title: Intestinal epithelial cells (RYU) and Mesenchymal stromal cells (LONG)

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary: The columnar epithelial cells comprising the intestinal tract, stomach, and uterus can be cultured in vitro as organoids or in adherent culture. However, the proliferation of these columnar epithelial cells in adherent culture is limited. Likewise, human pluripotent stem cell (hPSC)-derived intestinal epithelial cells do not show extensive or clonal propagation in vitro. In this study, we induced proliferation of hPSC-derived small intestinal epithelium for a longer time by utilizing mesenchymal stromal cells derived from self-organized intestinal organoids as feeders. The proliferating cells exhibited columnar form, microvilli and glycocalyx formation, and cell polarity, as well as expression of drug-metabolizing enzymes and transporters. It is noteworthy that small intestinal epithelial stem cells cannot be cultured in adherent culture alone, and the stromal cells cannot be replaced by other feeders. Organoid-derived mesenchymal stromal cells resemble the trophocytes essential for maintaining small intestinal epithelial stem cells and play a crucial role in adherent culture. The high proliferative expansion, productivity, and functionality of hPSC-derived small intestinal epithelial stem cells could have potential applications in pharmacokinetic and toxicity studies and regenerative medicine.

overall_design: Comprehensive gene expression analysis of small intestinal epithelial cells and mesenchymal stromal cells derived from human pluripotent stem cells (hESC or hiPSC) was performed. We also prepared a group where small intestinal epithelial cells were treated with puromycin to kill mesenchymal stromal cells used as feeder cells. Adult human small intestine and hESC cell-derived hepatocyte-like cells were used as controls.

first: JunLong

last: Chen

first: Shinichiro

last: Horiuchi

first: So

last: Kuramochi

first: Tomoyuki

last: Kawasaki

first: Hayato

last: Kawasumi

first: Saeko

last: Akiyama

first: Tomoki

last: Arai

first: Kenichi

last: Morinaga

first: Tohru

last: Kimura

last: Kiyono

first: Hidenori

last: Akutsu

first: Seiichi

last: Ishida


title: Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via regulation of key regenerative pathways (RNA-Seq I)

status: Public on Dec 22 2023

city: Tampa

first: Xuewei

last: Wang

state: FL

address: 4001 E Fletcher Ave, ALZ 339

department: Molecular Medicine

country: USA

institute: University of South Florida

type: Expression profiling by high throughput sequencing

summary: Current treatments for neurodegenerative diseases and neural injuries fall short of success. One primary reason is that neurons in the mammalian central nervous system (CNS) lose their regeneration ability as they mature. Here, we investigated the role of Ezh2, a histone methyltransferase, in regulation of mammalian axon regeneration. We found that Ezh2 declined in the mouse nervous system during maturation but was upregulated in adult dorsal root ganglion neurons to support spontaneous axon regeneration following peripheral nerve injury. In addition, overexpression of Ezh2 in retinal ganglion cells in the CNS promoted optic nerve regeneration via both histone methylation-dependent and -independent mechanisms. Further investigation revealed that Ezh2 supported axon regeneration by systematically silencing the transcription of genes regulating synaptic function and inhibiting axon regeneration, while simultaneously activating various axon regeneration promoting factors. In particular, our study demonstrated that the GABA transporter 2 encoded by the gene Slc6a13 acted downstream of Ezh2 to control axon regeneration. Our study suggested that modulating chromatin accessibility was a promising strategy to promote CNS axon regeneration.

overall_design: To study how Ezh2 supports axon regeneration of retinal ganglion cells, we profiled the transcriptomic changes in retinal ganglion cells induced by Ezh2 overexpression with RNA-seq. We intravitreally injected AAV2-GFP (control) or AAV2-Ezh2 and crushed the optic nerve after two weeks. Three days after the optic nerve crush, retinal ganglion cells were enriched from dissociated retinal cells.

first: Xue-Wei

first: Shu-Guang

last: Yang

first: Ming-Wen

last: Hu

first: Rui-Ying

first: Chi

last: Zhang

first: Anish

middle: R

last: Kosanam

first: Arinze

middle: J

last: Ochuba

first: Jing-Jing

last: Jiang

first: Ximei

last: Luo

first: Yun

last: Guan

first: Jiang

last: Qian

first: Chang-Mei

last: Liu

first: Feng-Quan

last: Zhou


title: BTLA contributes to acute-on-chronic liver failure infection and mortality through CD4+ T-cell exhaustion

status: Public on Dec 21 2023

city: Quanzhou

first: Xueping

last: Yu

state: Fujian

address: No. 250 East Street

department: Infection Disease

country: China

institute: Fujian Medical University Affiliated First Quanzhou hospital

summary: B- and T-lymphocyte attenuator (BTLA) levels are increased in patients with hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF). This condition is characterized by susceptibility to infection and T-cell immune exhaustion. However, whether BTLA can induce T-cell immune exhaustion and increase the risk of infection remains unclear. Here, we report that BTLA levels are significantly increased in the circulating and intrahepatic CD4+ T cells from patients with HBV-ACLF, and are positively correlated with disease severity, prognosis, and infection complications. BTLA levels are upregulated by the IL-6 and TNF signaling pathways, and are abolished or partially weakened by IL-6 and TNF inhibitors. Antibody crosslinking of BTLA activated the PI3K-Akt pathway to inhibit the activation, proliferation, and cytokine production of CD4+ T cells while promoting their apoptosis. In contrast, BTLA knockdown promoted their activation and proliferation.  BTLA-/- ACLF mice exhibited increased cytokine secretion, and reduced mortality and bacterial burden. The administration of a neutralizing anti-BTLA antibody reduced Klebsiella pneumoniae load and mortality in ACLF mice. These data help elucidate HBV-ACLF pathogenesis and aid in identifying novel drug targets.

overall_design: To explore the mechanisms by which BTLA induces CD4+ T-cell exhaustion in HBV-ACLF patients and to seek drug targets for recovering the function of CD4+ T cells, we analyzed gene expression profiles in PBMC from NC, CHB, and HBV-ACLF patients with or without BTLA Ab treatment through next-generation high-throughput RNA-Seq.

first: Feifei

first: Zhongliang

last: Shen

first: Yao


title: Impact of the vitamin B12 on the transcriptional regulation of the Mycobacterium tuberculosis Complex

city: Zaragoza

first: Jesus

last: Gonzalo-Asensio

state: Zaragoza

address: C/ Domingo Miral sn

department: Microbiology

country: Spain

institute: University of Zaragoza

summary: The transcriptome in response to vitamin B12 was interrogated in three M. tuberculosis Complex species: M. tuberculosis H37Rv, M. tuberculosis GC1237, and M. bovis AF2122/97. Examination of the core B12 transcriptome resulted in a robust differential regulation of 7 genes in the three species analysed

sample_organism: Mycobacterium tuberculosis variant bovis

overall_design: Each Mycobacterium tuberculosis heterotypic synonym (M. tuberculosis H37Rv, M. tuberculosis GC1237, and M. bovis AF2122/97) was grown in standard laboratory media supplemented with or without vitamin B12. Two replicates of each strain were processed in each condition (2 with B12 and 2 without B12 for each strain). RNA was extracted and subjected to RNA-seq. Expression profiles for each DNA strand (plus and minus) were obtained for the three species analysed.

first: Jesús

first: Elena

last: Campos-Pardos


title: A TLR4/Traf6-dependent signaling pathway mediates NCoR co-activator complex formation for inflammatory gene activation

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A TLR4/Traf6-dependent signaling pathway mediates NCoR co-activator complex formation for inflammatory gene activation [RNA-seq]

summary:
To investigate the cooperative function NCoR/HDAC3/PGC1β complex in TLR4-regulated inflammatory genes, we used bone marrow-derived macrophages treated with or without KLA.
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 bone marrow-derived macrophages treated with or without KLA

first: Yohei

last: Abe

first: Eric

last: Kofman

first: Zhengyu

last: Ouyang

first: Grisel

last: Cruz-Becerra

first: Nathanael

last: Spann

first: Jason

middle: S

last: Seidman

first: Ty

middle: D

last: Troutman

first: Joshua

last: Stender

first: Havilah

last: Taylor

first: Weiwei

last: Fan

first: Verena

middle: M

last: Link

first: Zeyang

first: Juro

last: Sakai

first: Michael

last: Downes

first: Ronald

last: Evans

first: James

middle: T

last: Kadonaga

middle: G

last: Rosenfeld

middle: K


title: A TLR4/Traf6-dependent signaling pathway mediates NCoR co-activator complex formation for inflammatory gene activation [ChIP-seq]

first: Christopher

last: Glass

summary:
To investigate the genomic localization of NCoR/HDAC3/PGC1β complex and the enhancer/promoter activity in inflammatory genes, we used NCoR KO or PGC1β KO bone marrow-derived macrophages and Traf6 siRNA knockdown bone marrow-derived macrophages.
We then performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27ac, NCoR, HDAC3, PGC1β, ERK1, p65, Fosl2, PU.1 and p300.

overall_design: Genomic localization of NCoR/HDAC3/PGC1β and transcription factors with H3K27 acetylation depending on TLR4 signal

last: Shen


title: TRPS1 modulates chromatin accessibility to regulate estrogen receptor (ER) binding and ER target gene expression in luminal breast cancer cells (3 clone PRO-seq)

city: Charlottesville

first: Thomas

last: Scott

state: VA

address: 1340 Jefferson Park Ave, Pinn Hall 6225

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: Breast cancer is the most frequently diagnosed cancer in women. The most common subtype is luminal breast cancer, which is typically driven by estrogen receptor alpha (ER), a transcription factor (TF) that activates many genes required for proliferation. Multiple effective therapies target this pathway, but individuals often develop resistance. Thus, there is a need to identify additional targets that regulate ER activity and contribute to breast tumor progression. TRPS1 is a repressive GATA-family TF that is overexpressed in breast tumors. Common genetic variants in the TRPS1 locus are associated with breast cancer risk, and luminal breast cancer cell lines are particularly sensitive to TRPS1 knockout. However, we do not know how TRPS1 regulates target genes to mediate these breast cancer patient and cellular outcomes. We introduced an inducible degron tag into the native TRPS1 locus within a luminal breast cancer cell line to identify the direct targets of TRPS1 and determine how TRPS1 mechanistically regulates gene expression. We acutely deplete over eighty percent of TRPS1 from chromatin within 30 minutes of inducing degradation. We find that TRPS1 regulates transcription of hundreds of genes, including those related to estrogen signaling. TRPS1 directly regulates chromatin structure, which causes ER to redistribute in the genome. ER redistribution causes direct repression of ER targets and indirectly activates dozens of ER target genes. Downstream from these primary effects, TRPS1 depletion represses cell cycle-related gene sets and reduces cell doubling rate. Finally, we show that high TRPS1 activity, calculated using a gene expression signature defined by primary TRPS1-regulated genes, is associated with worse breast cancer patient prognosis. Taken together, these data suggest a model in which TRPS1 modulates the activity of other TFs, both activating and repressing transcription of genes related to cancer cell fitness.

overall_design: 3 independent clones of T47D cells with TRPS1 tagged with an inducible degron tag were treated with a drug to induce TRPS1 degradation for 90 minutes, and collected for PRO-seq

last: Guertin


title: A TLR4/Traf6-dependent signaling pathway mediates NCoR co-activator complex formation for inflammatory gene activation [ATAC]

summary:
To investigate the enhancer/promoter activity in TLR4-regulated inflammatory genes, we used bone marrow-derived macrophages treated with or without KLA.
We then analyzed open chromatin regions obtained from ATAC-seq data.

overall_design: ATAC peak-associated H3K27ac analysis for active enhancer/promoter regions

first: Yohei

last: Abe

first: Eric

last: Kofman

last: Ouyang

last: Cruz-Becerra


title: Single nuclei transcriptomic profiling of adult Drosophila upon oxidative stress

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

country: Germany

institute: Freiburg Medical Center

summary: Environmental factors, infection, or injury, can cause oxidative stress in diverse tissues and loss of tissue homeostasis. Effective stress response cascades, conserved from invertebrates to mammals, ensure reestablishment of homeostasis and tissue repair. Hemocytes, the Drosophila blood-like cells, rapidly respond to oxidative stress by immune activation. However, the precise signals how they sense oxidative stress and integrate these signals to modulate their immune response during oxidative stress are ill-defined. Furthermore, it remains unclear if all hemocytes respond similarly to oxidative stress or if there is a specification in distinct subsets. here, we employes single nuclei RNA-sequencing (snRNA-seq) to elcuidate the induced transcriptomic chnages in hemocytes and other cell types by Paraquat feeding compared to control food. Paraquat induces a pronounced oxidative stress response in Drosophila and we used this mdoel to study the diversification of immune cells upon this immune challenge in the adult fly.

overall_design: The data sets include two samples of sorted nuclei from flies on control food (100 flies/sample) and 2 samples on 15mM paraquat food (100 flies/sample)

first: Katrin

last: Kierdorf

first: Fabian

last: Hersperger

first: Chintan

last: Chhatbar


title: Human cardiac organoids to model COVID‐19 cytokine storm induced cardiac injuries

status: Public on Dec 20 2023

city: Charleston

first: Dimitrios

last: Arhontoulis

state: South Carolina

address: 68 President St

department: Bioengineering

institute: MUSC

summary: Acute cardiac injuries occur in 20%–25% of hospitalized COVID‐19 patients. Herein, we demonstrate that human cardiac organoids (hCOs) are a viable platform to model the cardiac injuries caused by COVID‐19 hyperinflammation. As IL‐1β is an upstream cytokine and a core COVID‐19 signature cytokine, it was used to stimulate hCOs to induce the release of a milieu of proinflammatory cytokines that mirror the profile of COVID‐19 cytokine storm. The IL‐1β treated hCOs recapitulated transcriptomic, structural, and functional signatures of COVID‐19 hearts. The comparison of IL‐1β treated hCOs with cardiac tissue from COVID‐19 autopsies illustrated the critical roles of hyper‐inflammation in COVID‐19 cardiac insults and indicated the cardioprotective effects of endothelium. The IL‐1β treated hCOs thus provide a defined and robust model to assess the efficacy and potential side effects of immunomodulatory drugs, as well as the reversibility of COVID‐19 cardiac in- juries at baseline and simulated exercise conditions.

first: Charles

last: Kerr

first: Nathaniel

last: Hyams

first: Ying

last: Mei


title: Control of lateral root formation by rapamycin-induced dimerization of engineered RGI/BAK1 and by BIR3 chimera

city: Gwangju

first: Jungmook

last: Kim

address: 77, yongbong-ro

department: Bioenergy science and technology

country: South Korea

institute: Chonnam national university

summary: Leucine-rich repeat receptor kinases (LRR-RKs) play a pivotal role in diverse aspects of growth, development, and immunity in plants by sensing extracellular signals. Typically, LRR-RKs are activated through the ligand-induced interaction with a SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) coreceptor, triggering downstream signaling. ROOT MERISTEM GROWTH FACTOR1 (RGF1) INSENSITIVEs (RGIs) LRR-RLK receptors promote primary root meristem activity while inhibiting lateral root (LR) development in response to RGF peptide. In this study, we employed rapamycin-induced dimerization (RiD) and BAK1-INTERACTING RECEPTOR-LIKE KINASE3 (BIR3) chimera approaches to explore the gain-of-function of RGI1, RGI4, and RGI5. Rapamycin induced the association of cytosolic kinase domains (CKDs) of RGI1 and the BAK1 coreceptor, activating both mitogen-activated protein kinase 3 (MPK3) and MPK6. Rapamycin significantly inhibited LR formation in RiD-RGI1/RGI4/RGI5-BAK1 plants. Using transgenic Arabidopsis expressing RGI1CKD fused to the BIR3-LRR chimera under estradiol control, we observed a substantial reduction in LR density upon β-estradiol treatment. Additionally, we identified a decrease in root gravitropism in BIR3 chimera plants. In contrast, RiD-RGI/BAK1 plants did not exhibit defects in root gravitropism, implying the importance of combinatorial interactions between RGIs and SERK coreceptors in the inhibition of root gravitropism. Constitutive activation of RGIs with BAK1 in RiD-RGI/BAK1 plants by rapamycin treatment resulted in the inhibition of primary root growth, resembling the inhibitory effects observed with high concentrations of phytohormones on primary root elongation. Our findings highlight that the interactions between CKDs of RGIs and BAK1, constitutively induced by rapamycin or BIR3 chimera, efficiently control LR development.

overall_design: Arabidopsis plants at 7 days after germination were transferred on a filter paper containing 1/2 MS solution with mock, 100 nM rapamycin (for RiD-RGI5/BAK1) or 1 µM rapamycin (for RiD-RGI1/BAK1) and incubated for 4 hours with gentle shaking in light at 23°C. Wild-type (Col-0) plants were treated with 100 nM RGF1 peptide for 4 hours. RNA-seq and data analyses were performed as described previously (Jeon et al. 2023. Journal of Experimental Botany, 74, 1475–1488)


title: Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial-Mesenchymal Transition [RNA-seq]

city: Shenzhen

first: Wei

last: Chen

state: Guangdong

address: No. 1088 Xueyuan Avenue, Nanshan District

department: School of Life Sciences

institute: Southern University of Science and Technology

summary: Epithelial-mesenchymal transition (EMT) is a fundamental cellular process frequently hijacked by cancer cells to promote tumor progression, especially metastasis. EMT is orchestrated by a complex molecular network acting at different layers of gene regulation. In addition to transcriptional regulation, post-transcriptional mechanisms may also play a role in EMT. Here, we performed a pooled CRISPR screen analyzing the influence of 1547 RNA binding proteins (RBPs) on cell motility in colon cancer cells and identified multiple core components of P-bodies (PBs) as negative modulators of cancer cell migration. Further experiments demonstrated that PB depletion by silencing DDX6 or EDC4 could activate hallmarks of EMT thereby enhancing cell migration in vitro as well as metastasis formation in vivo. Integrative multi-omics analysis revealed that PBs could repress the translation of the EMT-driver gene HMGA2, which contributed to PB-meditated regulation of EMT. This mechanism is conserved in other cancer types. Furthermore, endoplasmic reticulum (ER) stress was an intrinsic signal that induced PB disassembly and translational derepression of HMGA2. Taken together, this study has identified a function of PBs in the regulation of EMT in cancer.

overall_design: Gene expression profiling analysis of RNA-seq data for HCT116 cell line and its KO/KD derivatives (DDX6 KO, EDC4 KO, DDX6 KO shHMGA2).

first: Mengran

last: Wang

first: Li

last: Zhang

first: Jiao

last: Yang

first: Liang

last: Fang


title: Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial-Mesenchymal Transition [RIP-seq]

overall_design: eCLIP-seq data analysis of DDX6 for HCT116 cell line in two replicates.


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [Bisulfite-seq]

city: Milano

first: Sara

last: Valsoni

state: MI

address: via Olgettina 60

department: TIGET

country: Italy

institute: SR-TIGET

type: Methylation profiling by high throughput sequencing

summary: Permanent epigenetic silencing with programmable editors equipped with transcriptional repressors holds great promise for the treatment of human diseases. However, to unlock its full therapeutic potential, a formal proof of durable epigenetic silencing upon transient editors’ delivery in vivo is needed. To this end, we targeted here Pcsk9, a hepatocyte-expressed gene involved in cholesterol homeostasis. In vitro screening of different editors’ designs indicated zinc finger proteins as the best-performing DNA binding platform to efficiently silence murine Pcsk9, with minimal genome-wide transcriptional and epigenetic perturbations. A single administration of lipid nanoparticles loaded with the editors’ mRNAs halved circulating levels of Pcsk9 for nearly 1 year  in mice. Notably, Pcsk9 silencing and accompanying epigenetic repressive marks persisted following forced also upon liver regeneration, further corroborating heritability of the newly installed epigenetic state. This study lays the foundation for the development of in vivo therapeutics  modalities based on epigenetic silencing.

overall_design: Comparative analysis of in vivo methylation status of Pcsk9 promoter in kidney, lung, spleen and pancreas from mice treated with EvoETRs 8 targeting Pcsk9 and PBS

first: Martino

middle: A

last: Cappelluti

first: Valeria

last: Mollica Poeta

first: Piergiuseppe

last: Quarato

first: Ivan

last: Merelli

first: Angelo

middle: L

last: Lombardo


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [RNAseq_2]

overall_design: Comparative analysis of transcriptome from Hepa 1-6 cells treated with ZFP-based epi-editors, targeting Pcsk9 promoter. As a control, cells transfected with the mRNA of a GFP were used

last: Poeta


title: Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial-Mesenchymal Transition

overall_design: Gene expression profiling analysis of RNA-seq data for HCT116 cell line and its KO/KD derivatives (DDX6 KO, EDC4 KO, DDX6 KO shHMGA2). The eCLIP-seq data analysis of DDX6 for HCT116 cell line in two replicates.


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [targetBSseq_offTargets]

overall_design: Comparative analysis of Arid1b e Shroom1 in vitro DMR methylation status from hepatocytes treated with ZFP-ETRs targeting Pcsk9 and PBS


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [deep_sequencing_ZFPoff8]

overall_design: Comparative analysis of genome editing status of hepatocytes treated with EvoETRs 8 targeting Pcsk9 and PBS


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [targetBSseq_CpG_Pcsk9_2]

overall_design: Comparative analysis of Pcsk9 CpG island methylation status from hepatocytes treated with ZFP-ETRs targeting Pcsk9, EvoETRs 8 targeting Pcsk9 and PBS


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [targetBSseq_DMRs_2]

overall_design: Comparative analysis of in vitro DMR methylation status from hepatocytes treated with EvoETRs 8 targeting Pcsk9 and PBS


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [targeBSseq]

overall_design: Comparative analysis of Pcsk9 CpG island methylation status of hepotocyte extracted from mice treated with ZFP-ETRs pre- and post-partial hepatectomy procedure.


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [WGMS]

overall_design: Comparative analysis of whole genome methylation status from Hepa 1-6 cells treated with ZFP-based or dCas9-based epi-editors, targeting Pcsk9 promoter. Three controls was added: i) untargeted ETRs, i.e. ZFP-based ETRs targeting the GFP; ii) Cas9 and a sgRNA targeting Pcsk9 exon 1; iii) cells transfected with the mRNA of a GFP


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [RNA-seq]

overall_design: Comparative analysis of transcriptome from Hepa 1-6 cells treated with ZFP-based or dCas9-based epi-editors, targeting Pcsk9 promoter. Three controls was added: i) untargeted ETRs, i.e. ZFP-based ETRs targeting the GFP; ii) Cas9 and a sgRNA targeting Pcsk9 exon 1; iii) cells transfected with the mRNA of a GFP


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [targetBSseq_DMRs]

overall_design: Comparative analysis of in vitro DMR (chr2 and chr8-B) methylation status from hepatocytes treated with EvoETRs 8 targeting Pcsk9 and PBS


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [deep_sequencing_Cas9]

overall_design: Comparative analysis of genome editing status of hepatocytes treated with Cas9 targeting Pcsk9 and PBS


title: Multi-omic and spatial dissection of immunotherapy response groups in non-small cell lung cancer (NSCLC)

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

summary: DSP RNA profiling was performed on a cohort of immunotherapy treated NSCLC patients

overall_design: Differential expression was performed in tumour and stromal compartments for response to immunotherapy outcome

first: James

last: Monkman


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [WGMS_invitro_revision]

overall_design: Comparative analysis of whole genome methylation status from Hepa 1-6 cells treated with ZFP-based epi-editors, targeting Pcsk9 promoter


title: Theileria parasites sequester host eIF5A to escape elimination by host-mediated autophagy

status: Public on Dec 19 2023

city: Paris

first: Aristeidis

last: Panagiotou

address: 35 Rue Hélène Brion

department: UMR7216 Epigenetics and Cell Fate

country: France

institute: CNRS

summary: Intracellular pathogens develop elaborate mechanisms to survive within the hostile environments of host cells. Theileria parasites infect bovine leukocytes and cause devastating diseases in cattle in developing countries.  Theileria spp. have evolved sophisticated strategies to hijack host leukocytes, inducing proliferative and invasive phenotypes characteristic of cell transformation. Intracellular Theileria parasites secrete proteins into  the host cell and recruit host proteins to induce oncogenic signaling for parasite survival. It is unknown how Theileria parasites evade host cell defense mechanisms, such as autophagy, to survive within host cells. Here, we show that Theileria annulata parasites sequester the host eIF5A protein to their surface to escape elimination by autophagic processes. We identified a small-molecule compound that reduces parasite load by inducing autophagic flux in host leukocytes, thereby uncoupling Theileria parasite survival from host cell survival. We took a chemical genetics approach to show that this compound induced host autophagy mechanisms and the formation of autophagic structures via AMPK activation and the release of the host protein eIF5A which is sequestered at the parasite surface. The sequestration of host eIF5A to the parasite surface offers a strategy to escape elimination by autophagic mechanisms. These results show how intracellular pathogens can avoid host defense mechanisms and identify a new anti-Theileria drug that induces autophagy to target parasite removal.

overall_design: 5x10^6 cells (BL3 or TBL3) were used as starting material to extract RNA. In this dataset, we explore the transcriptomes of 4 conditions: - Uninfected BL3 cells - Theileria annulata-Infected TBL3 cells - BL3 cells, treated with MC2646 4μM, 24 hours - TBL3 cells, treated with MC2646 4μM, 24 hours

first: Marie

last: Villares

first: Nelly

last: Lourenço

last: Ktorza

first: Jeremy

last: Berthelet

first: Aurelie

last: Richard

first: Angélique

last: Amo

first: Yullianna

last: Koziy

first: Souhila

last: Medjkane

first: Sergio

last: Valente

first: Rossella

last: Fioraventi

first: Catherine

last: Durieu

first: Laurent

last: Lignière

first: Guillaume

last: Chevreux

first: Antonello

last: Mai

first: Jonathan

middle: B

last: Weitzman


title: Biphasic Regulation of Epigenetic State by Matrix Stiffness during Cell Reprogramming [ATAC-seq]

city: Los Angeles

first: Song

last: Li

state: California

address: 404 Westwood Plaza, Eng VI

institute: UCLA

summary: In this study, we investigate how matrix stiffness regulates chromatin reorganization and cell reprogramming, and find that matrix stiffness acts as a biphasic regulator of epigenetic state and fibroblast-to-neuron conversion efficiency, maximized at an intermediate stiffness of 20 kPa. ATAC-sequencing analysis shows the same trend of chromatin accessibility to neuronal genes at these stiffness levels. Concurrently, we observe peak levels of histone acetylation and histone acetyltransferase (HAT) activity in the nucleus on matrices at 20 kPa, and inhibiting HAT activity abolishes matrix stiffness effects. G-actin and cofilin, the co-transporters shuttling HAT into the nucleus, rises with decreasing matrix stiffness; however, reduced importin-9 on soft matrices limits nuclear transport. These two factors result in a biphasic regulation of HAT transport into the nucleus, which is directly demonstrated on matrices with dynamically tunable stiffness. These findings unravel a mechanism of the mechano-epigenetic regulation that is valuable for cell engineering in disease modeling and regenerative medicine applications.

overall_design: To investigate the effect of matrix stiffness on the epigenetic state during induced neuronal reprogramming, mouse dermal fibroblasts were cultured on polyacrylamide hydrogels of varying stiffness or glass, which served as control, for 3 days and then samples were collected for ATAC-seq.

first: Yang

last: Song

first: Jennifer

last: Soto

first: Yifan

last: Wu


title: NRF2 Is Required for Neonatal Beta-Cell Growth by Maintaining Redox Balance and Promoting Mitochondrial Biogenesis and Function

city: Duarte

first: Sharon

last: Baumel Alterzon

address: 1500 East Duarte road

department: Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute

institute: City of Hope

summary: Due to the limited expression of several antioxidant enzymes, β-cells are highly vulnerable to high ROS levels, which can lead to the reduction of functional β-cell mass.     During early postnatal ages, both human and rodent β-cells go through a burst of proliferation that quickly declines with age. Here we discovered that the expression of the master antioxidant regulator, Nrf2, is increased during this postnatal burst of β-cell proliferation in humans. Additionally, data from β-cell specific Nrf2 deletion in mice demonstrated that Nrf2 is required for β-cell proliferation, β-cell survival, β-cell identity and β-cell mass expansion at early stages of life. Daily administration of antioxidant NAC to newborn mice showed that Nrf2 mechanism of action strongly relies on maintaining normal redox balance. Interestingly, RNAseq of islets isolated from β-cell specific Nrf2 deleted mice suggests that Nrf2 regulates neonatal β-cell proliferation by promoting mitochondrial ATP synthesis. Our study highlights Nrf2 as an essential transcription factor for maintaining redox balance as well as mitochondrial biogenesis and function to support neonatal β-cell growth and for maintaining functional β-cell mass in adulthood under metabolic stress.

overall_design: To investigate mechanisms by which Nrf2 stimulates β-cell proliferation in neonatal mice islets from 7-day old β-cell specific Nrf2 deletion mouse model (βNrf2KO) vs Nrf2lox/lox mice

last: Baumel-Alterzon

first: Luca

last: Lambertini

first: Adolfo

last: Garcia-Ocaña

first: Donald

last: Scott


title: Biphasic Regulation of Epigenetic State by Matrix Stiffness during Cell Reprogramming [RNA-seq]

overall_design: To investigate the effect of matrix stiffness on the epigenetic state during induced neuronal reprogramming, mouse dermal fibroblasts were cultured on polyacrylamide hydrogels of varying stiffness or glass, which served as control, for 3 days and then samples were collected for RNA-seq.


title: Bulk RNA-seq was performed on murine Lin-Sca+Kit+ (LSK) bone marrow cells from a transgenic SCLtTA/BCR-ABL (DTG) mouse BM cells (CD45.2) in which BCR-ABL1 was expressed or not expressed

city: Glasgow

first: David

last: Vetrie

address: Wolfson Wohl Cancer Research Centre

department: Institute of Cancer Sciences

country: United Kingdom

institute: Glasgow University

summary: Bulk RNA-seq was performed on murine Lin-Sca+Kit+ bone marrow cells from a transgenic SCLtTA/BCR-ABL (DTG) mouse BM cells (CD45.2) to understand the molecular consequences of BCR-ABL1 expression on the global mRNA programme of these cells.

overall_design: Eight to twelve week old B6.SJL recipient mice (CD45.1) were irradiated with two doses of 4.25Gy, 3hrs apart and transplanted with 2 x 106 SCLtTA/BCR-ABL (DTG) mouse BM cells (CD45.2) via tail vein injection. Tetracycline (TET) was included in the drinking water for two weeks post-transplant to allow time for recovery and engraftment. Two weeks post irradiation, TET was removed for two weeks in one cohort, allowing BCR-ABL1 expression and leukaemia development (n=6; CML group), while TET administration was continued In a second cohort (n=6; CTRL group). RNA was extracted and libraries made for RNA-seq analysis. Both male and female age-matched recipient mice  were used for this study.

first: Thomas

last: Stevens

first: Mary

first: Wei

last: Liu


title: Generation of induced pluripotent stem cells from Bornean orangutans

city: Taipei

first: Wei-Ni

last: Lyu

state: Daan

address: 4th Floor, No. 81, Changxing Street

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

summary: Bornean orangutans (Pongo pygmaeus) are an endangered non-human primate species. Induced pluripotent stem cells (iPSCs) offer a promising avenue for preserving genetic resources and studying evolutionary processes. In this study, we successfully generate Bornean orangutan iPSCs (o-iPSCs) from peripheral blood mononuclear cells using Sendai virus-mediated reprogramming. Furthermore, we transform primed o-iPSCs into a naïve pluripotent state using a novel 4i/L/A culture system. The resulting naïve o-iPSCs exhibit key features similar to human naïve stem cells, including upregulation of KLF17, DNMT3L, and DPPA3/5. We also observe significant activation of the WNT signaling pathway and X chromosome reactivation in the 4i/L/A o-iPSCs. Transcriptome analysis confirmed their resemblance to human naïve embryonic stem cells. Our findings contribute to the molecular understanding of naïve o-iPSCs and provide a foundation for orangutan conservation using advanced technologies.

overall_design: To enhance their utility for developmental and therapeutic studies, we subjected the primed o-iPSCs to a transformation process to induce a naïve pluripotent state using the 4i/L/A culture system with feeder cells.


title: Expanded T lymphocytes in the cerebrospinal fluid of multiple sclerosis patients are specific for Epstein-Barr virus infected B cells

city: Houston

first: John

middle: William

last: Lindsey

state: TX

address: 6431 Fannin St, Ste 7.044 MSB, Neurology Dept

institute: University of Texas Health Science Center At Houston

summary: Our hypothesis is that a major fraction of the expanded clones of T lymphocytes in the cerebrospinal fluid (CSF) are specific for autologous EBV-infected B cells.  We obtained blood and CSF samples from 8 relapsing-remitting patients in the process of diagnosis.  We stimulated cells from the blood with autologous EBV-infected lymphoblastoid cell lines (LCL), EBV, varicella zoster virus, influenza, and candida, and sorted the responding cells with flow cytometry after 6 days.  We sequenced the RNA for T cell receptors (TCR) from CSF, unselected blood cells, and the antigen-specific cells.  We used the TCR Vβ CDR3 sequences from the antigen-specific cells to assign antigen specificity to the sequences from the CSF and blood.  LCL-specific cells comprised 13.0±4.3% (mean±standard deviation) of the total reads present in CSF and 13.3±7.5% of the reads present in blood.  The next most abundant antigen specificity was flu, which was 4.7±1.7% of the reads in the CSF and 9.3±6.6% in the blood.  The prominence of LCL-specific reads was even more marked in the top 1% most abundant CSF clones with statistically significant 47% mean overlap with LCL.

overall_design: T cell receptor sequences from cerebrospinal fluid, peripheral blood mononuclear cells (PBMC), and proliferating CD3+  cells from PBMC stimulated with Epstein-Barr virus, autologous EBV-infected cell lines, varicella zoster virus, influenza, or candida.

middle: W

first: Assaf

last: Gottlieb


title: Multi-omic and spatial dissection of immunotherapy response groups in NSCLC

first: Arutha

last: Kulasinghe

summary: Nanostring protein DSP was performed on 42 TMA cores of immunotherapy treated NSCLC patients

overall_design: DE proteins between patient response were identified in tumour and stroma compartments

first: James

last: Monkman


title: Vascular endothelial cells drive organ fibrosis by inducing the transcription factor Sox9 (scRNA-Seq I)

city: Mannheim

first: Joerg

last: Heineke

state: Baden Wuttemberg

address: Ludolf-Krehl-Str. 7-11

department: – Department of Cardiovascular Research (HKF)

institute: Medizinische Fakultät Mannheim

summary: Chronic fibrosis is a hallmark of pathologic tissue remodelling that deteriorates organ function and eventually leads to death. Although fibroblasts are typically made responsible, it was recently suggested that endothelial cells contribute to fibrosis, although the functional importance of this phenomenon remained unclear. In this study, we addressed this question by genetic manipulation of the fibrogenic HMG-box transcription factor SOX9 specifically in vascular endothelial cells. Induced transgenic overexpression of SOX9 in these cells in mice triggered extensive fibrosis, organ growth and dysfunction in the heart, lung, liver and spleen. We found an upregulation of endogenous Sox9 in endothelial cells during cardiac, lung and liver fibrosis, and endothelial specific Sox9 deletion prevented fibrosis and organ dysfunction in mouse models of systolic and diastolic heart failure, as well as in mouse bleomycin induced pulmonary and non-alcoholic steato-hepatitis (NASH) triggered liver fibrosis. Mechanistically, a combined approach of bulk and single cell RNA sequencing of endothelial cells across multiple vascular beds revealed that Sox9 promoted the expression of extracellular matrix and matrix remodelling genes, growth factors, and inflammatory mediators, which triggered the expression of extracellular matrix directly by endothelial cells, but also activated fibroblasts. As we found the upregulation of endothelial Sox9 also in failing human hearts, we propose that endothelial Sox9 could be a target for anti-fibrotic therapy.

overall_design: Cardiac EC lysates from mice with 1 M continuous endothelial Sox9 expression

first: Felix

last: Trogisch

first: Julio

last: Cordero

first: Aya

last: Abouissa

first: Merve

last: Keles


title: Vascular endothelial cells drive organ fibrosis by inducing the transcription factor Sox9 (bulk RNA-Seq IV)

overall_design: Liver EC lysates from mice with CDAA diet after endothelial Sox9 knock-out


title: Vascular endothelial cells drive organ fibrosis by inducing the transcription factor Sox9 (bulk RNA-Seq III)

overall_design: Cardiac or pulmonal EC lysates from mice with either HFpEF diet or bleomycin injection after endothelial Sox9 knock-out


title: Vascular endothelial cells drive organ fibrosis by inducing the transcription factor Sox9 (scRNA-Seq II)

overall_design: Cardiac EC lysates from mice with TAC operation after endothelial Sox9 knock-out


title: Biphasic Regulation of Epigenetic State by Matrix Stiffness during Cell Reprogramming

first: Song

last: Li

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

overall_design: Refer to individual Series


title: Vascular endothelial cells drive organ fibrosis by inducing the transcription factor Sox9


title: Vascular endothelial cells drive organ fibrosis by inducing the transcription factor Sox9 (bulk RNA-Seq I)

overall_design: Cardiac bulk or EC lysates from mice with 1 M continuous endothelial Sox9 expression


title: Durable and efficient gene silencing in vivo by hit-and-run epigenome editing

first: Sara

last: Valsoni


title: Vascular endothelial cells drive organ fibrosis by inducing the transcription factor Sox9 (bulk RNA-Seq II)

overall_design: Cardiac, pulmonal or hepatic bulk or EC lysates from mice with either 1 M continuous endothelial Sox9 expression or TAC operation after endothelial Sox9 knock-out


title: Inosine Induces Stemness Features in HA-CAR-T cells and Enhances Potency

status: Public on Dec 18 2023

city: Stanford

first: Yiyun

last: Chen

address: 265 Campus Dr Room G2105

department: Stanford Cancer Institute

institute: Stanford University

relation:
SuperSeries of: GSE250439
SuperSeries of: GSE250442


title: Inosine Induces Stemness Features in HA-CAR-T cells and Enhances Potency [RNA-seq]

summary: Adenosine (Ado) mediates immune suppression in the tumor microenvironment and exhausted CD8+ HA-CAR-T cells commonly express CD39 and CD73, which mediate proximal steps in Ado generation. Here we sought to enhance HA-CAR-T cell potency by knocking out CD39, CD73 or adenosine receptor 2a (A2aR), but observed only modest effects. In contrast, overexpression of Ado deaminase (ADA-OE), which metabolizes Ado to inosine (INO), induced stemness features and potently enhanced HA-CAR-T functionality. Similarly, and to a greater extent, exposure of HA-CAR-T cells to INO augmented HA-CAR-T cell function and induced hallmark features of T cell stemness. INO induced profound metabolic reprogramming, diminishing glycolysis and increasing oxidative phosphorylation, glutaminolysis and polyamine synthesis, and reprogrammed the epigenome toward greater stemness. Clinical scale manufacturing using INO generated enhanced potency HA-CAR-T cell products meeting criteria for clinical dosing. These results identify INO as a potent modulator of T cell metabolism and epigenetic stemness programming and deliver a new enhanced potency platform for immune cell manufacturing.

overall_design: On day 14, CD39+ and CD39- CD4+ or CD8+ subsets were isolated using a BD FACSAria cell sorter (Stem Cell FACS Core, Stanford University School of Medicine). ADA-OE, CD39KO, CD73KO, A2aRKO and AAVS1KO HA-CAR-T cells were collected at day 15 post-activation. HA-CAR-T cells cultured in regular media or in the media containing INO but not GLC were collected at day 14.

first: Dorota

last: Klysz

first: Amaury

last: Leruste

first: Katherine

last: Freitas

first: Elena

last: Sotillo

first: Crystal

last: Mackall


title: Drug repositioning of inflammatory bowel disease based on co-target gene expression signature of glucocorticoid receptor and TET2

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

summary: The glucocorticoid receptor (GR) and ten-eleven translocation 2 (TET2) respectively play a crucial role in regulating immunity and inflammation, and GR interacts with TET2. However, their syn-ergetic roles in inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), remain unclear. This study aimed to investigate the co-target gene signatures of GR and TET2 in IBD and provide potential therapeutic interventions for IBD. By integrating public data, we identified 179 GR- and TET2-targeted differentially expressed genes (DEGs) in CD and 401 in UC. These genes were closely associated with immunometabolism, inflammatory responses, and cell stress pathways. In vitro inflammatory cellular models were constructed using LPS-treated HT29 and HCT116 cells, respectively. Drug repositioning based on the co-target gene signatures of GR and TET2 derived from transcriptomic data of UC, CD, and the in vitro model were performed using the Connectivity Map (CMap). BMS-536924 emerged as a top therapeutic candidate, and its validation experiment within the in vitro inflammatory model confirmed its ef-ficacy in mitigating the LPS-induced inflammatory response. This study sheds light on the path-ogenesis of IBD from a new perspective and may accelerate the development of novel therapeutic agents for inflammatory diseases including IBD.

overall_design: To compare the similarities and differences between  two cell lines with different GR basal expression in response to LPS-induced inflammation and identify sepecific expression signatures useful for screening anti-inflammatory compounds, we utilized two types of intestinal epithelial-derived cells, HT29 and HCT116, stimulating them with 1 ug/mL LPS for 24 h. Subsequently, next-generation RNA sequencing was performed.

first: Xianglin

last: Zhao

first: Chenghao

last: Hu

first: Shuqiang

last: Ren


title: Cord blood donor characteristics determine the efficacy of IL-15 armored CAR-transduced natural killer cells against CD19-positive B cell tumors

first: Katy

last: Rezvani

address: Zayed Building, 5th floor 6565 MD Anderson Blvd. Unit 1061 Houston, TX 77030

department: Stem Cell Transplantation & Cellular Therapy department

institute: MD Anderson Cancer Center

summary: We conducted a phase I-II clinical trial at our institution that was designed to assess the safety and efficacy of escalating doses of CAR19/IL-15 CB-NK cells as treatment for relapsed/refractory CD19-positive malignancies. NK cells from these optimal CBs were highly functional and enriched in effector-related genes. In contrast, NK cells from suboptimal CBs had upregulation of inflammation, cellular stress and apoptosis programs. Finally, using multiple mouse models, we confirmed the superior anti-tumor activity of CAR-NK cells from optimal CBs.

overall_design: The objective of this study was to investigate the molecular profiles difference between suboptimal and optimal CBs.

first: Katayoun


title: Different Transcriptome Features of Peripheral Blood Mononuclear Cells in Non-Emphysematous Chronic Obstructive Pulmonary Disease [COPD_PBMC]

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

country: Japan

institute: Chiba University

summary: Non-emphysematous COPD, which is defined based on chest computed tomography (CT) findings, may present different transcriptome features of peripheral blood mononuclear cells (PBMCs) derived from bone marrow (BM). In obstructive disorder-fixed COPD, including the airway-dominant phenotype, the upregulated differentially expressed genes (DEGs) were mainly related to Th2 inflammation, suppression of pulmonary vascular remodeling, and the function of BM-derived progenitor cells. Airway-dominant phenotypes are associated with less obstructive impairment. The upregulated DEGs in emphysematous COPD could be associated with airway inflammation and remodeling, suggesting an asthmatic component. Upregulated XCL1, PRKCZ, TMEM102, CD200R1, and AQP1 levels are associated with the activation of T lymphocytes and eosinophils. The upregulation of keratan sulfate biosynthesis and metabolic processes is associated with protection against destruction of the distal airways. The upregulation of ITGA3 could augment interactions with extracellular matrix proteins. COL6A1 may augment the profibrotic mast cell phenotype during the deposition of alveolar collagen VI. The upregulated HSPG2, PDGFRB and PAK4 may contribute to airway wall thickening. The upregulated SERPINF1 could explain the better preserved vascular bed, and the upregulation of SERPINF1 and ISM1 seem to protect against emphysema formation. These patterns in PBMCs may be related to the pathogenesis of nonemphysematous COPD.

overall_design:
To investigate the pathogenesis of COPD in PBMCs, we compared COPD (n=26) and healthy controls (n=13) samples by RNA-seq.
Then, to investigate the pathogenesis of non-emphysematous COPD, we compared samples between non-emphysematous COPD (n=14) and emphysematous COPD (n=8), respectively, by RNA-seq.

first: Takuro

last: Imamoto

first: Hironori

last: Sato

first: Koichiro

last: Tatsumi

first: Daisuke

last: Ishii

first: Keiichiro

last: Yoshioka

first: Yoshinori

last: Hasegawa

first: Osamu

last: Ohara

first: Takuji

last: Suzuki


title: Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian Hamsters

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Hybrid immunity (vaccination + natural infection) to SARS-CoV-2 provides superior protection to re-infection. We performed immune profiling studies during breakthrough infections in mRNA-vaccinated hamsters to evaluate hybrid immunity induction. Vaccine was dosed to induce binding antibody titers against ancestral spike, but not efficient virus neutralization of ancestral SARS-CoV-2 or variants of concern (VoCs). Vaccination reduced morbidity and controlled lung virus titers for ancestral virus and Alpha but allowed breakthrough infections in Beta, Delta and Mu-challenged hamsters. Vaccination primed for T cell responses that were boosted by infection. Infection back-boosted neutralizing antibody responses against ancestral virus and VoCs. Hybrid immunity resulted in more cross-reactive sera, reflected by smaller antigenic cartography distances. Transcriptomics post infection reflects both vaccination status and disease course, and suggests a role for interstitial macrophages in vaccine-mediated protection. Therefore, protection by vaccination, even in the absence of neutralizing antibodies, correlates with recall of broadly reactive B- and T-cell responses.

overall_design: Transcriptomic profiling of vaccinated and unvaccinated hamsters infected with SARS-CoV-2 variants of concern.

first: Juan

last: García-Bernalt Diego

first: Gagandeep

last: Singh

first: Sonia

last: Jangra

first: Michael

last: Schotsaert


title: Mitol dysfunction triggers apoptosis of hematopoietic stem cell via ER stress response

city: Kumamoto

first: Toshio

last: Suda

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

summary: Cellular metabolism exceedingly determines hematopoietic stem cells (HSCs) divisional fate and functioning through organelles interaction upon stress-induced response. The outer mitochondrial membrane-localized E3 ubiquitin ligase Mitol/Marchf5 (encoded by Mitol gene) is known to regulate mitochondrial and endoplasmic reticulum (ER) interaction and promote cell survival. To investigate the precise functional involvement of Mitol in HSC maintenance, we analyzed MX1-cre inducible Mitol knockout mice. Mitol deletion in bone marrow (BM) leads to HSCs exhaustion and impairment of BM reconstitution capability. Moreover, Mitol deletion induced prolonged ER stress in HSCs, which triggers cellular apoptosis that is mainly regulated by IRE1a signaling. Inhibition of ER stress by KIRA6 could partially reduce apoptosis of long term-HSC. Our observations indicated that Mitol is principal to maintain hematopoietic homeostasis and protects HSCs from apoptosis mainly through ER function via IRE1a signaling.

overall_design: HSC fraction (CD150+ CD48- EPCR+ Lineage-) were sorted from bone marrow of control and Mitol knockout (KO) mice, and subsequently mRNA profiles were generated by deep sequencing using Next-seq.

first: Michihiro

last: Hashimoto

first: Miho

last: Kataoka

first: Wenjuan

last: Ma

first: Ahad

last: Khalilnezhad

first: Shah

last: Ahmad


title: FGF19 and its analog Aldafermin cooperate with MYC to induce aggressive hepatocarcinogenesis

city: Montpellier

first: Damien

last: Grégoire

address: 1919, route de Mende

summary: Fibroblast growth factor 19 (FGF19) gene amplification is a common event in human hepatocellular carcinoma (HCC). The protein it encodes acts as a hormone with multiple metabolic functions beneficial for the liver, which has led to the development of analogues for the treatment of metabolic disorders such as Nonalcoholic Steatohepatitis (NASH). The most studied analogue is Aldafermin (NGM282), with previous reports showing the absence of oncogenic properties when given alone. However, potential oncogenic cooperation with frequent disrupted pathways in HCC have not been studied. Here, we used hydrodynamic gene transfer and recombinant protein injection to study oncogenic cooperation between FGF19 and its rodent orthologue FGF15, FGF19 analogue Aldafermin and common HCC events. We found a strong cooperation between FGF15/19 or Aldafermin and hepatocyte overexpression of Myc. The resulting tumours appeared in a short frame (2 to 4 weeks), were well differentiated, and expressed typical HCC markers (alpha foetoprotein and glypican 3). Transcriptomic and pathological analyses showed that Myc/FGF19 and Myc/Aldafermin tumours were almost identical. Our findings could be clinically relevant since clinical studies are currently ongoing in patients with cirrhosis, a condition associated with high susceptibility to HCC development.

overall_design: Hydrodynamic gene transfer was made a C57Bl6 mice (n=5/conditions) to express FGF19, Aldafermin and MYC in a subtype of hepatocytes. Tumoral or healthy liver was collected and sent for Bulk RNAseq.

first: José

last: Ursic-Bedoya

first: Guillaume

last: Desandré

last: Gregoire


title: Circulating tumor DNA for monitoring classic Hodgkin lymphoma patients: correlation with FDG-PET/CT

city: Madrid

first: Sara

last: Fernández

state: Madrid

address: C/Arturo Soria 270

institute: MD Anderson Cancer Centre

type: Genome variation profiling by high throughput sequencing

summary: Circulating tumor DNA (ctDNA) as a biomarker of disease activity in classic Hodgkin lymphoma (cHL) patients are still not well-defined. By profiling primary tumors and ctDNA, we identified common variants between primary tumors and longitudinal plasma samples in most of the cases, confirming high PBatial and temporal heterogeneity. Though ctDNA analyses mirrored HRS cell genetics overall, the prevalence of variants shows that none of them can be used as a single biomarker. Conversely, the estimation of hGE/mL, based in total ctDNA quantification, reflects disease activity and is almost perfectly correlated with standard parameters such as PET/CT that are associated with refractoriness.

overall_design: The study includes blood, tissue (FFPE) and bone marrow samples from patients with a confirmed diagnosis of classical Hodgkin lymphoma

first: Laura

last: Cereceda

first: Eva

last: Díaz

first: Sasha

last: Figueroa

last: Reguera

first: Victoria

last: Menéndez

last: Solñorzano

first: Carlos

last: Montalbán

first: Mónica

last: Estevez

middle: F

last: García


title: Small noncoding RNA profiles and sperm nuclear basic protein properties in semen of young men living in a high environmental impact area

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

type: Non-coding RNA profiling by high throughput sequencing

summary: We present a pilot study based on a multi-level molecular profiling of semen from 33 healthy young subjects residing in a high (n=18) and low (n=15) polluted area in Italy. Samples were analyzed for spermiogram parameters, protamine/histone ratio, Sperm Nuclear Basic Proteins (SNBP) and DNA interaction, oxidative DNA damage, trace metals in semen, and spermatocyte small-noncoding RNA expression. Although comparable mobility and concentration of sperm cells were observed between  samples from the two areas, a higher immature/immune cell concentration characterized the semen of subjects from the high-polluted area. These subjects also showed a lower ratio of protamine to histone and a reduced ability of SNBP to bind and protect DNA from oxidative damage. Trace metal analysis showed an altered ratio of copper to zinc in their semen. In spermatocytes from the high-polluted area, altered levels of 32 microRNAs involved in intraflagellar transport, response to oxidative species, nuclear envelope organization, and lipid metabolism were observed. These miRNA profiles resemble those of spermatocytes undergoing differentiation, including a decrease of miR-23b-3p and let-7f-5p and an increase of miR-34b-3p levels. MicroRNAs expression profiles were coherently related to the sperm concentration in both study groups. In addition, a significant decrease of piRNA levels was also observed. These results support a model that provides new insights into the environmental impact on male germ cells.

overall_design: Thirty-three boys were involved, distributed and residing in two areas, with different environmental pressures based on environmental data from ARPA Campania of which one with high environmental impact in LF municipalities and one with low environmental impact in Upper Middle Sele municipalities in the province of Salerno (namely, Valley of the Sele, VSL). The inclusion criteria used in this project were the following: boys between the ages of 18 and 22 years; healthy; non-drinkers, non-regular (daily) alcohol users (≤ 5 alcoholic units per week); not drug users; not previous oncological diseases and/or chemo/radiotherapy; body mass index (BMI) between 18.5 and 30.5; abdominal circumference <102 cm. After 3-4 days of sexual abstinence, human sperm was collected at the time of morning masturbation and stored in sterile containers. In line with the WHO recommendations (WHO Laboratory Manual for the Examination and Processing of Human Semen, 6th edn. Geneva: World Health Organization, 2021), regular tests were performed on sperm samples to assess their quality (volume, pH, sperm concentration, total and progressive motility, morphology, and round cell concentration).

last: Follia

first: Alessio

last: Naccarati

first: Sonia

last: Tarallo

first: Barbara

last: Pardini

first: Marina

last: Piscopo

first: Antonella

last: Giarra

first: Gennaro

last: Lettieri

first: Rosaria

last: Festa

first: Tiziana

last: Notari

first: Luigi

last: Montano


title: Staufen1 Represses the FOXA1-Regulated Transcriptome by Destabilizing FOXA1 mRNA in Colorectal Cancer Cells

city: Bethesda

first: Ashish

last: Lal

state: Maryland

address: 37 Convent Drive, Room 6134

department: NCI

institute: NIH

summary: Transcription factors play key roles in development and diseases by controlling gene expression. Forkhead Box A1 (FOXA1) is a pioneer transcription factor essential for mouse development that plays important roles in prostate and breast cancer. In colorectal cancer (CRC), we have found that FOXA1 is significantly downregulated, suggesting potential tumor suppressive functions. However, the mechanism(s) by which FOXA1 is downregulated in CRC cells remain largely unclear. We investigated the regulation of FOXA1 expression in CRC, focusing on well-differentiated CRC cells where it is robustly expressed. Genome-wide stability assays identified FOXA1 as an unstable mRNA in CRC cells. We validated FOXA1 mRNA instability in multiple CRC lines and patient-derived CRC organoids and found FOXA1 mRNA is degraded via its 3’UTR. Through FOXA1 3’UTR RNA pulldowns, we identified Staufen1 (STAU1) as a potential regulator of FOXA1. Indeed, knockdown of STAU1 results in increased expression of FOXA1 mRNA and protein due to increased FOXA1 mRNA stability. A subset of the STAU1-regulated transcriptome is enriched for FOXA1 targets, whose expression also increases upon STAU1 knockdown. Collectively, this study uncovers the molecular mechanism by which FOXA1 is regulated in CRC and provides insights into our understanding of the complex mechanisms of gene regulation in cancer.

overall_design: mRNA profiles from LS180 upon siCTRL, or siSTAU1 after 72 + 72 hours of transfection. mRNA profiles from LS180 and HCT116 upon 5 ug/ml Actinomycin D treatment at different time points.

first: Katherine

last: Pasterczyk

first: Meira

last: Zibitt

first: Corrine

last: Hartford

first: Xiao

last: Li

first: Lorinc

last: Pongor

first: Lisa

last: Jenkins

first: Yue

last: Hu

first: Patrick

middle: X

last: Zhao

first: Bruna

last: Muys

first: Suresh

last: Kumar

first: Nitin

last: Roper

first: Mirit

middle: I

last: Aladjem

first: Yves

last: Pommier

first: Ioannis

last: Grammatikakis


title: PRC1 directs PRC2-H3K27me3 deposition to shield adult spermatogonial stem cells from differentiation

city: Davis

first: Satoshi

last: Namekawa

address: One Shields Avenue

institute: UC Davis


title: Inosine Induces Stemness Features in HA-CAR-T cells and Enhances Potency [ATAC-seq]

first: Yiyun

last: Chen

first: Dorota

last: Klysz

first: Bence

last: Daniel

first: Katalin

last: Sandor

first: Stefanie

last: Meier

first: Crystal

last: Mackall


title: Effect of S1P on gene expression in human primary keratinocytes

city: Toulouse

first: Nathalie

last: ANDRIEU-ABADIE

address: 2 Avenue Hubert Curien

institute: INSERM

summary: To investigate the effect of the sphingolipid S1P secreted by melanoma cells on epidermal keratinocytes, we treated human primary keratinocytes with exogenous S1P.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of HPK treated or not with S1P (1µM) for 24 h. Each condition was performed in 5 replicates.

first: Justine

last: Noujarède

first: Lorry

last: Carrié

first: Matthieu

last: Genais

first: Joelle

last: Riond

last: Andrieu-Abadie


title: Single cell analysis of newly diagnosed AML patients

first: Hussein

last: Abbas

state: Texas

address: 1515 Holcombe Blvd

institute: The University of Texas at MD Anderson Cancer cent

summary: Acute Myeloid Leukemia (AML) is a heterogenous disease characterized by immature blasts at different maturation stage. We used single cell sequencing technique to analyze newly diagnosed AML patients.

overall_design: Bone marrow biopsies were routinely collected before treatment initiation. Samples were freshly frozen with freezing medium containing 20% fetal calf serum (FCS) and 10% dimethyl sulfoxide (DMSO) in Dulbecco’s modified Eagle medium (DMEM) and stored in liquid nitrogen. All frozen BM samples were retrieved immediately before sample processing. The 5 prime gene expression libraries were prepared using a 10x Genomics Chromium Controller instrument and Chromium Single-Cell 5 V5.1 reagent kits (10x Genomics).

first: Bofei

last: Wang

first: Patrick

last: Reville


title: H3K9me2 profile of tumor infiltrated Treg from the WT and the jmjd1c TregcKO mice and chromatin accessibility profile of tumor treg and spleen treg

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

summary: Tumor infiltrated treg cells are considered as a crucial in the cancer immunotherapy. We used H3K9me2 CUT&RUN to analyze the differences between WT and jmjd1cTreg cko mice and clarify the important function of jmjd1c in tumor treg. We use ATACseq to analyze the difference between tumor treg and spleen treg and characterize the epigenetic characters in tumor treg.

overall_design: Tumor infiltrated treg of the WT and jmjd1c tregcKO mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of fluorence signal and analyzed using H3K9me2 CUT&RUN. Tumor infiltrated treg and spleen treg were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of fluorence signal and analyzed using ATACseq. Tumor infiltrated treg of the WT and jmjd1c tregcKO mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of fluorence signal and analyzed using and H3K9me2 CUT&RUN.

first: Xiaoming

first: Xuehui

last: Long

first: Yuliang


title: B-cell-intrinsic DNase1L3 is essential for T-cell-independent type II response in mice

city: Noda

first: Daisuke

last: Kitamura

state: Chiba

address: Yamazaki 2669

institute: Tokyo University of Science

summary: T-cell independent type II (TI-II) antigens, such as capsular polysaccharides, have multivalent epitope, which induce B cell activation, plasma cell differentiation and antibody production by strongly cross-linking B cell receptors. However, the mechanism of B cell activation by TI-II antigens remains unclear. In this study, we demonstrate that DNA endonuclease DNase1L3 (also termed DNase g) is required for the TI-II response. The production of antigen-specific antibodies was severely diminished in DNase1L3-deficient mice upon immunization with TI-II antigens, but not with TD antigens. Bone-marrow chimeric mice and B cell transfer experiments revealed that B-cell-intrinsic DNase1L3 was required for the TI-II response. DNase1L3-deficient B cells were defective in cell proliferation and plasma cell differentiation in the TI-II response in vivo as well as in vitro, which was not rescued by co-culture with DNase1L3-sufficient B cells in vitro, disproving an involvement of a secretory DNase1L3. In vitro stimulation with TI-II antigen transiently increased expression of DNase1L3 and its translocation into the nucleus. RNA-seq analysis of ex-vivo B cells having been responded to TI-II antigen in vivo revealed a marked reduction of Myc-target gene sets in DNase1L3-deficient B cells. Expression of IRF4, the gene of which is a target of Myc, was diminished in the ex-vivo DNase1L3-deficient B cells, in which forced expression of IRF4 restored the TI-II response in vivo. These data revealed an unexpected role of DNase1L3 in a missing link between B cell receptor signaling and B cell activation in the TI-II response, giving a valuable clue to molecularly dissect this response.

overall_design: Marginal zone B cells purified from pooled spleens of CD45.1+ VHB1-8 knock-in gene (B1-8f/+), Dnase1l3+/+ (WT) or Dnase1l3-/- (KO) mice were intravinously(i.v.) transferred into C57BL/6NCrSlc mice, which were immunized i.v. with 4-hydroxy-3-nitrophenyl acetyl (NP)-Ficoll on the following day. Two days later, donor cells (CD45.1+ B220+ CD138- FSChi) were sorted by cell sorter. RNA-sequencing was performed to identify the difference of gene expression between Dnase1l3+/+  and Dnase1l3-/- marginal zone B cells.

first: Kei

last: Kato

last: Haniuda

first: Saori

last: Fukao


title: PRC1 directs PRC2-H3K27me3 deposition to shield adult spermatogonial stem cells from differentiation [RNA-seq]

first: Satoshi

last: Namekawa

summary:
To understand the functional role of PRC1 in defining the epigenomic and transcriptional landscape in Aundiff, we eliminated PRC1 function in germ cells using Ddx4-Cre to mutate the E3 ubiquitin ligase RNF2 on a background lacking its partially redundant paralog RING1 (RING1A) to create PRC1 conditional knockout (PRC1cKO) mice. We discover a key role of Polycomb complexes in shielding the undifferentiated state of mouse adult spermatogonia.
We then performed gene expression profiling analysis using data obtained from RNA-seq of  WT, PRC1ctrl and PRC1cKO spermatogonial cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for (1) WT Aundiff and Adiff spermatogonia; (2) PRC1ctrl and PRC1cKO Aundiff spermatogonia; (3) PRC1ctrl and PRC1cKO Aundiff spermatogonia after win18,446 inhibition.

first: Mengwen

last: Hu

middle: H


title: AA2P-mediated DNA demethylation synergizes with stem cell agonists to promote expansion of stem cells via activation of GAS6/AXL signaling axis [scRNA-Seq]

city: Ottawa

first: Nicolas

last: Pineault

state: Nicolas Pineault

address: 1800 Alta Vista Dr

country: Canada

institute: Canadian Blood Services

summary: To investigate the graft composition of SCACs expanded and non cultured CD34+ cells

overall_design: CD34+ cells were cultured in respective conditions (X2A,X2B,C6) for 14 days and then FACS sorted for CD34+ populations followed by Sc-RNA sequencing. As a control, the matched non-cultured FACS sorted CD34+ cells were also subjected to Sc-RNA sequencing.

first: Harinad

last: Maganti

first: Javed

last: Manesia


title: PRC1 directs PRC2-H3K27me3 deposition to shield adult spermatogonial stem cells from differentiation [CUT&Tag, CUT&RUN]

summary:
To understand the functional role of PRC1 in defining the epigenomic and transcriptional landscape in Aundiff, we eliminated PRC1 function in germ cells using Ddx4-Cre to mutate the E3 ubiquitin ligase RNF2 on a background lacking its partially redundant paralog RING1 (RING1A) to create PRC1 conditional knockout (PRC1cKO) mice. We discover a key role of Polycomb complexes in shielding the undifferentiated state of mouse adult spermatogonia.
CUT&RUN or CUT&Tag for H2AK119ub, H3K27me3 and H3K4me3 in WT, PRC1ctrl and PRC1cKO spermatogonial cells.

overall_design: Comparative chromatin profiling analysis of quantitative CUT&Tag or CUT&RUN data for (1) WT Aundiff and Adiff spermatogonia; (2) PRC1ctrl and PRC1cKO Aundiff spermatogonia; (3) PRC1ctrl and PRC1cKO Aundiff spermatogonia after win18,446 inhibition.


title: AA2P-mediated DNA demethylation synergizes with stem cell agonists to promote expansion of stem cells via activation of GAS6/AXL signaling axis [bulkRNA-Seq]

summary: To investigate the transcriptional profile of SCACs, STFL expanded and non-cultured CD34+CD45RA- cells

overall_design: CD34+ cells were cultured in respective condition (X2A,X2B,SM6,C6, STFL) for 14 days and then FACS sorted for CD34+CD45RA- populations followed by RNA sequencing. As a control, the matched non-cultured FACS sorted CD34+CD45RA- cells were also subjected to RNA sequencing.


title: Epigenetic Rewiring of Metastatic Cancer to the Brain: Focus on Lung and Colon Cancers

status: Public on Dec 17 2023

city: MILANO

first: VALENTINA

last: VAIRA

address: VIA FRANCESCO SFORZA 35

department: PATHOPHISIOLOGY AND TRANSPLANTATION

institute: UNIVERSITY OF MILANO

summary: Genome wide DNA methylation profiling of brain metastasis from colorectal and lung cancer. The Illumina Infinium MethylationEPIC was used to obtain DNA methylation profiles across approximately 850,000 CpGs in brain metastasis samples. Samples included 1 breast ductal invasive carcinoma, 4 colon adenocarcinoma, 1 melanoma, 1 multiple mieloma, 7 non small cell lung cancer adenocarcinoma,  3 non small cell lung cancer G3, 4 non small cell lung cancer SCC, 1 prostate cancer adenocarcinoma and 1 serous carcinoma.

overall_design: Bisulfite-converted DNA was amplified, fragmented and precipitated. The DNA was subsequently hybridized to probes on the BeadChips and scanned using the NextSeq 550 System (Illumina).

first: Annamaria

last: Morotti

first: Francesco

last: Gentile

first: Gianluca

last: Lopez

first: Giulia

last: Passignani

first: Luca

last: Valenti

first: Marco

last: Locatelli

first: Manuela

last: Caroli

first: Claudia

last: Fanizzi

first: Stefano

last: Ferrero

first: Valentina

last: Vaira


title: Single Cell RNA-sequencing analyasis of mouse glutamatergic myenteric neurons

city: Storrs

first: Bin

last: Feng

state: CT

address: 4S2 67 N Eagleville Road

department: Biomedical Engineering

institute: University of Connecticut

summary: The study aimed to uncover the molecular profile of mouse Vglut2-possitive enteric neurons (VGLUT2-ENs) by single-cell mRNA sequencing (scRNA-seq). Method: We performed scRNA-seq of VGLUT2-ENs from distal intestine extracted from 6-8 weeks mice. We removed the non-neuronal cells, performed Principal Component Analysis (PCA) on the gene expression level of 15 well accepted and curated myenteric neuron markers, and analyzed the expression of the mechanosensitive ion channels. Results: clustering analysis results from PCA on the 15 gene markers indicates a dominant cluster of VGLUT2-ENs; By comparing the expression levels of the mechanosensitive ion channels Piezo1 and Piezo2 in the non-VGLUT2- ENs and VGLUT2-ENs, we find significantly less expression level of piezo1 and piezo2 genes in the VGLUT2-EN population as compared with myenteric neurons negative for VGLUT2. Conclusion: Molecular profiling of VGLUT2-ENs through single-cell mRNA sequencing unveiled a unique expression profile, distinguishing them from typical interneurons. Additionally, VGLUT2-ENs displayed minimal expression of mechanosensitive ion channels (Piezo1 and Piezo2), setting them apart from mechanosensitive interneurons.

overall_design: We isolated single Vglut2-possitive enteric neurons from distal colorectum of VGLUT2-tdTomato mice using fluorescence-assisted manual cell picking, and obtained transcriptomes by single cell mRNA-sequencing.

first: Jia

last: Liu

first: Shaopeng

last: Zhang

first: Sharareh

last: Emadi


title: Impaired interferon response in plasmacytoid dendritic cells from children with persistent wheeze

city: Nedlands

first: Jonatan

last: Leffler

state: WA

address: 15 Hospital Ave

institute: Telethon Kids Institute

summary:
Background Impaired interferon response and allergic sensitisation may contribute to virus induced wheeze and asthma development in young children. Plasmacytoid dendritic cells (pDC) play a key role in antiviral immunity as critical producers of type I interferons (IFN-I). pDC also express the high affinity IgE receptor (FcRI) through which IFN-I production may be negatively regulated. If antiviral function of pDC is associated with recurrent episodes of wheeze in young children is not well understood. This study aimed to evaluate the phenotype and function of circulating pDC in children with a longitudinally defined wheezing phenotype.
Methods We performed multiparameter flow cytometry on peripheral blood mononuclear cells from 38 children presenting to the emergency department with an acute episode of respiratory wheeze and 19 controls. RNA sequencing on isolated pDC from the same individuals was also performed. For each subject, their longitudinal exacerbation phenotype was determined using the Western Australia public hospital database.
Results We observed a significant depletion of circulating pDC in young children with a persistent phenotype of wheeze. The same individuals also displayed upregulation of the IgE receptor (FcRI) on their pDC. Based on transcriptomic analysis, pDC from these individuals did not mount a robust systemic antiviral response as observed in children who displayed a non-recurrent wheezing phenotype.
Conclusion Our data suggests that circulating pDC phenotype and function are altered in young children with a persistent longitudinal exacerbation phenotype. Expression of FcRI is increased and their function as major IFN producers is impaired during acute exacerbations of wheeze.

overall_design: Clinical samples obtained children with an acute respiratory wheeze, control samples were sampled from children in the community

first: Isabelle

last: Coenen

first: Emma

last: de Jong

first: Anya

middle: C

last: Jones

first: Kim

last: Khoo

first: Shihui

last: Foo

first: Shanshan

last: Wu Howland

first: Florent

last: Ginhoux

first: Peter

last: Le Souëf

first: Patrick

last: Holt

first: Deborah

last: Strickland

first: Ingrid

last: Laing


title: Transcriptomic Profiling of Myosin 1e WT and KO 4T1 Cell Pools

city: SYRACUSE

first: Mira

last: Krendel

state: New York

address: 505 Irving Ave

institute: Upstate Medical University

summary: Myosin 1e may influnece the metastatic spread of breast cancer cells as determined using the MMT-PyMT mouse model deficient in myo1e, which demonstrated no lung metastases. Therefore, we used CRISPR to knock out Myosin 1e (myo1e) in the 4T1 breast cancer line to study the effect on the propensity to metastasize. The Myosin 1e (Myo1e) WT and KO 4T1 cell pools were generated by Synthego using gRNA sequence 'CUUCUUCAGGUUCUCUACAA'.

overall_design: Three biological replicates of Myosin 1e WT and KO 4T1 cells were using for RNA extraction.

first: Michael

last: Garone

first: Sharon

last: Chase

first: Chunling


title: Single-cell immunophenotyping revealed the association of CD4+ central and CD4+ effector memory T cells linking exacerbating chronic obstructive pulmonary disease and NSCLC

city: Szeged

first: Gabor

middle: Janos

last: Dr. Szebeni

state: Csongrád

address: Temesvári krt. 62.

country: Hungary

institute: Biological Research Centre

summary: Introduction: Tobacco smoking generates airway inflammation in chronic obstructive pulmonary disease (COPD), and its involvement in the development of lung cancer is still among the leading causes of early death. Therefore, we aimed to have a better understanding of the disbalance in immunoregulation in chronic inflammatory conditions in smoker subjects with stable COPD (stCOPD), exacerbating COPD (exCOPD), or non-small cell lung cancer (NSCLC). Methods: Smoker controls without chronic illness were recruited as controls. Through extensive mapping of single cells, surface receptor quantification was achieved by single-cell mass cytometry (CyTOF) with 29 antibodies. The CyTOF characterized 14 main immune subsets such as CD4+, CD8+, CD4+/CD8+, CD4 −/CD8−, and g/d T cells and other subsets such as CD4+ or CD8+ NKT cells, NK cells, B cells, plasmablasts, monocytes, CD11cdim, mDCs, and pDCs. The CD4+ central memory (CM) T cells (CD4+/CD45RA−/CD45RO+/CD197+) and CD4+ effector memory (EM) T cells (CD4+/CD45RA−/CD45RO+/CD197−) were FACSsorted for RNA-Seq analysis. Plasma samples were assayed by Luminex MAGPIX® for the quantitative measurement of 17 soluble immuno-oncology mediators (BTLA, CD28, CD80, CD27, CD40, CD86, CTLA-4, GITR, GITRL, HVEM, ICOS, LAG-3, PD-1, PD-L1, PD-L2, TIM-3, TLR-2) in the four studied groups. Results: Our focus was on T-cell-dependent differences in COPD and NSCLC, where peripheral CD4+ central memory and CD4+ effector memory cells showed a significant reduction in exCOPD and CD4+ CM showed elevation in NSCLC. The transcriptome analysis delineated a perfect correlation of differentially expressed genes between exacerbating COPD and NSCLCderived peripheral CD4+ CM or CD4+ EM cells. The measurement of 17 immuno-oncology soluble mediators revealed a disease-associated phenotype in the peripheral blood of stCOPD, exCOPD, and NSCLC patients. Discussion: The applied single-cell mass cytometry, the whole transcriptome profiling of peripheral CD4+ memory cells, and the quantification of 17 plasma mediators provided complex data that may contribute to the understanding of the disbalance in immune homeostasis generated or sustained by tobacco smoking in COPD and NSCLC.

overall_design: FACS sorted CD4+ human central memory and effector memory T-cells: 1. CD4+ CM T-cell contol, 2. CD4+ CM T-cell stable COPD, 3. CD4+ CM T-cell COPD with exacerbation, 4. CD4+ CM T-cell NSCLC, 5. CD4+ EM T-cell contol, 6. CD4+ EM T-cell stable COPD, 7. CD4+ EM T-cell COPD with exacerbation, 8. CD4+ EM T-cell NSCLC

first: Nikolett

last: Gémes

first: Ágnes

last: Zvara

first: László

last: Puskás

first: Zsolt

last: Czimmerer

first: Máté

last: Manczinger

first: Gergő

last: Balogh

first: Gábor

middle: J

last: Szebeni


title: Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization [RNA-seq]

status: Public on Dec 15 2023

city: Houston

first: Priyatansh

last: Gurha

address: 6770 Bertner Ave

department: School of Medicine

institute: UTHealth

summary: Rationale: Human pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) provide a platform to identify and characterize factors that regulate the maturation of CMs. The transition from an immature fetal to adult CM state entails coordinated regulation of the expression of genes involved in myofibril formation and OXPHOS among others. Lysine demethylase 5 (KDM5) specifically demethylate H3K4me1/2/3 and have emerged as potential regulators of expression of genes involved in cardiac development and mitochondrial function.Objectives: The purpose of this study is to determine the role of KDM5 in iPSC-CM maturation.Methods and Results:  KDM5A, B, and C proteins were mainly expressed in the early post-natal stages and their expressions were progressively downregulated in the postnatal cardiomyocytes and were absent in adult hearts and CMs. In contrast, KDM5 proteins were persistently expressed in the iPSC-CMs up to 60 days after the induction of myogenic differentiation, consistent with the immaturity of these cells. Inhibition of KDM5 by KDM5-C70 -a pan-KDM5 inhibitor, induced differential expression of 2,372 genes, including upregulation of genes involved in fatty acid oxidation (FAO), OXPHOS, and myogenesis in the iPSC-CMs. Likewise, genome-wide profiling of H3K4me3 binding sites by the CUT&RUN (Cleavage Under Targets & Release Using Nuclease) assay showed enriched of the H3K4me3 peaks at the promoter regions of genes encoding FAO, OXPHOS, and sarcomere proteins. Consistent with the chromatin and gene expression data, KDM5 inhibition increased expression of multiple sarcomere proteins and enhanced myofibrillar organization. Furthermore, inhibition of KDM5 increased H3K4me3 deposits at the promoter region of the ESRRA gene and increased its RNA and protein levels. Knockdown of ESRRA in KDM5-C70-treated iPSC-CM suppressed expression of a subset of the KDM5 targets. In conjunction with changes in the gene expression, KDM5 inhibition increased oxygen consumption rate and contractility in iPSC-CMs.

overall_design: IPSC-CM and treated groups were used for RNA-seq.

first: Manisha

last: Deogharia

first: A

last: Marian


title: Deciphering the Differential Impact of Thrombopoietin/MPL Signaling on Hematopoietic Stem Cell Function in Bone Marrow and Spleen

status: Public on Dec 16 2023

city: Stony Brook

first: Huichun

last: Zhan

state: NY

address: 101 Nicolls Rd

institute: Stony Brook Univeristy

summary: Thrombopoietin (TPO) and its receptor MPL play crucial roles in hematopoietic stem cell (HSC) function and platelet production. However, the precise effects of TPO/MPL signaling on HSC regulation in different hematopoietic niches remain unclear. Here, we investigated the effects of TPO/MPL ablation on marrow and splenic hematopoiesis in TPO-/- and MPL-/- mice during aging. Despite severe thrombocytopenia, TPO-/- and MPL-/- mice did not develop marrow failure during a 2-year follow-up. Marrow and splenic HSCs exhibited different responses to TPO/MPL ablation and exogenous TPO treatment. Splenic niche cells compensated for marrow HSC loss in TPO-/- and MPL-/- mice by upregulating CXCL12 levels. These findings provide new insights into the complex regulation of HSCs by TPO/MPL and reveal a previously unknown link between TPO and CXCL12, two key growth factors for HSC maintenance. Understanding the distinct regulatory mechanisms between marrow and spleen hematopoiesis will help develop novel therapeutic approaches for hematopoietic disorders.

overall_design: To gain insight into the transcriptomic changes associated with TPO/MPL ablation and enhanced HSC function in the spleen, we performed RNA sequencing on Lineage-cKit+ HSPCs from the marrow and spleen of wild-type, TPO-/- , and MPL-/- mice.

first: Sandy

last: Lee


title: The miRNA expression profile in the progression of the gastric cancer

city: wuxi

first: fangmei

last: an

state: jiangsu

address: NO 299,QingYang Road

institute: Wuxi Public Hospital

summary:
miRNA expression profiles in the progression of the gastric cancer
According to the development of intestinal gastric cancer(GC), the normal gastric mucosa gradually evolves into gastric cancer through CSG(Chronic superficial gastritis), CAG(Chronic atrophic gastritis), IM (intestinal metaplasia) and Dys(Dysplasia). H. pylori is the main risk factor for GC, but the mechanism  is still unclear. In this study, we indentified the miRNA, lncRNAs and mRNAs expression profiles in GC progression, analyzed the fuctions and pathways and investigated the relationship between non coding RNAs and H. pylori infection. Our study provided new ideas for the study of the pathogenesis of GC and a basis for the early diagnosis and treatment of GC and precancerous lesions.

overall_design: we reported the expression profile in gastric mucosa with chronic surficial gastritis, chronic atrophy gastritis, dysplasia and cancer

first: Qiang

first: Fangmei

last: An


title: KRAS inhibition impacts chromatin organization and transcriptional performance in colorectal cancer cells [SW480 RNA-seq]

city: Porto

first: Flávia

middle: Oliveira

last: Martins

address: Rua Alfredo Allen, 208

country: Portugal

summary: Preclinical and clinical data revealed that targeting KRAS mutant tumors is more challenging than expected. While initially sensitive to the treatment, cancer cells have the capability to rapidly bypass dependence on this oncogene to acquire a drug-tolerant phenotype. Gaining a comprehensive understanding of the mechanisms underlying the transition from a drug-sensitive to a drug-tolerant state holds the key to invaluable insights. Such insights will inform the development of therapeutic strategies aimed at disrupting intrinsic or adaptive resilience, ultimately enhancing therapeutic outcomes. Building upon this rationale, we established three-dimensional culture models of mutant KRAS CRC cell lines with distinct KRAS dependencies to investigate the cellular response to KRAS silencing. Our approach revealed a unique response in KRAS-dependent cells, characterized by G0/G1 cell cycle arrest and entry into a quiescent-like state. Proteomics analysis identified nucleosome assembly, regulation of gene expression, mRNA splicing, and mRNA processing as the top biologic processes specifically up-regulated in KRAS-dependent CRC cell lines upon KRAS silencing. Additionally, alterations in histone 3 post-translational modifications and chromatin compaction were also observed, along with enhanced transcriptional performance revealed by longitudinal RNA-Seq analysis. Our discoveries substantiate the existence of an epigenetic mechanism responsible for inducing tolerance to KRAS loss. This mechanism relies on both chromatin reorganization and transcriptional upregulation, illuminating the cancer cells' remarkable capacity to swiftly adapt, survive, and sustain malignancy even in the absence of oncogenic KRAS.

overall_design: To investigate the effect of KRAS inhibition in transcription dynamics os colorectal cancer cell lines, we used 3 different KRAS mutant colorectal cancer cell lines (HCT116, LS174T and SW480). We then silenced cells using siRNA and performed gene expression profilling analysis using data obtained from RNA-seq of the different cell lines at four different-time points from silenced cells (siKRAS) or its control (siControl).

first: Ana

last: Machado

first: Andreia

last: Ribeiro

first: Susana

last: Oliveira

first: Joana

last: Carvalho

first: Rune

last: Matthiesen

first: Sérgia

last: Velho


title: ATM-ESCO2-SMC3 axis regulates cohesin-dependent chromatin structure dynamics in response to DNA damage and safeguards genome integrity by promoting 53BP1 recruitment

city: Beijing

first: Jianfeng

last: Fu

address: Yiheyuan Road

institute: Peking university

summary: 53BP1 is primarily known as a key regulator in DNA double-strand break (DSB) repair. However, the mechanism of DSB-triggered cohesin modification-modulated chromatin structure on the recruitment of 53BP1 remains largely elusive. Here we identified acetyltransferase ESCO2 as a regulator for DSB-induced cohesin-dependent chromatin structure dynamics, which promotes 53BP1 recruitment. Mechanistically, in response to DNA damage, ATM phosphorylates ESCO2 S196 and T233. MDC1 recognizes phosphorylated ESCO2 and recruits ESCO2 to DSB sites. ESCO2-mediated acetylation of SMC3 stabilizes cohesin complex conformation and regulates the chromatin structure at DSB breaks, which is essential for the recruitment of 53BP1 and the formation of 53BP1 microdomains. Furthermore, depletion of ESCO2 in both colorectal cancer cells and xenografted nude mice sensitizes cancer cells to chemotherapeutic drugs. Collectively, our results reveal a molecular mechanism for the ATM-ESCO2-SMC3 axis in DSB repair and genome integrity maintenance with a vital role in chemotherapy response in colorectal cancer.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for rH2AX as well as 53BP1 and ac-SMC3 in WT/ESCO2 KD HCT116 cells.

first: Siru

last: Zhou

first: Huilin

last: Xu

first: Xiaofeng

last: Zheng


title: AA2P-mediated DNA demethylation synergizes with stem cell agonists to promote expansion of stem cells via activation of GAS6/AXL signaling axis

first: Nicolas

last: Pineault

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

overall_design: Refer to individual Series


title: Immunosuppressive CD29+ Treg accumulation in the liver in mice upon checkpoint inhibitor therapy

first: Tim

last: Greten

address: Building 10, Room 3B45, 9000 ROCKVILLE PIKE RM

department: TGMB

institute: NCI

summary: We report that anti-PD1 treatment expands regulatory T cells (Tregs) in the liver of tumor-bearing mice and this contributes to the resistance mechanism of metastatic liver cancer to immunotherapy. Using FoxP3-GFP strain, Tregs after anti-PD1 treatment were sorted and Tregs from the liver and spleen were sequenced. CD29 positive cluster expanded in PD1-treated mouse liver. CD29-positive Tregs had also a suppression function in vitro validation study. And we identified CD29-positive Tregs in the public database of human liver cancer. We propose that CD29+ Tregs constitute a unique subpopulation of hepatic Tregs that are primed to respond to ICI agents and mediate resistance.

overall_design: Intrahepatic MC38 tumors were established in FoxP3-GFP mice (JAX:006772). Seven days following establishment, 200 μg of either IgG2b isotype or αPD-1 were delivered intraperitoneally. Three days following treatment, tumor-bearing livers and spleens were harvested and processed. CD3+CD4+GFP+ cells were lysed and partitioned. Single-cell barcoding of reverse transcribed mRNA was performed on the Chromium controller. 3’ immune cell profiling chemistry v1.0 and v1.1 (10x Genomics, USA) was used. Single-cell cDNA amplification, and library preparation was proceeded via the manufacturer guidelines. Expression libraries were sequenced on a NextSeq 550 (Illumina).

first: Benjamin

last: Green

first: Yuta

last: Myojin


title: KRAS inhibition impacts chromatin organization and transcriptional performance in colorectal cancer cells [HCT116 RNA-seq]

overall_design:
To investigate the effect of KRAS inhibition in transcription dynamics os colorectal cancer cell lines, we used 3 different KRAS mutant colorectal cancer cell lines (HCT116, LS174T and SW480). We then silenced cells using siRNA and performed gene expression profilling analysis using data obtained from RNA-seq of the different cell lines at four different-time points from silenced cells (siKRAS) or its control (siControl).
This Series represents HCT116 data.

middle: M


title: Identification of genes regulated by the transcription factor RFX1 (CR_06110C) in the yeast Candida albicans

first: Jose

middle: Christian

last: Perez

address: 6431 Fannin

institute: UTHealth Houston

summary: The regulatory factor X (RFX) gene family comprises a functionally diverse group of transcription factors characterized by a highly conserved and unique winged-helix DNA binding domain. The RFX proteins control a variety of processes ranging from genome integrity and cell cycle in model yeasts to immune functions and tissue differentiation in higher eukaryotes. The yeast Candida albicans encodes two RFX homologs, one of which (CR_06110C, termed RFX1) remains uncharacterized. In this study we employed RNA-seq to identify downstream targets of the transcriptional regulator Rfx1 in C. albicans.

overall_design: Transcriptome comparison between two isogenic Candida albicans strains: WT reference strain and rfx1 deletion mutant. The strains were grown in triplicates on YP (yeast extract, peptone) maltose agar at 30°C for 48 hours. RNA was prepared from colonies scraped off the agar. Directional mRNA library preparation (with poly A enrichment) and sequencing using NovaSeq PE150 mode was executed at Novogene Corporation Inc.

first: Christian

first: Elena

last: Lindemann-Perez


title: A COMPASS histone H3K4 trimethyltransferase pentamer transactivates drought tolerance and growth/biomass production in Populus trichocarpa

city: Harbin

first: Baofeng

last: Zhang

address: Hexing Road 26#, Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

summary: ChIP-seq was carried out with H3K4me3 antibody using Stem differentiating xylem from wild-type plants under drought conditions

overall_design: Twelve samples were analyzed: 3 biological replicates of input DNA and IP DNA under drought treatment,  3 biological replicates of input DNA and IP DNA under well-watered treatment (Control for drought treatment)


title: KRAS inhibition impacts chromatin organization and transcriptional performance in colorectal cancer cells [LS174T RNA-seq]

first: Flávia

last: Martins

first: Ana

last: Machado

first: Andreia


title: XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells [CUT&Tag]

city: Los Angeles

first: Kathrin

last: Plath

state: CA

institute: UCLA

summary: X-chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X-chromosome in cis to mediate chromosome-wide gene silencing. In female naïve human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration and XCI does not occur, raising questions about XIST’s function. We found that XIST spreads across the X-chromosome and induces dampening of X-linked gene expression in naïve hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences on autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X-chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences on autosomes. Dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our results identify XIST as the regulator of X-chromosome dampening, uncover an evolutionarily conserved trans-acting role of XIST/Xist, and reveal a correlation between XIST/Xist dispersal and autosomal targeting.

overall_design: We examined the K27me3 in multiple cells: female human naive hESCs (H9) WT and in XIST KO (two clones) and in male human naive hESC (WIN1)

first: Iris

last: Dror

first: Weixian

last: Deng

first: Tsotne

last: Chitiashvili


title: XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells [scRNA-seq]

summary: X-chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X-chromosome in cis to mediate chromosome-wide gene silencing. In female naïve human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration and XCI does not occur, raising questions about XIST’s function. We found that XIST spreads across the X-chromosome and induces dampening of X-linked gene expression in naïve hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences on autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X-chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.

overall_design: Single cell RNA in naive hESCs (H9) and in XIST KO (clone18 and clone7)


title: XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells [ChIP-seq]

overall_design: We examined multiple histone marks in female human naive iPSCs and in male human naive hESCs (WIN1)

first: Constantinos

last: Chronis