title: Identification of TREM1+CD163+ myeloid cells as a deleterious immune subset in HCC [bulk_RNA-seq]

overall_design: Single-cell RNA-seq (10x Genomics) on FACS-sorted CD45 + panTCRαβ - CD19 - innate immune cells freshly isolated from tumors (HCC) and adjacent non-tumoral (NT) liver sections were realized for 10 patients (10 HCC/CHC samples and 10 NT/TS samples). In parallel, we applied spatial transcriptomics (ST; Visium ® , 10x Genomics) on frozen tissue sections from the two of the previous patients (2 CHC visium samples). Furthermore, bulk RNA-seq sequencing were performed on innate immunity cells that were isolated using the same sorting strategy designed for scRNAseq experiments, for six of the previous patients. Bulk RNA-seq sequencing were also realized on FACS-sorted cell population, namely THBS1_M (c0, c3 and c4) populations that were isolated according to specific sorting strategy. In summary, available data concerns 20 scRNA-seq samples, 2 visium spatial transcriptomics and 9 bulk RNA-seq.


title: The BAF complex does not mediate GLI repression (ATAC-Seq)

status: Public on Feb 03 2024

city: Austin

first: Steven

middle: A.

last: Vokes

state: Texas

address: 2500 Speedway, STOP A5000

department: Molecular Biosciences

country: USA

institute: University of Texas at Austin

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Purpose: This study seeks to determine whether Smarcc1 mediates GLI repression through chromatin compaction in the limb.
Methods: To determine if Smarcc1 mediated GLI repression through chormatin compaction, we used genomic approached to determine changes in chromatin accessibility in control and Smarcc1-conditional mutants. We performed ATAC-seq on individually genotyped anterior forelimbs at E11.5 (40-48s) on control (2 replicates) and PrxCre/+;Smarcc1c/c (3 replicates) embryos. From this experiment we identified ~10,000 differentially accessible regions (FDR<0.05).
Results: We find that SMARCC1 is required to maintain chromatin accessibility at thousands of regions within the mouse limb, including most HH-responsive GLI enhancers

overall_design: ATAC-seq on individual E11.5 (40-48s) anterior forelimb buds from control (2 replicates) and PrxCre/+;Smarcc1c/c (3 replicates) embryos.

first: Janani

last: Ramachandran

first: Rachel

last: Lex

first: Wanlu

last: Chen

first: Kathryn

last: Windsor

first: Tingchang

last: Wang

first: Weiqiang

last: Zhou

first: Hongkai

last: Ji


title: Identification of TREM1+CD163+ myeloid cells as a deleterious immune subset in HCC [scRNA-seq]

status: Public on Feb 04 2024

city: Laval

first: Maya

last: Saleh

state: Qc

address: 531 Boulevard des Prairies

department: Armand Frappier Santé Biotechnologie

country: Canada

institute: INRS

type: Expression profiling by high throughput sequencing

summary: Hepatocellular carcinoma (HCC) is an inflammation-associated cancer arising from viral and non-viral etiologies. Expansion of suppressive myeloid cells is a hallmark of chronic inflammation and cancer, but their heterogeneity in HCC is not fully resolved and might underlie immunotherapy resistance in the steatohepatitis setting. Here, we present a high resolution atlas of hepatic innate immune cells from patients with HCC that unravels a steatohepatitis contexture characterized by influx of inflammatory and immunosuppressive myeloid cells. A discrete myeloid cell population identified by selective expression of TREM1 and CD163 expands in steatohepatitis-HCC. We refer to this population as TREM1+ regulatory myeloid cells (Mreg), as it potently suppresses T cell effector functions, highly expresses TGFB1 and IL13RA1 and localizes to HCC fibrotic lesions.

first: Julie

last: Giraud

first: Domitille

last: Chalopin

first: Eloïse

last: Ramel

first: Thomas

last: Boyer

first: Atika

last: Zouine

first: Marie-Alix

last: Derieppe

first: Nicolas

last: Larmonier

first: Olivier

last: Adotevi

first: Brigitte

last: Le Bail

first: Jean-Frédéric

last: Blanc

first: Christophe

last: Laurent

first: Laurence

last: Chiche

first: Marc

last: Derive

first: Macha

last: Nikolski


title: The BAF complex does not mediate GLI repression (WT Cut&RUN)

first: Steven

last: Vokes

summary:
Purpose: This study seeks to identify SMARCC1-bound regions in the mouse limb.
Methods: To identify SMARCC1 bound regions in the limb, we performed Cut&Run on pooled anterior and posterior wild-type forelimbs at E11.5 (43-44s; 3 replicates each) and on whole forelimb pairs at E9.5 (21-24s; 2 replicates). We identified 28,082 SMARCC1-bound regions in the anterior forelimb at E11.5, 42,530 regions in the E11.5 posterior limb, and 10,792 SMARCC1-bound regions at E9.5 (FDR<0.05).
Results: We find that SMARCC1 is bound to most limb enhancer regions at late stages (E11.5). Additionally, We find that SMARCC1 is bound to the majority of HH-responsive GLI enhancers at E11.5 but only a small portion of GLI enhancers at E9.5.

overall_design: Cut&Run E11.5 (43-44s; 3 replicates per condition) anterior and posterior forelimb buds, and E9.5 (21-24s; 2 replicates) forelimb buds from wild-type embryos.

first: Janani

last: Ramachandran

first: Rachel

last: Lex

first: Wanlu

last: Chen

first: Kathryn

last: Windsor

first: Tingchang

last: Wang

first: Weiqiang

last: Zhou


title: The BAF complex does not mediate GLI repression (Gli3 null Cut&RUN)

summary:
Purpose: This study seeks to determine whether GLI3 is required to recruit the SMARCC1 complex to GLI enhancers in the limb.
Methods: To determine if Gli3 is required to recruit SMARCC1 to its anhancers, we performed differential chromatin binding to compare SMARCC1 binding in control and Gli3 mutants.  We performed Cut&Run for SMARCC1 binding on individually genotyped E11.5 (40-43s) anterior forelimb pairs from control (Gli3+/+; 3 replicates) and Gli3 mutant (Gli3-/-; 4 replicates) embryos.
Results: We found that there is no major difference in SMARCC1 binding in Gli3-mutants compared to controls.

overall_design: Cut&Run on E11.5 (40-43s) control and Gli3-/- anterior forelimb pairs (3-4 replicates per condition).

first: Hongkai

last: Ji


title: The BAF complex does not mediate GLI repression (RNA-Seq)

summary:
Purpose: This study seeks to determine whether Smarcc1 co-regulates Hedgehog (HH) target genes in the limb.
Methods: To determine if Smarcc1 is required to regulate HH targets, we used genomic approaches to identify Smarcc1-regulated genes within the forelimb. We performed bulk RNA-seq on individually genotyped forelimb-bud pairs at E11.5 (39-40s) on control (2 replicates) and PrxCre/+;Smarcc1c/c (2 replicates) embryos. From this experiment we identified 928 differentially expressed genes (FDR<0.05).
Results: We find that while certain HH target genes are co-regulated by SMARCC1, the majority of HH target genes do not require Smarcc1.

overall_design: Bulk RNA-seq on individual E11.5 (39-40s) forelimb bud pairs from control (2 replicates) and PrxCre/+;Smarcc1c/c (2 replicates) embryos.


title: SWI/SNF Chromatin Remodeling Complex Orchestrates Sequential Binding of Key Transcription Factors in B Cells and Restricts Aggressive Lymphoma [mouse RNA-Seq]

status: Public on Feb 02 2024

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

summary: ARID1A, a subunit of the canonical BAF nucleosome remodeling complex, is commonly mutated in lymphomas. Our study shows that ARID1A orchestrates B-cell fate during the germinal center (GC) response, facilitating cooperative and sequential binding of PU.1 and NF-kB at crucial genes for cytokine and CD signaling. The absence of ARID1A tilts GC cell-fate towards immature IgM+CD80-PDL2- memory B-cells, known for their potential to re-enter new GCs. When combined with BCL2 oncogene, ARID1A haploinsufficiency hastens the progression of aggressive follicular lymphomas in mice. Remarkably, follicular lymphoma patients with ARID1A-inactivating mutations preferentially display an immature memory B-cell-like state with increased transformation risk to aggressive disease. These observations offer mechanistic understanding into the emergence of both indolent and aggressive lymphomas in ARID1A-mutant patients through formation of immature memory-like clonal precursors. Lastly, we demonstrate that ARID1A mutation induces synthetic lethality to SMARCA2/4 inhibition, paving the way for potential precision therapy for high-risk patients.

overall_design: To determine the role of ARID1A in germinal center B cells, we sorted centroblasts (CB) and centrocytes (CC) from primary mouse tissues (spleen), and performed RNA-seq, for two genotypes; Arid1a+/- and Arid1a+/+.

first: Barisic

last: Darko

first: Chris

first: Meydan

last: Cem

first: Teater

last: Matt

first: Melnick

last: Ari


title: SWI/SNF Chromatin Remodeling Complex Orchestrates Sequential Binding of Key Transcription Factors in B Cells and Restricts Aggressive Lymphoma [human FHD286 ATAC-Seq]

overall_design: ATAC-seq was performed as per Omni-ATAC-seq protocol, on two biological replicates (clones; DQ1 and DQ2 for WT; TQ1 and TQ2 for HET) and each clone had two technical replicates, with each being subjected to either DMSO or 100nM of FHD-286 for 24h.

first: Darko

last: Barisic

first: Cem

last: Meydan

first: Matt

last: Teater

first: Ari

last: Melnick


title: The BAF complex does not mediate GLI repression

first: Steven

last: Vokes

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

overall_design: Refer to individual Series


title: SWI/SNF Chromatin Remodeling Complex Orchestrates Sequential Binding of Key Transcription Factors in B Cells and Restricts Aggressive Lymphoma [human RNA-Seq]

overall_design: RNA was isolated using Rneasy mini kit from Arid1a WT (WT/WT) and HET (Q474*/WT) RIVA cell line isogenic clones (CRISPR). Two technical replicates per clone, and two clones per genotype was processed. RIVA parental cell lines were processed (two technical replicates) for comparison.


title: SWI/SNF Chromatin Remodeling Complex Orchestrates Sequential Binding of Key Transcription Factors in B Cells and Restricts Aggressive Lymphoma [human ATAC-Seq]

overall_design: ATAC-seq was performed as per Omni-ATAC-seq protocol, on three biological replicates for each condition. WT and HET (for Arid1a) were processed in a separate experiment compared to sh-knockdown. Therefore, sh-uninduced control was added (KD and sh-control). Sh-experiment was perfomred with two different sh-constructs targeting Arid1a, each with two biological replicates.


title: SWI/SNF Chromatin Remodeling Complex Orchestrates Sequential Binding of Key Transcription Factors in B Cells and Restricts Aggressive Lymphoma [mouse ATAC-Seq]

overall_design: ATAC-seq was performed as per Omni-ATAC-seq protocol, on 3-5 biological replicates (mice), for each cell type profiled (centroblast or centrocyte) 10 days post SRBC immunization.


title: SWI/SNF Chromatin Remodeling Complex Orchestrates Sequential Binding of Key Transcription Factors in B Cells and Restricts Aggressive Lymphoma [human Mnase-Seq]

overall_design: Mnase was performed using standard protocol, on 2-3 replicates per genotype (WT or HET) with either 3U or 5U of Mnase (5U was only used for HET sample to match the digestion levels of 3U WT).


title: Murine MHC-Deficient Nonobese Diabetic Mice Carrying Human HLA-DQ8 Develop Severe Myocarditis and Myositis in Response to Anti–PD-1 Immune Checkpoint Inhibitor Cancer Therapy

city: Bar Harbor

first: Dave

last: Serreze

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Myocarditis has emerged as an immune-related adverse event of immune-checkpoint inhibitor (ICI) cancer therapy associated with significant mortality. Our new NOD-cMHCI/II-/-.DQ8 mouse strain expresses human HLA-DQ8 in the absence of classical murine MHC class I and II. These mice are highly susceptible to myocarditis and acute heart failure following anti-PD-1 ICI-induced treatment. Additionally, anti-PD-1 administration accelerates skeletal muscle myositis development. Using RNA sequencing analyses we performed a thorough characterization of cardiac and skeletal muscle infiltrating T-cells, identifying shared and unique characteristics of both populations.

overall_design: In order to determine the molecular features of heart and skeletal muscle infiltrating T-cells, and how those features may differ, we sorted CD90+ TCRβ+ T-cells from heart or skeletal muscle (diaphragm & soleus) of NOD-cMHCI/II-/-.DQ8 mice within one hour of a fourth injection of anti-PD-1 (administered twice a week starting at 10-12 weeks of age). We then performed gene expression analysis from RNA-seq data obtained from these heart or skeletal muscle T-cells. Each sequenced sample is derived from a pool of cells isolated from between 2-12 mice individual mice.

first: Jeremy

middle: J

last: Racine

first: John

middle: F

last: Bachman

first: Ji-Gang

last: Zhang

first: Adel

last: Misherghi

first: Raheem

last: Khadour

first: Sana

last: Kaisar

first: Olivia

last: Bedard

first: Catherine

last: Jenkins

first: Annie

last: Abbott

first: Elvira

last: Forte

first: Peter

last: Rainer

first: Nadia

last: Rosenthal

first: Susanne

last: Sattler

first: David

middle: V


title: LIN28B promotes differentiation of fully transformed AML cells but is  LIN28B promotes differentiation of fully transformed AML cells but is dispensable for fetal leukemia suppression

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

summary: MLL-AF9 driven AML cells regress when LIN28B is ectopically expressed.RNA-seq was performed to measure LIN28B expression and associated changes in gene expression

overall_design: MLL-AF9 virus was used to induce AML from widtype or tet-on LIN28B rogenitors. After leukemia engraftment, LIN28B expression was induced in experimental mice by feeding Doxycycline chow. AML were harvested 6 days later to assess gene expression.

first: Magee

last: Jeffrey


title: Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance [ChIP-chips_H3-FLAG]

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

type: Genome binding/occupancy profiling by genome tiling array

summary: Occupancy profiling of FLAG-tagged H3 in fission yeast.

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  FLAG-tagged histone H3 from nucleosome turnover experiments.

first: Patroula

last: Nathanailidou

first: Jothy

last: Dhakshnamoorthy

first: Martin

last: Zofall

first: Sahana

last: Holla

last: Wheeler

middle: I


title: Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance [ChIP-chip H3K9me3]

summary: Occupancy profiling of lysine 9 trimethylated histone H3 in fission yeast.

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  K9-trimethylated histones from asynchronous culture of fission yeast.


title: Kaempferol Improves Exercise Performance and Its Potential Mechanism

city: Beijing

first: Xiaoning

last: Ji

address: No.16, Nanxiao street, Dongzhimen, Dongcheng District, Beijing, 100700, China

country: China

institute: China Academy of Chinese Medical Sciences

summary: Kaempferol is a natural flavonoid with reported bioactivities, however its effects on exercise performance and muscle metabolism are unclear. This study investigated kaempferol for improving exercise performance and potential underlying mechanism in vivo and in vitro. In vitro, kaempferol promoted glucose uptake, protein synthesis and mitochondrial function along with decreasing oxidative stress in C2C12 myotubes. Moreover, the PI3K-AKT and MAPK signaling pathways were proved be activated with kaempferol by transcriptomic analysis.

overall_design: To investigate the molecular mechanisms of kaempferol influence on muscle function, C2C12 myotubes were exposed to 25 μM kaempferol for  24 hours. Analysis unveiled differential gene expression between the treated and untreated groups.


title: ARID1A Orchestrates SWI/SNF-mediated Sequential Binding of Transcription Factors and Its Deficiency Drives Pre-memory B-cell Fate and Lymphomagenesis [Arid1a_multiome]

first: Christopher

last: Chin

summary: ARID1A, a subunit of the canonical BAF nucleosome remodeling complex, is commonly mutated in lymphomas. Our study shows that ARID1A orchestrates B-cell fate during the germinal center (GC) response, facilitating cooperative and sequential binding of PU.1 and NF-kB at crucial genes for cytokine and CD40 signaling. The absence of ARID1A tilts GC cell-fate towards immature IgM+CD80-PDL2- memory B-cells, known for their potential to re-enter new GCs. When combined with BCL2 oncogene, ARID1A haploinsufficiency hastens the progression of aggressive follicular lymphomas in mice. Remarkably, follicular lymphoma patients with ARID1A-inactivating mutations preferentially display an immature memory B-cell-like state with increased transformation risk to aggressive disease. These observations offer mechanistic understanding into the emergence of both indolent and aggressive lymphomas in ARID1A-mutant patients through formation of immature memory-like clonal precursors. Lastly, we demonstrate that ARID1A mutation induces synthetic lethality to SMARCA2/4 inhibition, paving the way for potential precision therapy for high-risk patients.

overall_design: GC cells from splenocytes were sorted and underwent the manufacturer's nuclei preparation procedure. Then, about 20,000 nuclei were placed into a 10x Chromium X instrument. The remainder of the library preparation steps were conducted in accordance with the manufacturer's protocol

middle: R

first: Darko

last: Barisic

first: Cem

last: Meydan

first: Matt

last: Teater


title: Placenta accreta spectrum disorder at single cell resolution: a loss of boundary limits in the uterine endothelium and decidua.

city: Los Angeles

first: Jina

last: Kim

state: CA

address: 8700 Beverly Blvd

institute: cedars-sinai medical center

summary: Objective: The objective of this study is to utilize advances in single-cell RNAsequencing to characterize cellular heterogeneity and transcriptomic signatures of PAS. Our findings can elucidate mechanisms of abnormal placental invasion and identify targets for potential diagnostic and therapeutic biomarkers of PAS. Results: Placental samples from PAS participants and non-PAS cesarean births were included. In total, we analyzed 31,406 individual cells expressing an average of 1,493 genes. Clustering analysis of gene expression identified multiple populations of cells representing syncytiotrophoblasts, cytotrophoblasts, extravillous trophoblasts, decidua,endothelial cells, myeloid, natural killer, and lymphoid cells. When analyzed by disease phenotype, AI showed a unique gene signature most prominently in the endothelial population. The highest expression in AI compared to AO and C was seen in the following genes: DLK1, EGFL6, HGF, APOLD1, and EDNRB. Gene set enrichment analysis of AI endothelial cells identified the following key pathways: blood vessel development, response to growth factors and hormones, regulation of cell adhesion and migration, and pathways in cancer. Conclusions: We present a comprehensive single-cell atlas of PAS across the site of invasion and site of non-adherence. By integrating expression from individual genes per cell, we identified endothelial cells as a key subpopulation in invasive accreta, with expression of genes involved in multiple angiogenic, growth, and mechanical-signaling pathways. After validation, these gene targets may be used to refine diagnostic assays for placenta accreta in early gestation, track disease progression over time, and inform Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation therapeutic discoveries.

overall_design: Study Design: We generated a single-cell atlas of gene expression at the site of accreta invasion (AI) versus site of accreta opposite, non-invasion (AO) in PAS placentas versus controls (C). Mechanical and enzymatic dissociation of single cell suspensions of placentas was performed with confirmation of high cell viability and RNA quality prior to library creation. We utilized a high-throughput whole-transcriptome system for single-cell sequencing.

first: Yalda

last: Afshar


title: Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis [scTreg]

city: New York

first: Nicholas

last: Arpaia

address: 701 West 168th Street

department: Microbiology & Immunology

institute: Columbia University

summary: We study the effect of Treg cell-derived Areg in chronic liver injury. Here we look at the transcriptional changes of Treg cells in NASH compared to normal chow.

overall_design:
Single cell RNA-seq of Treg cells enriched via FACS from the liver, spleen and visceral adipose tissue from Foxp3GFP mice fed normal chow or a NASH diet.
Hashtag 1-3 are normal diet and Hashtag 4-7 are NASH.

first: Thomas

middle: M

last: Savage

first: Katherine

middle: T

last: Forton

first: Kenia

last: de los Santos

first: Mathieu

last: Rouanne

first: Angelica

last: Oliveras Alsina

first: Renzo

last: Cavero

first: Fangda

last: Li

first: Rebecca

middle: A

last: Haeusler

first: Julien

last: Adam

first: Robert

last: Schwabe

first: Hani

last: Shayya

first: Sarah

middle: S

last: Rae


title: Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis I

summary: We study the effect of Treg cell-derived Areg in chronic liver injury. Here we look at the transcriptional changes of Treg cells in fibrosis compared to control and conventional T cells in vivo.

overall_design: Treg (TCRb+CD4+Foxp3+) and Tconv (TCRb+CD4+Foxp3-) cells were sorted from liver and spleen of Foxp3GFP mice, either control or CCl4 treated mice.

middle: O

last: Alsina


title: Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis


title: Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis II

summary: We study the effect of Treg cell-derived Areg on hepatic stellate cells. Here we look at the transcriptional effect of Areg on hepatic stellate cells in vitro.

overall_design: Quiescent hepatic stellate cells were isolated and cultured for 5 hours, then stimulated with recombinant mouse Areg (500 ng/mL) for 4 hours in starving media.


title: Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance [ChIP-seq]

first: Shiv

last: Grewal

summary: Heterochromatin domains defined by distinct histone methylation patterns are a major feature of mammalian genomes. Epigenetic pathways ensure stable heterochromatin inheritance through cell division to prevent the expression of lineage-inappropriate genes and defects in this process can lead to many diseases including cancer. Previous studies have shown that heterochromatin maintenance requires a critical threshold of methylated histones, but how modified parental histones are transferred to daughter strands during DNA replication is unclear. We find that heterochromatin domains are specialized replication zones enriched in replisome components, which load factors that help retain parental histones. This mechanism is further supported by the boundary elements surrounding the heterochromatin domains. DNA replication is thus coordinated with histone preservation to facilitate epigenetic inheritance of heterochromatin.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the proteins Mcl1, Mcm2 and Rix1, the BrdU analogue, and the lysine 9 trimethylated histone H3 in fission yeast. Input control and immunoprecipitation samples are provided for each experiment.

first: Patroula

last: Nathanailidou

first: Jothy

last: Dhakshnamoorthy

first: Hua

last: Xiao

first: Martin

last: Zofall

first: Sahana

last: Holla

first: David

last: Wheeler


title: Tunable DNMT1 degradation reveals cooperation of DNMT1 and DNMT3B in regulating DNA methylation dynamics and genome organization (Hi-C).

status: Public on Feb 01 2024

city: Worcester

first: Nezar

last: Abdennur

state: MA

address: 368 Plantation Street

department: Genomics and Computational Biology

institute: UMass Chan Medical School

summary: DNA methylation (DNAme) is a key epigenetic mark that regulates critical biological processes maintaining overall genome stability. Given its pleiotropic function, studies of DNAme dynamics are crucial, but currently available tools to interfere with DNAme have limitations and major cytotoxic side effects. Here, we present cell models that allow inducible and reversible DNAme modulation through DNMT1 depletion. By dynamically assessing whole genome and locus-specific effects of induced passive demethylation through cell divisions, we reveal a cooperative activity between DNMT1 and DNMT3B, but not of DNMT3A, to maintain and control DNAme. We show that gradual loss of DNAme is accompanied by progressive and reversible changes in heterochromatin, compartmentalization, and peripheral localization. DNA methylation loss coincided with a gradual reduction of cell fitness due to G1 arrest, but with minor level of mitotic failure. Altogether, this system allows DNMTs and DNA methylation studies with fine temporal resolution, which may help to reveal the etiologic link between DNAme dysfunction and human disease.

overall_design: Chromosome conformation capture (Hi-C) in DLD1 cells derived cell lines with or without DNMTs

first: Andrea

last: Scelfo

first: George

last: Spracklin

first: Leonid

last: Mirny

first: Daniele

last: Fachinetti


title: Tunable DNMT1 degradation reveals cooperation of DNMT1 and DNMT3B in regulating DNA methylation dynamics and genome organization

overall_design: Refer to individual Series


title: RNA sequencing data of Ing4;Ing5 double knock-out embryonic mouse hearts

city: Parkville

first: Connie

middle: S. N.

last: Li-Wai-Suen

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

summary: Inhibitor of growth 4 and 5 (ING4 and ING5) are chromatin-binding proteins in the KAT6A, KAT6B and KAT7 histone acetyltransferase protein complexes. Heterozygous mutations in the KAT6A or KAT6B gene cause human disorders with cardiac defects, but the contribution of their chromatin adaptor proteins to development is unknown. We found that Ing5–/– mice had isolated cardiac ventricular septal defects. ING4 and ING5 are structurally similar proteins, suggesting a degree of redundancy. Combined loss of ING4 and ING5 caused developmental arrest at embryonic day E8.5, loss of histone H3 lysine 14 acetylation (H3K14ac), a reduction in H3K23ac levels and disruption of developmental gene expression in Ing4–/–Ing5–/– compared to control embryos. E12.5 Ing4+/–Ing5–/– hearts showed a paucity of epicardial cells and epicardium-derived cells, failure of myocardium compaction and coronary vasculature defects, accompanied by a reduction in the expression of epicardium genes compared to control hearts. In addition, a reduction in the expression of genes required for cell adhesion, both in whole E8.75 Ing4–/–Ing5–/– embryos and in E10.5 Ing4+/–Ing5–/– hearts compared to controls was observed. In vitro assessment of fibroblast and proepicardium explants revealed cell spreading and outgrowth defects. Our findings suggest that ING4 and ING5 are essential for heart development and promote epicardium and epicardium-derived cell fates and mutation of the human ING5 gene as a possible cause of isolated ventricular septal defects.

overall_design: RNA seqencing data was generated from embryonic mouse hearts taken at embryonic day 8.25 or 8.75 (E8.25 or E8.75). The embryos were either wild type (WT) or Ing4-/-;Ing5-/- double knock-outs. Each genotype group has n=5 biological repcliates.  Differential expression analyses were conducted between the genotype groups.

first: Alexandra

middle: L

last: Garnham

first: Anne

middle: K

last: Voss

first: Tim

last: Thomas


title: Transcriptomic Analysis of Cortical and Medullary Thick Ascending Limb  of Henle's loop (CTAL and MTAL)  from WT or Cldn-10 Knock-out mice

city: PARIS

first: Caroline

last: Prot-Bertoye

address: 15 rue Ecole de Médecine

country: France

institute: CNRS EMR8228, INSERM UMRS 1138

summary: We applied RNAseq analysis on microdissected cortical and medullary thick ascendind limb of Henle’s loop from WT and Cldn10 KO mice (cKO). Among 11369 genes sequenced 291 have an expression significantly modified (p<0.05) between MTAL and CTAL from WT mice. In cKO mice, among 12023 genes sequenced 359 were signicantly modified (p<0.05) between MTAL and CTAL. surprisingly, while 637 genes have significantly (p<0.05) different expression between MTAL WT and cKO only 66 were in this case between CTAL WT and cKO.

overall_design: Comparison of gene abundance by RNA-sequencing between CTAL and MTAL from WT or Cldn10 kncok out mice.

first: Pascal

last: Houillier

first: Gaëlle

last: Brideau

first: Lydie

last: Cheval


title: Widespread prevalence of a post-translational modification in activation of an essential bacterial DNA damage response (RNA-seq)

city: Bengaluru

first: Anjana

last: Badrinarayanan

state: Karnataka

address: Bellary Road

country: India

institute: National Centre for Biological Sciences

summary: DNA methylation plays central roles in diverse cellular processes, ranging from error-correction during replication to regulation of bacterial defense mechanisms. Nevertheless, certain aberrant methylation modifications can have lethal consequences. The mechanisms by which bacteria detect and respond to such damage remain incompletely understood. Here, we discover a highly conserved but previously uncharacterized transcription factor (Cada2), which orchestrates a methylation-dependent adaptive response inCaulobacter. This response operates independently of the SOS response, governs the expression of genes crucial for direct repair, and is essential for surviving methylation-induced damage. Our molecular investigation of Cada2 reveals a cysteine methylation-dependent post-translational modification and mode of action distinct from itsE. colicounterpart, a trait conserved across all bacteria harboring a Cada2-like homolog instead. Extending across the bacterial kingdom, our findings support the notion of divergence and co-evolution of adaptive response transcription factors and their corresponding sequence-specific DNA motifs. Despite this diversity, the ubiquitous prevalence of adaptive response regulators underscores the significance of a transcriptional switch, mediated by methylation post-translational modification, in driving a specific and essential bacterial DNA damage response.

overall_design: RNA-seq was performed on Caulobacter crescentus strains upon exposure to various forms of DNA damage.

first: Aditya

last: Kamat

first: Ngat

last: Tran

first: Mohak

last: Sharda

first: Neha

last: Sontakke

first: Tung

last: Le


title: Tunable DNMT1 degradation reveals cooperation of DNMT1 and DNMT3B in regulating DNA methylation dynamics and genome organization (ChIP-Seq).

first: Nezar

last: Abdennur

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27me3 and H3K9me3 in DLD1 cells.

first: Andrea

last: Scelfo

first: George

last: Spracklin


title: Obesity during preclinical Alzheimer's disease development exacerbates brain metabolic decline

city: Atlanta

first: Marise

last: Parent

email: mbparent@gsu.edu, tanderson80@gsu.edu

state: GA

address: PO Box 5030

department: Neuroscience Institute

institute: Georgia State University

summary: Alzheimer's disease (AD) is the most common form of dementia. Obesity in middle age increases AD risk and severity, which is alarming given that obesity prevalence peaks at middle age and obesity rates are accelerating worldwide. Midlife, but not late-life obesity increases AD risk, suggesting that this interaction is specific to preclinical AD. AD pathology begins in middle age, with accumulation of amyloid beta (Aβ), hyperphosphorylated tau, metabolic decline, and neuroinflammation occurring decades before cognitive symptoms appear. We used a transcriptomic discovery approach in young adult (6.5 months old) male and female TgF344-AD rats that overexpress mutant human amyloid precursor protein and presenilin-1 and wild-type (WT) controls to determine whether inducing obesity with a high-fat/high-sugar “Western” diet during preclinical AD increases brain metabolic dysfunction in dorsal hippocampus (dHC), a brain region vulnerable to the effects of obesity and early AD. Analyses of dHC gene expression data showed dysregulated mitochondrial and neurotransmission pathways, and up-regulated genes involved in cholesterol synthesis. Western diet amplified the number of genes that were different between AD and WT rats and added pathways involved in noradrenergic signaling, dysregulated inhibition of cholesterol synthesis, and decreased intracellular lipid transporters. Importantly, the Western diet impaired dHC-dependent spatial working memory in AD but not WT rats, confirming that the dietary intervention accelerated cognitive decline. To examine later consequences of early transcriptional dysregulation, we measured dHC monoamine levels in older (13 months old) AD and WT rats of both sexes after long-term chow or Western diet consumption. Norepinephrine (NE) abundance was significantly decreased in AD rats, NE turnover was increased, and the Western diet attenuated the AD-induced increases in turnover. Collectively, these findings indicate obesity during prodromal AD impairs memory, potentiates AD-induced metabolic decline likely leading to an overproduction of cholesterol, and interferes with compensatory increases in NE transmission.

overall_design: To investigate the gene expression dynamics in the dorsal hippocampus in an Alzheimer's disease model (TgF344-AD rats) exposed to standard and western diets

first: Sharma

last: Sumeet

first: Anderson

last: Thea


title: DDX20 is required for cell cycle reentry of prospermatogonia and establishment of spermatogonial stem cell pool during testicular development in mice

city: beijing

first: dingfeng

last: zou

state: 北京

address: Beijing, Dong Dan San Tiao 5

institute: Institute of Basic Medical Sciences  Chinese Academy of Medical Sciences & Peking Union Medical College

summary: DDX20 is required to promote spermatogonial stem cell pool formation by regulating mRNA translation during postnatal prospermatogonia differentiation in mice.

overall_design: We used THY1-positive cells isolated from Ddx20 knockout mice and littermate controls for low-input Ribo-seq.

first: Dingfeng

last: Zou

first: Luying

last: Su


title: Amphiregulin from regulatory T cells promotes liver fibrosis and insulin resistance in non-alcoholic steatohepatitis [scHSC]

first: Nicholas

last: Arpaia

summary: We study the effect of Treg cell-derived Areg in chronic liver injury. Here we look at the transcriptional changes of hepatic stellate cells in NASH in response to Treg cell-derived Areg.

overall_design: Single cell RNA-seq of hepatic stellate cells enriched via FACS from the liver of AregFl/Fl (control) or AregFl/Fl Foxp3YFP-cre (conditional knockout) mice fed a NASH diet.

first: Thomas

last: Savage

first: Katherine

last: Forton

first: Kenia

last: de los Santos

first: Mathieu

last: Rouanne

first: Angelica

last: Oliveras Alsina

first: Renzo

last: Cavero

first: Fangda

last: Li

first: Rebecca

last: Haeusler

first: Julien

last: Adam

first: Robert

last: Schwabe

first: Hani

last: Shayya

first: Sarah

last: Rae


title: RNA sequencing data of Kat6a (Moz) mutant embryonic mouse hearts (ING4 and ING5 are essential for histone H3 lysine 14 acetylation and epicardial cell lineage development)

first: Connie

last: Li-Wai-Suen

summary: Inhibitor of growth 4 and 5 (ING4 and ING5) are chromatin-binding proteins in the KAT6A, KAT6B and KAT7 histone acetyltransferase protein complexes. Heterozygous mutations in the KAT6A or KAT6B gene cause human disorders with cardiac defects, but the contribution of their chromatin adaptor proteins to development is unknown. We found that Ing5-/- mice had isolated cardiac ventricular septal defects. ING4 and ING5 are structurally similar proteins, suggesting a degree of redundancy. Combined loss of ING4 and ING5 caused developmental arrest at embryonic day E8.5, loss of histone H3 lysine 14 acetylation (H3K14ac) and a reduction in H3K23ac levels. Ing4+/-Ing5-/- hearts showed a paucity of epicardial cells and epicardium-derived cells, failure of myocardium compaction and coronary vasculature defects, accompanied by a reduction in the expression of epicardium genes. Our findings suggest that ING4 and ING5 are essential for heart development and promote epicardium and epicardium-derived cell fates and mutation of the human ING5 gene as a possible cause of isolated ventricular septal defects.

overall_design: RNA-sequencing data of N = 3 Kat6a-/- and 5 Kat6a+/+ E10.5 hearts.

first: Anne

last: Voss

first: Alexandra

last: Garnham


title: Anthracyclines induce cardiotoxicity through a shared gene expression response signature

city: Galveston

first: Michelle

middle: C.

last: Ward

email: miward@UTMB.edu, ermatthe@UTMB.edu

state: TX

address: 301 University Blvd., MRB 7.150

department: Biochemistry and Molecular Biology

institute: UTMB-Galveston

summary: TOP2 inhibitors (TOP2i) are effective drugs for breast cancer treatment. However, they can cause cardiotoxicity in some women. The most widely used TOP2i include anthracyclines (AC) Doxorubicin (DOX), Daunorubicin (DNR), Epirubicin (EPI), and the anthraquinone Mitoxantrone (MTX). It is unclear whether women would experience the same adverse effects from all drugs in this class, or if specific drugs would be preferable for certain individuals based on their cardiotoxicity risk profile. To investigate this, we studied the effects of treatment of DOX, DNR, EPI, MTX, and an unrelated monoclonal antibody Trastuzumab (TRZ) on iPSC-derived cardiomyocytes (iPSC-CMs) from six healthy females. All TOP2i induce cell death at concentrations observed in cancer patient serum, while TRZ does not. A sub-lethal dose of all TOP2i induces limited cellular stress but affects calcium handling, a function critical for cardiomyocyte contraction. TOP2i induce thousands of gene expression changes over time, giving rise to four distinct gene expression response signatures, denoted as TOP2i early-acute, early-sustained, and late response genes, and non-response genes. There is no drug- or AC-specific signature. TOP2i early response genes are enriched in chromatin regulators, which mediate AC sensitivity across breast cancer patients. However, there is increased transcriptional variability between individuals following AC treatments. To investigate potential genetic effects on response variability, we first identified a reported set of expression quantitative trait loci (eQTLs) uncovered following DOX treatment in iPSC-CMs. Indeed, DOX response eQTLs are enriched in genes that respond to all TOP2i. Next, we identified 38 genes in loci associated with AC toxicity by GWAS or TWAS. Two thirds of the genes that respond to at least one TOP2i, respond to all ACs with the same direction of effect. Our data demonstrate that TOP2i induce thousands of shared gene expression changes in cardiomyocytes, including genes near SNPs associated with inter-individual variation in response to DOX treatment and AC-induced cardiotoxicity.

overall_design: We collected RNA-seq data from iPSC-derived cardiomyocytes derived from six healthy female individuals (1-6). Each individual was treated with 0.5 uM of one of the following breast cancer drugs: Doxorubicin (DOX), Epirubicin (EPI), Daunorubicin (DNR), Mitoxantrone (MTX), Trastuzumab (TRZ), or a vehicle control (VEH) for three or 24 hours.

first: Elizabeth

last: Matthews

middle: C


title: Ascorbic acid reprogrames epigenome and epitranscriptome by recycling Fe (III) into Fe (II) in the catalytic cycle of dioxygenases (RNA-Seq)

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Ascorbic acid has been reported to stimulate DNA iterative oxidase TET enzymes, Jumonji C-domain-containinghistone demethylase and potentially RNA m6A demethylase FTO and ALKBH5 as a cofactor. Although ascorbic acid has been widely investigated in reprogramming DNA and histone methylation status in vitro, in cell lines and mouse models, its specific role in the catalytic cycle of dioxygenases remains enigmatic. Here we systematically investigated the stimulation of ascorbic towards TET2, ALKBH3, histone demethylases and FTO. We find that ascorbic acid reprograms epitranscrip-tome by erasing the hypermethylated m6A sites. Biochemistry and Electron spin resonance (ESR) assays demonstrate that ascorbic acid enters the active pocket of dioxygenases, reduces Fe (III), either incorporated upon protein synthesis or generated upon rebounding the hydroxyl radical during oxidation, into Fe (II). Finally, we propose a new model for the catalytic cycle of dioxygenases by adding in the essential dynamic cofactor, ascorbic acid. Ascorbic acid refreshes and regenerates inactive dioxygenase through recycling Fe (III) into Fe (II) in a dynamic “hit-and-run” manner.

overall_design: Gene expression profiling analysis of RNA-seq data  after Ascorbic acid treatment

first: He

last: Weizhi


title: Ascorbic acid reprogrames epigenome and epitranscriptome by recycling Fe (III) into Fe (II) in the catalytic cycle of dioxygenases (m6A)

overall_design: Comparation m6A profiling analysis of RNA-seq data  after Ascorbic acid treatment


title: Ascorbic acid reprogrames epigenome and epitranscriptome by recycling Fe (III) into Fe (II) in the catalytic cycle of dioxygenases

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


title: FOXP4-mediated induction of PTK7 activates the Wnt/β-catenin pathway and promotes ovarian cancer development

city: Lianyungang

first: Yasong

last: Wang

state: Jiangsu

address: Jiangsu Ocean University, School of Pharmacy, 108 Tongguan South Road, Haizhou District, Lianyungang City, Jiangsu Province,

institute: Jiangsu Ocean University

summary: Ovarian cancer (OC) presents a significant challenge in clinical settings due to its difficulty in early diagnosis and its resistance to treatment. FOXP4 is a member of the FOXP subfamily and is involved in various biological processes including embryonic development, cell cycle regulation, and tumorigenesis. Despite its potential role in cancer, the exact function and significance of FOXP4 in OC remain uncertain. Here we showed that FOXP4 was expressed at high levels in OC, and its high expression was associated with poor prognosis. Furthermore, RNA sequencing and functional analysis of cells lacking FOXP4 suggest that FOXP4 contributes to the activation of the Wnt signaling pathway, leading to the amplification of the malignant phenotype in OV. Mechanistically, FOXP4 directly induces the expression of protein tyrosine kinase 7 (PTK7), a Wnt-binding receptor tyrosine pseudokinase, leading to abnormal activation of the Wnt signaling pathway. Disrupting the FOXP4-Wnt feedback loop by inactivating the Wnt signaling pathway or reducing FOXP4 expression resulted in the reduction of the malignant phenotype of OC cells, while restoring PTK7 expression reversed this effect. In conclusion, our findings highlight the importance of FOXP4 in the activation of the Wnt signaling pathway in OC and provide evidence for the potential therapeutic value of targeting this pathway in the treatment of the disease.

overall_design: In order to study the FOXP4 role in ovarian cancer as well as the mechanism, we established the FOXP4 knockout (KO) and FOXP4 wild - type of 293 t cell line (WT). We then performed gene expression profiling using RNA-seq data from FOXP4_Con and FOXP4_KO1 cells.

first: Jing

last: Ji

first: Qilan

last: Qian

first: Aixin

last: Jing

first: Ting

last: Geng

first: Yuanyuan

last: Ding

first: Xinhui

last: Ma

first: Qian

last: Sun

first: Xiujun

first: Shaojie

first: Qing

last: Yuan

first: Menghan

last: Xu

first: Jingting

last: Qin

first: Lin

first: Jiayan

last: Yang

first: Meiqi

last: Zhang

first: Wenhao

last: Cheng

first: Seng

first: Shunfang

last: Liu

first: Bin


title: Endothelial TDP-43 controls sprouting angiogenesis and vascular barrier integrity, and its deletion triggers neuroinflammation

city: Hospitalet de Llobregat

first: Victor

last: Arribas

state: Barcelona

address: Carrer de la Feixa Llarga, s/n

country: Spain

institute: Universitat de Barcelona

summary: TDP-43 is a DNA/RNA-binding protein that regulates gene expression and its malfunction in neurons has been causally associated with multiple neurodegenerative disorders. Although progress has been made in understanding the functions of TDP-43 in neurons, little is known about its role in endothelial cells (ECs), angiogenesis and vascular function. Using inducible EC-specific TDP-43 knockout mice, we show that TDP-43 is required for sprouting angiogenesis, vascular barrier integrity and blood vessel stability. Postnatal EC-specific deletion of TDP-43 leads to retinal hypovascularization due to defects in vessel sprouting associated with reduced EC proliferation and migration. In mature blood vessels, loss of TDP-43 disrupts the blood-brain barrier and triggers vascular degeneration. These vascular defects are associated with an inflammatory response in the central-nervous system with activation of microglia and astrocytes. Mechanistically, deletion of TDP-43 disrupts fibronectin matrix around sprouting vessels and reduces -catenin signaling in ECs. Together, our results indicate that TDP-43 is essential for the formation of a stable and mature vasculature.

overall_design: The RNA Sequencing analysis was performed using endothelial cells (EC) from the spinal cord of control and EC-specific knock-out mice at postnatal day 16. TDP-43 gene deletion was inducied via tamoxifen injection every 24 hours and three times at P5-P7,. Three animals were used per experimental group.

first: Arribas

last: Víctor

first: Onetti

last: Yara

first: Ramiro-Pareta

last: Marina

first: Villacampa

last: Pilar

first: Beck

last: Heike

first: Merkel

last: Angelika

first: Alberola

last: Mariona

first: Esteve-Codina

last: Anna

first: Sperandio

last: Markus

first: M

last: Ofelia

first: Schmid

last: Bettina

first: Montanez

last: Eloi


title: ING4 and ING5 are essential for histone H3 lysine 14 acetylation and epicardial cell lineage development

first: Connie

last: Li-Wai-Suen


title: Single cell analysis of follicular lymphoma patient-derived xenograft in avian embryos

city: OULLINS

first: Pierre

last: Sujobert

address: 165 Chemin du Grand Revoyet 1er eta, Faculte Medecine Lyon Sud BP12

institute: CIRI - Centre International de Recherche en Infectiologie

summary: Despite achieving high rates of complete remission with RCHOP immuno-chemotherapy, almost all patients with follicular lymphoma (FL) will experience multiple relapses after treatment. The understanding of the heterogeneity of treatment responses is limited by the absence of in vitro or in vivo experimental models. Here, we develop a primary FL cell xenograft model in chicken embryos to capture treatment response heterogeneity and analyze the mechanisms of response to immune-chemotherapy. Using light sheet microscopy, we observed that tumor volume reduction achieved with RCHOP treatment in ovo predicted progression free survival in multivariate analysis. To further explore the model, we used single-cell RNA sequencing to discover a signature of 21 genes upregulated after RCHOP exposure, with significant intratumoral heterogeneity. As a proof of concept, we functionally validated the involvement of BAX as a critical effector of RCHOP which can be targeted with venetoclax in vitro and in ovo.

overall_design: Human lymph nodes from follicular lymphoma samples before and after avian transplantation with RCHOP or vehicle treatment

first: Manon

last: Zala


title: Viral reprogramming of host transcription initiation [ChIP-seq]

city: New Orleans

first: Erik

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

summary: Viruses are master remodelers of the host cell environment in support of infection and virus production. For example, viruses typically regulate cell gene expression through modulating canonical cell promoter activity. Here, we show that Epstein Barr virus (EBV) replication causes “de novo” transcription initiation at 29,674 new transcription start sites throughout the cell genome. De novo transcription initiation is facilitated in part by the unique properties of the viral pre-initiation complex (vPIC) that binds a simple TATT[T/A]AA, TATA box-like sequence and activates transcription with minimal support by additional transcription factors. Other de novo promoters are driven by the viral transcription factors, Zta and Rta and are influenced by directional proximity to existing canonical cell promoters, a configuration that fosters transcription through existing promoters and transcriptional interference. These studies reveal a new way that viruses interact with the host transcriptome and shed light on primal features driving promoter function.

overall_design: ChIP-Seq of latent or reactivated (anti-IgG treated) Akata cells after 24h

first: Nate

last: Ungerleider


title: Temporal dynamics and genomic programming of plasma cell fates

city: Pittsburgh

first: Harinder

last: Singh

state: PA

address: 5051 Centre Avenue

department: Center for Systems Immunology and Department of Immunology

institute: University of Pittsburgh

summary: Bone marrow plasma cells (BMPCs) of varying lifespans are generated through a germinal center response (GC). The developmental dynamics and genomic programs of antigen-specific plasma cell (PC) precursors remain to be elucidated. Using a model antigen, we demonstrate biphasic generation of BMPC precursors, with those generating long-lived PCs preferentially produced in late phase of GC response. Clonal tracing using scRNA-seq+BCR-seq in spleen and bone marrow compartments, coupled with adoptive transfer experiments, reveal a novel PC transition state that gives rise to functionally competent PC precursors, the latter undergo clonal expansion, dependent on inducible expression of TIGIT. We propose a model for the proliferation and programming of precursors of long-lived BMPCs, based on extended antigen encounters.

overall_design: Splenic and bone marrow CD138+ cells or subsets were isolated using positive selection or flow cytometry based sorting from C57BL6/J mice immunized with NP-KLH, alum and LPS at indicated days post-immunization (d.p.i.)

first: Godhev

last: Manakkat Vijay


title: Multi-ome profiling (paired RNAseq and ATACseq) of human iPSC-derived renal organoids over the period of MET

city: Cambridge

first: Katja

last: Röper

state: Cambridgeshire

address: Cambridge Biomedical Campus,, Francis Crick Ave

department: Cell Biology Division

country: United Kingdom

institute: MRC LMB

summary: Nephron epithelial cells arise through a mesenchymal-to-epithelial transition (MET) during kidney development. We used scRNA-seq and multi-ome profiling to investigate transcriptional mechanisms driving MET in human renal organoids.

overall_design: Renal organoids were generated from human iPSCs and collected at days 10, 12 and 14 of the protocol, which covers the period of MET, and analysed by multi-ome profiling. Organoids were harvested at day 24, when they are considered mature, and analysed by scRNA-seq.

first: John-Poul

last: Ng-Blichfeldt


title: Viral reprogramming of host transcription initiation [ATAC-seq]

summary: Viruses are master remodelers of the host cell environment in support of infection and virus production. For example, viruses typically regulate cell gene expression through modulating canonical cell promoter activity. Here, we show that Epstein Barr virus (EBV) replication causes “de novo” transcription initiation at 29,674 new transcription start sites throughout the cell genome. De novo transcription initiation is facilitated in part by the unique properties of the viral pre-initiation complex (vPIC) that binds a TATT[T/A]AA, TATA box-like sequence and activates transcription with minimal support by additional transcription factors. Other de novo promoters are driven by the viral transcription factors, Zta and Rta and are influenced by directional proximity to existing canonical cell promoters, a configuration that fosters transcription through existing promoters and transcriptional interference. These studies reveal a new way that viruses interact with the host transcriptome and shed light on primal features driving promoter function.

overall_design: Mutu and Akata cells were reactivated with Zta or anti-IgG, respectively. Latent and lytic cells from each population were subjected to ATAC-sequencing.


title: Widespread prevalence of a post-translational modification in activation of an essential bacterial DNA damage response (ChIP-seq)

first: Anjana

last: Badrinarayanan

overall_design: Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on exponential-growing Caulobacter crescentus

first: Aditya

last: Kamat

first: Ngat

last: Tran

first: Mohak

last: Sharda

first: Neha

last: Sontakke

first: Tung

last: Le


title: A common set of genes responding to florigenic and photoperiodic induction at the shoot apical meristem of rice

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

summary: Flowering of rice is triggered by transcriptional reprogramming at the shoot apical meristem (SAM) mediated by florigenic proteins produced in leaves in response to changes in the photoperiod. Florigens are more rapidly expressed under short day (SD) and include the HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1) Phosphatidyl Ethanolamine Binding Proteins (PEBP). Hd3a and RFT1 are largely redundant at converting the SAM into an inflorescence, but whether they activate the same target genes and convey all photoperiodic information that modifies gene expression at the SAM is currently unclear.  We uncoupled the contribution of Hd3a, RFT1 and SD to transcriptome reprogramming at the SAM, by RNA-sequencing of dex-inducible over-expressors of single florigens and wild type plants exposed to photoperiodic induction. Fifteen highly differentially expressed genes common to Hd3a, RFT1 and SD were retrieved, ten of which still uncharacterized. Detailed functional studies on some candidates revealed a role for LOC_Os04g13150 in determining tiller angle and bract development and the gene was renamed BROADER TILLER ANGLE 1 (BRT1). We identified a core set of genes common to florigenic and photoperiodic induction and defined the function of a novel florigen target controlling tiller angle.

overall_design: RNA-seq on naturally induced plants and florigen overexpressing plants

first: Lorenzo

last: Mineri

first: Martina

last: Cerise

first: Francesca

last: Giaume

first: Giulio

last: Vicentini

first: Damiano

last: Martignago

last: Galbiati

first: Alberto

last: Spada

first: David

last: Horner

first: Fabio

last: Fornara

first: Vittoria

last: Brambilla


title: Binding Changes in Chromatin Factors Upon Targeted XPO1 Inhibition in T Cells

city: Cleveland

first: Yi Fan

last: Chen

state: OH

address: 2109 Adelbert Road Biomedical Research Building 747A

institute: Case Western Reserve University School of Medicine

summary:
We assessed the chromatin localization of XPO1, different histone markers, and transcription factors associated with T cell activation with and without SP100030 treatment
We used CUT&RUN sequencing as a lower-input (500,000 cells per sample), higher-sensitivity alternative to ChIP-Seq to assess chromatin binding of different factors

overall_design: Differential binding analysis and overlap analysis of different chromatin factors in T cells at baseline conditions (DMSO), activated conditions (50 nM PMA + 1 uM Ionomycin), or activated + SP100030 (PMA/Iono + 1 uM SP100030)

first: Yi

first: Drew

last: Adams


title: RNA sequencing data of Ing4;Ing5 compound mutant embryonic mouse hearts (ING4 and ING5 are essential for histone H3 lysine 14 acetylation and epicardial cell lineage development)

first: Connie

last: Li-Wai-Suen

overall_design: RNA-sequencing data of Ing4+/-Ing5-/-, Ing4+/+Ing5-/-, Ing4+/-Ing5+/+, Ing4+/+Ing5+/+ embryonic day 10.5 (E10.5) mouse hearts. N = 4 embryonic hearts per genotype.

first: Anne

last: Voss

first: Alexandra

last: Garnham


title: RNA-sequencing of MDA-MB-231 breast cancer cells with and without treatment of BAY 2506856

city: Berlin

first: Andreas

last: Schlicker

address: Muellerstr 178

department: Translational Sciences Oncology Computational Biology

country: Germany

institute: Bayer AG

summary: MDA-MB-231 cancer cells were treated for 24h with DMSO or BAY 2506856. RNA-sequencing was performed to identify changes induced by treatment on the transcriptome level.

overall_design: Cell lines MDA-MB-231 were grown overnight prior to treatment with DMSO or with BAY 2506856 at a concentration of 0.1 µM, 0.3 µM or 1 µM. The cells were harvested 24 h post-treatment for RNA isolation and sequencing.

first: Anna

last: Montebauer


title: Effect of XPO1 Inhibition on Jurkat T Cell Activation

summary: To assess the effects of small molecules SP100030 and Selinexor on Jurkat T cells activated by PMA/Ionomycin after 6 hours of activation and treatment

overall_design: Comparative gene analysis of Jurkat cells at baseline (DMSO), baseline + SP100030 (1 uM SP100030), baseline + Selinexor (1 uM Selinexor), activated (50 nM PMA + 1 uM Ionomycin), activated + SP100030 (PMA/Ionomycin + 1 uM SP100030), and activated + Selinexor (PMA/Ionomycin + 1 uM Selinexor)


title: Single Cell Gene Expression and ATAC-seq of Mouse Brain Following Multiple Infections with Murine Cytomegalovirus (MCMV)

first: Kevin

last: Zwezdaryk

address: 1430 Tulane Ave, Mail code #8638

department: Micro/Immuno

institute: Tulane University

summary: Evidence supporting the role of pathogen exposure in the development of dementia has been mounting for decades. We used murine cytomegalovirus (MCMV) as our model pathogen. We repeated infected mice every 3 months modeling the re-activation/re-infection with MCMV that occurs throughout life. We used Multiome ATAC-seq and RNA-seq to examine changes to the brain of infected animals.

overall_design: 2 month old mice were either mock- or MCMV-infected with 5x10^4 plaque forming units. Repeated reactivation or reinfection over the course of the lifetime of the animal was modeled by re-infection with MCMV every 3 months. Mice were sacrificed at 14 months of age and brains were collected for Multiome ATAC-seq RNA-seq

first: Mark

last: Harrison


title: Targeting the chromatin-binding of XPO1 disrupts NFAT and T cell activation

overall_design: Refer to individual Series


title: The role and function of YAP in cancer-associated fibroblasts

city: Cincinnati

first: Yuhang

last: Zhang

address: 3230 Eden Ave

institute: University of Cincinnati

summary: To investigate how YAP activity contributes to the functional properties of cancer-associated fibroblasts (CAFs), we established YAP-deficient cancer-associated fibroblast cell line, in which YAP expression can be inducibly silenced using shRNA, for RNA-Seq compared to wildtype CAFs.

overall_design: Total RNA was extracted from both wildtype CAFs and YAP-deficient CAFs for RNA-Seq. RNA-Seq data were analyzed using DESeq2 on the AIR platform (https://transcriptomics.sequentiabiotech.com/).

first: Linli

last: Zhou

first: Yao

last: Xiao


title: Effect of PBX1 overexpression in PCM6 and MM1S myeloma cell lines

status: Public on Jan 31 2024

city: Indianapolis

first: Brian

last: Walker

state: IN

address: 980 W Walnut St

department: Medicine

institute: Indiana University

summary: Multiple Myeloma is an incurable plasma cell malignancy with a poor survival rate that is usually treated with immunomodulatory drugs (iMiDs) and proteosome inhibitors (PIs). The malignant plasma cells quickly become resistant to these agents causing relapse and uncontrolled growth of resistant clones. From whole genome sequencing (WGS) and RNA sequencing (RNA-seq) studies, different high-risk translocation, copy number, mutational, and transcriptional markers have been identified. One of these markers, PHF19, epigenetically regulates cell cycle and other processes and has already been studied using RNA-seq. In this study a massive (325,025 cells and 49 patients) single cell multiomic dataset was generated with jointly quantified ATAC- and RNA-seq for each cell and matched genomic profiles for each patient. We identified an association between one plasma cell subtype with myeloma progression that we have called relapsed/refractory plasma cells (RRPCs). These cells are associated with 1q alterations, TP53 mutations, and higher expression of PHF19. We also identified downstream regulation of cell cycle inhibitors in these cells, possible regulation of the transcription factor (TF) PBX1 on 1q, and determined that PHF19 may be acting primarily through this subset of cells.

overall_design: To investigate the effect of PBX1 expression of PHF19 expression we performed and overexpression experiment in two myeloma cell lines. A vector was created to overexpress PBX1 and an empty vector was used as a control two replicates were used for each group.

first: Sylvia

last: Robertson

first: Nathan

last: Becker

first: Travis

last: Johnson


title: Myocardial KLF15 epigenomic changes with single ZT0 prednisone pulse

first: Mattia

last: Quattrocelli

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: this dataset encompasses the cardiac KLF15 epigenomic changes elicited in 4-month-old mice with a single ZT0 prednisone (1mg/kg i.p.) injection

overall_design: 4 months-old mice (KLF15-3x-FLAG+/- mice, C57BL/6J background) were injected with either vehicle, or one i.p. injection of 1mg/kg prednisone (#P6254; Sigma-Aldrich; St. Louis, MO) at ZT0. The injectable solution was diluted from a 5mg/ml stock in DMSO (#D2650; Sigma-Aldrich; St. Louis, MO) in 50ml volume. Injections were conducted at the beginning of the light-phase (ZT0; lights-on). Hearts were collected 4 hours after last injection.

first: Hima

last: Bindu Durumutla

first: Fadoua

last: El Abdellaoui Soussi

first: Saptarsi

last: Haldar


title: Structural atlas of human primary microRNAs generated by SHAPE-MaP

first: Seungchan

last: Baek

state: Massachusetts

address: 22 Water St, Apt 326

institute: Broad Institute

summary: MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here we employed SHAPE-MaP, a high-throughput RNA structure probing method, to unravel the secondary structures of 476 high-confidence human pri-miRNAs. Our SHAPE-based structures diverge substantially from those inferred solely from computation, particularly in the apical loop and basal segments, underlining the need for experimental data in RNA structure prediction. By comparing the structures with high-throughput processing data, we determined the optimal structural features of pri-miRNAs. The sequence determinants are influenced substantially by their structural contexts. Moreover, we identified an element termed the bulged GWG motif (bGWG) with a 3′ bulge in the lower stem, which promotes processing. Our structure-function mapping better annotates the determinants of pri-miRNA processing and offers practical implications for designing small hairpin RNAs and predicting the impacts of miRNA mutations.

overall_design: SHAPE-MaP experiments were performed on all 519 high-confidence human pri-miRNAs curated by MirGeneDB (v1). The pri-miRNAs were synthesized by in vitro transcription using minigene constructs of 125 nt, which contain a miRNA hairpin in the middle. As structural probing controls, we included three well-defined RNAs: human U1 snRNA, yeast tRNAAsp, and HCV IRES domain II. The pooled RNAs, including the controls, were incubated with 1M7. The acylated residues cause base substitutions or indels during reverse transcription. Through high-throughput sequencing, we obtained mutational rates for each nucleotide, which allowed us to quantify the reactivity of 1M7, referred to as “SHAPE reactivity.” This reactivity was then used to model the RNA secondary structure.

first: S

first: Boseon

last: Kim

first: Harim

last: Jang

first: Kijun

first: Il-Soo

last: Park

first: Dal-Hee

last: Min

first: V

middle: N


title: Deep mutational scanning reveals a tight correlation between protein degradation and toxicity of thousands of non-native aspartoacylase protein variants

city: Copenhagen

first: Kristoffer

last: Johansson

address: Ole Maaløes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

summary: When the structural stability of a protein is compromised, the protein may form non-native interactions with other cell proteins and thus becomes a hazard to the cell. To mitigate this danger, destabilized proteins are targeted by the cellular protein quality control (PQC) network, which either corrects the folding defect or targets the protein for degradation. However, the details of how the protein folding and degradation systems collaborate to combat potentially toxic non-native proteins are unknown. To address this issue, we performed systematic studies on destabilized variants of the cytosolic aspartoacylase, ASPA, where loss-of-function variants are linked to Canavan’s disease, an autosomal recessive and lethal neurological disorder, characterized by the spongy degeneration of the white matter in the brain. Using Variant Abundance by Massively Parallel sequencing (VAMP-seq), we determined the abundance of 6152 out of the 6260 (~98%) possible single-site missense and nonsense ASPA variants in cultured human cells. The majority of the low abundance ASPA variants are degraded through the ubiquitin-proteasome system (UPS) and become toxic upon prolonged expression. Variant cellular abundance data correlates with predicted thermodynamic stability, evolutionary conservation, and separates most known disease-linked variants from benign variants. Systematic mapping of degradation signals (degrons) shows that inherent primary degrons in ASPA are located in buried regions, and reveals that the wild-type ASPA C-terminal region functions as a degron. Collectively, our data can be used to interpret Canavan’s disease variants and also offer mechanistic insight into how ASPA missense variants are targeted by the PQC system. These are essential steps towards future implementation of precision medicine for Canavan’s disease.

overall_design: To investigate cellular abundance levels of ASPA single amino acid variants, a site saturation library was GFP labeled and FACS sorted in 4 bins with 3 replicates and 4 biological replicates

first: Martin

last: Grønbæk-Thygesen

first: Vasileios

last: Voutsinos

middle: E

first: Rasmus

last: Hartmann-Petersen


title: In vitro cultured-cells from Homo sapiens control and treated with BHB and LPS raw sequence reads

city: California

first: Natalia

middle: Faraj

last: Murad

address: 500 Parnassus Ave

department: HemOnc

institute: University of California, San Francisco

summary: Beta-hydroxybutyrate (BHB) is a ketone body synthesized during fasting or strenuous exercise. Our previous study demonstrated that a cyclic ketogenic diet (KD), which induces BHB levels similar to fasting every other week, reduces midlife mortality and improves memory in aging mice. BHB actively regulates gene expression and inflammatory activation through non-energetic signaling pathways. Neither of these activities has been well-characterized in the brain and they may represent mechanisms by which BHB affects brain function during aging. First, we analyzed hepatic gene expression in an aging KD-treated mouse cohort using bulk RNA-seq. In addition to the downregulation of TOR pathway activity, cyclic KD reduces inflammatory gene expression in the liver. We observed via flow cytometry that KD also modulates age-related systemic T cell functions. Next, we investigated whether BHB affects brain cells transcriptionallyin vitro. Gene expression analysis in primary human brain cells (microglia, astrocytes, neurons) using RNA-seq shows that BHB causes a mild level of inflammation in all three cell types. However, BHB inhibits the more pronounced LPS-induced inflammatory gene activation in microglia. Furthermore, we confirmed that BHB similarly reduces LPS-induced inflammation in primary mouse microglia and bone marrow-derived macrophages (BMDMs). BHB is recognized as an inhibitor of histone deacetylase (HDAC), an inhibitor of NLRP3 inflammasome, and an agonist of the GPCR Hcar2. Nevertheless, in microglia, BHB's anti-inflammatory effects are independent of these known mechanisms. Finally, we examined the brain gene expression of 12-month-old male mice fed with one-week and one-year cyclic KD. While a one-week KD increases inflammatory signaling, a one-year cyclic KD reduces neuroinflammation induced by aging. In summary, our findings demonstrate that BHB mitigates the microglial response to inflammatory stimuli, like LPS, possibly leading to decreased chronic inflammation in the brain after long-term KD treatment in aging mice.

overall_design: Three brain cell types: astrocytes, microglia and neurons. For each cell type, four treatments: control, BHB, LPS and BHB+LPS. For each treatment: 3 samples. Total samples 36


title: The CoREST Repressor Complex Mediates Phenotype Switching and Therapy Resistance in Melanoma

city: Boston

first: Robert

last: Fisher

address: 609 Albany St

department: Dermatology

institute: Boston University

summary: Virtually all patients with BRAF-mutant melanoma develop resistance to MAPK inhibitors largely through non-mutational events. Although the epigenetic landscape is shown to be altered in therapy-resistant melanomas and other cancers, a specific targetable epigenetic mechanism has not been validated to date. Here, we evaluate the CoREST repressor complex and the recently developed bivalent inhibitor, corin, within the context of melanoma phenotype plasticity and therapeutic resistance. We find that CoREST is a critical mediator of the major distinct melanoma phenotypes and that corin treatment of melanoma cells leads to phenotype reprogramming. Global assessment of transcript and chromatin changes conferred by corin reveals specific effects on histone marks connected to EMT-associated transcription factors and the dual-specificity phosphatases (DUSPs). Remarkably, treatment of BRAF inhibitor (BRAFi)-resistant melanomas with corin promotes resensitization to BRAFi therapy. DUSP1 is consistently downregulated in BRAFi-resistant melanomas which is reversed by corin treatment and associated with inhibition of p38 MAPK activity and resensitization to BRAFi therapies. Moreover, this activity can be recapitulated by the p38 MAPK inhibitor, BIRB 796. These findings identify the CoREST repressor complex as a central mediator of melanoma phenotype plasticity and resistance to targeted therapy and suggest that CoREST inhibitors may prove beneficial to patients with BRAFi- resistant melanoma.

overall_design: 451Lu BRAFi-R and 1205Lu BRAFi-R cells were treated for 24 h with 5 μM PLX4032, 2.5 μM corin, 5 μM PLX4032 + 2.5 μM corin, or DMSO as a control. RNA was isolated from cells using an RNeasy Plus Mini kit (Qiagen Inc.) following the manufacturer's instructions. Paired-end RNA-Seq reads were quality- and adapter-trimmed using trimmomatic and gene expression was quantified using the salmon software package against the GENCODE v32 transcriptome summarized to the gene level. Differential expression analysis for pairwise cell type/treatment conditions was conducted using DESeq2 modeling counts as a function of treatment vs the relevant control.

first: Muzhou

last: Wu

first: Ailish

last: Hanly

first: Frederick

last: Gibson

first: Samantha

last: Rogers

first: Kihyun

first: Angelina

last: Zuger

first: Kevin

last: Kuang

first: Jay

last: Kalin

first: Sarah

last: Nocco

first: Matthew

last: Cole

first: Amy

last: Xiao

first: Filisia

last: Agus

first: Adam

last: Labadorf

first: Samuel

last: Beck

first: Marianne

last: Collard

first: Philip

first: Rhoda

last: Alani


title: Single-cell RNA sequencing identifies dysregulated NOTCH3 signaling in tumor stroma of lung adenocarcinoma

first: Marc

last: Sze

address: 320 Bent Street

institute: Merck

summary: Cancer immunotherapy has revolutionized the treatment of lung adenocarcinoma (LUAD); however, a significant fraction of patients fails to respond. Recent studies to understand transcriptomic determinants of immunotherapy response have pinpointed stroma-mediated resistance mechanisms. To gain a better understanding of the stromal biology at the cellular and molecular levels in LUAD, we obtained the transcriptomes of 256,379 single cells with 13,857 mesenchymal cells from 9 treatment-naïve patients. Among the mesenchymal cells, we identify subsets of FAP+PDPN+ cancer-associated fibroblasts (CAFs) and ACTA2+MCAM+ pericytes, which enrich in tumors, differentiate from lung resident fibroblasts and possess a myofibroblast phenotype.  By utilizing imaging-mass cytometry, we found that both subsets are topographically adjacent to the perivascular niche and have close spatial interaction with endothelial cells (ECs). Modelling of ligand and receptor interactomes between mesenchymal and ECs identifies that NOTCH3/NOTCH signaling drives the cell-cell interaction in tumors, with pericytes and CAFs as the signal receivers and arterial and PLVAPhigh immature neovascular ECs as the signal senders. Either pharmacologically blocking NOTCH signaling or tuning down NOTCH3 level in mesenchymal cells reduced collagen production and suppressed cell invasion. By evaluating the clinical relevance of NOTCH signaling using bulk-RNA sequencing data, we demonstrate that NOTCH3 correlates with poor survival in stroma-rich patients and that a T-cell inflammation gene signature predicts survival only in low-NOTCH3 expressing patients.  Our study underscores the importance of NOTCH3 in regulating tumor stroma biology and may serve as a potential target for immunotherapy combination strategies.

overall_design: All tissue samples from 9 patients for the scRNA sequencing (cohort A) were obtained from Brigham and Women’s Hospital, with patient consent approved by the Institutional Review Board protocol DFCI #98-063. LADC samples from a cohort B of 7 patients for IMC were purchased from commercial suppliers with patient informed consents. Tumors (T) or Adjacent Non-Tumor (ANT) tissues from cohort A were minced with scissors and digested with a human tumor dissociation kit (Miltenyi Biotec, 130-095-929) as per the manufacturer’s protocol with some modifications. For digesting lung samples for MRC001-005, the digestion cocktail from the kit was used, whereas the digestion cocktail with the addition of 0.8 mg/mL dispase II (Sigma, 4942078001) was used to digest the rest of samples.

first: Sze

last: Marc

first: Xiang

last: Handan


title: Gene expression of clonal subpopulations derived from the 4T1 murine mammary carcinoma cell line

city: Princeton

first: Celeste

last: Nelson

state: NJ

address: 25 William Street

institute: Princeton Univerisity

summary: Breast tumors often exhibit intratumoral heterogeneity. We hypothesized that phenotypically distinct clonal subpopulations in heterogeneous tumors may affect overall tumor morphology and cancer cell invasion. In order to study heterogeneous tumors, we isolated individual cells from a parental 4T1 murine mammary carcinoma cell line and generated four clonal subpopulations (E1, E2, A, and M). To characterize these subpopulations, we examined gene expression by performing bulk RNA-sequencing.

overall_design: We performed gene expression analysis on clonal, iRFP-expressing subpopulations derived from a parental population of 4T1 murine mammary carinoma cells. We collected RNA from three biological replicates for each sample.

first: Molly

last: Brennan

first: Susan

last: Leggett


title: PTH treatment prior to cyclic joint loading improves cartilage health and attenuates load-induced osteoarthritis development in mice

city: Ithaca

first: Marjolein

last: van der Meulen

state: NY

address: Weill Hall

department: BME

institute: Cornell University

summary: Osteoarthritis (OA) treatment is limited by the lack of effective non-surgical interventions to slow disease progression. Here, we examined the contributions of the subchondral bone properties to OA development. We used parathyroid hormone (PTH) to modulate bone mass prior to OA initiation and alendronate (ALN) to inhibit bone remodeling during OA progression. We examined the spatiotemporal progression of joint damage by combining histopathological and transcriptomic analyses across joint tissues. The additive effect of PTH pretreatment prior to OA initiation and ALN treatment during OA progression most effectively attenuated load-induced OA pathology. Individually, PTH directly improved cartilage health and slowed the development of cartilage damage, whereas ALN primarily attenuated subchondral bone changes associated with OA progression. Joint damage reflected early transcriptomic changes. With both treatments the structural changes were associated with early modulation of immunoregulation and -response pathways that may contribute to disease mechanisms. Overall, our results demonstrate the potential of subchondral bone-modifying therapies to slow the progression of OA.

overall_design:
Parathyroid hormone (PTH (1-34), 40mg/kg/day, SQ (66)) or vehicle (VEH, saline, same volume, SQ) pretreatment was administered for 8 weeks (5 days/week) to 18-week-old male C57BL/6J mice (202 animals total). Following pretreatment, cyclic mechanical loading was applied to the left tibia at a peak load of 9N for 0 (pretreatment only, no loading, Fig.1A), 1, 2, or 6 weeks (Fig.2A) (8, 29, 30). Concurrent with loading, pretreated mice received either alendronate (73mg/kg/day, intraperitoneal (18)) or vehicle (saline, same volume, intraperitoneal) treatment (5 days/week, Fig.2A). Mice were placed under general anesthesia during loading (2% isoflurane, 1.0L/min, Webster). Loading was applied to the left tibiae at 4Hz for 1200 cycles (5 min) per day, 5 days per week (8, 29, 30). The right tibiae served as contralateral controls. Following completion of the loading periods, mice were euthanized.
In a subset of mice following 1, 2, and 6 weeks of loading, knee joints were harvested and fixed in 4% paraformaldehyde (PFA) overnight at 4° C for tissue level analysis (n=7-8/group). In the pretreatment only group, right limbs were harvested and fixed in 4% paraformaldehyde overnight at 4° C, and left limbs were frozen in PBS-soaked gauze immediately following dissection for nanoindentation analysis. In a separate group of mice following 0, 1, or 2 weeks of loading, different tissues (cartilage, inguinal lymph nodes, and metaphyseal cancellous and cortical bone, after bone marrow removal) were retrieved. Cartilage samples were stabilized in RNAlater while inguinal lymph node and bone samples were snap frozen in liquid nitrogen for for RNA isolation and bulk RNA sequencing analyses (RNA-seq, n=4-8/group). RNA was extracted from tibial cartilage, metaphyseal cortical bone, cancellous bone and inguinal lymph node tissues using protocols previously described (67, 68) (n=4-8/ea). Samples were not pooled.
All experimental procedures were approved by the Institutional Animal Care and Use Committee at Cornell University and by the USAMRMC Animal Care and Use Review Office, and are reported following ARRIVE guidelines (69) and best practices to implement and report experiments using the tibial loading model (70).

first: Adrien

middle: Y

last: Antoinette

first: Sophia

last: Ziemian

first: Carolyn

last: Chlebek

first: Miguel

last: Otero


title: Identification of the downstream target genes of TGFbeta

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: This study aimed to explore the downstream target genes of TGFbeta in normal gastric cell line GES-1.

overall_design: The GC cell lines were treated with or without recombinant human TGF-beta protein. After effective transcrection, the genes downregulated by TGF-beta were screened by RNA sequencing. The transcriptome sequencing studies were performed by deep sequencing, using Illumina NovaSeq 6000.

first: Shanshan

last: Qin

first: Dandan

last: Li


title: Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: Infection with chikungunya virus (CHIKV) causes disruption of draining lymph node (dLN) organization, including paracortical relocalization of B cells, loss of the B cell-T cell border, and lymphocyte depletion that is associated with infiltration of the LN with inflammatory myeloid cells. Here, we find that during the first 24 h of infection, CHIKV RNA accumulates in MARCO-expressing lymphatic endothelial cells (LECs) in both the floor and medullary LN sinuses. The accumulation of viral RNA in the LN was associated with a switch to an antiviral and inflammatory gene expression program across LN stromal cells, and this inflammatory response, including recruitment of myeloid cells to the LN, was accelerated by CHIKV-MARCO interactions. As CHIKV infection progressed, both floor and medullary LECs diminished in number, suggesting further functional impairment of the LN by infection. Consistent with this idea, antigen acquisition by LECs, a key function of LN LECs during infection and immunization, was reduced during pathogenic CHIKV infection.

overall_design: Identification and characterization of cells harboring CHIKV RNA using single-cell RNA sequencing.

first: Cormac

middle: J

last: Lucas

first: Jay

last: Hesselberth

first: Thomas

last: Morrison


title: SRRM2 Phase Separation Drives Assembly of Nuclear Speckle Subcompartments

city: Xiamen

first: Mengjun

last: Zhang

address: State Key Laboratory of Cellular Stress Biology

department: Department of biochemistry

institute: Xiamen university

summary: Nuclear speckles (NSs) are nuclear biomolecular condensates that are postulated to arise through liquid-liquid phase separation (LLPS), although the detailed underlying forces driving NS formation remain elusive. SRRM2 and SON are 2 non-redundant scaffold proteins for NSs. How each individual protein governs assembly of NS protein network and the functional relationship between SRRM2 and SON are largely unknown. Here, we uncover immiscible multiphase of SRRM2 and SON within NSs. SRRM2 and SON are functionally independent, specifically regulating alternative splicing of subsets of mRNA targets, respectively. We further uncover that SRRM2 forms multicomponent liquid phase in cells to drive NS subcompartmentalization, which is reliant on homotypic interaction and heterotypic non-selective protein-RNA complex coacervation-driven multicomponent LLPS. SRRM2 RS domains form high-order oligomers, and can be replaced by oligomerizable synthetic modules, the serine residues within the RS domains, however, play an irreplaceable role in fine-tuning the liquidity of NSs.

overall_design: Compared the changes of RNA alternative splicing after SRRM2 and SON gene knockdown in HeLa cells (siSRRM2, siSON).

first: Zhuang

last: Gu

first: Bo

last: Wang


title: TCR signaling induces STAT3 phosphorylation to promote TH17 cell differentiation

city: Guangzhou

first: Tao

last: Xu

address: Forested street

institute: Sun Yat-Sen University

summary: To systematically evaluate the effect of inhibition of Lck/Fyn kinase activity on the differentiation of TH17 and Treg cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TH17 (with DMSO/Srci1 or STAT3 KO) and Treg(with DMSO/Srci1) cells.

first: Zhen

first: Ping

last: Hou


title: Acute spinal cord injury induces systemic muscle wasting by lesion-level dependent neuroendocrine tone

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

summary: A limited mechanistic understanding of skeletal muscle wasting after acute spinal cord injury (SCI) precludes targeted molecular interventions. Here, we demonstrate marked systemic wasting also affecting neurologically intact non-paralyzed (supralesional) muscle early after SCI. Systemic muscle mass loss propagates muscle weakness, affects fast type 2 myofibers preferentially, and becomes exacerbated after high (T3) compared to low (T9) thoracic paraplegia indicating lesion-level dependent (“neurogenic”) mechanisms. The wasting of non-paralyzed muscle, its rapid onset and severity beyond what can be explained by disuse implies additional systemic drivers. Muscle transcriptome and biochemical analysis revealed a glucocorticoid-mediated catabolic signature of SCI-induced systemic muscle wasting that was mitigated i) by endogenous glucocorticoid ablation (adrenalectomy), ii) by pharmacological glucocorticoid receptor (GR) blockade, and was iii) completely prevented, relative to T9 SCI, by genetic muscle-specific GR deletion. We provide evidence of neurogenic hypercortisolism underlying a rapid systemic and functionally relevant muscle wasting syndrome after acute SCI.

overall_design: 4 to 6 replicates of sham, high-thoracic (T3), or low-thoracic (T9) spinal cord injuries from Gastrocnemius Muscle or Triceps Brachii Muscle

last: Webb

first: Markus

last: Harrigan

first: Jan

last: Schwab


title: Transcriptome of senescence-committed vs uncommitted cells upon oncogenic RAS signaling

city: Montréal

first: Gerardo

last: Ferbeyre

state: Québec

address: 900 rue Saint-Denis

institute: Centre de recherche du CHUM (CRCHUM)

summary:
To investigate how cells distinguish physiological signaling from aberrant RAS signaling to engage the senescence program, we used a model of conditional expression of oncogenic RASG12V.
This allowed us to discover a Senescence Restriction Point (SeRP) where cells are not yet senescent but committed towards that cell fate. We then used transcriptomics to compare committed vs uncommitted cells, in order to identify the downstream effectors of that engagement program.

overall_design: Comparative gene expression analysis of RNA-seq data from IMR90 cells expressing ER-RASG12V and treated with 4OHT for 3 days or 1.5 days.

first: Stéphane

last: Lopes-Paciencia


title: RNA sequencing of embryonic and abembryonic compartments of euploid human blastocysts of good and poor morphology.

city: La Jolla

first: Heidi

last: Cook-Andersen

state: California

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

summary: Implantation of the early embryo—the blastocyst—in the uterine wall to establish a pregnancy is remarkably inefficient in humans for reasons that remain largely unexplained1–3. In recent years, the volume of gene expression data from human preimplantation embryos has rapidly accumulated; however, prioritization of these data to discover specific genes that determine successful implantation is significantly hindered by ethical and experimental constraints. Here, we combine clinical morphologic grading with transcriptome analysis of matched trophectoderm (TE) and inner cell mass (ICM) samples to identify specific genes and cell-cell interactions differentially activated in human blastocysts of high and low implantation potential genome-wide. This allowed us to develop the first prioritized list of genes and cell-cell interactions associated with successful implantation. Employing multiple machine learning approaches, we identified TE and ICM genes that distinguish embryos of high and low implantation potential and found that gene expression within the ICM best predicts implantation. Unexpectedly, we discovered that blastocysts of low implantation potential share defects in the formation of the extraembryonic primitive endoderm (PrE) and the PrE-associated extracellular matrix network. Our results support a model in which successful implantation is most strongly influenced by factors and signals from the ICM, and suggest that defective PrE development, in particular, is a common cause of failed implantation in humans.

overall_design: Examination of gene expression changes within the embryonic and abembryonic compartments between human blastocysts graded as good morphology (highly likely to implant and generate a successful pregnancy), versus those graded as poor morphology (unlikely to implant in the uterus).

first: Jennifer

last: Chousal


title: Chromatin Binding Deubiquitinase MYSM1 in Dendritic Cell Development and Activation

city: Montreal

first: Anastasia

last: Nijnik

state: Quebec

address: Rm 368 - 3649 Promenade Sir William Osler

department: Physiology

institute: McGill University

summary: Dendritic cells (DCs) are the most significant antigen presenting cells of the immune system, critical for the activation of naïve T cells. The pathways controlling DC development, maturation, and effector function therefore require precise regulation to allow for an effective induction of adaptive immune response. MYSM1 is a chromatin binding deubiquitinase (DUB), known to act as an activator of gene expression via its catalytic activity for monoubiquitinated histone H2A (H2A-K119ub), which is a highly abundant repressive epigenetic mark. MYSM1 is an important regulator of hematopoiesis in mouse and human, and a systemic constitutive loss of Mysm1 in mice results in a depletion of many hematopoietic progenitors, including DC precursors, with the downstream loss of most DC lineage cells. However, the roles of MYSM1 at the later checkpoints in DC development, maturation, activation, and effector function at present remain unknown. In the current work, using a range of mouse models (Mysm1flCreERT2, Mysm1flCD11c-cre, Mysm1DN), we further the understanding of MYSM1 functions in the DC lineage: assessing the requirement for MYSM1 in DC development independently of other complex developmental phenotypes, exploring its role at the later checkpoints in DC maintenance and activation in response to microbial stimulation, and testing the requirement for the DUB catalytic activity of MYSM1 in these processes. Surprisingly, we demonstrate that MYSM1 expression and catalytic activity in DCs are dispensable for the maintenance of DC numbers in vivo or for DC activation in response to microbial stimulation.  In contrast, MYSM1 and its DUB catalytic activity in hematopoietic progenitors are essential for normal DC development, and its loss results not only in a severe depletion of DC lineage cells, but also in the production of functionally altered DCs, with a dysregulation of many housekeeping transcriptional programs and significantly altered responses to microbial stimulation.

overall_design:
To further analyze the effects of a pan-hematopoietic loss of MYSM1 function on DC responses to microbial stimulation, bulk RNA-seq of BMDCs was carried out using BMDCs derived from tamoxifen treated CreERT2 transgenic mice of Mysm1fl/DN and control Mysm1fl/+ genotypes, at steady-state and following LPS stimulation.
To be more specific, tamoxifen treated CreERT2Mysm1fl/DN mice (Δ/DN, group C) express a catalytically inactive MYSM1, whereas CreERT2Mysm1fl/+ control mice (Δ/+, group A) express wild type MYSM1.  Bone marrow was extracted at >12 weeks after the tamoxifen treatment, BMDCs derived in vitro over 9 days of culture, and subsequently harvested and cultured for further 18 hours either untreated (US) or with LPS stimulation (10 ng/mL). The samples (US Δ/DN, LPS Δ/DN, US Δ/+, LPS Δ/+) were send to Institut de recherches cliniques de Montréal (IRCM) for RNA-Seq gene expression profilling.

first: Marwah

last: Mousa

first: Yue

last: Liang

first: Lin Tze

last: Tung

first: Hanchen

first: David

last: Langlais

first: Connie

last: Krawczyk


title: Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils [Hi-C]

status: Public on Jan 30 2024

city: Bunkyo-ku

first: Naoko

last: Yokota

state: Tokyo

address: 1-1-1 yayoi

department: Department of Cell and Molecular Biology

country: Japan

institute: The University of Tokyo

summary: The Structural Maintenance of Chromosome (SMC) protein complexes cohesin, condensin and the Smc5/6 complex (Smc5/6) are essential for chromosome function. At the molecular level, these complexes fold DNA by loop extrusion. Accordingly, cohesin creates chromosome loops in interphase, and condensin compacts mitotic chromosomes. However, the role of Smc5/6’s recently discovered DNA loop extrusion activity is unknown. Here, we uncover that Smc5/6 controls the spatial organization of supercoiled chromosomal regions. The results show that Smc5/6 associates with transcription-induced positively supercoiled chromosomal DNA at cohesin-dependent chromosome loop boundaries. Mechanistically, single-molecule imaging reveals that dimers of Smc5/6 specifically recognize the tip of positively supercoiled DNA plectonemes, and efficiently initiates loop extrusion to gather the supercoiled DNA into a large plectonemic loop. Finally, Hi-C analysis shows that Smc5/6 links chromosomal regions containing transcription-induced positive supercoiling in cis. Altogether, our findings indicate that Smc5/6 controls the three-dimensional organization of chromosomes by recognizing and initiating loop extrusion on positively supercoiled DNA.

overall_design: Analysis of chromosome structure by Hi-C in various mutants in Saccharomyces cerevisiae

first: Kristian

last: Jeppsson

first: Biswajit

last: Pradhan

first: Takashi

last: Sutani

first: Toyonori

last: Sakata

first: Miki

middle: U

last: Igarashi

first: Davide

middle: G

last: Berta

first: Takaharu

last: Kanno

first: Ryuichiro

last: Nakato

first: Katsuhiko

last: Shirahige

first: Eugene

last: Kim

first: Camilla

last: Björkegren


title: Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils [ChIP-seq]

overall_design: Analysis of Smc5/6, cohesin and RNA pol II chromosomal association by ChIP-seq in Saccharomyces cerevisiae


title: Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils [RNA-seq]

overall_design: Analysis of transcription levels by RNA-seq in wild-type and top2-4 mutated Saccharomyces cerevisiae cells


title: Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils.

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

overall_design: Refer to individual Series


title: Neonatal CD4+ T cells have a characteristic transcriptome and epigenome and respond to TCR stimulation with proliferation and yet a limited immune response

city: Cuernavaca

first: LInda

middle: AImara

last: Kempis

state: Morelos

address: Avenida Universidad 1001

department: CIDC

country: Mexico

institute: UAEM

summary:
The adaptive immune response is coordinated by CD4+ T cells, which determine the type and strength of the immune response and the
effector cells involved. It has been reported that CD4+ T cells are less responsive in neonates, leading to low activation of the cellular
response and poor antibody production by B cells. This low response is essential for the tolerant window that favors birth transition
from the sterile environment in the womb to the outside world but leaves neonates vulnerable to infection, which is still an important
health issue. Neonates have a high morbidity and mortality rate due to infections, and the molecular reasons are still understudied.
We asked whether the neonatal naive CD4+ T cells have a genomic program that predisposes them to a low response. Therefore, we
evaluated the transcriptome and epigenome of human neonatal and adult naive CD4+ T cells. Our results point to a gene expression
profile forming a distinct regulatory network in neonatal cells, which favors proliferation and a low T-cell response. Such expression
profile is supported by a characteristic epigenetic landscape of neonatal CD4+ T cells, which correlates with the characteristic
transcriptome of the neonatal cells. These results were confirmed by experiments showing a low response to activation signals,
higher proliferation, and lower expression of cytokines of neonatal CD4+ T cells as compared to adult cells. Understanding this
network could lead to novel vaccine formulations and better deal with life-threatening diseases during this highly vulnerable period
of our lives.

overall_design: CD4+T cells were cultured in RPMI 1640 medium supplemented with 2 mM glutamine, commercial antibiotics (50 U/mL penicillin,50lg/mL streptomycin) and 5% fetal coalf serum. Cells were activated with 1µg/mL anti-CD3 (OKT3; TONBO Bio-sciences) and 1µg/mL anti-CD28 (CD28.2;TONBO Biosciences) , cross-linked with 1ug/mL goat anti-mouse (Polyclonal,Bioss) and incubated for 6 h under 5% CO2 at 37°C

first: Otoniel

last: Rodríguez-Jorge

first: Darely

last: Gutiérrez-Reyna

first: Carlos

last: Martínez

first: Salvatore

last: Spicuglia

first: Alejandra

last: Medina-Rivera

first: Denis

last: Thieffry

first: Aitor

last: González

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last: Santana