and single-cell RNA sequencing analyses revealed that Mga functions through, at least partially, repression of MHC-II genes and related immune responses. Consistently, we observed that low MGA expression in breast cancer patients correlates with a favorable prognosis, particularly in those with active interferon-g signaling. Our findings provide new insights into tumor immune escape and pave the way for further exploration of MGA inhibition for clinical benefits in triple-negative breast cancer.

overall_design: To investigate the effect of depletion of Mga on transcriptomics, we generated Mga KO 4T1 cells, together with WT cells treated with IFN-g (100ng/ml, 24h). 3 replicates for each group.

first: Xu

last: Feng

first: Dadi

last: Jiang

first: Junjie


title: Next Generation Sequencing Facilitates Quantitative Analysis of  transcriptome and epigenome in skeletal stem cell sorted from Ptipfl/fl and Ptipf/f;Col2-Cre mice

city: wuhan

first: Jianfei

last: Liang

address: No. 237, Luoyu Road, Hongshan District,

institute: wuhan university

summary:
Purpose: the goals of this study are to map epigenetic alterations drive the trajectory of skeletal stem and progenitor cells by integrating their cis-regulatory landscape(ChIP-seq) with the transcriptomic profiling(RNA-seq)
Methods:  freshly sorted SSCs, pBCSPs, and BCSPs by FACS (Fluorescence activated Cell Sorting) from 3-day-old Ptipf/f mice and conditional knockout Ptip by crossing col2a1-cre mice and Ptipfl/fl mice (Ptipf/f;Col2-Cre mice) were performed RNA-seq and ChIP-seq (H3K4me1/H3K4me3/H3K27ac-ChIPseq).
Results: using an optimized data analysis workflow, we integrated their cis-regulatory landscape with the transcriptomic profiling. As expected, expression levels of genes were associated with the activity of their related cis-regulatory elements in SSCs, pBCSPs and BCSPs.
Conclusions: Ptip play a crucial role in epigenetic alterations governing the developmental trajectory of skeletal stem and progenitor cells.

overall_design: The RNA-seq and ChIP-seq (H3K4me1,H3K4me3,H3K27ac) of SSC, pBCSP and BCSP sorted from Ptipf/f mice and Ptipf/f;Col2-Cre mice at P3.


title: Spatiotemporal transcriptomic mapping of regenerative inflammation in skeletal muscle reveals a dynamic multilayered tissue architecture

status: Public on Sep 05 2024

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

summary: Tissue regeneration is orchestrated by macrophages that clear damaged cells and promote regenerative inflammation. How macrophages spatially adapt and diversify their functions to support the architectural requirements of actively regenerating tissue remains unknown. In this study, we reconstructed the dynamic trajectories of myeloid cells isolated from acutely injured and early-stage dystrophic muscles. We identified divergent subsets of monocytes/macrophages and dendritic cells (DCs) and validated markers (e.g., GPNMB) and transcriptional regulators associated with defined functional states. In dystrophic muscle, specialized repair-associated subsets exhibited distinct macrophage diversity and reduced DC heterogeneity. Integrating spatial transcriptomics analyses with immunofluorescence uncovered the ordered distribution of subpopulations and multilayered regenerative inflammation zones (RIZs) where distinct macrophage subsets are organized in functional zones around damaged myofibers supporting all phases of regeneration. Importantly, intermittent glucocorticoid treatment disrupted the RIZs. Our findings suggest that macrophage subtypes mediated the development of the highly ordered architecture of regenerative tissues, unveiling the principles of the structured yet dynamic nature of regenerative inflammation supporting effective tissue repair.

overall_design: Capture-Hi-C in WT bone marrow-derived macrophages (BMDMs).

first: Dora

last: Bojcsuk

first: Petros

last: Tzerpos

first: Andreas

last: Patsalos


title: Label-free single-cell RNA Multiplexing leveraging genetic variability [scRNA-seq]

first: Tore

last: Bleckwehl

summary: Single cell RNA sequencing has enabled unprecedented insights into the molecular cues and cellular heterogeneity underlying human disease. However, the high costs and complexity of single cell methods remain a major obstacle for generating large scale human cohorts. Here we compare current state-of-the-art single cell multiplexing technologies, and provide a new widely applicable demultiplexing method, SNP-Fishing, that enables simple, robust high-throughput multiplexing leveraging genetic variability of patients.

overall_design: Single-cell and single-nuclei RNA-sequencing were pooled from different patients and demultiplexed with matching bulk-RNA-seq of the same individuals.


title: Genome-wide histone 3 lysine 27 trimethylation patterns in wild type and CLF-deficient Arabidopsis plants after high humidity treatment [ChIP-seq]

summary: We report the H3K27 trimethylation profiles in Arabidospsis wild type and clf mutant plants before and after high humidity treatment. We find that many genes display a different H3-lysine 27 trimethylation level in the clf mutant plant compared to Col-0 plant. In addition, high humidity also influences H3K27 trimethylation profiles in both genotypes.

overall_design:
Examination of global profiles of histone 3 lysine 27 trimethylation in two plant genotypes in response to high air humidity.
Please note that each processed data was generated from both *input and *H3K27me3 samples and is linked to the corresponding *H3K27me3 sample records.


title: Label-free single-cell RNA Multiplexing leveraging genetic variability [bulk RNA-seq]

overall_design: Matching RNA-seq of the pooled single-cell RNA-seq experiments


title: Nitrogen source effect (ammonium and nitrate) on Brachypodium distachyon B21 root transcriptome

city: Leioa

first: Daniel

last: Marino

address: Barrio Sarriena s/n

country: Spain

institute: University of the Basque Country (UPV/EHU)

summary: Nitrogen (N) fertilization is essential to maximize crop production. However, around half of the applied N is lost to the environment causing water and air pollution and contributing to climate change. Understanding the natural genetic and metabolic basis underlying plants N use efficiency is of great interest to reach an agriculture with less N demand and thus, more sustainable. The study of ammonium (NH4+) nutrition is of particular interest, because it mitigates N losses due to nitrate (NO3-) leaching or denitrification. In this work, we performed gene expression analysis in the root of the model plant for C3 grasses Brachypodiyum distachyon, reference accession Bd21, grown with exclusive NH4+ or NO3- supply.

overall_design: 7-day old seedlings were transfered to hydroponic tanks and grown for 19 days with 2,5 mM ammonium or nitrate as exclusive source of nitrogen.

first: María

middle: B

last: González-Moro

first: Marlon

last: de La Peña


title: Combined targeting of GPX4 and BCR-ABL tyrosine kinase selectively compromises BCR-ABL+ leukemia stem cells

city: Guangzhou

first: Xiangbo

last: Zeng

address: Jinan University

institute: JNU

summary: Background In the ongoing battle against BCR-ABL+ leukemia, despite significant advances with tyrosine kinase inhibitors (TKIs), the persistent challenges of drug resistance and the enduring presence of leukemic stem cells (LSCs) remain formidable barriers to achieving a cure.  Methods In this study, we demonstrated that Disulfiram (DSF) induces ferroptosis to synergize with TKIs in inhibiting BCR-ABL+ cells, particularly targeting resistant cells and LSCs, using cell models, mouse models, and primary cells from patients. We elucidated the mechanism by which DSF promotes GPX4 degradation to induce ferroptosis through immunofluorescence, co-immunoprecipitation (CO-IP), RNA sequencing, lipid peroxidation assays, and rescue experiments. Results Here, we present compelling evidence elucidating the sensitivity of DSF, an FDA-approved drug for alcohol dependence, towards BCR-ABL+ cells. Our findings underscore DSF's ability to selectively induce a potent cytotoxic effect on BCR-ABL+ cell lines and effectively inhibit primary BCR-ABL+ leukemia cells. Crucially, the combined treatment of DSF with TKIs selectively eradicates TKI-insensitive stem cells and resistant cells. Of particular note is DSF's capacity to disrupt GPX4 stability, elevate the labile iron pool, and intensify lipid peroxidation, ultimately leading to ferroptotic cell death. Our investigation shows that BCR-ABL expression induces alterations in cellular iron metabolism and increases GPX4 expression. Additionally, we demonstrate the indispensability of GPX4 for LSC development and the initiation/maintenance of BCR-ABL+ leukemia. Mechanical analysis further elucidates DSF's ability to circumvent resistance by reducing GPX4 levels through the disruption of its binding with HSPA8, thereby promoting GPX4 ubiquitination and subsequent degradation. Furthermore, the combined treatment of DSF with TKIs effectively targets both BCR-ABL+ blast cells and drug-insensitive LSCs, conferring a significant survival advantage in mouse models. Conclusion In summary, the dual inhibition of GPX4 and BCR-ABL presents a promising therapeutic strategy to synergistically target blast cells and drug-insensitive LSCs in patients, offering potential avenues for advancing leukemia treatment.

overall_design: KBM5 RNA-seq followed treatment of Ctrl, IM, DSF and IM+DSF


title: H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [RNA-Seq]

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

summary: Facultative heterochromatin is formed by Polycomb repressive complex 2 (PRC2)-deposited H3K27 tri-methylation (H3K27me3) and PRC1-deposited H2AK119 mono-ubiquitylation (H2AK119ub1). How it is newly established after fertilization remains unclear. To delineate the establishment kinetics, here we profiled the temporal dynamics of H3K27 di-methylation (H3K27me2), which represents the de novo PRC2 catalysis, in mouse preimplantation embryos. H3K27me2 is newly deposited at CpG islands (CGIs), the paternal X-chromosome (Xp), and putative enhancers during the 8-cell-to-morula transition, all of which follow H2AK119ub1 deposition. We found that JARID2, a PRC2.2-specific accessory protein possessing an H2AK119ub1-binding ability, colocalizes with SUZ12 at CGIs and Xp in morula embryos. Upon JARID2 depletion, SUZ12 chromatin binding and H3K27me2 deposition were attenuated and H3K27 acetylation was increased at putative enhancers in morulae, and subsequently H3K27me3 failed to be deposited in blastocysts. These data reveal that facultative heterochromatin is established by PRC2.2-driven stepwise H3K27 methylation along pre-deposited H2AK119ub1 during early embryogenesis.

overall_design: RNA-seq were performed in control and Jarid2 KO morula embryos. Then comparative analysis was done between these two mutants.

first: Masahiro

last: Matsuwaka

first: Mami

last: Kumon


title: The histone demethylase JMJ27 acts during the UV-induced modulation of H3K9me2 landscape and facilitates photodamage repair

city: Strasbourg

first: Jean

last: Molinier

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

summary: We used ChIP-seq to identify changes in H3K9me2 contents upon UV-C exposure in WT Arabidopsis plants and in plants deficient for the expression of the histone demethylase, Jumonji27 (JMJ27)

overall_design: Chromatin immmunoprecipitation DNA sequencing (ChIP-seq) for H3K9me2 of UV-C -irradiated Arabidopsis WT and jmj27 plants

first: Philippe

last: Johann to Berens

first: Jackson

last: Peter

first: Sandrine

last: Koechler

first: Mathieu

last: Bruggeman

first: Sebastien

last: Staerck


title: Peculiar transcriptional reprogramming with functional impairment of dendritic cells upon exposure to transformed HTLV-1-infected cells

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

institute: oncovirology and Biotherapies, UMR5239, LBMC

summary: Manipulation of immune cell functions, independently of direct infection of these cells, emerges as a key process in viral pathophysiology. Chronic infection by Human T-cell Leukemia Virus type 1 (HTLV-1) is associated with immune dysfunctions, including misdirected responses of dendritic cells (DCs). Here, we interrogate the ability of HTLV-1-infected T cells to indirectly manipulate human DC functions. We show that upon coculture with chronically infected T cells, monocyte-derived DCs (MDDCs) fail to fully mature. We further show that exposure to HTLV-1-infected T cells induces a unique transcriptional signature in MDDCs, which differs from a typical maturation program, and which is correlated with a dampened ability of HTLV-1-exposed MDDCs to subsequently respond to restimulation. Induction of this tolerogenic behavior is not strictly dependent on capture of HTLV-1 viral particles by MDDCs, nor on cell-cell contacts between HTLV-1-infected T cells and MDDCs, but is instead the result of a molecular dialogue between HTLV-1-infected T cells and MDDCs upon coculture, illustrating how HTLV-1 might indirectly induce a local tolerogenic immune microenvironment suitable for its own persistence.

overall_design:
To understand how HTLV-1 infected transformed cell lines could modulate innate cell functions, we used dendritic cells generated from monocytes isolated from human blood using culture with GM-CSF and IL-4 (100ng/ml each) for 5 days. Then monocyte-derived dendritic cells (MDDCs) were co-cultured with HTLV-1 infected cell lines (C91PL, or C8166) or control non-infected T cells (Jurkat) for 24h and retsimulated or not with LPS for anaother 24h. MDDCs were then isolated from T cells using magnetic negative selection on CADM1 expression.
Samples from 3 independent experiment performed using MDDCs generated from monocytes isolated from 3 independent blood donors (identified as 118, 155 and 156)  were subjected to RNA extraction and gene expression profiling by RNA sequencing.
Comparative gene expression profiling analysis of RNAseq data from MDDCs cultured with (i) control jurkat cells for 24h (A118_1, A155_1, A156_1) and restimulated for additional 24h with LPS (AL118_4, AL155_4, AL156_4),  (ii) HTLV-1 infected cells (C91PL : B118_2, B155_2, B156_2 or C8166 : C118_3, C155_3, C156_3)  and restimulated for additional 24h with LPS (BL118_5, BL155_5, BL156_5, or CL118_6, CL155_6, CL156_6)

first: Auriane

last: Carcone

first: Franck

last: Mortreux

last: Alais

first: Cyrille

last: Mathieu

first: Chloé

last: Journo

first: Hélène

last: Dutartre


title: Transcriptomic analysis of HSF1 knockout cardiomyocytes

first: Alyssa

last: Holman

summary: Transcriptomic analysis revealed differences in gene expression between control and HSF1 knockout cells, revealing how HSF1 gene regulation may be altered when knocked out.

overall_design: We performed differentiations based on a 3D hPSC-cardiomyocyte (CM) differentiation protocol using control and three HSF1 knockout clones to determine the transcriptomic impacts of a HSF1 loss of function.

first: Eugin

last: Destici

first: Neil

last: Chi


title: H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq]

first: Azusa

last: Inoue

overall_design:
H3K27me2 and H3K36me3 Carrier DNA assisted ChIP-seq (CATCH-seq) and JARID2 and H3K36me3 CUT&RUN were performed in WT mouse ES cells, oocytes and B6/PWK F1 hybrid preimplantation embryos. H3K27me2, H3K27me3 and H3K27ac CATCH-seq and SUZ12 CUT&RUN were performed in BDF1/PWK F1 hybrid Jarid2 CTR and KO morula and blastocyst embryos.
H3K27me2 CATCH-seq with spike-in was performed in BDF1/BDF1 F1 WT preimplantation embryos. H3K27me3 CUT&RUN was performed in BDF1/BDF1 WT and Jarid2 overexpressed 2-cell embryos. H3K27me3 CATCH-seq was performed in BDF1/PWK hybrid WT and Jarid2 overexpressed morula embryos.

first: Masahiro

last: Matsuwaka

last: Kumon


title: Genome-wide histone 3 lysine 27 trimethylation patterns and expression analysis of WT and CLF-deficient Arabidopsis plants after high humidity treatment

first: Minhang

last: Yuan

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

overall_design: Refer to individual Series


title: Single-cell multiome uncovers differences in glycogen metabolism underlying species-specific speed of development

city: Leiden

first: Max

last: Fernkorn

address: Einsteinweg 55

department: Leiden Academic Centre for Drug Research (LACDR)

institute: University Leiden

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus


title: Targeting EGLN2/PHD1 protects motor neurons and normalizes the astrocytic interferon response.

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: The egl-9 family hypoxia-inducible factor (EGLN) enzymes, also known as prolyl hydroxylase domain (PHD) enzymes, are metabolic sensors regulating inflammatory responses and cellular metabolism. Both neuroinflammation and dysregulated energy metabolism are linked to motor neuron degeneration leading to amyotrophic lateral sclerosis (ALS) and correlate with disease progression. Therefore, the aim of this study was to explore the role of EGLN2 in ALS. Using a genetic and an oligonucleotide-based approach, we showed that downregulation of EGLN2 protects motor neurons and mitigates the ALS-like phenotypes in a mouse and a zebrafish model of ALS. Single-nuclei RNA sequencing of murine spinal cord revealed that loss of EGLN2 induced an astrocyte-specific downregulation of pro-inflammatory interferon-stimulated genes. In addition, we found that genetic deletion of EGLN2 restored the disturbed interferon response in iPSC-derived astrocytes from an ALS patient, confirming the novel link between EGLN2 and astrocytic interferon signaling. In conclusion, we identified EGLN2 as a potential novel ALS therapeutic target normalizing the astrocytic interferon-dependent inflammatory axis in vivo as well as in patient-derived cells.

overall_design: To study the effect of EGLN2-KO in amyotrophic lateral sclerosis (ALS) patient-derived astrocytes, we performed RNA-seq analysis on three differentiations (DIFF) of iPSC-derived astrocytes from an ALS patient (SOD1-A4V), the isogenic control (SOD1-A4A) and a CRISPR-Cas9 generated EGLN2-KO (SOD1-A4V/EGLN2-/-) that were vehicle (VEH) treated or treated with TNFα, IL-1α and C1q  (TIC) to provoke A1-like astrogliosis.

first: Christine

last: Germeys

first: Tijs

last: Vandoorne

first: Kristofer

last: Davie

first: Suresh

last: Poovathingal

first: Kara

last: Heeren

first: Wendy

last: Vermeire

first: FatemehArefeh

last: Nami

first: Matthieu

last: Moisse

first: Annelies

last: Quaegebeur

first: Annerieke

last: Sierksma

first: Laura

last: Rué

first: Adrià

last: Sicart

first: Caroline

last: Eykens

first: Bart

last: De Strooper

first: Peter

last: Carmeliet

first: Philip

last: Van Damme

first: Katrien

last: De Bock

first: Ludo

last: Van Den Bosch


title: Identifying Coordinated Gene Regulatory Networks That Direct Cardiomyocyte Development

first: Alyssa

last: Holman

summary: Illuminating the precise stepwise genetic programs directing cardiac development provides insights into the mechanisms of congenital heart disease and strategies for cardiac regenerative therapies. Here, we integrated in vitro and in vivo human single-cell multi-omic studies with high-throughput functional genomic screening to reveal dynamic, cardiac-specific gene regulatory networks and transcriptional regulators during human cardiomyocyte development. Interrogating developmental trajectories reconstructed from single-cell data unexpectedly revealed divergent cardiomyocyte lineages with distinct gene programs based on developmental signaling pathways. High-throughput functional genomic screens identified key transcription factors from inferred gene regulatory networks (GRNs) that were functionally relevant for cardiomyocyte lineages derived from each pathway. Notably, we discovered a critical HSF1-mediated cardiometabolic GRN controlling cardiac mitochondrial/metabolic function and cell survival, also observed in fetal human cardiomyocytes. Overall, these multi-modal genomic studies enabled the systematic discovery and validation of coordinated gene regulatory networks and transcriptional regulators controlling the development of distinct human cardiomyocyte populations.

overall_design: Refer to individual Series.


title: TFEB controls syncytiotrophoblast formation and estrogen production in placenta

city: Pozzuoli

first: Francesco

last: Panariello

state: Napoli

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

summary: TFEB, a bHLH-leucine zipper transcription factor belonging to the MiT/TFE family, is a renowned global modulator of cell metabolism by regulating autophagy and lysosomal functions. Remarkably, loss of TFEB in mice causes embryonic lethality due to severe defects in placentation associated with aberrant vascularization and resulting hypoxia. However, the molecular mechanism underlying the described phenotype has yet to be elucidated. By integrating multi-omics approaches with functional assays, we uncover an unprecedented function for TFEB in promoting the formation of a functional syncytiotrophoblast in the placenta. Here, we showed that syncytiotrophoblast formation is marked by TFEB nuclear translocation and its association with the promoters of crucial placental genes, including fusogenic proteins (Syncytin-1 and Syncythin-2) and enzymes involved in the steroidogenic pathway, such as CYP19A1, the rate-limiting enzyme for the synthesis of 17β-Estradiol (E2). Conversely, the depletion of TFEB negatively impacts both the syncytial fusion and the endocrine properties of the syncytiotrophoblast, as demonstrated by a significant decrease in the secretion of placenta hormones and E2 production. Notably, the restoration of TFEB expression resets the syncytiotrophoblast identity. Finally, we identified reduced expression levels of TFEB and its target CYP19A1 in the placenta of pre-eclampsia women, suggesting that dysregulation of the TFEB-CYP19A1 axis might underlie the impairment of placental steroidogenesis described in pre-eclampsia. Our findings elect TFEB as a central controller of the metabolic properties of the placenta by orchestrating both the transcriptional program underlying trophoblast fusion and the acquisition of endocrine function, which are crucial for the bioenergetic requirements of embryonic development.

overall_design: RNAseq of BeWo (WT and TFEB KO) cells undergoing syncitiotrophoblast differentiation, with or wihout transfection of siRNA against TFEB and BeWo TFEB KO cells overexpressing TFEB ORF in the presence of Forskolin or Torin-1.

first: Marcella

last: Cesana


title: TFEB controls syncytiotrophoblast formation and estrogen production in placenta [ChIP-Seq]

summary: To stimulate BeWo trophoblast differentiation, cells were treated with 100uM of Forskolin (F6886, Sigma-Aldrich). 250nM of Torin-1 was used to promote TFEB nuclear translocation.

overall_design: ChIP-seq of TFEB in HeLa cells undergoing starvation and BeWo WT cells stimulated to differentiate into syncytiotrophoblast

first: Margherita

last: Mutarelli


title: In Vivo Direct Reprogramming by AAV Improves Cardiac Function after Myocardial Infarction. [RNA-seq]

city: Tsukuba

first: Koji

last: Nakano

institute: Tsukuba University

summary: The overexpression of cardiac transcription factors, Gata4/Hand2/Tbx5, and Mef2c (GHT/M) has been indicated that directly reprogram cardiac fibroblasts (CFs) into induced cardiomyocytes (iCMs) in vivo, and improve cardiac function after MI in mice. Previous studies demonstrated in vivo reprogramming by using Sendai virus vectors. Here we show that in vivo reprogramming by using Adeno-associated virus (AAV) vectors. Additionally, we use Mef2cM3 (M3), a fusion of Mef2c with a strong MyoD transcriptional activation domain. RNA-seq revealed that directly cardiac reprogramming of GHT/M3 by AAV vector activated the cardiac program and concomitantly suppressed fibroblast and inflammatory signatures.

overall_design: Hearts were harvested 4 weeks after myocardical infarction experiment from two groups (PBS, 4FM3) for RNA-seq.

first: Taketaro

last: Sadahiro


title: In vivo dendritic cell reprogramming for cancer immunotherapy [T cell scRNA + TCR]

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

institute: Lund University

summary: Immunotherapy can lead to long-term survival for some cancer patients, yet generalized success has been hampered by insufficient antigen presentation and exclusion of immunogenic cells from the tumor microenvironment. Here, we developed an approach to reprogram tumor cells in vivo by adenoviral delivery of the transcription factors PU.1, IRF8, and BATF3, which enabled them to present antigens as type 1 conventional dendritic cells. Reprogrammed tumor cells remodeled their tumor microenvironment, recruited, and expanded polyclonal cytotoxic T cells, induced tumor regressions, and established long-term systemic immunity in multiple mouse melanoma models. In human tumor spheroids and xenografts, reprogramming to immunogenic dendritic-like cells progressed independently of immunosuppression, which usually limits immunotherapy. Our study paves the way for human clinical trials of in vivo immune cell reprogramming for cancer immunotherapy.

overall_design: To characterize T cell responses elicited by in vivo cDC1 reprogramming, we profiled T cells from tumors, tdLN and blood using single cell 5'RNA and TCR-sequencing. At day 21, T cells were harvested from animals injected subcutaneously with PIB- or eGFP-transduced YUMM1.7 cells (1:1 mixed with parental cell line) and combined with anti-PD-1 or isotype control antibody treatment.

first: Ervin

last: Ascic

first: Carlos-Filipe

last: Pereira


title: A high-fat plus high-sucrose diet induces age-related macular degeneration in an experimental rabbit model

city: Chengdu

first: Danian

last: Chen

address: 37 Guoxue Xiang Street

institute: West China Hospital, Sichuan University

summary: Age-related macular degeneration (AMD) is a leading cause of blindness. Metabolic disorders and diets are risk factors. We compared lipid profiles and retinal phenotypes with long-term feeding of four diets in male Chinchilla rabbits. Animals were fed a normal diet (ND), high-fat diet (HFD), high-sucrose diet (HSD) or a high-fat plus high-sucrose diet (HFSD) for 6 months. Eyes were examined using multimodal imaging modalities and electroretinograms. Retinal sections were analyzed using H&E staining, Toluidine Blue staining, immunostaining and transmission electron microscopy. Lipids and complement C3 protein (C3) in serum or aqueous humor were measured. RNA sequencing was performed to evaluate the retinal transcriptomes. HFD and HSD had minor effects on lipid profiles but, when fed concomitantly, synergistically induced severe dyslipidemia. None of the four diets caused obesity. HFSD induced retinal lesions, such as reticular pseudodrusen (RPDs) and other pigmentary abnormalities. RPD-like lesions were mainly lipid droplets around cells of the retinal pigment epithelium. HFSD also induced elevated levels of ocular C3 and reduced the density of retinal vessels. In conclusion, HFD and HSD can - when combined - induce normal-weight dyslipidemia and RPD-like retinal lesions. HFSD-fed male Chinchilla rabbits are a good model of early AMD.

overall_design: To understand the underlying mechanism, we analyzed the transcriptome of the retinas of male Chinchilla rabbits at the age of about ten months, fed with a regular control diet group (ND, standard rabbit chow), HFD group (adding 10% lard and 0.5% cholesterol in the standard chow), HSD (adding 40% sucrose in the standard chow) and HFSD (adding 10% lard, 0.5% cholesterol, and 35% sucrose in the standard chow) for six months RNA sequencing. Each group had two retinas for sequencing.

first: Yujiao

last: Wang

first: Zhongping

last: Lv

first: Yongjiang

first: Xiaobo

last: Cen

first: Hui

last: Zhang


title: BDNF-TrkB signalling depletion from the indirect pathway spiny projection neurons (iSPN) leads to age-dependent spontaneous hyperlocomotion.

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

summary: Therefore, we have established a unique mouse model that provides a rare example of an age-dependent locomotor defect to identify the genes and associated molecular pathways relevant to maintaining locomotor control. Thus, we performed gene expression profiling analysis using data from RNA-seq of 2 different striatal populations at two time points in the presence and absence of the TrkB signalling.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from a limited number of purified adult or aged murine brain neurons lacking BDNF-TrkB signalling versus control mice.

first: Liliana

last: Minichiello

first: Chinnavuth

last: Vatanashevanopakorn

first: Amit

last: Grover


title: Inhibiting EZH2 Targets Atypical Teratoid Rhabdoid Tumor by Triggering Viral Mimicry via Both RNA and DNA Sensing Pathways

city: Toronto

first: Sajid

last: Marhon

state: ON

address: 101 College Street

institute: Princess Margaret Cancer Centre


title: Inhibiting EZH2 Targets Atypical Teratoid Rhabdoid Tumor by Triggering Viral Mimicry via Both RNA and DNA Sensing Pathways [CUT&RUN]

summary: Loss of function mutations in SMARCB1 are prevalent in pediatric atypical teratoid rhabdoid tumors (ATRTs) and confer an oncogenic dependency on EZH2, providing a compelling rationale for treating these genetically defined cancers via EZH2 inhibition (EZH2i). EZH2i results in tumor regression in SMARCB1-deficient tumors in preclinical studies, but the molecular mechanism has not been fully elucidated. Here we found that the sensitivity of SMARCB1-deficient tumors to EZH2i is associated with the viral mimicry response that depends on both double-stranded RNA (dsRNA) and cytoplasmic DNA sensing pathways. Unlike other epigenetic therapies targeting transcriptional repressors, viral mimicry by EZH2i in SMARCB1-deficient tumors is not triggered by crypt initiation of endogenous retroelements, but rather mediated by increased expression of genes enriched for intronic inverted-repeat Alu (IR-Alu) elements. Interestingly, we found that interferon-stimulated genes (ISGs) are highly enriched for dsRNA-forming intronic IR-Alu elements, suggesting a positive feedback loop whereby interferon response leads to dsRNA formation from intronic ISGs and activation of viral mimicry. Moreover, EZH2i in ATRT cells also enhances the expression of full-length LINE-1 elements, leading to genomic instability and cGAS/STING response in a process dependent on reverse transcriptase activity. Supporting this mechanism, co-depletion of dsRNA sensing and cytoplasmic DNA sensing completely rescues the viral mimicry response to EZH2i in SMARCB1-deficient tumors.

overall_design: UNC1999 and UNC24000 treatments. Day 4 and Day 6. 3 replicates.

first: Shengrui

last: Feng

first: Dustin

last: Sokolowski

first: Daniel

middle: D

last: De Carvalho


title: Single-cell multiome uncovers differences in glycogen metabolism underlying species-specific speed of development [UGP2 KO]

first: Max

last: Fernkorn

summary: Embryos from different mammalian species develop at characteristic timescales. These timescales are recapitulated during the differentiation of pluripotent stem cells in vitro. Specific genes and molecular pathways that modulate cell differentiation speed between mammalian species remain to be identified. Here we use single-cell multi-omic analysis of neural differentiation of mouse, cynomolgus monkey and human pluripotent cells to identify new regulators for differentiation speed. We demonstrate that species-specific differences in transcriptome dynamics are mirrored at the chromatin level, but that, contrary to other developmental contexts, the speed of neural differentiation is insensitive to manipulations of cell growth and cycling. Exploiting the single-cell resolution of our data, we identify glycogen storage levels regulated by UGP2 expression as a new species-specific trait of pluripotent cells, and show that lowered glycogen storage in UGP2 mutant cells is associated with accelerated neural differentiation. The control of energy storage could be a general strategy for the regulation of cell differentiation speed.

sample_organism:
Macaca fascicularis
Homo sapiens

platform_organism:
Macaca fascicularis
Homo sapiens

overall_design: Neural differentiation of a UGP2 KO lines was performed with sequencing samples collected at 0 hours and 7 days post-induction.

first: Alexandra

last: de la Porte

first: Julia

last: Schröder

first: Moritz

last: Thomas

first: Johanna

last: Geuder

first: Michael

last: Sterr

first: Wolfgang

last: Enard

first: Christian

last: Schröter

first: Carsten

last: Marr

first: Micha

last: Drukker


title: Differential contribution of P73+ Cajal-Retzius cells and Reelin to cortical morphogenesis

status: Public on Sep 04 2024

city: paris

first: Frederic

last: Causeret

address: 24 bd de montparnasse

department: Imagine Institute

institute: Inserm

summary: Cajal-Retzius cells (CRs) are a peculiar neuronal type within the developing mammalian cerebral cortex. One of their best documented feature is the robust secretion of Reln, a glycoprotein essential for the establishment of cortical layers through the control of radial migration of glutamatergic neurons. Although CRs and Reln are tightly associated, a direct assessment of their relative contribution to cortical morphogenesis is still lacking. Here we took advantage of the Gmnc-/- mouse model, in which CRs are initially produced but abnormally specified and undergo early apoptosis leading to a severe depletion, to investigate the consequences of CRs loss on neocortical lamination and hippocampal morphogenesis. We then compared to the phenotype of CRs-specific conditional Reln deletion in order to evaluate the relative contribution of CRs and Reln. We found that neocortical lamination defects upon CRs depletion are relatively modest, and partially recapitulated by Reln loss. By contrast, hippocampal morphogenesis was far more affected by CRs depletion than Reln loss. In addition, we found the lateral cortex especially sensitive to CRs depletion, but not Reln loss. These data support a model whereby CRs-derived Reln and Reln-independent signals differentially contribute to the morphogenesis of distinct regions of the developing cortex.

overall_design: The forebrain of four Gmnc-/- P0 animals originating from two distinct litters and four wild-type littermates were collected. The region encompassing the lateral and dorsal cortex as well as the hippocampus was dissected on both hemispheres and samples were pooled according to their genotype. Cells were dissociated and two Next GEM Single Cell 3’ v3.1 libraries were produced (one per genotype).

first: Vicente

last: Elorriaga

first: Frédéric


title: The role of fatty acid metabolism on Th9 cells differentiation

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

institute: KAZUSA DNA Research Institute

summary: T helper 9 cells (Th9) are interleukin 9 (IL-9)–producing cells that have diverse functions ranging from anti-tumor immune responses to driving allergic inflammation. Th9 cells differentiate from naïve CD4+ T cells in the presence of IL-4 and transforming growth factor-beta (TGF-β). In this reports, we have found that suppression of fatty acid biosynthesis increased IL-9 production in murine and human Th9 cells. This dataset include a set of data showing the effects of suppression of fatty acid synthesis on gene expression, chromatin remodelling and histone modifications in Th9 cells as analyzed by RNA-seq, ATAC-seq and ChIP-seq, respectively.

overall_design: Related to Fig 3-5.   RNA-seq, ATAC-seq, and ChIP-seq was performed to investigate the role of fatty acid metabolism on the regulation of Th9 cells specific gene expression.

first: Takahiro

last: Nakajima

first: Yuki

last: Ueda

first: Keisuke

last: Miyako

first: Takeru

last: Endo

first: Souta

last: Yoshida

first: Satoru

last: Yokoyama

first: Hikari

middle: K

last: Asou

first: Kazuko

last: Yamada

first: Kazutaka

last: Ikeda

first: Yosuke

last: Togashi

first: Yusuke


title: Translational profiling of stress-induced small proteins uncovers a connection among distinct signaling systems

city: Piscataway

first: Srujana

middle: Samhita

last: Yadavalli

state: NJ

address: 190 Frelinghuysen Rd

department: Genetics

institute: RUTGERS UNIVERSITY

summary: Bacteria utilize sophisticated mechanisms to detect and adapt to challenging environmental conditions by activating specific genes that help counteract stressors. Over 150 small proteins (≤ 50 amino acids long) are documented in Escherichia coli, but only a fraction of them are well-studied. Many of these proteins do not have an associated phenotype and their biological roles remain elusive. Here, we investigate small proteins induced in response to magnesium limitation using ribosome profiling, RNA sequencing, and transcriptional reporter assays. We uncover 17 small proteins with increased translation initiation, a majority of which are transcriptionally upregulated by the PhoQ-PhoP two-component signaling system, central for magnesium homeostasis. Next, we describe small protein-specific deletion and overexpression phenotypes, which underscore the significance of their expression to cellular physiology in low magnesium stress. Most remarkably, our study reveals the small protein YoaI as a connector of the major signaling networks – PhoR-PhoB and EnvZ-OmpR in E. coli.

overall_design: To investigate low magnesium stress induced small proteins in E. coli K-12 MG1655 strain, we utilized translation initiation profiling (Ribo-RET) and RNA-Seq under conditions of magnesium starvation and no stress. Code for processing the data can be found at https://github.com/yadavalli-lab/Small-proteins-induced-under-low-magnesium-stress

first: Sangeevan

last: Vellappan

first: Junhong

last: Sun

first: John

last: Favate

first: Pranavi

last: Jagadeesan

first: Debbie

last: Cerda

first: Premal

last: Shah


title: Quantification of tumour-infiltrating immune cells through deconvolution of DNA methylation data in Ewing sarcomas

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

institute: Ospedale Pediatrico Bambino Gesù

summary: Ewing Sarcomas (EWS, OMIM#612219) presents a major challenge in pediatric oncology due to its aggressive nature and poor prognosis, particularly in metastatic cases. Genetic fusions involving the EWSR1 gene and ETS family transcription factors are common in EWS, though other rarer fusions have also been identified. Current standard techniques like immunohistochemistry have failed to fully characterize the immune tumor microenvironment of EWS, hindering insights into tumor development and treatment strategies. Recent efforts apply gene expression datasets to quantify tumor-infiltrating immune cells in EWS. Similar deconvolution techniques can be also applied to DNA methylation (DNAm) arrays, which are much more stable compared to RNA-based methods. This study aims to characterize immune cell infiltration in EWS using DNAm array data. We collected 32 EWS samples from 32 consecutive patients referred to Bambino Gesù Children’s Hospital. DNAm analysis was performed by EPIC arrays; data loading, normalization, deconvolution and survival analysis were then performed in R programming environment. We observed a higher content of dendritic cells and longer overall survival in samples with EWSR1::FLI1 translocation compared to samples with rarer fusions. Moreover, T-memory lymphocytes and monocytes emerged as a significant predictor of overall survival. This study underscores the potential of DNAm arrays in providing robust insights into EWS immune profiles, offering a promising avenue for future research. Further investigations with larger cohorts are warranted to validate these findings and explore additional immune cell types influencing EWS outcomes.

overall_design: We performed immune cell content deconvolution of the normalized DNA methylation data through package MethylResolver. Then, we used two-tailed heteroschedastic Student’s T-test to evaluate the statistical significance of differences in immune cell content between sample groups (canonical vs. non-canonical), and Kaplan-Meier analysis to assess the relationship between immune cell content and overall survival.


title: Epigenetic evidence of an Ac/Dc axis by VPA and SAHA

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

summary: Valproic acid (VPA) is one of the most commonly used anti-epileptic drugs with pharmacological actions on GABA and blocking voltage-gated ion channels. VPA also inhibits histone deacetylase (HDAC) activity. Suberoylanilide hydroxamic acid is also a member of a larger class of compounds that inhibit HDACs. At the time of this article, there are 123 active international clinical trials for VPA (also known as valproate, convulex, divalproex, and depakote) and SAHA (vorinostat, zolinza). While it is well known that VPA and SAHA influence the accumulation of acetylated lysine residues on histones, their true epigenetic complexity remains poorly understood. Primary human cells were exposed to VPA and SAHA to understand the extent of histone acetylation (H3K9/14ac) using chromatin immunoprecipitation followed by sequencing (ChIP-seq). Because histone acetylation is often associated with modification of lysine methylation, we also examined H3K4me3 and H3K9me3. To assess the influence of the HDAC inhibitors on gene expression, we used RNA sequencing (RNA-seq).

overall_design: ML16 fibroblasts were exposed to VPA and SAHA for 16 hours before processing for ChIP and RNA sequencing

first: Sebastian

last: Lunke

first: Scott

last: Maxwell

first: Ishant

last: Khurana

first: K

last: Harikrishnan

first: Jun

last: Okabe


title: Small changes in cultivability, big changes in heat treated yeast transcriptome

city: Dijon

first: Stéphane

last: GUYOT

address: 1 Esplanade Erasme

institute: Institut Agro Dijon

summary: During the application of thermal treatment, cell survival depends on biological factors (such as growth stage, culture conditions, and the composition of the stress medium) as well as physical factors inherent to the thermal process (including amplitude, duration at the stress temperature, and the rate of temperature increase). In this study, the yeast Saccharomyces cerevisiae BY4742 was exposed to two different thermal treatment kinetics in a nutrient medium after being cultivated in YPD medium at 25 °C for 48 hours (to reach the stationary growth phase). The thermal treatments were applied between 25 °C and 50 °C, followed by a 30-minute hold at 50 °C before returning to 25 °C. The yeast cells were exposed either to a heat shock (heating kinetics: 50 °C/min) or to a gradual temperature increase (heating kinetics: 0.5 °C/min). Generally, it is known that heat shock induces lower survival (30%) compared to the gradual increase (80%). In this study, we demonstrate that despite the small difference in survival rate (less than one logarithmic reduction in both cases), the transcriptomes vary significantly. The use of bioinformatics tools such as WGCNA revealed a correlation between differentially expressed gene clusters and phenotypic traits (measured by spectroscopy, fluorescence microscopy, flow cytometry, among others). Here, we focused on both mRNA and ncRNA (non coding RNA).

overall_design: Yeast were submitted to a heat shock (HS) or a heat ramp (HR) and then imediatly recpvered at 25°C before extracting mRNA and ncRNA. Controls (CTL) corresponded to untreated yeasts (collected before the heat treatment).

first: Lucie

last: BERTHEAU

first: Hazel

last: DAVEY


title: LncRNA Expression Profiling in Renal Cancer Tissues

city: Ube

first: Takanori

last: Tokunaga

address: 1-1-1 Minami-kogushi

institute: Yamaguchi University

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

summary: This study investigates the expression profiles of LncRNA in renal cancer tissues from patients treated with immune checkpoint inhibitors.

overall_design: We used a microarray approach to assess LncRNA expression in renal cancer tissues. A total of 4 samples were analyzed, comparing treated and untreated patients.

first: Hiroshi

last: Hirata


title: In vivo dendritic cell reprogramming for cancer immunotherapy [organoid scRNA]

first: Ilia

last: Kurochkin

overall_design: To verify that a cDC1 program was established in cancer spheroids and to uncover potential differences in cDC1 reprogramming progressing in 2D or 3D cultures, we FACS-purified CD45+ and HLA-DR+ T98G cells at days 3, 7, and 9 of reprogramming and performed scRNA-seq. This submission includes only 2 of the 2D samples (day 7 and day9). We used 2 of the 2D samples (day 0 and day3) from previous submission GSE224941 (GSM7035968, GSM7035969).

first: Ervin

last: Ascic

first: Carlos-Filipe

last: Pereira


title: Spatiotemporal Single-Cell Roadmap of Human Skin Wound Healing (Single-cell-VU)

city: Nanjing

first: Dongqing

last: Li

address: No.12, Jiangwangmiao Street, Xuanwu District, Nanjing, China

institute: Hospital for Skin Diseases, Institute of  Dermatology, Chinese Academy of Medical Sciences &  Peking Union Medical College

summary: The process of wound healing in humans is poorly understood. To identify spatiotemporal gene expression patterns during human wound healing, we performed single cell and spatial transcriptomics profiling of human in vivo wound samples.

overall_design:
We obtained the human skin chronic wound tissues by recruiting venous ulcer (VU) patients (n=4) and matched healthy controls (n=5). Samples were anaylsed using single cell gene expression sequencing.

*** The raw sequencing data are available for controlled access in European Genome–phenome Archive (EGA) under the accession code EGAS50000000571 ***

first: Jiating

last: Wang


title: Paraspeckle-Independent Co-Transcriptional Regulation of Nuclear microRNA Biogenesis by SFPQ [PRO-seq]

city: Montreal

first: Thomas

middle: Francis

last: Duchaine

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

institute: McGill University

summary: MicroRNAs (miRNAs) play crucial roles in physiological functions and diseases such as cancer, but the regulation of their nuclear biogenesis remains poorly understood. Here, BioID on Drosha, the catalytic subunit of the microprocessor complex, revealed its proximity to SFPQ, a multifunctional RNA-binding protein (RBP) notably involved in forming the paraspeckle nuclear condensates. SFPQ depletion impacted both primary and mature miRNA expression, while other crucial paraspeckle proteins or the paraspeckle scaffolding lncRNA NEAT1 did not, indicating a unique paraspeckle-independent role. Comprehensive transcriptomic analyses showed that SFPQ loss broadly affects RNA and miRNA host gene (miRNA HG) expression, influencing both their transcription and stability. Notably, SFPQ protects specific miRNA HGs, including the oncogenic miR-17~92 polycistron, from degradation by the nuclear NEXT-exosome complex. Lastly, we show that high SFPQ is tightly linked with overexpression miR-17~92 and its mature miRNAs across a broad variety of cancers. Our findings reveal a dual role for SFPQ in the regulation of miRNA HGs transcription and stability, as well as its significance in cancers.

overall_design: We used a multi-omic approach to uncover a dual role for SFPQ in the regulation of pri-miRNAs’ transcription and stability. We established an SBC-3 cell line in which SFPQ has been knocked down by siRNAs. We then performed nascent transcription profiling analysis using data obtained from PRO-seq at the 72h time point post-transfection.

first: Caroline

last: Thivierge

first: Maxime

last: Bellefeuille

first: Sarah-Slim

last: Diwan

first: Boris

last: Dyakov

first: Rania

last: Leventis

first: Gabrielle

last: Perron

first: Hamed

middle: S

last: Najafabadi

first: Simon-Pierre

last: Gravel

first: Anne-Claude

last: Gingras

middle: F


title: Impact of phlebotomy induced anemia on whole retinal transcriptome at P15 and P20 in the rat 50/10 OIR model

city: Minneapolis

first: Ellen

middle: Coley

last: Ingolfsland

state: MN

address: 516 Delaware St SE

institute: University of Minnesota

summary: Phlebotomy-induced-anemia (PIA), which induces tissue hypoxia and angiogenesis, occurs universally among infants at risk for severe retinopathy of prematurity (ROP). We hypothesized that PIA exacerbates pathologic retinal neovascularization in ROP. Methods: We induced PIA to a hematocrit of 18% among rats undergoing the established 50/10 oxygen-induced retinopathy (OIR) model. Rats were euthanized at P15 and P20, during the avascular and neovascular phases of OIR, respectively. Whole retinal transcriptomes were compared to non-PIA controls. Results: RNA sequencing showed dampened pathways of angiogenesis, inflammation, and neural development in anemic OIR females at P20. Conclusion: PIA dampened transcriptomic pathways central to retinal vascular and neural development in neonatal rats. These data suggest PIA provides a protective effect from ROP.

overall_design: Samples for RNA isolation were selected from 4-8 pups/group that were 50% male, 50% female/ group and weight-matched within the group. RNA was extracted from single whole retina using RNAqueous RNA Isolation Kits (Ambion, Waltham, MA). RNA concentration and purity were measured as previously described19. The University of Minnesota Genomic Center performed qualification analysis (RIN score > 8.0), coded library construction, and next generation sequencing, as previously described19. Differentially expressed genes (DEGs) between RA versus RA+PIA pups and OIR versus OIR+PIA pups were identified by the EdgeR package (negative binomial feature in CLCGWB, Qiagen, Redwood City, CA) using raw read counts and a corrected-false discovery rate < 0.05. Additionally, P20 groups (n=8/group) were divided by sex (4 male, 4 female) and DEGs calculated between OIR versus OIR+PIA females and OIR versus OIR+PIA males.

first: Juan

last: E.Abrahante Llorens


title: Senescence and Inflamm-Aging Are Associated With Endothelial Dysfunction in Men But Not Women With Atherosclerosis

city: Montréal

first: Pauline

last: Mury

state: QC

address: 5000 rue Bélanger

institute: Montreal Heart Institute

summary: Coronary artery disease (CAD) is a major cause of death worldwide, and more prevalent in men than in women. This study examines explored the differences in endothelium-dependent relaxation and associated transcriptomic signature in plaque-free internal thoracic arterial segments of age-matched men and women undergoing CABG procedure. Endothelium-dependent relaxations were better in female arteries compared to male. Using single nuclei mRNA sequencing, our analysis revealed the prevalence of senescence-associated inflammation in male but not female endothelial cells (EC), that also had longer telomeres than male EC. Furthermore, we found a large common transcriptomic signature in EC of men with severe endothelial dysfunction and in EC expressing CDKN1A (p21), a canonical marker of cellular senescence, validating the link between senescence, inflammation and endothelial dysfunction in men. In contrast, compared to male, female EC overexpressed pathways suggestive of a better stress resistance in association with the better endothelial function.

overall_design: Nuclei were isolated from internal thoracic arteries from 12 patients with coronary artery disease (CAD) undergoing an in-patient CABG, including 6 men and 6 women

first: Gael

last: Cagnone

first: Olina

last: Dagher

first: Florian

last: Wünnemann

first: Guillaume

last: Voghel

first: Melissa

last: Beaudoin

first: Melanie

last: Lambert

first: Geraldine

last: Miquel

first: Pierre-Emmanuel

last: Noly

first: Louis

middle: P

last: Perrault

first: Michel

last: Carrier

first: Nathalie

last: Thorin-Trescases

first: Jean-Sebastien

last: Joyal

last: Lettre

first: Eric

last: Thorin


title: Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

summary: Genomic enhancers are key transcriptional regulators which, upon the binding of sequence-specific transcription factors, can activate their cognate promoter. Although enhancers have been extensively studied in isolation, a substantial number of genes have more than one simultaneously active enhancer, and it remains unclear how these distinct elements cooperate to regulate transcription. In this work, we report that developmental enhancers – that regulate tissue-specific genes – and housekeeping enhancers rely on distinct modes of enhancer-enhancer cooperativity: while developmental enhancers are synergistic, housekeeping enhancers are additive (meaning that their combined activity mirrors the sum of their individual activities). Developmental enhancer synergy is promiscuous in our system and is not associated with specific combinations of transcription factors. However, developmental transcription factors globally contain higher fraction of intrinsically disordered domains, which might support such synergistic interactions.

overall_design: The enhancer activity of three different pools of enhancer-enhancer pairs were measured using the STARR-Seq method in Drosophila S2 cells (with or without ecdysone) and OSC cells.

first: Vincent

last: Loubiere

first: Bernardo

last: de Almeida

first: Michaela

last: Pagani


title: The transcriptional landscape of cancer stem-like cells functionality in breast cancer

city: Cluj-Napoca

first: Oana

last: Baldasici

state: Cluj

address: Republicii 34-36

country: Romania

institute: The Oncology Institute Cluj-Napoca

summary: To further explore the signaling mechanisms underlying breast CSCs maintenance in breast tissues, we employed microarray analysis, to compare the 3 observed mammosphere formation groups: M0, M1, and M2, identified by in vitro cultivation of breast biopsy tissue samples.

overall_design: Gene expression in breast tissue samples was evaluated in relation to mammosphere formation in vitro, from matching fresh biopsies.

first: Olga

last: Soritau

first: Andrei

last: Roman

first: Carmen

last: Lisencu

first: Simona

last: Visan

first: Laura

last: Maja

first: Bogdan

last: Pop

last: Fetica

last: Cismaru

first: Laurian

last: Vlase

first: Loredana

last: Balacescu

first: Ovidiu

first: Aman

last: Russom

last: Tudoran


title: AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancer [ChIP-seq]

city: Philadelphia

first: Christopher

last: McNair

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

summary: Castration resistant prostate cancer (CRPC) remains an incurable disease stage with ineffective treatments options. Here, the androgen receptor (AR) coactivators CBP/p300, which are histone acetyltransferases, were identified as critical mediators of DNA damage repair (DDR) to potentially enhance therapeutic targeting of CRPC. Key findings demonstrate that CBP/p300 expression increases with disease progression and selects for poor prognosis in metastatic disease. CBP/p300 bromodomain inhibition enhances response to standard of care therapeutics. Functional studies, CBP/p300 cistrome mapping, and transcriptome in CRPC revealed that CBP/p300 regulates DDR. Further mechanistic investigation showed that CBP/p300 attenuation via therapeutic targeting and genomic knockdown decreases homologous recombination (HR) factors in vitro, in vivo, and in human prostate cancer (PCa) tumors ex vivo. Similarly, CBP/p300 expression in human prostate tissue correlates with HR factors. Lastly, targeting CBP/p300 impacts HR-mediate repair and patient outcome. Collectively, these studies identify CBP/p300 as drivers of PCa tumorigenesis and lay the groundwork to optimize therapeutic strategies for advanced PCa via CBP/p300 inhibition, potentially in combination with AR-directed and DDR therapies.

overall_design: Genome binding/occupancy profiling by high throughput sequencing. Human prostate cancer cells treated with vehicle and CBP/p300 bromodomain inhibitor (CCS1477). ChIP-Seq performed for AR, CBP, and p300 in these conditions to determine impact on cistrome with AR coactivator inhibition.

first: A

last: Shafi

first: C

middle: M


title: Paraspeckle-Independent Co-Transcriptional Regulation of Nuclear microRNA Biogenesis by SFPQ [RNA-seq]

first: Thomas

last: Duchaine

overall_design: We used a multi-omic approach to uncover a dual role for SFPQ in the regulation of pri-miRNAs’ transcription and stability. We established an SBC-3 cell line in which SFPQ/NONO/NEAT1 have been knocked down by siRNAs or ASOs. We then performed gene expression profiling analysis using data obtained from RNA-seq at the 72h time point post-transfection.

first: Caroline

last: Thivierge

first: Maxime

last: Bellefeuille

first: Sarah-Slim

last: Diwan

first: Boris

middle: J

last: Dyakov

first: Rania

last: Leventis

first: Gabrielle

last: Perron

first: Hamed

last: Najafabadi

first: Simon-Pierre

last: Gravel

first: Anne-Claude

last: Gingras


title: Mechanistic Insights and In Vivo Efficacy of Thiosemicarbazones Against Methicillin-Resistant Staphylococcus aureus

city: London

first: David

last: Heinrichs

address: Microbiology and Immunology, 3014 Dental Sciences Building, 1151 Richmond Street

institute: University of Western Ontario

summary: Thiosemicarbazone R91 targets drug-resistant S. aureus by inducing copper and oxidative stress

overall_design: A total of 6 samples were analyzed. Samples were acquired from 3 independent experiments. 3 samples were WT S. aureus treated with a vehicle control, 3 samples were WT S. aureus treated with R91.

first: Avery

last: Gaudreau

last: Watson


title: AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancer [RNA-seq: 22RV1]

overall_design: Gene expression profiling by high throughput sequencing in human prostate cancer cells (cell lines 22RV1).


title: G-quadruplexes within the SVA retrotransposon modulate TAF1 gene expression in X-linked Dystonia Parkinsonism [ChIP-seq]

city: Padova

first: Giulia

last: Nicoletto

address: Via Gabelli 63

department: Molecular Medicine

institute: UNIPD

summary: By ChIP-seq with the anti-G4 antibody BG4, we assessed that G4s are present in the folded state in ctrl and XDP cell tested.

overall_design: XDP, NMC and ctrl fibroblasts analysed by G4 ChIP-seq to detect the presence of G-quadruplexes. Experiment performed in duplicate.

first: Filippo

last: Cernilogar

first: Gunnar

last: Schotta

first: Sara

middle: N

last: Richter


title: Eukaryotic Initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs

city: Cambridge

first: Anne

middle: E

last: Willis

address: Gleeson Building, Tennis Court Road

department: MRC Toxicology Unit

institute: University of Cambridge

summary: In diffuse large B-cell lymphoma (DLBCL) poor outcome is associated with eIF4B-dependent stimulation of the DEAD box helicase eIF4A that unwinds RNA structures in 5’ untranslated regions (UTRs) in mRNAs that encode proteins with a role in cell proliferation. We carried out iCLIP to examine differences in RNAs bound by eIF4B in DLBCL-derived versus -control B-cells.

overall_design: iCLIP analysis of eIF4B binding in DLBCL (DoHH2) (n=4) and non-cancerous B-cells (GM01953) (n=2)


title: Stroma reprogramming by FAK synergizes with MAPK inhibition and renders PDAC responsive to cytotoxic- and immuno-therapies

city: Saint Louis

last: DeNardo

address: 425 South Euclid Ave

institute: Washington University in Saint Louis

summary: Pancreatic ductal adenocarcinoma(PDAC) is a highly lethal malignancy with poor response rate to therapy. An immune suppressive tumor microenvironment (TME) and oncogenic mutations in KRAS have been implicated as drivers of resistance to both conventional and immune therapies.  As such, targeting RAS/MAPK signaling is an attractive strategy. However, in practice, MAPK inhibition has not yet shown clinical efficacy, likely due to rapid acquisition resistance in PDAC cells. Tumor intrinsic mechanisms of resistance to RAS/MAPK have been studied, however, the unique PDAC TME may also be a key driver in resistance. Previous studies have shown that FAK inhibition can reprogram the PDAC TME and delay PDAC progression in animal models. Herein, we found that long-term FAK inhibitor treatment leads to hyperactivation of the MAPK pathway in both genetically engineered mouse models and in post-treatment PDAC tissues from FAK inhibitor clinical trials. Concomitant inhibition of both FAK (VS4718) and RAF/MEK (V6766) signaling dramatically suppressed tumor cell growth, leading to increased survival across multiple PDAC mouse models. The mechanisms of synergy include both changes in tumor-intrinsic signaling and modulation of tumor/stroma interactions that drive MEK resistance. In the TME, we found that cancer associated fibroblasts (CAFs) can impair the downregulation of cMyc by MEK inhibition in PDAC cells. This results in de-novo resistance to MEK inhibition in fibrotic conditions. By contrast, FAK inhibitors reprogram CAFs to suppress the production of key growth factors, including FGF1, that drives resistance to RAF/MEK inhibition. While combined FAK and RAF/MEK inhibition only leads to disease stasis, the addition of chemotherapy to the combination led to tumor regression and improved long-term survival in PDAC mouse models. Analysis of tumor immunity showed that the combination of FAK and MEK inhibition improved anti-tumor immunity and improved priming of T cell responses, which was further improved with the addition of chemotherapy. These findings led to testing of FAK (Defactinib) plus RAF/MEK (Avutometinib) inhibition in combination with gemcitabine and nab-paclitaxel in advanced pancreatic cancer patients (NCT05669482). Finally, we tested if the addition of immunotherapy could enhance the efficacy of the FAKi/MEKi/chemotherapy and found adding in either PD1 or CTLA4/PD1 blockade led to long term disease control in PDAC animal models.  Together, these studies identified novel FAK inhibition as a route to overcome both tumor intrinsic and stromal-derived resistance to MAPK inhibition and showed that this combination can be exploited to increase the efficacy of cytotoxic and immunotherapy approaches.

overall_design: Cancer-associated fibroblast (CAF) and Immune cells of PDAC Tumor tissue from KPPC (p48-Cre;LSL-KrasG12D;Trp53flox/flox) mice were isolated by Fluorescence-activated cell sorting (FACS) according to CD45+ staining and analyzed

first: Xiuting

last: Liu


title: G-quadruplexes within the SVA retrotransposon modulate TAF1 gene expression in X-linked Dystonia Parkinsonism [RNA-Seq]

summary: X-linked dystonia parkinsonism (XDP) is an inherited neurodegenerative disease characterized by the antisense insertion of an SVA retrotransposon into the TAF1 gene, encoding for the largest subunit of the basal transcription factor TFIID, which is essential for RNA polymerase II activity. This SVA insertion has been associated with altered TAF1 expression levels, but the cause of this outcome and its link to the development of XDP remain unknown. Unique to the XDP SVA compared to other SVA retrotransposons in the human genome is the amplification of the (GGGAGA)n repeat domain, creating a unique G4-prone region, whose length correlates with age at onset and disease severity. By ChIP-seq and ChIP-qPCR with the anti-G4 antibody BG4, we assessed that G4s are present in the folded state in the XDP SVA of these cells. Using available G4 ligands, we demonstrated that stabilization of the XDP SVA G4s reduces TAF1 transcripts in the exons around and downstream of the SVA, while increasing the transcription of the upstream exons, possibly through a positive feedback loop.

overall_design: To investigate the effects of XDP SVA G4s formation, we performed RNA-seq of healthy ctrl and XDP-affected cells from two cell types, human fibroblasts (hFib) and neuronal progenitor cells (NPCs). We treated cells with two G4 ligands, namely BRACO-19 (B19) and quarfloxin (Q), for 24 h to modulate XDP SVA G4s and evaluate the effects on the TAF1 gene by DE analysis. The experiment was repeated in triplicate for all cell lines.


title: Single-molecule chromatin configurations link transcription factor binding to expression in human cells [ATAC-seq]

city: Stanford

first: Benjamin

middle: Rosenstock

last: Doughty

state: CA

address: 279 Campus Drive W

institute: Stanford University

summary: The binding of multiple transcription factors (TFs) to genomic enhancers activates gene expression in mammalian cells. However, the molecular details that link enhancer sequence to TF binding, promoter state, and gene expression levels remain opaque. We applied single-molecule footprinting (SMF) to measure the simultaneous occupancy of TFs, nucleosomes, and components of the transcription machinery on engineered enhancer/promoter constructs with variable numbers of TF binding sites for both a synthetic and an endogenous TF. We find that activation domains enhance a TF’s capacity to compete with nucleosomes for binding to DNA in a BAF-dependent manner, TF binding on nucleosome-free DNA is consistent with independent binding between TFs, and average TF occupancy linearly contributes to promoter activation rates. We also decompose TF strength into separable binding and activation terms, which can be tuned and perturbed independently. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the binding microstates observed at the enhancer and subsequent time-dependent gene expression. This work provides a template for quantitative dissection of distinct contributors to gene activation, including the activity of chromatin remodelers, TF activation domains, chromatin acetylation, TF concentration, TF binding affinity, and TF binding site configuration.

overall_design: Bulk omni-ATAC was performed as in69 with 50,000 cells and two biological replicates per sample. Libraries were sequenced 2x36 with an NextSeq 500/550 High Output v2.5 75 cycles kit (Illumina, 20024906) on a NextSeq 550. Bulk ATAC-seq data processing of fastq files was performed with snakeATAC (https://github.com/GreenleafLab/snakeATAC_singularity) and alignment to hg38.   To compare SMF and ATAC data, ATAC peaks were first standardized to 200 bp wide and grouped by signal into 100 quantile bins. Average ATAC coverage was computed per bin. Methylation signal from SMF was computed by averaging over all GpCs in all reads overlapping the ATAC peaks and averaged by quantile.  Visualization of ATAC peaks at ISGs was performed by loading BigWig files with 100 bp windows into the Integrative Genomics Viewer70. BAM files were then further processed with ChrAccR (https://github.com/GreenleafLab/ChrAccR) to perform chromVar71 (IFN_ATAC_chraccr.rmd) and ATAC footprinting analyses. ATAC footprinting of ISREs was performed on genome-wide matches to Vierstra Non-redundant TF motif clustering (V2.1 BETA-HUMAN)1 cluster AC0188 IRF/STAT|IRF using ChrAccR function getMotifFootprints and RPM and Tn5 bias normalization (IFN_ATAC_footprinting.R). Computing average ATAC signal around IFN promoters, a list of hg38 TSS was extended by 250 bp in either direction, and average ATAC-seq coverage was computed over these peaks using bedtools coverage (vX). Signal was RPM normalized and averaged across all ISGs, which were defined as genes with >2-fold increase in expression 24 hours after IFN-β stimulation (as measured by bulk RNA-seq, see below) and which contained ≥3 ISRE motifs in the promoter. A null set of genes was selected by choosing the expressed gene with the closest TPM to each ISG pre-stimulation.

middle: R


title: Mouse enteric neurons control intestinal plasmacytoid dendritic cell function via serotonin-HTR7 signaling [Cd45 RNAseq]

city: boston

first: Hailong

last: Zhang

state: MA

address: 181 longwood ave

institute: Brigham and Women's Hospital, Harvard Medical School

summary: Serotonergic neurons have multiple roles, including regulating mood and behavior1,2, yet it remains unclear which of these phenotypes are caused by serotonin produced by the central versus the peripheral nervous system. Neuronal serotonin is produced by the enzyme tryptophan hydroxylase 2 (Tph2)3. Mice that lack Tph2 exhibit decreased gut motility4 and several behavioral disorders, including decreased anxiety-like behavior and increased aggression5. To clarify the specific role of peripheral serotonergic circuits, here we engineered mice with intact Tph2 in central neurons but lacking Tph2 in peripheral neurons (Tph2fl/fl; Hand2-Cre). We discovered that PSN contribute to gut motility and are important in the control of anxiety-like behavior but do not contribute to impulsive aggression. Thus, central and peripheral serotonergic neurons have different roles in behavioral regulation. Intriguingly, animals lacking peripheral neuronal Tph2 had deficiencies in enteric immune cells, including reduced abundance of dendritic cells (DC) and IgA+ B cells in the small intestine and elevated susceptibility to oral Salmonella infection. Mechanistic studies suggest that serotonin produced by PSN promotes activation of DC through the 5-HT7 receptor, thereby facilitating DC-mediated differentiation of IgA+ B cells. Our findings highlight the importance of serotonin produced by peripheral neurons for control of behavior and gut defense and suggest that these circuits could be valuable targets for therapeutics.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lamina propria CD45 from co-housed WT and Tph2 KO mice

first: Matthew

last: Waldor


title: Mouse enteric neurons control intestinal plasmacytoid dendritic cell function via serotonin-HTR7 signaling

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

overall_design: Refer to individual Series


title: Mouse enteric neurons control intestinal plasmacytoid dendritic cell function via serotonin-HTR7 signaling [16S]

overall_design: Comparative microbiota in WT and Tph2 KO mice, as well as between Tph2fl/fl and Tph2fl/fl; Hand2-Cre


title: Mouse enteric neurons control intestinal plasmacytoid dendritic cell function via serotonin-HTR7 signaling [Sep_Epi]

summary: Serotonergic neurons have multiple roles, including regulating mood and behavior1,2, yet it remains unclear which of these phenotypes are caused by serotonin produced by the central versus the peripheral nervous system. Neuronal serotonin is produced by the enzyme tryptophan hydroxylase 2 (Tph2). Mice that lack Tph2 exhibit decreased gut motility4 and several behavioral disorders, including decreased anxiety-like behavior and increased aggression5. To clarify the specific role of peripheral serotonergic circuits, here we engineered mice with intact Tph2 in central neurons but lacking Tph2 in peripheral neurons (Tph2fl/fl; Hand2-Cre). We discovered that PSN contribute to gut motility and are important in the control of anxiety-like behavior but do not contribute to impulsive aggression. Thus, central and peripheral serotonergic neurons have different roles in behavioral regulation. Intriguingly, animals lacking peripheral neuronal Tph2 had deficiencies in enteric immune cells, including reduced abundance of dendritic cells (DC) and IgA+ B cells in the small intestine and elevated susceptibility to oral Salmonella infection. Mechanistic studies suggest that serotonin produced by PSN promotes activation of DC through the 5-HT7 receptor, thereby facilitating DC-mediated differentiation of IgA+ B cells. Our findings highlight the importance of serotonin produced by peripheral neurons for control of behavior and gut defense and suggest that these circuits could be valuable targets for therapeutics.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for intestinal epithelial cell from separate-housed WT and Tph2 KO mice


title: Mouse enteric neurons control intestinal plasmacytoid dendritic cell function via serotonin-HTR7 signaling [scRNA-seq]

overall_design: Single cell RNA-seq of FACS-sorted enteric neuron


title: Expression data from ELC52 cells

status: Public on Sep 03 2024

city: Kasugai

first: Yukiya

last: Yamamoto

state: Aichi

address: 1200 Matsumoto-cho,  Biomedical Sciences, 11F, Building#51

institute: Chubu University

summary: Microarray analysis showed that TPO addition induced mRNA expression of chemokine families in ELC52 cells, and ruxolitinib treatment reduced mRNA expression of certain chemokine families in ELC52 cells. IFN-α inhibited ELC52 cell proliferation, and this was accompanied by induction of IFN-stimulated genes.

overall_design: Total RNA from treated ELC52 cells was isolated using a RNeasy Plus Mini Kit (QIAGEN). Total RNA was subjected to human Clarion S assay (Applied Biosystems). Reagent concentrations were DMSO (0.01%), ruxolitinib (1 microM), TPO (100 ng/ml), and IFNalpha2b (200 ng/ml).


title: Prenatal exposure to valproic acid induces sex-specific alterations in rat cortical and hippocampal neuronal structure and function in vitro

city: Guelph

first: Olivia

middle: Olga Fraser

last: Williams

address: 50 Stone Road West

department: Biomedical Sciences

institute: Unviersity of Guelph

summary: In this dataset we include the expression data obtained by dissected prefrontal cortical tissue from sprague-dawley rats exposed to saline or valproic acid on gestation day 12.5 in utero. This data was used to obtain prefrontal cortical genes to determine sex differences in a model of autism spectrum disorder.

overall_design: 20 Total samples were analyzed

first: Williams

last: Olivia

first: Perreault

last: Melissa


title: Regular exercise suppresses steatosis-associated liver cancer development by degrading E2F1 and c-Myc via circadian gene upregulation

city: Osaka-City

first: Kanae

last: Echizen

state: Osaka

address: Asahimachi 1-4-3, Abeno-Ku

department: Graduate School of Medicine

institute: Osama Metropolitan University

summary: Regular exercise is believed to suppress cancer progression. However, the precise molecular mechanisms by which exercise prevents cancer development remain unclear. In this study, using a steatosis-associated liver cancer mouse model, we found that regular exercise at a speed of 18 m/min for 20 min daily suppressed liver cancer development. To explore the underlying mechanisms, we examined the gene expression profiles in the livers of the exercise and non-exercise groups. We extracted RNA from non-tumor and tumor tissues from each mouse liver and performed bulk RNA-seq analysis. The expressions of circadian genes, such as Per1 and Cry2, were upregulated in the exercise group. We further found that the expression of a series of E2F1 and c-Myc target genes that directly affect the proliferation of cancer cells was downregulated in the exercised group. However, the expression of these genes was transcriptionally unchanged but degraded at the post-translational level by exercise. Cry2, which is regulated by the Skp1-Cul1-FBXL3 (SCFFBXL3) ubiquitin ligase complex by binding to FBXL3, can form a complex with E2F1 and c-Myc, which we think is the mechanism to degrade them. Our study revealed a previously unknown mechanism by which exercise prevents cancer development.

overall_design: To analyze effects of  excercise on tumor promotion, we used  liver carcinogenesis model mice by  7,12-dimethylbenz(a)anthracene (DMBA) trearment and high fat diet (HFD) feeding. Total RNA was extracted from the frozen liver tissues of exercised and non-exercised mice.

first: Vu

last: Thuong Huyen

first: Ryota

last: Yamagishi

first: Miho

last: Kumagai

first: Yoshiki

last: Nonaka

first: Takahiro

last: Kodama

first: Tatsuya

last: Ando

first: Megumu

last: Yano

first: Naoki

last: Takada

first: Masaki

last: Takasugi

first: Fumitaka

last: Kamachi

first: Naoko

last: Ohtani


title: Inhibiting EZH2 Targets Atypical Teratoid Rhabdoid Tumor by Triggering Viral Mimicry via Both RNA and DNA Sensing Pathways [RNA-Seq]

city: Toronto

first: Sajid

middle: A

last: Marhon

address: 101 College Street

institute: Princess Margaret Cancer Centre

summary: Loss of function mutations in SMARCB1 are prevalent in pediatric atypical teratoid rhabdoid tumors (ATRTs) and confer an oncogenic dependency on EZH2, providing a compelling rationale for treating these genetically defined cancers via EZH2 inhibition (EZH2i). EZH2i results in tumor regression in SMARCB1-deficient tumors in preclinical studies, but the molecular mechanism has not been fully elucidated. Here we found that the sensitivity of SMARCB1-deficient tumors to EZH2i is associated with the viral mimicry response that depends on both double-stranded RNA (dsRNA) and cytoplasmic DNA sensing pathways. Unlike other epigenetic therapies targeting transcriptional repressors, viral mimicry by EZH2i in SMARCB1-deficient tumors is not triggered by crypt initiation of endogenous retroelements, but rather mediated by increased expression of genes enriched for intronic inverted-repeat Alu (IR-Alu) elements. Interestingly, we found that interferon-stimulated genes (ISGs) are highly enriched for dsRNA-forming intronic IR-Alu elements, suggesting a positive feedback loop whereby interferon response leads to dsRNA formation from intronic ISGs and activation of viral mimicry. Moreover, EZH2i in ATRT cells also enhances the expression of full-length LINE-1 elements, leading to genomic instability and cGAS/STING response in a process dependent on reverse transcriptase activity. Supporting this mechanism, co-depletion of dsRNA sensing and cytoplasmic DNA sensing completely rescues the viral mimicry response to EZH2i in SMARCB1-deficient tumors.

overall_design: UNC1999 and UNC24000 treatments. Day 4 and Day 6. 3 replicates.

first: Shengrui

last: Feng

first: Dustin

last: Sokolowski

first: Daniel

last: De Carvalho


title: selenocysteine tRNA methylation promotes oxidative stress resistance in melanoma metastasis [Xenograft Human]

city: New York

first: Elena

last: Piskounova

state: NY

address: 52 East 78th Street, Apt 4A

institute: Weill Cornell Medicine

summary: Oxidative stress has been shown to limit metastasis of numerous cancer types including melanoma. A specialized group of 25 proteins containing the 21st amino acid, selenocysteine, plays a central role in oxidative stress resistance, which is a key driver of metastasis. A single selenocysteine tRNA methylation, Um34, is required for the translation of several stress-related selenoproteins in a selenium-dependent manner. Herein, we characterize FTSJ1 as the Um34 methyltransferase and show that its activity is required for the Sec tRNA (tRNASec) Um34 modification. Loss of Um34 affects translation of a subset of selenoproteins and increases melanoma cell sensitivity to oxidative stress while increased Um34 levels promote oxidative stress resistance. Loss of FTSJ1  does not affect primary melanoma tumor growth but abolishes metastatic spread in vivo. Overexpression of FTSJ1 specifically increases melanoma metastasis in vivo. Our work establishes FTSJ1 as the Um34 methyltransfearse and tRNASec Um34 modification as a central regulator of oxidative stress resistance during melanoma metastasis.

overall_design: Patient-derived melanoma cells were injected subcutaneously into NSG mice. Liver metastases and primary tumor samples were collected at endpoint and ribosome profiling was completed to investigate changes in selenoprotein translation during metastasis


title: Paraspeckle-Independent Co-Transcriptional Regulation of Nuclear microRNA Biogenesis by SFPQ [miRNA-seq]

city: Montreal

first: Thomas

last: Duchaine

address: 3655 Promenade Sir-William-Osler

institute: McGill University

summary: MicroRNAs (miRNAs) play crucial roles in physiological functions and diseases such as cancer, but the regulation of their nuclear biogenesis remains poorly understood. Here, BioID on Drosha, the catalytic subunit of the microprocessor complex, revealed its proximity to SFPQ, a multifunctional RNA-binding protein (RBP) notably involved in forming the paraspeckle nuclear condensates. SFPQ depletion impacted both primary and mature miRNA expression, while other crucial paraspeckle proteins or the paraspeckle scaffolding lncRNA NEAT1 did not, indicating a unique paraspeckle-independent role. Comprehensive transcriptomic analyses showed that SFPQ loss broadly affects RNA and miRNA host gene (miRNA HG) expression, influencing both their transcription and stability. Notably, SFPQ protects specific miRNA HGs, including the oncogenic miR-17~92 polycistron, from degradation by the nuclear NEXT-exosome complex. Lastly, we show that high SFPQ is tightly linked with overexpression miR-17~92 and its mature miRNAs across a broad variety of cancers. Our findings reveal a dual role for SFPQ in the regulation of miRNA HGs transcription and stability, as well as its significance in cancers.

overall_design: We used a multi-omic approach to uncover a dual role for SFPQ in the regulation of pri-miRNAs’ transcription and stability. We established an SBC-3 cell line in which SFPQ/NONO/NEAT1 have been knocked down by siRNAs or ASOs. We then performed miRNA expression profiling analysis using data obtained from miRNA-seq at the 72h time point post-transfection.

first: Caroline

last: Thivierge

first: Maxime

last: Bellefeuille

first: Sarah-Slim

last: Diwan

first: Boris

last: Dyakov

first: Rania

last: Leventis

first: Gabrielle

last: Perron

first: Hamed

last: Najafabadi

first: Simon-Pierre

last: Gravel

first: Anne-Claude

last: Gingras


title: Genomic and transcriptomic analyses reveal insights into cadmium resistance mechanisms of Cupriavidus nantongensis E324

city: Mueang Khon Kaen

first: Todsapol

last: Techo

state: Khon Kaen

department: Biology

country: Thailand

institute: Khon Kaen University

summary: The cadmium-resistant Cupriavidus  sp. E324 strain has been previously shown to have a high potential  for use in cadmium (Cd) remediation,  due to its high capacity for  cadmium bioaccumulation. According to the comparative genomic analysis, the E324 strain was  most closely related to C.  nantongensis X1 T , indicating that the E324 strain should be re-identified as C. nantongensis. To unravel the Cd tolerance mechanisms of  C. nantongensis E324,  the transcriptional response of this strain to Cd stress was assessed using RNA-seq-based transcriptome analysis,  followed by validation through qRT- PCR. The results showed that the upregulated Differentially Expressed Genes (DEGs) were significantly enriched in categories related to  metal binding and transport, phosphate transport, and oxidative stress response. Consistently, we observed significant increases in both the cell wall and intracellular contents of certain essential metals (Cu, Fe, Mn, and Zn) upon Cd exposure). Among these, only the Zn pretreatment resulting in  high Zn accumulation in the cell walls could enhance bacterial growth under Cd stress conditions through its role in inhibiting Cd accumulation. Additionally, the promotion of catalase activity and glutathione metabolism upon Cd exposure to cope with Cd-induced oxidative stress was demonstrated. Meanwhile, the  upregulation of phosphate transport-related genes upon Cd treatment seems to be the bacterial response to Cd-induced phosphate depletion. Altogether, our findings suggest that these adaptive responses are critical mechanisms contributing to increased Cd tolerance in C. nantongensis E324 strain via the enhancement of metal-chelating and antioxidant capacities of the cells.

overall_design: To investigate the Cd tolerance mechanism in C. nantongensis E324, we examined the transcriptome profile of this strain in response to Cd exposure. We analyzed the sequencing data for six samples: three treated with 4 mM CdCl2 and three control samples without CdCl2 treatment

first: Kittikhun

last: Kerdsomboon

first: Choowong

last: Auesukaree


title: Mouse enteric neurons control intestinal plasmacytoid dendritic cell function via serotonin-HTR7 signaling [Co_Epi]

first: Hailong

last: Zhang

overall_design: Comparative gene expression profiling analysis of RNA-seq data for intestinal epithelial cell  from co-housed WT and Tph2 KO mice

first: Matthew

last: Waldor


title: selenocysteine tRNA methylation promotes oxidative stress resistance in melanoma metastasis

overall_design: A375 control or FTSJ1 KO cells were treated with 0 or 30nM sodium selenite. Ribosome profiling was completed to look at effects on selenoprotein translation when Um34 Sec tRNA was lost


title: Effect of A20 deletion in a retroviral mouse model of AML

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: We show that AML patients who experience induction failure have elevated expression of the NF-kB target gene TNFAIP3/A20 and impaired necroptotic cell death, leading to a worse prognosis with chemotherapy. A20High AML samples display resistance to anthracyclines, while A20Low AML samples show sensitivity. Loss of A20 in AML cells restores sensitivity to anthracycline treatment by inducing necroptosis. Moreover, our studies revealed that A20 plays a critical role in AML development as deletion or knockdown of A20 effectively suppresses leukemic cells by mediating spontaneous necroptosis. A20 prevents necroptosis in AML by targeting the necroptosis effector RIPK1, and anthracycline-induced necroptosis is abrogated in A20High AML cells. These findings suggest that NF-kB-driven A20 overexpression plays a role in failed chemotherapy induction and highlights the potential of targeting an alternative cell death pathway in AML. The data contained here provide a platform in which to examine the effects of A20 loss in a retroviral mouse model of AML.

overall_design: A retroviral mouse model of AML was generated by transducing lineage negative hematopoietic cells from A20+/+ Rosa Cre-ER and A20f/f Rosa Cre-ER mice with the oncogene MLL-AF9. Cells were treated with 1uM 4-hydoxy-tamoxifen for 48hr to induce deletion of A20 at which point they were harvested and RNA was isolated.

first: Ashley

last: Culver-Cochran

first: Aishlin

last: Hassan

first: Kathleen

last: Hueneman

first: Averil

last: Ma

first: Mark

last: Wunderlich

first: Daniel

middle: T

last: Starczynowski