title: In vitro organoid-based assays reveal SMAD4 tumor-suppressive mechanisms for serrated colorectal cancer invasion [RNA-seq]

city: Nutley

first: Kevin

last: Tong

state: NJ

address: 111 Ideation Way

department: CDI

institute: Hackensack Meridian Health

summary: We establish a model system where organoids derived from tumors found in the Smad4KO BRAFV600E/+ mouse model present multiple phenotypes characteristic of invasion both in ex vivo and in vivo systems.  Additionally, Smad4KO BRAFV600E/+ tumor organoids have the ability to infiltrate a transwell and initiate colonies on the culture plate below.  This invasive behavior can be suppressed when SMAD4 is re-expressed in the tumor organoids. RNA-Seq analysis reveals that SMAD4 expression in organoids rapidly regulates transcripts associated with extracellular matrix and secreted proteins, suggesting that the mechanisms employed by SMAD4 to inhibit invasion are associated with regulation of extracellular matrix and secretory pathways. These findings indicate new models to study SMAD4 regulation of tumor invasion and an additional layer of complexity in the tumor-suppressive function of the SMAD4/Tgfβ pathway.

overall_design: Tumor organoids were derived from macroscopic tumors tissue found in Smad4f/f; BRAFV600E/+;Villin-CreERT2 mice, and were lentivirally transduced with pINDUCER-SMAD4. Organoids were passaged and cultured in 1x CCM treated with either vehicle or 4ug/mL of doxycycline for 48 hours prior to collection for RNA-Seq.

first: Manisha

last: Bandari

first: Jillian

middle: N

last: Carrick

first: Om

last: Kothari

first: Eman

last: Shamshad

first: Katherine

last: Haro

first: Katarina

last: Stefanik

first: Anastasia

last: Zenkevich

first: Ansu

last: Perekatt

first: Michael

middle: P

last: Verzi


title: Single Cell Multiome Atlas of the Human Fetal Retina

status: Public on May 30 2024

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: As the light-sensing part of the visual system, the retina is comprised of five classes of neurons, including photoreceptors, horizontal, amacrine, bipolar, and retinal ganglion cells, along with several non-neuronal cell types such as Muller glia. These major cell classes can be further classified into hundreds of distinct cell subtypes. The development of the retina is under tight temporal control where multipotent progenitor cells differentiate into specific mature cell types in a sequential, but overlapping, order. Additionally, the developmental process is under tight spatial control, with cells at the central retina developing earlier than cells at the periphery. To provide a comprehensive view of the human fetal retina at the molecular level and investigate transcriptional regulatory mechanisms controlling the differentiation process, we profiled more than 300,000 single nuclei of the human fetal retina from 12 donors spanning post conception week 10 and 23 with Multiome RNA-seq and ATAC-seq.

overall_design: snATAC-seq and snRNA-seq of macula lutea tissue, peripheral region of retina tissue from 12 fetal  human donors

first: Rui

last: Chen

first: Zhen

last: Zuo

first: Xuesen

last: Cheng

first: Salma

last: Ferdous

first: Jianming

last: Shao

first: Jin

last: Li

first: Jiaxiong

last: Lu

first: Antonio

last: Lopez

first: Juliette

last: Wohlschlegel

first: Aric

last: Prieve

first: Mervyn

last: Thomass

first: Thomas

last: Reh

first: Yumei

first: Ala

last: Moshiri

first: Yourong

last: Bao

first: Jean


title: In vitro organoid-based assays reveal SMAD4 tumor-suppressive mechanisms for serrated colorectal cancer invasion

first: Kevin

last: Tong

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: In vitro organoid-based assays reveal SMAD4 tumor-suppressive mechanisms for serrated colorectal cancer invasion [ChIP-seq]

overall_design: SW480 cells were then transduced serially with lentiviral vectors carrying avi-tagged SMAD4 expression constructs (pReceiver-Lv108, GeneCopoeia) with puromycin resistance cassette and BirA expression plasmid with hygromycin B (Addgene plasmid 29649). SW480 cells were cultured in RPMI, containing 10% FBS and 1% penicillin and streptomycin. Cells stably expressing both avi-tagged SMAD4 and BirA were selected with medium containing 2 μg/ml puromycin and 0.4 mg/ml Hygromycin B, respectively. Cells were fed 24 hours prior to harvest at approximately 95% confluency for ChIP-Seq.

first: Manisha

last: Bandari

first: Jillian

last: Carrick

first: Om

middle: A

last: Kothari

first: Eman

last: Shamshad

first: Katherine

middle: S

last: Haro

first: Katarina

last: Stefanik

first: Anastasia

last: Zenkevich

first: Ansu

middle: O

last: Perekatt

first: Michael

last: Verzi


title: The regulation of transcriptome in HCC cells by KDM1A inhibition [HepG2_SP2509_RNAseq]

city: Shanghai

first: Boshi

last: Wang

address: No.800 Dongchuan Road

country: China

institute: Shanghai Cancer Institute

summary: We investigated the impact of KDM1A inhibition on transcriptome in HCC cells through RNA-seq assays

overall_design: We analyzed gene expression profiles using RNA-seq assays in HepG2 cells with SP2509 treatment.

first: Tiantian

last: Jing


title: Mutant IDH modulates suppressive myeloid populations in malignant glioma

status: Public on May 29 2024

city: Boston

first: Eric

last: Grewal

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

summary: RNA-sequencing for myeloid inflammation-related genes was conducted on primary tumor samples from patients with IDH-wildtype glioblastoma (GBM) and grade 4 IDH-mutant astrocytoma (G4IMA). In addition, the IDH-wildtype murine glioma cell line GL261 and a strain of IDH-mutant GL261 were also sequenced using the murine counterpart of the RNA-sequencing myeloid innate immunity panel.

overall_design: Tissue from human cases of GBM (n=12) and G4IMA (n=12), and murine IDH-wildtype GL261 tumors (n=5) and IDH-mutant GL261 tumors (n=5) were isolated and subjected to bulk RNA sequencing using the Nanostring nCounter® Myeloid Innate Immunity Panel V2 (human and murine kits, respectively).


title: Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis [RNA-Seq2]

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ-cell genes during differentiation and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. Surprisingly, we find that genome organization also contributes to NPC formation, mediated by the transcription factor Stonewall (Stwl). As GSCs differentiate, Stwl accumulates at boundaries between silenced and active gene compartments. Stwl at these boundaries plays a pivotal role in transitioning germ-cell genes into a silenced state and activating a group of oocyte genes and Nucleoporins (Nups). The upregulation of these Nups during differentiation is crucial for NPC formation and further genome organization. Thus, crosstalk between genome architecture and NPCs is essential for successful cell fate transitions.

overall_design: RNA-seq was performed on duplicates of each genotype: Control  and BEAF32-AB KO ovaries

first: Noor

middle: M

last: Kotb

first: Gulay

last: Ulukaya

first: Ankita

last: Chavan

first: Son

middle: C

last: Nguyen

first: Lydia

last: Proskauer

last: Joyce

first: Dan

last: Hasson

first: Madhav

last: Jagannathan

first: Prashanth

last: Rangan


title: Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [Cut&Run Foxp3 Batf Ets1]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: Nuclear factor Foxp3 determines regulatory T (Treg) cell fate and function via mechanisms that remain unclear. Here we investigate the nature of Foxp3-mediated gene regulation in suppressing autoimmunity and antitumor immune response. Contrasting with previous models, we find that Foxp3-chromatin binding is regulated by Treg activation states, tumor microenvironment, and antigen and cytokine stimulations. Proteomics studies uncovered dynamic proteins within the Foxp3 proximity upon TCR or IL-2 receptor signaling in vitro, reflecting intricate interactions among Foxp3, signal transducers, and chromatin. Pharmacological inhibition and genetic knockdown experiments indicate that NFAT and AP-1 protein Batf are required for enhanced Foxp3-chromatin binding in activated Treg cells and tumor-infiltrating Treg cells to modulate target gene expression. Furthermore, mutations at Foxp3 DNA-binding domain destabilize Foxp3-chromatin association. These representative settings delineate context-dependent Foxp3-chromatin interaction, suggesting that Foxp3 associates with chromatin by hijacking DNA-binding proteins resulting from Treg activation or differentiation, which is stabilized by direct Foxp3-DNA binding, to dynamically regulate Treg cell function according to immunological contexts.

overall_design: Cut&Run protocol were performed to detect Batf Ets1 or Foxp3 binding sites changed in various settings. Each have 2 or 3 replicates.

first: Minghong

last: He

first: Xinying

last: Zong

first: Yongqiang

last: Feng


title: Specific binding sites on Rhesus rotavirus capsid protein dictates the method of endocytosis inducing the murine model of biliary atresia

city: Cincinnati

first: Erica

last: DePasquale

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology

institute: Cincinnati Children's Hospital

summary: Biliary atresia (BA) is the leading indication for pediatric liver transplantation. Rhesus rotavirus (RRV) induced murine BA develops an obstructive cholangiopathy that mirrors the human disease. We have previously demonstrated the "SRL" motif on RRV's VP4 protein binds to heat shock cognate 70 protein (Hsc70) facilitating entry into cholangiocytes. In this study, we analyzed how binding to Hsc70 affects viral endocytosis, intracellular trafficking, and uniquely activates the signaling pathway that induces murine BA. Inhibition of clathrin- and dynamin-mediated endocytosis in cholangiocytes following infection demonstrated blocking dynamin decreased the infectivity of RRV whereas clathrin inhibition had no eaffect. Blocking early endosome trafficking resulted in decreased viral titers of RRV while late endosome inhibition had no effect. Following infection, p-NF-?B levels and TLR3 expression increased in cholangiocytes, leading to increased release of CXCL9 and CXCL10. Infected mice knocked out for TLR3 had decreased levels of CXLC9 and CXCL10, resulting in reduced NK cell numbers. Human BA patients experienced an increase in CXCL10 levels, suggesting this as a possible pathway leading to biliary obstruction. Viruses that utilize Hsc70 for cell entry exploit a chlathrin-independent pathway and traffic to the early recycling endosome uniquely activating NF-kB through TLR3, releasing leading to the release of CXCL9 and CXCL10, and inducing NK cell recruitment. These results define how the "SRL" peptide found on RRV's VP4 protein modulates viral trafficking, inducing the host response leading to bile duct obstruction.

overall_design:
3 infected and 3 non-infected (control) samples of cholangiocytes laser captured from 7 day old mouse bile ducts

*** Submitters state that the complete processed/normalized data has been lost and thus only the reduced data set (of 633 data rows) after filtering for differential expression and fold-change is provided (as described in the sample data processing field)***

first: Haley

last: Temple

first: Bryan

last: Donnelly

first: Sujit

middle: K

last: Mohanty

first: Sarah

last: Mowery

first: Holly

last: Poling

first: Rajamouli

last: Pasula

first: Stephen

last: Hartman

first: Akaljot

last: Singh

first: Reena

last: Mourya

first: Alexander

last: Bondoc

first: Jaroslaw

last: Meller

first: Anil

middle: G

last: Jegga

first: Kei

last: Oyama

first: Monica

last: McNeal

first: Paul

last: Spearman

first: Greg

last: Tiao


title: Mis-splicing of mitotic regulators sensitizes SF3B1-mutated human HSCs to CHK1 inhibition [scRNA-seq]

city: Pavia

first: Martina

last: Sarchi

address: Via Ferrata 9

department: Dept. of Molecular Medicine

country: Italy

institute: University of Pavia

summary: Splicing factor SF3B1 mutations are frequent somatic lesions in myeloid neoplasms that transform hematopoietic stem cells (HSCs) by inducing mis-splicing of target genes. However, the molecular and functional consequences of SF3B1 mutations in human HSCs remain unclear. Here, we identify the mis-splicing program in human HSCs as a targetable vulnerability by precise gene editing of SF3B1 K700E mutations in primary CD34+ cells. Mutant SF3B1 induced pervasive mis-splicing and reduced expression of genes regulating mitosis in single cell transcriptomics, critically BUBR1 and CDC27, leading to altered differentiation and delayed G2/M progression. Mutant SF3B1 mis-splicing or reduced expression of BUBR1 and CDC27 was sufficient to delay G2/M transit, leading to activation of CHK1, sensitizing cells to CHK1 inhibition. Clinical CHK1 inhibitor prexasertib selectively targeted SF3B1-mutant HSCs and abrogated engraftment in vivo. These findings identify mis-splicing of mitotic regulators in SF3B1-mutant HSCs as a targetable vulnerability engaged by pharmacological CHK1 inhibition.

overall_design: Single cell RNA sequencing was performed on SF3B1 K700E mutant HSPCs and AAVS1 gene edited controls. Gene edited BFP+CD34+ HSPCs were flow-sorted 72 hours after gene editing.

first: Courtnee

last: Clough

first: Edie

middle: I

last: Crosse

first: Jason

last: Kim

first: Laura

middle: D

last: Baquero Galvis

first: Nelli

last: Aydinyan

first: Rachel

last: Wellington

first: Anna

last: Gallì

first: J

last: Creamer

first: Sintra

last: Stewart

first: Robert

last: Bradley

first: Luca

last: Malcovati

first: Sergei

last: Doulatov


title: Effect of whole-body deletion of Gclc on the liver

city: Rochester

first: Isaac

middle: Spencer

last: Harris

state: New York

address: 601 Elmwood Ave

department: Department of Biomedical Genetics

institute: University of Rochester Medical Center

summary: The rate-limiting step in glutathione (GSH) synthesis is controlled by glutamate-cysteine ligase catalytic subunit. To investigate the impact of GSH in vivo, we induced a deletion of Gclc using a Gclcf/f Rosa26-CreERT2 mouse model and harvested liver tissue for analysis.

overall_design: Liver tissue was harvested from WT and KO mice approximately two weeks after treatment with tamoxifen to induce Cre activity and Gclc deletion.

first: Gloria

last: Asantewaa


title: Comprehensive transcriptomic analysis of immune-related genes in diabetic foot ulcers: New insights into mechanisms and therapeutic targets

city: luzhou

last: Jiang

address: Zhong Shan Road

institute: SWMU

summary: We performed RNA-seq on tissue biopsies derived from patients with DFU and compared it to healthy controls who had similar foot surgery to identify the significant immune related differentially expressed genes between normal and DFU samples. Our results identified that there was a total of 8800 DEGs detected by RNA-seq data analysis, among which 2351 were upregulated and 6449 downregulated genes in DFU. 526 differential IRGs were obtained from intersection of DEGs and IRGs. These results suggest that a deregulated immune cells contribute to pathogenesis of DFUs.The purpose of this study was to identify the key biomarkers of the abnormally expressed genes and immune infiltration in the diabetic wound and to provide diagnostic and therapeutic targets for DFU.

overall_design: mRNA profiles of diabetic foot ulcers patients and healthy controls.

first: Qi

last: Chen

first: Jianying

last: Song

first: Lixin

last: Hu


title: Effect of liver-specific deletion of Gclc, Nrf2, and Gclc-Nrf2 on the liver

summary: The rate-limiting step in glutathione (GSH) synthesis is controlled by glutamate-cysteine ligase catalytic subunit. GSH is reported to buffer oxidative stress. In the absence of GSH, the antioxidant transcription factor Nrf2 is reported to be stabilized. The liver has the highest levels of GSH, but its impact on liver homeostasis is unclear. To investigate this, we induced a liver-specific deletion of Gclc (Gclc f/f), Nrf2 (Nrf2 f/f), or Gclc-Nrf2 (Gclc f/f Nrf2 f/f) by injecting my via tail-vein with AAV-TBG-Cre, which induces recombination specifically in hepatocytes.

overall_design: Gclc wt/wt (Control), Gclc f/f, Nrf2 f/f, and Gclc f/f Nrf2 f/f were injected via tail-vein with 2.5e11 pfu of AAV-TBG-Cre. Three weeks following injection with AAV-TBG-Cre, mice were sacrifice and liver was harvested for RNA analysis.


title: Progenitors of distinct lineages shape the diversity of mature type 2 conventional dendritic cells [scRNA-Seq]

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine in St. Louis

summary: Conventional Dendritic Cells (cDC) are antigen-presenting cells comprising cDC1 and cDC2 subsets, responsible for priming naïve CD8+ and CD4+ T cells, respectively. Recent studies have unveiled cDC2 heterogeneity and identified various cDC2 progenitors beyond the common DC progenitor (CDP), hinting at distinct cDC2 lineages. By generating Cd300ciCre-hCD2R26tdTomato reporter mice, we identified a bone marrow pro-cDC2 progenitor exclusively generating cDC2 in vitro and in vivo. Single-cell analyses and multiparametric flow cytometry demonstrated that pro-cDC2 encompass myeloid-derived pre-cDC2 and lymphoid-derived pDC-like precursors differentiating into a transcriptionally convergent cDC2 phenotype. Cd300c-traced cDC2 had distinct transcriptomic profiles, phenotypes, and tissue distributions compared to Ms4a3CreR26tdTomato lineage-traced DC3, a monocyte-DC progenitor-derived subset that bypasses CDP. Mice with reduced Cd300c-traced cDC2 showed impaired humoral responses to a blood-borne antigen. We conclude that progenitors of distinct lineages shape the diversity of mature cDC2 cells across tissues. Thus, ontogenesis may impact tissue immune responses.

overall_design: We performed single-cell RNA sequencing on splenic CD11c+ cells from three distinct mouse lines: CD300c-iCre-hCD2-, IL-7R-Cre-, and Ms4a3-Cre R26tdTomato. Each line included three biological replicates, uniquely identified by the labeling of three distinct Hashtag antibodies.

first: Patrick

last: Fernandes Rodrigues


title: YY1 is involved in homologous recombination inhibition at guanine quadruplex sites in human cells

first: Xinyu

last: Cui

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

summary: Homologous recombination (HR) is a key process for repairing DNA double strand breaks and for promoting genetic diversity, and it occurs unevenly throughout the genome. G-quadruplexes (G4s) are stable secondary structures widely present across the genome, which function in regulating gene transcription and maintaining genome stability. However, elevated G4 levels by BLM (RecQ like helicase unwinding G4) depletion can significantly drive HR at these G4 sites, which may threaten genome stability. Here, we investigated the role of Yin Yang-1 (YY1) in modulating HR at G4 sites. To elucidate G4 sites on the genome, cleavage under targets and tagmentation (CUT&Tag) of BG4, a G4 specific antibody, was conducted.

overall_design: Cleavage under targets and tagmentation (CUT&Tag) for BG4 in HEK293T cells.

first: Chengwen

last: Zhang

first: Chunqing

last: Fu

first: Jinlei

first: Tengjiao

last: Li

first: Lin


title: Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis

first: BiNGS

last: Core


title: Progenitors of distinct lineages shape the diversity of mature type 2 conventional dendritic cells.

overall_design: We performed single-cell RNA/ATAC (multiome) sequencing on Lin- B220- Flt3+ BM progenitor cells extracted from three CD300c-iCre-hCD2 R26tdTomato mice.


title: Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis [RNA-seq]

overall_design: RNA-seq was performed on duplicates of each genotype: Control nosGAL4 and nosGAL4>stwl GKD ovaries as well as control  bamGAL4 and bamGAL4>stwl GKD ovaries.

first: Noor

last: Kotb

first: Gulay

last: Ulukaya

first: Ankita

last: Chavan

first: Son

last: Nguyen

first: Lydia

last: Proskauer

first: Eric

last: Joyce

first: Dan

last: Hasson

first: Madhav

last: Jagannathan

first: Prashanth

last: Rangan


title: An activity regulated transcriptional program directly drives synaptogenesis

city: Stanford

first: Callista

last: Yee

state: California

address: 327 Campus Drive, Shen lab, Bass Biology 329

institute: Stanford University/HHMI


title: Intestinal ILC3s migrate to the kidney and promote renal fibrosis via PD-1-mediated activation

city: Guangzhou

first: Yi

last: Zhou

address: No.58 Zhongshan Er Road

institute: The First Affiliated Hospital, Sun Yat-Sen University

summary: Group 3 innate lymphoid cells (ILC3s) are enriched in mucosae, regulating inflammation and tissue repair, yet their role in renal fibrosis remains unclear. Here, we reported that renal fibrosis and dysfunction were associated with increased ILC3s in human kidney and blood. Using murine models, we showed that the rapid accumulated ILC3s in the kidney primarily originated from the intestinal mucosa. By performing scRNA-seq of ILC(3)s in kidneys and small intestines at different stage of renal fibrosis, we revealed the characteristic and migratory mechanism of these cells. Within the fibrotic kidney, ILC3s upregulated PD-1 to directly activate myofibroblasts and facilitate fibrotic niche formation by producing IL-17A. We also isolated ILCs from Pdcd1-knockout-UUO3d kidneys to gain the molecular mechanism of how PD-1 influence ILC3s' pro-fibrogenic effect. Collectively,  we reveal a hitherto unrecognized migration pathway of ILC3s from the intestine to the kidney and the PD-1-dependent function of ILC3s in promoting renal fibrosis.

overall_design: Renal or intestinal ILC(3)s of the WT or Pdcd1-knockout mice were isolated by Fluorescence-activated cell sorting (FACS) according to the specific cell surface markers and analyzed using scRNA-seq.

first: Zhou

last: Liang

first: Ziwen

last: Tang

first: Changjian

last: Zhu

first: Feng

first: Xu

last: Han

first: Ruilin

last: Zheng

first: Xinrong

last: Hu

first: Ruoni

last: Lin

first: Qiaoqiao

last: Pei

first: Wei

last: Chen


title: Effect of diet-induced obesity on uterine function in mice.

status: Public on May 28 2024

first: Antonina

middle: I.

last: Frolova

address: 660 S. Euclid Ave, CB 8064

department: OBGYN

institute: Washington University in St. Louis

summary: To gain insight into the mechanism(s) by which obesogenic diet caused decreased uterine contractility at term, we collected uterine tissue from mice fed either a control (CON) or an obesogenic (DIO) diet at day 18.5 of pregnancy and performed RNA sequencing.

overall_design: Female mice were fed either a control or an obesogenic diet for 10 weeks and throughout pregnancy. Whole uterus was collected on day of pregnancy 18.5 (term non-labor) starting from the implantation site closest to the cervix (C-0). Fetal tissue, placenta, and amnion were removed, and the remaining uterine tissues (individual implantation sites) were flash frozen in liquid nitrogen until further analyses. C-1 was used for RNA analysis.

first: Kevin

last: Prifti


title: Oxidative stress-induced gene expression changes in prostate epithelial cells in vitro reveal a robust signature of normal prostatic senescence and aging

city: CDMX

first: Samael

last: Olascoaga

state: Iztapalapa

address: Av. San Rafael Atlixco

department: Health Sciences

country: Mexico

institute: Universidad Autonoma Metropolitana

summary:
Oxidative stress has long been postulated to play an essential role in aging mechanisms, and numerous forms of molecular damage associated with oxidative stress have been well documented. However, the extent to which changes in gene expression in direct response to oxidative stress are related to actual cellular aging, senescence, and age-related functional decline remains unclear.
We used microarrays to detail H2O2-induced oxidative stress and resulting gene expression alterations in prostate epithelial cells in vitro. While a broad range of significant changes observed in the expression of non-coding transcripts implicated in senescence-related responses, we also note an overrepresentation of gene-splicing events among differentially expressed protein-coding genes induced by H2O2

overall_design: The study compares control samples of normal human prostate epithelial cells (HPEC) (4 replicates) with HPEC cell samples treated with 12 μmol/L of H2O2 for 2 hours to induce SIPS (4 replicates). The gene expression profile was determined on day 12 after senescence induction.

first: Norma

middle: E

last: López Díaz-Guerrero


title: 5' droplet-based single-cell RNA sequencing of human gastric cancer tissue

city: HongKong

first: Suetyi

last: Leung

address: Queen Mary Hospital, Pokfulam Road

department: Department of Pathology

institute: The University of Hong Kong

summary: Using single-cell sequencing, we profiled single cells derived from one human gastric tumor.

overall_design: Gastric cancer tissue were dissociated and sorted to obtain single cells and were subjected to single cell RNA sequencing.

first: Suet

middle: Y


title: DNA methylation profiling of the Biomarkers of Aging Consortium Cohort

first: Jesse

last: Poganik

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

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

type: Methylation profiling by genome tiling array

summary: We generated DNA methylation profiles of 500 diverse individuals to enable to construction and validation of DNA methylation biomarkers of aging.

overall_design: We selected 500 subjects to generate a cohort that was evenly divided between male and female, and represented a broad range of ages and race/ethnicity. DNA isolated from the blood of these subjects was profiled with the Illumina Infinium MethylationEPIC v2.0 array.

middle: R

first: Mahdi

last: Moqri

first: Vadim

last: Gladyshev


title: Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis [CUT&RUN]

first: BiNGS

last: Core

summary: Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in Genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ-cell genes during differentiation and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. Surprisingly, we find that genome organization also contributes to NPC formation, mediated by the transcription factor Stonewall (Stwl). As GSCs differentiate, Stwl accumulates at boundaries between silenced and active gene compartments. Stwl at these boundaries plays a pivotal role in transitioning germ-cell genes into a silenced state and activating a group of oocyte genes and Nucleoporins (Nups). The upregulation of these Nups during differentiation is crucial for NPC formation and further genome organization. Thus, crosstalk between genome architecture and NPCs is essential for successful cell fate transitions.

overall_design: Sequencing of duplicate samples after performing CUT&RUN on Bam GKD ovaries (enriched for undifferentiated stages), WT (differentiated stages) and stwl GKD ovaries for the transcription factor Stwl, the boundary element BEAF as well as histone marks: H3K4me3, H3k27ac, H3k9me3, H3k27me3 and H3k4me1

first: Noor

last: Kotb

first: Gulay

last: Ulukaya

first: Ankita

last: Chavan

first: Son

last: Nguyen

first: Lydia

last: Proskauer

first: Eric

last: Joyce

first: Dan

last: Hasson

first: Madhav

last: Jagannathan

first: Prashanth

last: Rangan


title: R-loop landscapes during parental-to-zygotic transition in zebrafish

city: Beijing

first: li

last: kuan

address: zhongguancun

institute: Tsinghua University

summary: The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here, we developed a novel R-loop profiling technique, ULI-ssDRIP-seq, to decte global R-loops from a limited number of cells. Based on this method, we profiled the R-loop landscapes during parental-to-zygotic transition and early development regulatory in zebrafish, and revealed a series of important characters of R-loops.

sample_organism:
Escherichia coli
Arabidopsis thaliana
Danio rerio
synthetic construct

overall_design: ULI-ssDRIP-seq development, and R-loop profiling in zebrafish

first: Wei

last: Xu

first: Luxi

last: Chen

first: Jinjin

last: Li

first: Kuan

first: Changbin

last: Sun

first: Anming

last: Meng

first: Qianwen


title: The spliceosome impacts morphogenesis in the human fungal pathogen Candida albicans.

city: Berlin

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

country: Germany

institute: Freie Universität

summary: At human body temperature, the fungal pathogen Candida albicans can transition from yeast to filamentous morphologies in response to host-relevant cues. Additionally, elevated temperatures encountered during febrile episodes can independently induce C. albicans filamentation. However, the underlying genetic pathways governing this developmental transition in response to elevated temperature remain largely unexplored. Here, we conducted a functional genomic screen to unravel the genetic mechanisms orchestrating C. albicans filamentation specifically in response to elevated temperature, implicating 45% of genes associated with the spliceosome or pre-mRNA splicing in this process. Employing RNA-Seq to elucidate the relationship between mRNA splicing and filamentation, we identified greater levels of intron retention in filaments compared to yeast, which correlated with reduced expression of the affected genes. Intriguingly, homozygous deletion of a gene encoding a spliceosome component important for filamentation (PRP19) caused even greater levels of intron retention compared with wild-type and globally dysregulated gene expression. This suggests that intron retention is a mechanism for fine-tuning gene expression during filamentation, with perturbations of the spliceosome exacerbating this process and blocking filamentation. Overall, this study unveils a novel biological process governing C. albicans filamentation, providing new insights into the complex regulation of this key virulence trait.

overall_design: We compare mRNA expression and splicing changes in different growth conditions (yeast form at 30°C, 2 filament-inducing conditions: 37° C + Newborn Calf Serum, heat inactivated (NBCS), 39 °C) of Candida albicans wild-type and the spliceosomal gene deletion strain prp19Δ/Δ.

first: Emma

last: Lash

first: Corinne

last: Maufrais

first: Guilhem

last: Janbon

first: Nicole

last: Robbins

first: Leah

last: Cowen


title: Adjuvant COX inhibition augments STING signaling and cytolytic T cell infiltration in irradiated murine 4T1 TNBC tumors

city: Frederick

first: David

last: Wink

state: MD

address: 1050 Boyles St

department: CCR

institute: NCI

summary: Immune therapy has emerged as the new frontier of cancer treatment. Therapeutic radiation is a known inducer of an immune response that can be limited by immunosuppressive mediators including cyclooxygenase-2 (COX2), which is highly expressed in triple negative breast tumors. A clinical cohort of triple negative breast cancer (TNBC) tumors revealed that elevated COX2 tumor expression predicted poor radiation therapeutic efficacy. Using the aggressive murine 4T1 TNBC model, we show that treatment with ionizing radiation and adjuvant NSAID (indomethacin) therapy to inhibit COX2 provides a powerful combination to reduce both primary tumor growth and lung metastasis through immune modulation. Using whole tumor RNAseq and multiplex fluorescence imaging, this study reveals spatial immunological changes in the treated primary tumor. Indomethacin alone increased the infiltration of lymphoid populations into the primary tumor. Importantly, the combined treatment improved lymphoid infiltration into the tumor epithelium, augmented cGAS/STING1 and type I IFN gene expression and altered key immune checkpoints including PD1, IDO, and CTLA4. Markedly increased B cell and T cell populations with increased CD8+ T cell activation and reduced T cell exhaustion were observed. Thus, adjuvant NSAID treatment combined with radiation therapy shifts “immune desert phenotypes” toward anti-tumor immune mediators favoring M1/Th1 signatures in the immunologically challenging 4T1 tumor model. Importantly, radiation/indomethacin combination improved local control of the primary lesion, reduced metastatic burden, and increased median survival when compared to mice treated with single agent radiation. These results show that clinically available NSAID’s augment radiation therapeutic efficacy through improved antitumor immune response and augmented local generation of cGAS/STING1 and type I IFNs

overall_design: In this study, we explored the effects of pan-NOS and -COX inhibitors on radiation therapeutic efficacy in the murine 4T1 TNBC model. After implanted 200k 4T1 TNBC cells at the age of 8 weeks old, mice were divided into 4 groups: (1) control, (2) 6 Gy radiation, (3) indomethacin, and (4) 6 Gy radiation plus indomethacin.

first: Lisa

last: Ridnour

first: Robert

last: Cheng

first: Noemi

last: Kedei

first: Veena

last: Somasundarum

first: Dibyangana

last: Bhattacharyya

first: Debashree

last: Basudhar

first: Adelaide

middle: L

first: Abigail

middle: J

last: Walke

first: Caleb

last: Kim

first: William

middle: F

last: Heinz

first: Elijah

last: Edmondson

first: Donna

last: Butcher

first: Andrew

last: Warner

first: Tiffany

middle: H

last: Dorsey

first: Milind

last: Pore

last: Kinders

first: Stanley

last: Lipkowitz

first: Richard

last: Byrant

first: Jens

last: Rittscher

first: Stephen

middle: T

last: Wong

last: Hewitt

first: Jenny

last: Chang

first: Aliaa

last: Shalaby

first: Grace

last: Callagy

first: Sharon

last: Glynn

first: Stefan

last: Ambs

first: Steven

last: Anderson

first: Daniel

middle: W

last: McVicar

last: Lockett


title: JAK inhibitor overcomes resistance to immune checkpoint inhibitor treatment in gastric cancer peritoneal dissemination in mouse

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

country: Japan

institute: Kindai University Faculty of Medicine

summary: Objective Cancer immunotherapy aims to unleash the immune system's potential against cancer cells, providing sustained relief for tumors responsive to immune checkpoint inhibitors (ICIs). While promising in gastric cancer (GC) trials, the efficacy of ICIs diminishes in the context of peritoneal dissemination. Our objective is to identify strategies to enhance the impact of ICI treatment specifically for cases involving peritoneal dissemination in GC. Design The therapeutic efficacy of anti-PD1, CTLA4 treatment alone, or in combination, was assessed using the YTN16 peritoneal dissemination tumor model mice. Peritoneum and peritoneal exudate cells were collected for subsequent analysis. Immunohistochemical staining, flow cytometry, and bulk RNA-sequence analyses were conducted to evaluate the tumor microenvironment (TME). A JAK inhibitor (JAKi) was introduced based on the pathway analysis results. Results Anti-PD1 and anti-CTLA4 combination treatment (dual ICI treatment) demonstrated therapeutic efficacy in certain mice, primarily mediated by CD8+ T cells. However, in mice resistant to dual ICI treatment, even with CD8+ T cell infiltration, most of the T cells exhibited exhaustion phenotype. Notably, resistant tumors displayed abnormal activation of the JAK-STAT pathway compared to the untreated group, with observed infiltration of macrophages, neutrophils, and Tregs in the TME. The concurrent administration of JAKi rescued CD8+ T cells function and reshaped the immunosuppressive TME, resulting in enhanced efficacy of the dual ICI treatment. Conclusion Dual ICI treatment exerts its anti-tumor effects by increasing tumor- specific CD8+ T cell infiltration, and the addition of JAKi further improves ICI resistant by reshaping the immunosuppressive TME.

first: Wan-Ying

last: Du

first: Kazuhiro

last: Kakimi

first: Sachiyo

last: Nomura


title: Single-cell multi-omics analysis revealing immune features of inactivated SARS-CoV-2 vaccination in systemic lupus erythematosus patients

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: The COVID-19 vaccine-induced immunity has been widely reported in the general population, but the protective immune response of COVID-19 vaccines in SLE patients (SLEs) remains largely unknown. Here, we performed a comprehensive and time-series investigation of immunological alterations induced by inactivated COVID-19 vaccines in SLEs and healthy controls using single-cell multi-omics methods. Compared with healthy controls (HCs), the lower titres of neutralizing antibodies and global transcriptomic and epigenomic changes in peripheral immune cells were detected in SLEs. Increased expression levels of inflammatory responses related genes and AP-1 family members were commonly detected in SLEs and HCs, along with increased activation of T cells and diversity of T cell receptor repertoire. However, this vaccine enhanced chromatin accessibility at interferon response factors (IRF) loci in monocytes and conventional dendritic cells (cDCs) from SLEs at the late stage after vaccination, which was confirmed by transcriptome data and distinct from HCs. Vaccine induced less differentiations of B cells, expanded clonotypes and class switching clonotypes in SLEs, which was associated with impaired neutralization antibodies. Our study provides a system biology assessment of the transcriptomic and epigenomic landscape during an immune response induced by COVID-19 vaccine within SLEs, providing insights that will be useful in the optimization of vaccination strategies in immune compromised populations.

overall_design:
We generated a single-cell multi-omics landscape for peripheral blood, including single-cell RNA sequencing (scRNA-seq), single-cell lymphocyte antigen receptor repertoire (single B/T cell receptor [BCR/TCR] sequencing), and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq). In this study, we collected single-cell data from four systemic lupus erythematosus patients and two health controls before (day 0) and after vaccination (day 28) using 10× Genomics platform.
Due to human patient privacy concerns, the raw sequencing data have been deposited in Genome Sequence Archive (GSA) for Human under the accession number HRA004028.

first: Siyuan

last: Wang

first: Xingyu

last: Zhou

first: Shitong

last: Qiao

first: Xin

last: Zhao

first: Yuan

last: Chen

first: Zijun

last: Li

first: Zhanguo

first: Xiaolin

last: Sun

first: Shuguang

last: Tan

first: Jing

last: He

first: George

last: F Gao


title: Single-cell RNA sequencing  of antigen specific CD4+ T cells induced by high vs low doses of MHC-II restricted neoantigens

first: Vladimir

last: Sukhov

address: 660. S Euclid Ave.

department: Immunology

summary: Here, we report the impact of the dose of the MHC-II restricted neoantigens on the phenotypic and the effector function of tumor-specific CD4  T cells. Whereas vaccines containing low doses of MHC-II-restricted neoantigen (LDVax) generated helper CD4 T cells that promote the proliferation and the cytotoxic functions of CD8 T cells, vaccines containing high doses of MHC-II restricted neoantigen (HDVax) elicited type 1 regulatory T cells that suppress the antitumor immunity.

overall_design: T3 tumor-bearing 129S6 male mice were vaccinated on day 6 post-tumor implantation, and 7 days later, tumors were harvested and processed into single-cell suspension. CD4+ T cells were then enriched using positive selection beads and then FACS sorted to ensure high purity (>95%).

first: Robert

last: Schreiber

first: Hussein

last: Sultan


title: Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [Cut&Run Foxp3 Batf]

first: Beisi

last: Xu

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hosipital

summary: Nuclear factor Foxp3 determines regulatory T (Treg) cell fate and function via mechanisms that remain unclear. Here we investigate the nature of Foxp3-mediated gene regulation in suppressing autoimmunity and antitumor immune response. Contrasting with previous models, we find that Foxp3-chromatin binding is regulated by Treg activation states, tumor microenvironment, and antigen and cytokine stimulations. Proteomics studies uncovered dynamic proteins within the Foxp3 proximity upon TCR or IL-2 receptor signaling in vitro, reflecting intricate interactions among Foxp3, signal transducers, and chromatin. Pharmacological inhibition and genetic knockdown experiments indicate that NFAT and AP-1 protein Batf are required for enhanced Foxp3-chromatin binding in activated Treg cells and tumor-infiltrating Treg cells to modulate target gene expression. Furthermore, mutations at Foxp3 DNA-binding domain destabilize Foxp3-chromatin association. These representative settings delineate context-dependent Foxp3-chromatin interaction, suggesting that Foxp3 associates with chromatin by hijacking DNA-binding proteins resulting from Treg activation or differentiation, which is stabilized by direct Foxp3-DNA binding, to dynamically regulate Treg cell function according to immunological contexts.

overall_design: Cut&Run protocol were performed to detect Batf binding sites changed in various settings. Each have 2 replicates.

first: Minghong

first: Xinying

last: Zong

first: Yongqiang

last: Feng


title: RNA sequencing  of antigen specific CD4+ T cells induced by high vs low doses of MHC-II restricted neoantigens

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

overall_design: Refer to individual Series


title: Gene expresion profile of different clusters of antigen specific CD4+ T cells induced by vaccines containing high doses of MHC-II restricted neoantigens

summary: CD4+ T cells induced by vaccines containing high doses of mItgb1 SLP were sorted into 3 different clusters based on the expression of CD25, CD200 and CD39. We found that cluster-3 cells (CD4+ CD25- and CD39+) express high levels of GZMB, Ccl5, Lilirb4 and Sema4a. The gene signature of cluster-3 matched those of mice and human Tr1.

overall_design: T3 tumor-bearing 129S6 male mice were vaccinated on day 6 post-tumor implantation, and 7 days later, tumors were harvested and processed into single-cell suspension. Antigen specific CD4+ T cells were then enriched using positive selection beads and then FACS sorted into 3 differtent clusters as listed.


title: Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [Cut&Tag Foxp3]

overall_design: Cut&Tag protocol were performed to detect Foxp3 binding sites changed in various settings. Each have 2 replicates.


title: Conserved Cis-Acting Range Extender Elements Mediate Long-Range Developmental Enhancer Activity in Mammals

city: Irvine

first: Evgeny

last: Kvon

address: 4310 McGaugh Hall

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: Long-range developmental enhancers can regulate cell-type specific target gene expression over distances that exceed hundreds of thousands of base pairs in mammals. Although higher-order chromatin organization provides support for such long-range enhancer—promoter interactions, the genetic factors that regulate these interactions during mammalian development remain largely unexplored. To address this central question, we replaced a limb enhancer, located >800,000 base pairs from its target promoter, with equivalent limb enhancers of similar strength from other genomic loci. We used this replacement strategy to generate six knock-in mouse strains, with enhancers from four distinct genomic loci. All enhancers drove strong expression in developing limb buds when placed adjacent to a reporter gene. However, when transplanted to a distal location, all four enhancers failed to activate remote gene expression and distal limb outgrowth, suggesting that proximally-active enhancers cannot activate transcription remotely. Including a highly conserved, but previously uncharacterized, sequence found adjacent to a long-range limb enhancer rescued gene expression and limb outgrowth. This cis-acting Range EXtender (REX) element does not have classical enhancer activity but is necessary and sufficient for enhancer–promoter communication over very long distances in vivo. The REX element contains highly conserved [C/T]AATTA consensus sequences that match binding preferences of LIM-homeodomain (LHX) transcription factors. We used multiomic single-cell ATAC-seq/RNA-seq profiling to identify [C/T]AATTA homeodomain motifs next to thousands of long-range limb enhancers. The presence of these motifs positively correlates with E–P distance genome-wide. Our data support a model where REX elements facilitate target gene activation by remote enhancers over very long distances in mammalian genomes.

overall_design: Whole hindlimb was dissected from an E11.5 FVB embryo, dissociated into single cells, lysed into nuclei and then single-cell multiomics (scRNA-seq and scATAC-seq) was performed.   For allele-specific ATAC-seq, both hindlimb ZPAs of individual E11.5 embryos from various enSWAP knock-in mice were dissected and slowly frozen using Mr. Frosty. Embryo genotypes were determined and single heterozygotes were chosen and bulk ATAC-seq was performed on the collected tissue.

first: Grace

last: Bower

first: Ethan

last: Hollingsworth

middle: Z


title: Single-cell transcriptional profiling of clear cell renal cell carcinoma reveals a tumor-associated endothelial tip cell phenotype

city: Vilnius

first: Justina

last: Zvirblyte

state: LT

address: Sauletekio av.7

department: Life Sciences Center, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

summary: Clear cell renal cell carcinoma (ccRCC) is the most prevalent form of renal cancer, accounting for over 75% of cases. The asymptomatic nature of the disease contributes to late-stage diagnoses and poor survival. Highly vascularized and immune infiltrated microenvironment are prominent features of ccRCC, yet the interplay between vasculature and immune cells, disease progression and response to therapy remains poorly understood. Using droplet-based single-cell RNA sequencing we profiled 50,236 transcriptomes from paired tumor and healthy adjacent kidney tissues. Our analysis revealed significant heterogeneity and inter-patient variability of the tumor microenvironment. Notably, we discovered a previously uncharacterized vasculature subpopulation associated with epithelial-mesenchymal transition. The cell-cell communication analysis revealed multiple modes of immunosuppressive interactions within the tumor microenvironment, including clinically relevant interactions between tumor vasculature and stromal cells with immune cells. The upregulation of the genes involved in these interactions was associated with worse survival in the TCGA KIRC cohort. Our findings demonstrate the role of tumor vasculature and stromal cell populations in shaping the ccRCC microenvironment and uncover a subpopulation of cells within the tumor vasculature that is associated with an invasive phenotype.

overall_design: Fresh ccRCC tumor (n=8) and healthy-adjacent (n=9) paired kidney tissues were obtained from the National Cancer Institute (Vilnius, Lithuania) with a bioethics committee approval No.2019/2˗1074˗586. No patient had received prior systemic therapy for their cancer. Samples were collected during an open or laparoscopic, partial or radical nephrectomy surgery, placed on ice and rapidly (<1 hour) transferred to the laboratory for dissociation. Briefly, patient derived tumor tissues were dissociated using Tumor Dissociation Kit (Miltenyi Biotec, cat.no.130-095-929) in an automated instrument gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) as per manufacturer’s instructions. Healthy-adjacent tissues were dissociated using Tissue Dissociation Kit I (Miltenyi Biotec, cat.no. 130-110-201). After dissociation, red blood cells were removed from the samples using RBC lysis reagent (Miltenyi Biotec, cat.no.130-094-183). After RBC lysis, cells were washed 3 times in ice-cold 1X DPBS (Gibco, cat.no. 14080-048) at 500g for 5 min. Cell viability and count was assessed using Trypan Blue dye (Gibco, cat.no. 15250061) on a hemocytometer. No further enrichment or selection of cells was performed. Cell suspension was immediately loaded onto inDrops platform for cell barcoding experiment.

first: Juozas

last: Nainys

first: Simonas

last: Juzenas

first: Karolis

last: Goda

first: Raimonda

last: Kubiliute

first: Darius

last: Dasevicius

first: Marius

last: Kincius

first: Albertas

last: Ulys

first: Sonata

last: Jarmalaite

first: Linas

last: Mazutis


title: Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [RNA-seq Foxp3 KO]

city: Memphis

first: Beisi

overall_design: RNA-seq were performed to detect the DEGs for Foxp3 knockout with or without TCR stimulation.

last: He


title: High-throughput sensitive screening of small molecule modulators of microexon alternative splicing using dual Nano and Firefly luciferase reporters

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: Disruption of alternative splicing frequently causes or contributes to human diseases and disorders. Consequently, there is a need for efficient and sensitive reporter assays capable of screening chemical libraries for compounds with efficacy in modulating important splicing events. Here, we describe a screening workflow employing dual Nano and Firefly luciferase alternative splicing reporters that affords highly efficient, sensitive, and linear detection of small molecule responses. Applying this system to a screen of ~95,000 small molecules, we identify compounds that selectively activate or repress a neuronal microexon network that is frequently disrupted in autism and overexpressed in neuroendocrine cancers. Remarkably, among the most potent and selective activating compounds are histone deacetylase (HDAC) inhibitors. We thus describe a high-throughput screening system for candidate splicing therapeutics, a resource of small molecule modulators of microexons, and insight into the mode of action and potential utility of HDAC inhibitors in the context of neurological disorders.

overall_design: Gene expression and alternative splicing analysis of RNA-seq of mouse neuroblastoma cells treated with small-molecule compounds (single replicates or duplicates) or DMSO control

first: Andrew

last: Best

first: Justin

last: Lim

first: Shaghayegh

last: Farhangmehr

first: Adrian

last: Pasculescu

first: Mingkun

last: Wu

first: Lim

middle: C

last: Comsa

first: Mark

last: Jen

first: Jenny

last: Wang

first: Alessandro

last: Datti

first: Jeffery

last: Wrana

first: Sabine

last: Cordes

first: Rima

last: Al-awar

first: Hong

last: Han

first: Benjamin

last: Blencowe


title: Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [ATAC-seq]

last: Xu

overall_design: ATAC-seq protocol were performed to detect the chromatin accessiblity different between Active Treg(ATreg) and Resting Treg(Rtreg) also the effect of Batf. Each have 2 replicates.

first: Minghong

first: Xinying

last: Zong

first: Yongqiang

last: Feng


title: Oncogenic Calreticulin Induces Immune Escape by Stimulating TGF-β Expression and Regulatory T Cell Expansion in the Bone Marrow Microenvironment

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg


title: Strand specific RNA-Seq of transcripts from cassava, Maihot esculenta variety TM12

city: Frederiksberg

first: Swetha

last: Chenna

state: Choose State

address: Bülowsvej

country: Denmark

institute: University of Copenhagen

summary: The gene expression profiling analysis from WT and cold treated samples of cassava that were used with other multi-omics data to build gene model annotation of Cassava.

overall_design: Comparative gene expression profiling analysis of strand specific RNA-Seq (ssRNA-Seq) data from wild type (WT) and cold treated (3 hours) cassava shoots.

first: Sebastian

last: Marquardt

first: Maxim

last: Ivanov


title: Transcriptome analysis of cassava, Manihot esculenta variety TM12


title: Oxford nanopore transcriptome of cassava, Manihot esculenta variety TM12

summary: Full length long read transcript sequences were used as guides along with other multi-omics data to build gene model annotation of Cassava.

overall_design: Comparative full length gene expression profiling analysis of ONT-Seq data from wild type (WT) and cold treated (3 hours) cassava shoots.


title: STRIPE-Seq of transcripts from cassava, Maihot esculenta variety TM12

summary: The start site analysis of transcripts from WT and cold treated samples of cassava that were used with other multi-omics data to build gene model annotation of Cassava.

overall_design: Comparative gene expression profiling analysis of STRIPE-Seq, a 5'-end sequencing method, from wild type (WT) and cold treated (3 hours) cassava shoots.


title: Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [RNA-seq]

first: Beisi

overall_design: We developed a comparative proteomics method by projecting the spatial information (PSI) of nuclear proteins with peroxidase–mediated proximity ligation, thus revealing the protein components of the cis-regulatory elements bound by Treg lineage–specifying factor Foxp3. We performed RNA sequencing for naïve CD4 T cells (Tn, CD4+ GFP- CD25- CD44low CD62Lhigh), effector CD4 T cells (aTe, CD4+ GFP- CD44high CD62Llow), resting Treg cells (rTreg, CD4+ GFP+ CD44low CD62Lhigh), and activated Treg cells (aTreg, CD4+ GFP+ CD44high CD62Llow) sorted from 8-10 week old male Foxp3-gfp knockin mice. To reveal signal-dependent transcriptional regulation, we first induced Treg cells in vitro (iTreg) from CD4 naïve T cells isolated from male Foxp3-gfp mice with TCR agonists, Interleukion-2 (IL-2), TGF-beta, and ascorbic acid and then stimulated them with IL-2 for 30 min or with plate-bound anti-CD3 and anti-CD28 antibodies for 3 hours. After stimulation, cells were immediately lysed with the TRIzol reagent for RNA extraction and sequencing.

first: Richard

last: Cross


title: Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [PSI-ChIP]

summary: Nuclear factor Foxp3 determines regulatory T (Treg) cell fate and function via mechanisms that remain unclear. Here we investigate the nature of Foxp3-mediated gene  regulation in suppressing autoimmunity and antitumor immune response. Contrasting with previous models, we find that Foxp3-chromatin binding is regulated by Treg activation states, tumor microenvironment, and antigen and cytokine stimulations. Proteomics studies uncovered dynamic proteins within the Foxp3 proximity upon TCR or IL-2 receptor signaling in vitro, reflecting intricate interactions among Foxp3, signal transducers, and chromatin. Pharmacological inhibition and genetic knockdown experiments indicate that NFAT and AP-1 protein Batf are required for enhanced Foxp3-chromatin binding in activated Treg cells and tumor-infiltrating Treg cells to modulate target gene expression. Furthermore, mutations at Foxp3 DNA-binding domain destabilize Foxp3-chromatin association. These representative settings delineate context-dependent Foxp3-chromatin interaction, suggesting that Foxp3 associates with chromatin by hijacking DNA-binding proteins resulting from Treg activation or differentiation, which is stabilized by direct Foxp3-DNA binding, to dynamically regulate Treg cell function according to immunological contexts.

overall_design: We developed a comparative proteomics method by projecting the spatial information (PSI) of nuclear proteins with peroxidase–mediated proximity ligation, thus revealing the protein components of the cis-regulatory elements bound by regulatory T cell lineage–specifying factor Foxp3. By incorporating this method with ChIP sequencing, we performed high efficient immunoprecipitation and ChIP sequencing.


title: 3'-end sequencing of transcripts from cassava, Manihot esculenta variety TM12

summary: Quant-Seq (3'-end sequencing technique) of mRNAs to identify the 3'-ends of transcripts to analyse the 3'-UTR that were used with other multi-omics data to build gene model annotation of Cassava.

overall_design: Comparative 3'-end gene expression profiling analysis of Quant-Seq data from wild type (WT) and cold treated (3 hours) cassava shoots.


title: Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [ATAC-seq iTreg]

overall_design: We developed a comparative proteomics method by projecting the spatial information (PSI) of nuclear proteins with peroxidase–mediated proximity ligation, thus revealing the protein components of the cis-regulatory elements bound by regulatory T cell lineage–specifying factor Foxp3. Open chromatins assessed by ATAC sequencing in regulatory T cells isolated ex vivo or induced in vitro were cross compared with Foxp3 traditional and PSI ChIP sequencing results to uncover the epigenetic features of Foxp3 targets.

first: Jun

last: Li


title: A natural loss-of-function deletion of the cytohesin 1 (Cyth1) gene in BALB/cByJ mice does not impact cardiomyocyte polyploidy

status: Public on May 27 2024

city: Charleston

first: Henry

last: Sucov

state: SC

address: 173 Ashley Ave

institute: Medical Univ. South Carolina

summary: Mammalian cardiomyocytes (CMs) mostly become polyploid shortly after birth. Because this feature may relate to several aspects of heart biology, including regeneration after injury, the mechanisms that cause polyploidy are of interest. BALB/cJ and BALB/cByJ mice are highly related sister strains that diverge substantially in CM ploidy. We identified a large deletion in the Cyth1 gene that arose uniquely in BALB/cByJ mice that creates a null allele. The deletion also results in ectopic transcription of the downstream gene Dnah17, although this transcript is unlikely to encode a protein. By evaluating the natural null allele from BALB/cByJ and an engineered knockout allele in the C57BL/6 background, we determined that absence of Cyth1 does not by itself influence CM ploidy. The ready availability of BALB/cByJ mice may be helpful to other investigations of Cyth1 in other biological processes.

overall_design: Bulk RNA-Seq from ventricles of BALB/cJ and BALB/cByJ neonatal (P4) mice. 3-4 hearts were pooled for each sample.


title: Transcriptomics Provide Insights into Early Responses to Sucrose Signaling in Lupinus albus.

city: Hayward

first: Claudia

last: Uhde-Stone

address: 25800 Carlos Bee Blvd

department: Biological Sciences

institute: California State University, East Bay

summary: Phosphorus (P) and iron (Fe) deficiency are major limiting factors for plant productivity worldwide. White lupin (Lupinus albus L.) has become a model plant for understanding plant adaptations to P and Fe deficiency, because of its ability to form cluster roots, bottle-brush-like root structures that play an important role in the uptake of P and Fe from soil. However, little is known about the signaling pathways involved in sensing and responding to P and Fe deficiency. Sucrose, sent in increased concentrations from the shoot to the root, has been identified as a long- distance signal of P and Fe deficiencies. To unravel responses to sucrose as a signal, we performed Oxford Nanopore cDNA sequencing of white lupin roots treated with sucrose for 10 min, 15 min, and 20 min, compared to untreated controls. We identified a set of 17 genes, including two bHLH transcription factors, that were upregulated at all three time points of sucrose treatment. GO (gene ontology) analysis revealed enrichment of auxin- and gibberellin-responses as early as 10 min after sucrose addition, and the emerging of ethanol-responses at 20 min of sucrose treatment, indicating a sequential involvement of these hormones in plant responses to sucrose.

first: Tahmina

last: Shammi

first: Yi

middle: S

last: Lee

first: Jayati

last: Trivedi

first: Dakota

last: Sierras

first: Aniqua

last: Mansoor

first: Jason

last: Maxwell

first: Matthew

last: Williamson

first: Mark

last: Mcmillan

first: Indrani

last: Chakravarty


title: Dynamic Foxp3-chromatin interaction controls tunable Treg cell function

last: Xu

department: Center for Applied Bioinformatics

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

Nuclear factor Foxp3 determines regulatory T (Treg) cell fate and function via mechanisms that remain unclear. Here we investigate the nature of Foxp3-mediated gene  regulation in suppressing autoimmunity and antitumor immune response. Contrasting with previous models, we find that Foxp3-chromatin binding is regulated by Treg activation states, tumor microenvironment, and antigen and cytokine stimulations. Proteomics studies uncovered dynamic proteins within the Foxp3 proximity upon TCR or IL-2 receptor signaling in vitro, reflecting intricate interactions among Foxp3, signal transducers, and chromatin. Pharmacological inhibition and genetic knockdown experiments indicate that NFAT and AP-1 protein Batf are required for enhanced Foxp3-chromatin binding in activated Treg cells and tumor-infiltrating Treg cells to modulate target gene expression. Furthermore, mutations at Foxp3 DNA-binding domain destabilize Foxp3-chromatin association. These representative settings delineate context-dependent Foxp3-chromatin interaction, suggesting that Foxp3 associates with chromatin by hijacking DNA-binding proteins resulting from Treg activation or differentiation, which is stabilized by direct Foxp3-DNA binding, to dynamically regulate Treg cell function according to immunological contexts.


title: Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney

city: Philadelphia

first: Liling

last: Wan

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania


title: Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney (scRNA-Seq)

summary: ENL is an epigenetic acetylation reader and represents the most frequently mutated epigenetic regulator in Wilms tumor. In this study, we established an in vivo mouse model with the ENL hotspot mutation Enl-T1. We performed single-cell RNA sequencing (scRNA-seq) analysis for the Enl-WT and T1 embryonic kidney to study the transcriptional mechanism underlying the kidney developing defeat induced by the Enl mutation.

overall_design: E15.5 kidneys with or without Enl-T1 mutation from B6 mice were isolated for the scRNA-seq assays, followed by corresponding analysis.

first: Qinglan

first: Lele

last: Song


title: Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney (snATAC-Seq)

summary: ENL is an epigenetic acetylation reader and represents the most frequently mutated epigenetic regulator in Wilms tumor. In this study, we established an in vivo mouse model with the ENL hotspot mutation Enl-T1. We performed single-nuclei ATAC sequencing (snATAC-seq) analysis for the Enl-WT and T1 embryonic kidney to study the open chromatin dynamics and gene regulatory mechanism underlying the kidney developing defeat induced by the Enl mutation.


title: Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney (RNA-Seq)

summary: ENL is an epigenetic acetylation reader and represents the most frequently mutated epigenetic regulator in Wilms tumor. In this study, we established an in vivo mouse model with the ENL hotspot mutation Enl-T1. Here we performed RNA sequencing (RNA-seq) analysis for human embryonuc kidney cell line HEK293 with ENL-WT, T1 or T2 to study the transcriptional changes induced by ENL mutations and whether those alterations can be rescued by treating the cells with the specific ENL inhibitor TDI-11055.

overall_design: HEK293 cells with ENL-WT or T1 treated with DMSO or TDI-11055 were collected for the RNA-seq assays, followed by corresponding analysis.


title: Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney (ChIP-Seq)

summary: ENL is an epigenetic acetylation reader and represents the most frequently mutated epigenetic regulator in Wilms tumor. In this study, we established an in vivo mouse model with the ENL hotspot mutation Enl-T1. Here we performed ChIP sequencing (ChIP-seq) analysis for human embryonuc kidney cell line HEK293 with ENL-WT or T1 to study the genomic binding site alterations induced by ENL mutation and whether those alterations can be rescued by treating the cells with the specific ENL inhibitor TDI-11055.


title: Two Broad Categories Overlapping With Rheumatoid Arthritis Observed in Synovial Biopsies from Patients With Juvenile Idiopathic Arthritis

status: Public on May 25 2024

city: Brussels

first: clement

last: triaille

address: avenue hippocrate

country: Belgium

institute: UCLouvain

summary: The purpose of this study was to investigate the transcriptomic heterogeneity in synovial tissue of JIA patients

overall_design: Comparative gene expression analysis (bulk RNA-seq) of JIA synovial tissue biopsie

first: Clément

last: Triaille

first: Axelle

last: Loriot

first: Nisha

last: Limaye


title: Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish

status: Public on May 26 2024

city: Tuebingen

first: Felicity

last: Jones

address: Max-Planck-Ring 9

institute: Friedrich Miescher Laboratory of the Max Planck Society

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

overall_design: Refer to individual Series


title: A KLF2-BMPER-Smad1/5 checkpoint regulates high fluid shear stress-mediated artery remodeling

status: Public on May 24 2024

city: New Haven

first: Hanqiang

last: Deng

state: CT

address: 116 Court Street

department: Yale Cardiovascular Research Center

institute: Yale University

summary: Vascular remodeling to match arterial diameter to tissue metabolic requirements commonly fails in ischemic disease. Endothelial cells (EC) sense fluid shear stress (FSS) from blood flow to maintain FSS within a narrow range in healthy vessels. Higher FSS induces vessel outward remodeling to return FSS to physiological levels, but mechanisms are poorly understood. We previously reported that Smad1/5 is maximally activated at physiological FSS and suppressed at higher flow. The Smad1/5 pathway opposes activation of Akt, suggesting that inhibiting Smad1/5 may be required for outward remodeling. Here, we report that suppression of Smad1/5 at high FSS is mediated by elevated KLF2, which induces the BMP pathway inhibitor BMPER, which suppresses Smad1/5 and de-inhibits Akt. In a mouse arteriovenous fistula (AVF) model, high FSS induces arterial outward remodeling coincident with elevated BMPER expression and Smad1/5 inactivation. Endothelial BMPER deletion impaired blood flow recovery and vascular remodeling in the AVF and a hindlimb ischemia (HLI) model, with the latter reversed by BMP9/10 blocking antibodies (bAbs). In both STZ-induced type 1 and HFD-induced type 2 diabetic mice that show poor recovery from HLI, BMP9/10 bAbs improved outcomes. Thus, suppression of Smad1/5 is required for high FSS-mediated outward remodeling and is a potential therapeutic approach for ischemic disease.

overall_design: Human umbilical vein endothelial cells (HUVECs) were transfected with Ctrl (siCtrl) or KLF2 (siKLF2) siRNA for 4 days, total RNA was extracted and subjected to RNAseq, n=4 samples for each group.


title: Mmp14-Dependent Remodeling of the Pericellular-Dermal Collagen Interface Governs Fibroblast Survival

city: Ann Arbor

first: Stephen

last: Weiss

state: MI

address: 210 Washtenaw Ave

institute: University of Michigan

summary: Dermal fibroblasts deposit type I collagen, the dominant extracellular matrix molecule found in skin, during early postnatal development.  Coincident with this biosynthetic program, fibroblasts proteolytically remodel pericellular collagen fibrils by mobilizing the membrane-anchored matrix metalloproteinase, Mmp14.  Unexpectedly, dermal fibroblasts in Mmp14-/- mice commit to a large-scale apoptotic program that leaves skin tissues replete with dying cells.  A requirement for Mmp14 in dermal fibroblast survival is recapitulated in vitro when cells are embedded within, but not cultured atop, 3-dimensional hydrogels of cross-linked type I collagen.  In the absence of Mmp14-dependent pericellular proteolysis, dermal fibroblasts fail to trigger β1 integrin activation and instead actuate a TGF-β1/phospho-JNK stress response that leads to apoptotic cell death in vitro as well as in vivo.  Taken together, these studies identify Mmp14 as a requisite cell survival factor that maintains dermal fibroblast viability in postnatal dermal tissues.

overall_design: To assess changes in transcription between control and MT1-MMP-null mouse dermal fibroblasts in 3D collagen, samples of 1X10^5 cells were embedded in 3D, type I collagen hydrogels and cultured for 40 hours prior to RNA isolation and sequencing. Two control and two wild-type samples were prepared for analysis.

first: Farideh

last: Sabeh

first: Xiao-Yan

last: Li

first: Adam

last: Olson

first: Elliot

last: Botvinick

first: Abhishek

last: Kurup

first: Jung-Sun

last: Cho


title: The Role of WTAP in Regulating Macrophage-Mediated Osteoimmune Responses and Tissue Regeneration in Periodontitis

city: Beijing

first: Yuman

address: No.22 , Zhongguancun South Avenue, Haidian District, Beijing

institute: Peking University School and Hospital of Stomatology

summary: Periodontitis, delineated by the destruction of structures that support teeth, is predominantly propelled by intricate immune responses. Immunomodulatory treatments offer considerable promise for the management of this ailment; however, the modulation of the periodontal immune microenvironment to facilitate tissue regeneration presents a substantial biomedical challenge. Herein, our study investigates the role of Wilms' tumor 1-associating protein (WTAP), a critical m6A methyltransferase, in the immunomodulation of periodontitis and assesses its viability as a therapeutic target. We observed heightened expression of WTAP in macrophages extracted from gingival tissues impacted by periodontitis, with a strong association with M1 polarization. Via loss-of-function experiments, we demonstrated that diminishing WTAP expression precipitates a transition from M1 to M2 macrophage phenotypes amidst inflammatory conditions, thus improving the periodontal immune landscape. Further, RNA sequencing and indirect co-culture assays indicated that suppressing of WTAP expression modulates osteoimmune responses and enhances the osteogenic differentiation of bone marrow stromal cells. The local deployment of adeno-associated virus-shWTAP in murine models of periodontitis robustly validated the therapeutic promise of targeting WTAP in this disease. Collectively, our findings highlight the crucial role of WTAP in orchestrating macrophage-mediated osteoimmune responses and tissue regeneration in periodontitis, proposing novel avenues for immunotherapeutic interventions in its treatment.

overall_design: To achieve a thorough understanding of WTAP's regulatory roles in macrophage-associated inflammation, we conducted RNA-seq on bone marrow-derived macrophages (BMDMs) treated with either shNC or shWTAP.

first: Yue

last: Yang

first: Yuting

last: Niu

first: Yao

first: Zhewen

last: Hu

first: Shiyu

last: Sun

first: Yiming

last: Chen

first: Bo

first: Ying

last: Huang

first: Xuliang


title: Placental co-transcriptional activator Vestigial-like 1 (VGLL1) drives tumorigenesis via increasing transcription of proliferation and invasion genes [ChIP-seq]

city: Houston

first: Heather

last: Sonnemann

address: 7455 Fannin St

institute: MD Anderson Cancer Center

summary: Vestigial-like 1 (VGLL1) is a co-transcriptional activator that binds to TEA domain-containing transcription factors (TEADs). Its expression is upregulated in a variety of aggressive cancer types, including pancreatic and basal-like breast cancer, and increased transcription of VGLL1 is strongly correlated with poor prognosis and decreased overall patient survival. In normal tissues, VGLL1 is most highly expressed within placental trophoblast cells, which share the common attributes of rapid cellular proliferation and invasion with tumor cells. The impact of VGLL1 in cancer has not been fully elucidated and no VGLL1-targeted therapy currently exists. The aim of this study was to evaluate the cellular function and downstream genomic targets of VGLL1 in placental, pancreatic, and breast cancer cells. Functional assays were employed to assess the role of VGLL1 in cellular invasion and proliferation, and ChIP-seq and RNA-seq assays were performed to identify VGLL1 target genes and potential impact using pathway analysis. ChIP-seq analysis identified eight transcription factors with a VGLL1-binding motif that were common between all three cell types, including TEAD1-4, AP-1, and GATA6, and revealed ~3,000 shared genes with which VGLL1 interacts. Furthermore, increased VGLL1 expression led to an enhancement of cell invasion and proliferation, which was supported by RNA-seq analysis showing transcriptional changes in several genes known to be involved in these processes.  This work expands our mechanistic understanding of VGLL1 function in tumor cells and provides a strong rationale for developing VGLL1-targeted therapies for treating cancer patients.

overall_design: ChiP-seq analysis of VGLL1 for different cancer cells: PANC10.05, BT20, and Bewo cells.

first: Greg

last: Lizee


title: Total RNA sequencing data for transcriptomic analysis of the effect of chronic ethanol administration on mouse testis

city: Gwangju

first: Gwidong

last: Han

address: GIST, Cheomdnagwagiro 123

department: School of Life Sciences

country: South Korea

institute: GIST

summary: Alcohol is a widely consumed beverage in human society, but it can cause toxic effects.Previous studies on the effects of alcohol consumption on male reproductive function have focused solely on hormonal regulation and physiological changes. However, spermatogenesis is a complex process that requires systemic regulation, including intrinsic regulation by germ cell-specific genes.This study presents a transcriptomic analysis of the effect of chronic ethanol administration on mouse testes.The administration of ethanol to the testis resulted in several alterations in the transcription of testicular genes. Although the changes in expression were mild, a group of genes related to sperm were observed.

overall_design: Chronic ethanol administration was designed for a period of 16 weeks.A daily administration of 10ml of the LDC liquid diet per head was carried out. Prior to the experiment, initial acclimatization was conducted by feeding the control LDC liquid diet for 5 days.

first: Chunghee


title: Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish [ChIP-Seq]

first: Felicity

last: Jones

summary: Despite deep evolutionary conservation, recombination varies greatly across the genome, among individuals, sexes and populations and can be a major evolutionary force in the wild. Yet this variation in recombination and its impact on adaptively diverging populations is not well understood. To elucidate the nature and potential consequences of recombination rate variation, we characterized fine-scale recombination landscapes by combining pedigrees, functional genomics and field fitness measurements in an adaptively divergent pair of marine and freshwater threespine stickleback populations from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic location of almost 50,000 crossovers and built recombination maps for 36 marine, freshwater, and hybrid individuals at 3.8 kilobase resolution. Using these maps, we quantified the factors driving variation in recombination rate: we find strong heterochiasmy between sexes (68% of the variation) but also differences among ecotypes (21.8%). Hybrids show evidence of significant recombination suppression, both in overall map length and in individual loci. We further tested and found reduced recombination rates both within single marine–freshwater adaptive loci and between loci on the same chromosome, suggestive of selection on linked ‘cassettes’. We tested theory supporting the evolution of linked selection using temporal sampling along a natural hybrid zone, and found that recombinants with shuffled alleles across loci show traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers whose mechanisms are disrupted in hybrids, may have an important role to play in the maintenance of differences among adaptively diverging populations.

overall_design: This GEO data deposit is part of a multipart study that includes functional genomic data related to meiosis in stickleback fish as described in Venu et al 2024.  This particular data series includes a ChIPseq dataset using a stickleback fish-specific DMC1 antibody and commercially available H3K4me3 antibody raised against a synthetic H3K4me3 peptide (Millipore; cat#07-473; testes only).  The experiments were performed in meiotic tissue (testes) of marine and freshwater strains of stickleback fish and ChIPseq in a control-somatic tissue (liver). The ChIP pulldown of DMC1-bound single stranded DNA was performed with "kinetic enrichment" following the protocols described in Smagulova et al (2011) Nature 472:375-8 and Khil et al (2012) Genome Research 22:957-65 and was followed sequentially by a ChIP pull down H3K4me3 on the same tissue lysate.  Meiotic tissue lysates comprised of a "freshwater ecotype testes pool" from 15 pairs of testes from freshwater-strain sticklebacks, a "marine ecotype testes pool" from 18 pairs of testes marine-strain sticklebacks.  Somatic-control tissue lysates comprised of a "freshwater ecotype liver pool" from tissue samples from 15 freshwater-strain stickleback livers. No replicates were performed.

first: Vrinda

last: Venu

first: Enni

last: Harjunmaa

first: Andreea

last: Dreau

first: Shannon

last: Brady

first: Devin

last: Absher

first: David

middle: M

last: Kingsley


title: Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms [RNA-seq]

city: Chapel Hill

first: Alexis

last: Stutzman

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

summary: Histone post-translational modifications and the proteins that bind them are proposed to be drivers of 3D genome organization, but whether and how they do so remain unanswered. Here, we evaluate the contribution of H3K9-methylated constitutive heterochromatin to 3D genome organization in Drosophila tissues. We find that the predominant organizational feature of wildtype tissues is segregation of euchromatic chromosome arms from heterochromatic pericentromeres. Reciprocal perturbation of HP1a•H3K9 binding, using a point mutation in the HP1a chromodomain or replacement of the replication-dependent H3 with H3K9R mutant histones, revealed that HP1a binding to methylated H3K9 in constitutive heterochromatin is required to restrict long-range interactions between pericentromeres and chromosome arms. Surprisingly, self-association of pericentromeric heterochromatin is largely preserved upon disruption of HP1a•H3K9 binding despite loss of pericentromeric H3K9 methylation and HP1a occupancy. Thus, the HP1a•H3K9 interaction contributes to, but does not solely drive, segregation of euchromatin and heterochromatin inside the nucleus.

overall_design: Comparative analysis of transposon and protein coding gene expression in total RNA-seq data collected from HP1a chromdomain mutant and H3.2-K9R mutant wing imaginal discs and their controls.

first: Stutzman

last: Alexis

first: Hill

last: Christina

first: Armstrong

last: Robin

first: Gohil

last: Riya

first: Duronio

last: Robert

first: Dowen

last: Jill

first: McKay

last: Daniel


title: Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms [Hi-C]

overall_design: Comparative analysis of Hi-C data collected from HP1a chromdomain mutant and H3.2-K9R mutant wing imaginal discs and their controls.

first: Christina

last: Hill

first: Robin

last: Armstrong

first: Riya

last: Gohil

first: Robert

last: Duronio

first: Jill

last: Dowen

first: Daniel

last: McKay


title: Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms[CUT&RUN]

summary: Whether and how histone post-translational modifications and the proteins that bind them drive 3D genome organization remains unanswered. Here, we evaluate the contribution of H3K9-methylated constitutive heterochromatin to 3D genome organization in Drosophila tissues. We find that the predominant organizational feature of wildtype tissues is segregation of euchromatic chromosome arms from heterochromatic pericentromeres. Reciprocal perturbation of HP1a•H3K9me binding, using a point mutation in the HP1a chromodomain or replacement of the replication-dependent histone H3 with H3K9R mutant histones, revealed that HP1a binding to methylated H3K9 in constitutive heterochromatin is required to limit contact frequency between pericentromeres and chromosome arms and regulate the distance between arm and pericentromeric regions. Surprisingly, self-association of pericentromeric regions is largely preserved despite loss of H3K9 methylation and HP1a occupancy. Thus, the HP1a•H3K9 interaction contributes to, but does not solely drive, segregation of euchromatin and heterochromatin inside the nucleus.

overall_design: Comparative analysis of CUT&RUN data collected from HP1a chromdomain mutant wing imaginal discs and their controls.


title: Whole genome sequencing of mouse sarcoma clones

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

overall_design: Primary autochthonous mouse sarcoma driven by KrasG12D, p53-/- expressing R26-Confetti reporters are sorted for different reporter tumor clones by FACS.  Genomic DNA from the sorted clones are used for whole genome sequencing (WGS).

first: Yuning

last: Tang

first: Jianhong

last: Ou

first: Benjamin

last: Alman


title: Identify H3K4Me3 occupancy on genome in Setd1a Knock out (KO) mouse undifferentiated pleomorphic sarcoma cells

summary:
As Setd1a is a methyltransferase targeting H3K4, we performed H3K4Me3 ChIP in control and Setd1a KO cell to observe the effects of Setd1a on H3K4Me3.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4Me in control mouse UPS and Setd1a KO mouse UPS cells  .

overall_design: Ga I Ban


title: Placental co-transcriptional activator Vestigial-like 1 (VGLL1) drives tumorigenesis via increasing transcription of proliferation and invasion genes [RNA-seq]

first: Heather

last: Sonnemann

overall_design: To determine the overall impact of VGLL1 expression on the transcriptomic profiles of the different cancer cells, RNAseq data from PANC10.05, BT20, and Bewo cells treated with siScramble versus siVGLL1 was compared

first: Greg

last: Lizee


title: Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms[FAIRE-seq]

first: Alexis

last: Stutzman

overall_design: Comparative analysis of FAIRE-seq data collected from HP1a chromdomain mutant wing imaginal discs and their controls.


title: Effect of depletion of Setd1a on gene expression in mouse Undifferentiated Pleomorphic Sarcoma (UPS)

summary:
To investigate the Setd1a function in the regulation of lung metastasis formation, we established mouse UPS cell lines in which each target gene has been knocked down by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse UPS cell and Setd1a KO derivatives

first: Ga

middle: I

last: Ban

first: Yu

last: Xiang


title: Dual specificity phosphatase 6 (DUSP6) deletion protects mice and reduces disease severity in autoimmune arthritis.

status: Public on May 23 2024

city: New York

first: Teresina

last: Laragione

state: NY

address: 1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Receptor tyrosine kinases (RTK) have an important role in arthritis severity and in models of rheumatoid arthritis (RA), but their regulation is not fully understood. The dual specificity phosphatase 6 (DUSP6) has been implicated in the regulation of RTK signaling, but never in the context of arthritis and autoimmunity. We used the KRN serum induced arthritis (KSIA) model of RA and show that DUSP6-/- mice were protected and had a 50% lower maximum arthritis score (P=0.006), and reduced joint damage than C57BL/6. Serum levels of IL10 were significantly increased (>two-fold), and IL6 decreased in DUSP6-/- mice. DUSP6-/- mice had increased numbers of IL10+ cells including Tr1 regulatory cells (P< 0.01). Introduction of the IL10-/- into DUSP6-/- (double KO) reversed the DUSP6-/- protection. In conclusion, this study reports a new pro-arthritic role for DUSP6. This new discovery has the potential generate a novel target for therapies for RA and inflammatory diseases.

overall_design: To investigate the role of DUSP6 in rheumatoid arthritis we studied spleen derived form WT and DUSP6-KO mice after inducing experimental arhritis. Gene expression profiling analysis obtained form RNA-seq of five different mice spleens per group.

first: Carolyn

last: Harris

first: Natasha

last: Rice

first: Percio

last: Gulko


title: COMPASS complex inhibition targets the metastasis initiating cell in undifferentiated pleomorphic sarcoma

first: Aenjamin

first: Joy

first: Vijitha

last: Puviindran


title: Naringenin modulates the NO-cGMP-PKG signaling pathway through AKT binding to enhance osteogenic differentiation in hPDLSCs

city: Luzhou

first: Xiaomei

last: Xu

state: None Selected

address: China

institute: Southwest medical univercity

summary: Naringenin (NAR) is a prominent flavanone, and it has been recognized for its capacity to promote osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs) in prior research. The present study aimed to explore how NAR promotes the osteogenic differentiation of hPDLSCs and to assess its efficacy in repairing alveolar bone defects. In the present study, the protein-protein interaction (PPI) network of NAR action was established by mRNA sequencing and network pharmacological analysis. Gene and protein expression were evaluated by PCR and western blotting. Alizarin red and alkaline phosphatase staining were employed to observe the osteogenic capacity of hPDLSCs, and immunofluorescence was used to examine the co-localization of NAR molecular probes and AKT in cells. Repair of mandibular defects was assessed by micro computed tomography (micro-CT), Masson staining and immunofluorescence. Additionally, computer simulation docking software was utilized to determine the binding affinity of NAR to the target protein AKT. The results demonstrated that activation of the nitric oxide (NO)-cyclic guanosine monophosphate (cGMP)-protein kinase G (PKG) signaling pathway promoted the osteogenic differentiation of hPDLSCs. Inhibition of AKT, endothelial nitric oxide synthase and soluble guanylate cyclase individually attenuated NAR’s ability to promote the osteogenic differentiation of hPDLSCs. Micro-CT and Masson staining revealed more new bone formation at the defect site in the NAR gavage group. Immunofluorescence assays confirmed upregulated expression of Runt-related transcription factor 2 and osteopontin in the NAR gavage group. In conclusion, the present study suggests that NAR promotes the osteogenic differentiation of hPDLSCs by activating the NO-cGMP-PKG signaling pathway through its binding to AKT.

overall_design: We did transcriptome sequencing of human periodontal stem cells in naringenin-treated group and control group.

first: XIAOMEI

last: XU

first: SHENGHONG

last: LI


title: Gene therapy for glaucoma using a combination targeting multiple genes with CRISPR-CasRx

city: Shanghai

first: Jinhai

last: Huang

address: 83 Fenyang Road, Xuhui District

institute: EYE & ENE Hospital of Fudan University

summary: Glaucoma affects approximately 80 million individuals worldwide, a condition for which current treatment options are inadequate. The primary risk factor for glaucoma is elevated intraocular pressure, which is currently the only controllable treatment approach. Elevated intraocular pressure is determined by the balance between the secretion and outflow of aqueous humor (AH). Utilizing CRISPR Cas9 to disrupt the expression of the AQP1 protein, which decreases the ciliary AH secretion, resulted in an approximate 22% reduction in intraocular pressure. Nevertheless, the effectiveness of single-gene therapies is limited. To address this limitation, we conducted experiments using two mouse models of ocular hypertension. Our findings indicate that reducing the expression of the genes Rock1 and Rock2, which are associated with the outflow of AH at the trabecular meshwork (TM), as well as the genes Aqp1 and Adrb2, which are related to the generation of AH at the ciliary body (CB), can significantly reduce intraocular pressure and provide protection to the retina ganglion cells (RGCs), ultimately delaying disease progression. In addition, we elucidated the mechanisms by which the knockdown of Rock1 and Rock2, or Aqp1 and Adrb2, reduces the IOP and secures RGCs by single-cell sequencing.

overall_design: The glucocorticoid-induced ocular hypertension model was prepared for single-cell RNA sequence. 10 weeks after mold and virus injection, eyes were surgically removed from the mice and trimmed, then surgical scissors were used to take samples 1mm before and after the ora serrata immediately and kept in a special preservation solution. All operations were performed on ice. The samples were delivered to CapitalBio Technology (Beijing, China) and sequenced for analysis.

first: Zhenhai

last: Zeng

first: Zhilin

last: Zou

first: Mingyu

last: Yao

first: Siheng

last: Li


title: High-throughput single-molecule long-read RNA sequencing analysis of tissue-specific genes and isoforms in lettuce (Lactuca sativa L.)

city: Guangzhou

first: Zhuoxing

last: Shi

state: GD

address: #7 Jinsui Road, Tianhe District

department: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: This study utilized the HIT-ISOseq method for high-throughput sequencing of RNA isoforms across multiple lettuce samples, generating millions of long reads per PacBio Sequel II SMRT Cell. Analysis of six tissue types revealed tissue-specific gene expression and RNA isoforms, facilitating updates to the lettuce reference genome annotation with expanded functional annotations.

overall_design: The experiment involved two samples each of lettuce leaves, roots, and stems. After RNA extraction and cDNA amplification, PacBio sequencing libraries were constructed using the HIT-ISOseq method. Each sample was tagged with a barcode SMRTbell adapter and sequenced in HiFi mode.


title: ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity [OE_MCF7]

city: Pamplona

first: Mirja

last: Rotinen

state: Navarre

address: Avenida Barañain s/n

department: Health Sciences

country: Spain

institute: Public University of Navarre

summary: Tumor heterogeneity complicates patient treatment and can be due to transitioning of cancer cells across phenotypic cell states. This process is associated with the acquisition of independence from an oncogenic driver, such as the estrogen receptor (ER) in breast cancer, resulting in tumor progression, therapeutic failure and metastatic spread. Here we identify the transcription factor ONECUT2 (OC2) as a lineage plasticity regulator of breast cancer (BC) that suppresses the estrogen axis and promotes luminal to basal transition. OC2 is highly expressed in a substantial subset of hormone receptor negative human BC tumors and is associated with poor clinical outcome, lymph node metastasis and heightened clinical stage. We also show that OC2 is required for cell growth and survival in metastatic BC models and that it can be targeted with a small molecule inhibitor providing a novel therapeutic strategy for patients with OC2 active tumors.

overall_design: To investigate the role of the transcription factor OC2 in the dynamic conversion between different molecular subtypes in  breast cancer, we performed RNA-Seq in MCF-7 and BT-474 cell lines after enforced expression of OC2 (OC2-OE vs C).


title: ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity

summary:
Purpose: Tumor heterogeneity complicates patient treatment and can be due to transitioning of cancer cells across phenotypic cell states. This process is associated with the acquisition of independence from an oncogenic driver, such as the estrogen receptor (ER) in breast cancer (BC), resulting in tumor progression, therapeutic failure and metastatic spread. The transcription factor ONECUT2 (OC2) has been shown to be a master regulator protein of metastatic castration-resistant prostate cancer (mCRPC) tumors that promotes lineage plasticity to a drug-resistant neuroendocrine (NEPC) phenotype. Here, we investigate the role of OC2 in the dynamic conversion between different molecular subtypes in BC.

Methods: We analyze OC2 expression and clinical significance in BC using public databases and immunohistochemical staining. In vitro, we perform RNA-Seq, RT-qPCR and western-blot after OC2 enforced expression. We also assess cellular effects of OC2 silencing and inhibition with a drug-like small molecule in vitro and in vivo.

Results: OC2 is highly expressed in a substantial subset of hormone receptor negative human BC tumors and tamoxifen-resistant models, and is associated with poor clinical outcome, lymph node metastasis and heightened clinical stage. OC2 inhibits ER expression and activity, suppresses a gene expression program associated with luminal differentiation and activates a basal-like state at the gene expression level. We also show that OC2 is required for cell growth and survival in metastatic BC models and that it can be targeted with a small molecule inhibitor providing a novel therapeutic strategy for patients with OC2 active tumors.

Conclusions: The transcription factor OC2 is a driver of BC heterogeneity and a potential drug target in distinct cell states within the breast tumors.

overall_design: Refer to individual Series


title: ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity [OE_BT474]

overall_design: To investigate the role of the transcription factor OC2 in the dynamic conversion between different molecular subtypes in  breast cancer, we performed RNA-Seq in MCF-7 and BT-474 cell lines after enforced expression of OC2 (OE vs C).


title: The establishment of a DNA replication timing program in the early embryo.

city: København

first: Jason

middle: A

last: Halliwell

address: Blegdamsvej 3B

institute: The University of Copenhagen

summary: Single Embryo Repli-Seq was utilized to investigate the replication timing in zygotes and 2-cell cleavage stage embryos. The aim was to understand the temporal progression of DNA replication during the early stages of embryonic development in mammals.

overall_design: The replication timing of zygotes and 2-cell stage embryos was analyzed using Single Cell RepliSeq.

first: Eva

last: Hoffmann

first: Adnan

last: Hashim

first: John

last: Dahl

first: Javier

last: Gonzalez

first: Mads

last: Lerdrup


title: Central nervous system-associated macrophages modulate the immune response following stroke in aged mice

status: Public on May 22 2024

city: Caen

first: Damien

last: Levard

address: Bd Henri Becquerel

country: France

institute: Inserm U1237 PhIND

summary: To study the differential role of central nervous system-associated macrophages (CAMs) in neuroinflammation after stroke between young and aged mice, we FACS sorted CD3-CD11b+CD45+CD206+ CAMs from brains of C57BL/6 mice aged 2 months (young) and 18 months (old)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CNS-associated macrophages from C57BL/6 mice aged 2 months (young) or 18 months (aged)

first: Levard

last: Damien