title: Ibrutinib effects on in vitro exhausted CTL

city: Rotterdam

first: Peter

middle: D.

last: Katsikis

state: Zuid-Holland

address: Dr. Molewaterplein 40

department: Department of Immunology

country: Netherlands

institute: Erasmus University Medical Center

summary: CTL exhaustion is driven by chronic antigen stimulation and is characterized by specific molecular, phenotypic and functional changes. Reversing CTLs exhaustion with immune checkpoint blockade (ICB) has provided clinical benefits in different types of cancer. However, the therapeutic effects of ICB varies among patients and cancer types. Ibrutinib, a potent BTK inhibitor, is reported that it improved T cell function in ibrutinib long-term treated chronic lymphocytic leukemia patients. However, the mechanism remains unclear. We hypothesized ibrutinib can directly act on CD8+ T cells and reinvigorates exhausted CTLs. To test this, we generated in vitro exhausted OT-I cells as previously described (Zhao M et al PLoS Pathog. 16(6): e1008555) by repeatedly stimulating cells with SIINFEKL peptide. We tested the effect of ibrutinib on inhibitory receptor, exhaustion-related transcription factor expression and cytokine (IFNγ, TNFα and IL-2) production. We found that ibrutinib decreased the expression of multiple inhibitory receptors on in vitro exhausted CTL while the critical transcription factor, Tox was downregulated. The cytokine production of exhausted cells was partially improved after ibrutinib treatment. Importantly, using btk deficient mice we found the effect of ibrutinib was independent of BTK expression. To conclude, these findings suggest that ibrutinib reduces CTL exhaustion. Our study provides evidence for ibrutinib’s synergistic use with cancer immunotherapy.

overall_design: CD8+ T cells are first exhausted in vitro for 5 days, then treated with either DMSO or Ibrutinib for 3 days before RNA isolation and sequencing.

first: Ling

last: Li

first: Manzhi

last: Zhao

first: Dwin

last: Grashof

first: Harmen

last: van de Werken


title: Tumorigenic effects of human mesenchymal stromal cells and fibroblasts on bladder cancer cells

status: Public on Sep 04 2023

city: Duesseldorf

first: Michèle

middle: J

last: Hoffmann

state: NRW

address: Moorenstr. 5

department: Urology

country: Germany

institute: Heinrich Heine University, Medical Faculty

type: Expression profiling by high throughput sequencing

summary: We sought for deeper understanding of interaction mechanisms between tumor microenvironment cells, like fibroblast (FB) and mesenchymal stem cells (MSC), and bladder cancer cells to develop new cancer treatment approaches overcoming therapy resistance. To this end the bladder cancer cell lines BFTC-905 and VMCUB-1 were treated with conditioned media from FB or MSC for 72h. RNA was submitted to RNA sequencing analysis on the HiSeq 3000/4000 system (Illumina).

overall_design: total RNA from urothelial carcinoma (UC) cell lines BFTC-905 and VMCUB-1 treated with conditioned media from fibroblasts (FB) or mesenchymal stem cells (MSC) for 72h compared to DMEM treated controls. Triplicates were analysed for each condition.

first: Lucie

middle: M

last: Frerichs

first: Bastian

first: Patrick

last: Petzsch

first: Karl

last: Köhrer

first: Joachim

last: Windolf

first: Bernd

last: Bittersohl

first: Vera

last: Grotheer


title: Induction of proteasomal activity in mammalian cells by lifespan-extending tRNA synthetase inhibitors

status: Public on Sep 05 2023

city: Tempe

first: Blaise

middle: L

last: Mariner

state: AZ

address: 427 E Tyler Mall, LSC 356

department: School of Life Sciences and Center for Evolution and Medicine

country: USA

institute: Arizona State University

summary:
ATF4-dependent differential transcription in response to tRNA synthetase inhibitor treatment in mouse embryonic fibroblasts
We performed RNAseq on wild type and ATF4 KO mouse embryonic fibroblasts with and without tRNA synthetase inhibitor as our block design described in
JAAA-D-23-00283R1 by Geroscience

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ATF4 downstream transcriptional activity.

first: Mariner

last: Blaise

first: McCormick

last: Mark


title: Acetyl-CoA is a Key Molecule for Nephron Progenitor Cell Pool Maintenance

city: New Orleans

first: Giovane

middle: G

last: Tortelote

state: LA

address: 1430 Tulane Ave. School of Medicine, Room 5112

department: Pediatrics

institute: Tulane University School of Medicine

summary: To uncover the effectors of metabolism-driven NPC differentiation, we compared the proteomic and transcriptomic signatures of renewing E13.5 NPC induced to differentiate with either glycolysis inhibition or Wnt activation. Acetate emerged as a key metabolite that play a role for NPC fate decision during kidney development.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data and proteomics  signatures of isolated NPCs treated with the Wnt agonist CHIR or with YN1-mediated glycolysis inhibition.
Freshly isolated E13.5 NPC (Six2+, Cited1+) were cultured for 24h in the presence or absence of either CHIR or YN1 separately. Then, NPCs were harvested and processed for bulk RNA seq or proteomics.

first: Samir

last: El-Dahr


title: Pathogen induced m6A dynamics regulate plant immunity

status: Public on Sep 08 2023

city: Philadelphia

first: Brian

middle: D

last: Gregory

state: PA

address: 433 South University Avenue

department: Biology

institute: University of Pennsylvania

summary: Post-transcriptional regulation of mRNA mediated by methylation at the N6 position of adenine (N6-methyladenosine (m6A)) can have profound effects on transcriptome regulation in plants. Focused studies across eukaryotes offer glimpses into the processes governed by m6A throughout developmental and disease states. However, we lack an understanding of the dynamics and scope of regulatory potential m6A possesses during biotic stress responses in plants. Here, we provide a comprehensive look into the effects m6A has on both the short-term and long-term response to pathogenic stress in Arabidopsis. m6A deposition influences transcript abundance and stability on populations of stress-responsive transcripts. Additionally, we demonstrate a time- and stress-dependent modulation of m6A highlighting specific stress-responsive transcripts regulated directly and indirectly by this mark. As a result, m6A deficient plants are more resistant to bacterial pathogen Pseudomonas syringae infection, and this mark is essential in dictating and coordinating transcript fate during a biotic stress reprograming event. Overall, we show m6A is a critical aspect in modulating the post-transcriptional regulation of the transcriptome in response to pathogenic stress in plants.

overall_design: 3 Replicates GMUCT seq on 14day old seedlings, 3 Replicates mRNA seq flg22-treated 14day old seedling, 3 Replicates 14day old seedlings m6A IP,  3 Replicates  m6A IP pair-end P.syringae maculicola-treated 4 week old leaves, 3 Replicates of mRNA seq pair-end P.syringae maculicola-treated 4 week old leaves

first: Wil

last: Prall

first: Arsheed

middle: H

last: Sheikh

first: Jeremie

last: Bazin

first: Jean

last: Bigeard

first: Marilia

last: Almeida-Trapp

first: Martin

last: Crespi

first: Heribert

last: Hirt


title: Glucocorticoid Receptor Activation in Lobular Breast Cancer is Associated with Reduced Cell Proliferation and Promotion of Metastases.

city: Dallas

first: Baylee

middle: A

last: Porter

state: TX

address: 5323 Harry Hines Blvd.

department: Internal Medicine

institute: UT Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Glucocorticoid Receptor Activation in Lobular Breast Cancer is Associated with Reduced Cell Proliferation and Promotion of Metastases; SUM44-GR-GFP

summary: Estrogen receptor-positive (ER+) invasive lobular breast cancer (ILC) comprises about ~15% of breast cancer.  ILC’s unique genotypic (loss of wild type E-cadherin expression) and phenotypic (small individual round cancer cells that grow in discontinuous nests) are thought to contribute to a distinctive pattern of metastases to serosal membranes. Unlike invasive ductal carcinoma (IDC), ILC metastases often intercalate into the mesothelial layer of the peritoneum and other serosal surfaces. While ER activity is a known driver of ILC proliferation, very little is known about how additional nuclear receptors contribute to ILC’s distinctive biology. In ER+ IDC, we showed previously that glucocorticoid receptor (GR) activity inhibits pro-proliferative gene expression and cell proliferation. Here we examined ER+ ILC models and find that GR activation similarly reduces S-phase entry gene expression and ILC proliferation. While slowing tumor growth rate, our data also suggest that GR activation results in an enhanced metastatic phenotype through increasing integrin-encoding gene expression, extracellular matrix protein adhesion, and mesothelial cell clearance. Moreover, in an intraductal mouse mammary gland model of ILC, we found that GR expression is associated with increased metastases despite slowed primary mammary tumor growth. Taken together, our findings suggest GR-mediated gene expression may contribute to the unusual characteristics of ILC biology.

overall_design: To investigate the role of GR in ILC tumor biology, we established a SUM44 cell line in which GR-GFP is ectopically expressed. We then performed gene expression prolifing analyisis using data obtained from RNA-seq of SUM44-GR-GFP from 4 treatment conditions.

first: Porter

last: Baylee

first: Frerich

last: Candace

first: Bennett

last: Lynda

first: Conzen

last: Suzanne


title: Glucocorticoid Receptor Activation in Lobular Breast Cancer is Associated with Reduced Cell Proliferation and Promotion of Metastases; MM134

overall_design: To investigate the role of GR in ILC tumor biology, we performed gene expression prolifing analyisis using data obtained from RNA-seq of MM134 from 4 treatment conditions.


title: TET-mediated DNA oxidation sustains intestinal homeostasis and protects from stressors.

city: Newark

first: Dahui

last: Wang

state: NJ

address: 73 Warren st

department: Biological Science

institute: Rutgers University, Newark

type: Methylation profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: DNA methylation pattern after salmonella typhimurium infection on human enterocyte [5hmeDIP-seq]

summary: We identified a differential enrichment of TET-medaited 5hmC in human enterocyte (Caco2BBE1 cells) upon infection with salmonella  typhimurium. Genes enriched with 5hmC are involved in Wnt and Notch signaling pathways.

overall_design: To investigate the role of DNA methylation in the response to challenege like bacteria infection. We infect the Caco2BBE1 cells with salmonella typhimurium and harvest after 3 hours.

first: Yue

last: Liu

first: Edward

last: Gonzalez


title: Effects of TET3 deletion on gene expression in ileum [RNA-seq]

summary: Bulk RNA-seq show differential gene expression profile beween Wild type (WT) and Tet3 knockout (KO) in ileum. We identified genes involved in innate immune defense, anti-microbial response and growth signaling to be affected by TET3 deletion.

overall_design: To invested the function of TET3 in ileum, we cross TET3 Flox mouse with VilinCre mouse to get TET3 Flox VilinCre mouse.


title: Redox state and altered pyruvate metabolism contribute to a dose-dependent metformin-induced lactate production of human myotubes

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Metformin-induced lactate production can lead to lactate acidosis as life-threatening side effect, whereas lactate in a physiological range might also be involved in the therapeutic effect. How metformin increases systemic lactate concentrations is only partly understood. Since human skeletal muscle has a high capacity to produce lactate, we aim to elucidate the potential contribution of skeletal muscle and the dose-dependent regulation of metformin-induced lactate production in primary human myotubes after 48 h of metformin treatment (16-776 μM). At 78 µM, metformin induced lactate production and glucose consumption. Investigating the cellular redox state by mitochondrial respirometry, we found metformin to inhibit the respiratory chain complex I (776 µM, p<0.01) along with a decreased [NAD+]:[NADH] ratio (776 µM, p<0.001). RNA sequencing and phospho-immunoblot data indicate inhibition of pyruvate oxidation mediated through phosphorylation of PDH complex (39 µM, p<0.01). In vivo in human skeletal muscle, we found pyruvate metabolism altered by exercise and not by metformin. Nonetheless, blood lactate levels in the pre-exercise condition are increased under metformin treatment (p<0.05). Metformin-induced inhibition of pyruvate oxidation combined with altered cellular redox state, both shift the equilibrium of the LDH reaction leading to enhanced lactate production of human myotubes.

overall_design: Primary human myoblasts treated with 16 – 776 µM metformin for 48 h.

first: Jennifer

last: Maurer

first: Xinjie

last: Zhao

last: Irmler

first: Anders

last: Gudiksen

first: Nanna

middle: S

last: Pilmark

first: Li

last: Qi

first: Thomas

last: Goj

first: Andreas

last: Birkenfeld

last: Peter

first: Rainer

last: Lehmann

first: Henriette

last: Pilegaard

first: Kristian

last: Karstoft

first: Guowang

last: Xu

first: Cora

last: Weigert


title: Ablation of dual specificity phosphatase 6 protects against non-alcoholic fatty liver disease via CYP4A and MAPK

city: Sendai

first: Can

last: Jiang

state: Miyagi

address: 2-1 Seiryomachi, Aobaku

department: Investigative Pathology

country: Japan

institute: Tohoku University

summary: Dual specificity phosphatase 6 (DUSP6) is a specific phosphatase for mitogen-activated protein kinase (MAPK). In this study, we used a high-fat diet (HFD)-induced murine non-alcoholic fatty liver disease (NAFLD) model to investigate the role of DUSP6 in this disease. Wild-type (WT) and Dusp6-haploinsufficient (HI) mice developed severe obesity and liver pathology consistent with NAFLD when exposed to HFD. In contrast, Dusp6-knockout (KO) mice completely eliminated these phenotypes. Furthermore, primary hepatocytes isolated from WT mice exposed to palmitic and oleic acids exhibited abundant intracellular lipid accumulation, while hepatocytes from Dusp6-KO mice showed minimal lipid accumulation. Transcriptome analysis revealed significant downregulation of genes encoding cytochrome P450 4A (CYP4A), known to promote ω-hydroxylation of fatty acids and hepatic steatosis, in Dusp6-KO hepatocytes compared with WT hepatocytes. Diminished CYP4A expression was observed in the liver of Dusp6-KO mice compared to WT and Dusp6-HI mice. Knockdown of DUSP6 in HepG2, a human liver-lineage cell line, also promoted a reduction of lipid accumulation, downregulation of CYP4A, and upregulation of phosphorylated/activated MAPK. Furthermore, inhibition of MAPK activity promoted lipid accumulation in DUSP6-knockdown HepG2 cells without affecting CYP4A expression, indicating that CYP4A expression is independent of MAPK activation. These findings highlight the significant role of DUSP6 in HFD-induced steatohepatitis through two distinct pathways involving CYP4A and MAPK.

overall_design: Transcriptome sequence analysis used RNA extracted from primary mouse hepatocytes that were treated or not with a mixture of palmitic and oleic acids.

first: Yuriko

last: Saiki

first: Shuto

last: Hirota

first: Kosei

last: Iwata

first: Xinyue

last: Wang

first: Yutaka

last: Ito

first: Keigo

last: Murakami

first: Takehiro

last: Imura

first: Jun

last: Inoue

first: Atsushi

last: Masamune

first: Akiyoshi

last: Hirayama

first: Masafumi

last: Goto

first: Toru

last: Furukawa


title: A tRNA modifying enzyme facilitates RNase P activity in Arabidopsis nuclei

city: Strasbourg

first: Philippe

last: Giegé

address: 12 rue du general Zimmer

country: France

institute: IBMP-CNRS

type: Non-coding RNA profiling by high throughput sequencing

summary: RNase P is the essential activity that performs the 5’ maturation of tRNA precursors. Beyond the ancestral form of RNase P containing a ribozyme, protein-only RNase P enzymes termed PRORP were identified in eukaryotes. In human mitochondria, PRORP forms a complex with two protein partners to become functional. In plants, although PRORP enzymes are active alone, we investigate their interaction network to understand their integration with gene expression pathways. Here we investigate functional interactions involving the Arabidopsis nuclear RNase P PRORP2. We show, using an immuno-affinity strategy, that PRORP2 occurs in a complex with the tRNA methyl transferases TRM1A and B in vivo. Beyond RNase P, these enzymes can also interact with RNase Z. We show that TRM1A/B localize in the nucleus and find that their double knock out mutation results in a severe macroscopic phenotype. Using a combination of immuno-detections, mass spectrometry and a transcriptome wide tRNAseq approach, we observe that TRM1A/B are responsible for the m2,2G26 modification of 70% of cytosolic tRNAs in vivo. We use the transcriptome wide tRNAseq approach as well as RNA blot hybridizations to show that RNase P activity is impaired in TRM1A/B mutants for specific tRNAs, in particular, tRNAs containing a m2,2G modification at position 26 that are strongly down-regulated in TRM1A/B mutants. Altogether, results indicate that the m2,2G adding enzymes TRM1A/B functionally cooperate with nuclear RNase P in  vivo for the early steps of cytosolic tRNAs biogenesis.

overall_design: Mim-tRNAseq analysis of Arabidopsis wild-type and TRM1A/B mutants

first: Mathilde

last: Arrivé

first: Mathieu

last: Bruggemann

first: Vassilis

last: Scaltsoyannes

first: Léna

last: Coudray

first: Yi-Fat

last: Quan

first: Cédric

last: Schelcher

first: Valérie

last: Cognat

last: Hammann

first: Johana

last: Chicher

last: Wolff

first: Anthony

last: Gobert


title: MicroRNA Profiling in Aplastic Anaemia (AA) Reveals Similarities between Secondary Myelodysplastic Syndromes (MDS) Arising from Clonal Progression and de novo MDS

status: Public on Sep 02 2023

city: Melbourne

first: Lynette

last: Chee

state: VIC

address: 305 Grattan Street

department: ACRF Laboratory

country: Australia

institute: The Royal Melbourne Hospital/ Peter MacCallum Cancer Centre

summary: Aplastic anaemia (AA) is a form of bone marrow failure (BMF) resulting in significant cytopenias and may progress with clonal evolution to myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML).  MicroRNA expression is dysregulated in MDS/AML but there are limited studies on its role in the pathogenesis of AA.  Using stored BM samples (n=81) from 2006-2019 from 52 patients, we demonstrate key differences in miRNA expression between AA patients at diagnosis and de novo MDS patients (n=21).  The five most significantly upregulated miRNA in MDS patients (downregulated in AA) were miR-130a-3p, miR-221-3p, miR-126-3p, miR-27b-3p and miR-196b-5p (adj p<0.001).  However, at the time of AA clonal progression to secondary MDS/AML, no significant miRNA differences were identified suggesting that the underlying mechanistic pathways are similar between AA progression to MDS/AML and de novo MDS.  At diagnosis, miR-127-3p, miR-1271-5p, miR-301b-5p, miR-3934-5p and miR-4531 (adj p=0.081) were upregulated in those whose AA eventually progressed in comparison to those without eventual clonal progression.  Using KEGG pathway analysis derived from miRPathDBv2.0, cytokine-cytokine receptor interaction, TGF-, MAP kinase, prolactin, Hippo, neurotrophin and FOXO signalling pathways were enriched in AA patients with clonal progression to MDS/AML; these pathways were similarly enriched in the de novo MDS cohort.  These studies highlight the differing miRNA expression profiles in AA and MDS and in AA clonal evolution to MDS/AML.

overall_design: 116 samples

first: Niko

last: Thio


title: Primate-specific ZNF808 is essential for pancreatic development in humans

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

country: United Kingdom

institute: University of Exeter Medical School

type: Genome binding/occupancy profiling by high throughput sequencing


title: Primate-specific ZNF808 is essential for pancreatic development in humans [RNA-seq]

summary: Functional investigation of the role primate-specific gene ZNF808 over pancreas differentiation. Loss of function of ZNF808 is a cause of pancreatic agenesis, which is a failure of pancreas development.

overall_design: Gene expression measured by RNA-seq over timecourse of pancreatic differentiation in WT and ZNF808 KO conditions.

first: Michael

last: Imbeault

first: Jouni

last: Kvist

first: Hossam

last: Montaser

first: Timo

last: Otonkoski


title: TAZ facilitates breast tumor growth by promoting an immune-suppressive tumor microenvironment [in-vitro]

city: Rehovot

first: Ori

last: Hassin

address: Hertzel 234

department: MCB

country: Israel

institute: Weizmann Institute

summary: The core Hippo pathway module consists of a tumor-suppressive kinase cascade that inhibits the transcriptional coactivators Yes-associated protein (YAP) and WW domain-containing transcription regulator protein 1 (WWTR1; also known as TAZ). When the Hippo pathway is downregulated, as often occurs in breast cancer, YAP/TAZ activity is induced. To elaborate the roles of TAZ in triple-negative breast cancer (TNBC), we depleted Taz in murine TNBC 4T1 cells, using either CRISPR/Cas9 or small hairpin RNA (shRNA). TAZ-depleted cells and their controls, harboring wild-type levels of TAZ, were orthotopically injected into the mammary fat pads of syngeneic BALB/c female mice, and mice were monitored for tumor growth. TAZ depletion resulted in smaller tumors compared to the tumors generated by control cells, in line with the notion that TAZ functions as an oncogene in breast cancer. Tumors, as well as their corresponding in vitro cultured cells, were then subjected to gene expression profiling by RNA sequencing (RNA-seq). Interestingly, pathway analysis of the RNA-seq data indicated a TAZ-dependent enrichment of ‘Inflammatory Response', a pathway correlated with TAZ expression levels also in human breast cancer tumors. Specifically, the RNA-seq analysis predicted a significant depletion of regulatory T cells (Tregs) in TAZ-deficient tumors, which was experimentally validated by the staining of tumor sections and by quantitative cytometry by time of flight (CyTOF). Strikingly, the differences in tumor size were completely abolished in immune-deficient mice, demonstrating that the immune-modulatory capacity of TAZ is critical for its oncogenic activity in this setting. Cytokine array analysis of conditioned medium from cultured cells revealed that TAZ increased the abundance of a small group of cytokines, including plasminogen activator inhibitor 1 (Serpin E1; also known as PAI-1), CCN family member 4 (CCN4; also known as WISP-1) and interleukin-23 (IL-23), suggesting a potential mechanistic explanation for its in vivo immunomodulatory effect. Together, our results imply that TAZ functions in a non-cell-autonomous manner to modify the tumor immune microenvironment and dampen the anti-tumor immune response, thereby facilitating tumor growth.

overall_design: 4T1 cells were infected with lentivirus expression of ShC or ShTAZ. Cells were grown in vitro and also injected into mice to create tumors. Tumors (ShC and ShTAZ), as well as their corresponding in vitro cultured cells, were  subjected to gene expression profiling by RNA sequencing using the MARS-seq protocol. Minimum 3 replicates from each condition. Also, in-vitro cell (4T1 TAZ WT and 4T1 TAZ KO) were subjected to  gene expression profiling by RNA sequencing using RNA-seq protocol.

first: Anat

last: Gershoni


title: Study the function of C17orf80

city: Beijing

first: Xianhua

last: Wang

address: 5 Summer Palace Road, Haidian District, Beijing

department: Institute of Molecular Medicine, College of Future Technology

country: China

institute: Peking University

summary: To study the function of C17orf80, we performed chromatin immunoprecipitation DNA-sequencing in HeLa cells.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for C17orf80  in HeLa cells.

first: Hao

last: Wu

first: Wanqiu

last: Ding


title: APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release

status: Public on Sep 01 2023

city: San Francisco

first: Ayushi

last: Agrawal

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

summary: Apolipoprotein E4 (APOE4) is an important driver of Tau pathology, gliosis, and degeneration in Alzheimer’s disease (AD). Still, the mechanisms underlying these APOE4-driven pathological effects remain elusive. In this study, we demonstrated in a tauopathy mouse model that APOE4 promoted the nucleo-cytoplasmic translocation and release of high mobility group box 1 (HMGB1) from hippocampal neurons, which correlated with the severity of hippocampal microgliosis and degeneration. Injection of HMGB1 into the hippocampus of young APOE4-tauopathy mice induced considerable and persistent gliosis. Selective removal of neuronal APOE4 reduced the nucleo-cytoplasmic translocation and release of HMGB1. Therapeutic treatment of APOE4-tauopathy mice with HMGB1 inhibitors effectively blocked the intraneuronal translocation and release of HMGB1 and ameliorated the development of prominent APOE4-driven AD pathologies, including gliosis, Tau pathology, neurodegeneration, and myelin deficits. Single-nucleus RNA-sequencing revealed that treatment with HMGB1 inhibitors diminished disease-associated and enriched disease-protective subpopulations of neurons, microglia, and astrocytes in APOE4-tauopathy mice. Thus, HMGB1 inhibitors represent a promising approach for treating APOE4-related AD.

overall_design: Single-nucleus RNA sequencing on isolated hippocampi from 9.5-month-old PS19-E3 and PS19-E4 mice that underwent a 12-week treatment with either saline or the HMGB1 inhibitors.

first: Nicole

last: Koutsodendris

first: Jessica

last: Blumenfeld

first: Michela

last: Traglia

first: Reuben

last: Thomas

first: Yadong

last: Huang


title: Preclinical Evidence for the Glucocorticoid-Sparing Potential of a Dual Toll-Like Receptor 7/8 Inhibitor in Autoimmune Diseases

city: Billerica

first: Andrew

last: Bender

state: MA

address: 45 Middlesex Turnpike

department: Research Unit - Neuroscience & Immunology

institute: EMD Serono

summary: Single cell RNA-seq analysis of PBMCs testing for a synergistic effect of TLR7/8 inhibition and the glucocorticoid dexamethasone

overall_design: Isolated PBMCs of four healthy human blood donor leukopaks, treated with a TLR7 and/or TLR8 inhibitor and/or dexamethasone

first: Geraci

last: Nicholas

first: Bender

last: Andrew

first: Tzvetkov

last: Evgeni

first: Deshmukh

last: Ankita

first: Vaidyanathan

last: Bharat


title: Primate-specific ZNF808 is essential for pancreatic development in humans [ChIP-seq]

first: Nick

last: Owens

overall_design: ChIP-seq for H3K27me3 and H3K27ac over timecourse of pancreatic differentiation in WT and ZNF808 KO conditions.

first: Michael

last: Imbeault

first: Jouni

last: Kvist

first: Hossam

last: Montaser

first: Timo

last: Otonkoski


title: Hippocampal single-nuclei RNA-sequencing identifies a role for Kdm5a in regulating cell identity

first: Maria

last: Chahrour

state: Texas

address: 6000 Harry Hines Boulevard, NB10.104

summary: KDM5A is a chromatin remodeler disrupted in neurodevelopmental disease. To investigate the effect of losing KDM5A on the development of the hippocampus, we profiled hippocampi from wild type (WT) and Kdm5a -/- mice using single-nuclei RNA sequencing (snRNA-seq). We found that KDM5A regulates the development of specific subtypes of excitatory (CA1, CA2, CA3) and inhibitory (SST+, PVALB+) neurons, that loss of KDM5A leads to a more mature cellular identity in the hippocampus, and that KDM5A functions early in development to specify proper CA1 cell identity.

overall_design: Nuclei were isolated from hippocampal tissue of 20-week old WT and Kdm5a -/- (KO) mice and snRNA-seq data were generated by sequencing of 4 biological replicates per genotype using Illumina NovaSeq 6000.

first: Lauretta

last: El Hayek

first: Ashlesha

last: Gogate


title: TAZ facilitates breast tumor growth by promoting an immune-suppressive tumor microenvironment [in-vivo and in-vitro]

first: Ori

last: Hassin

first: Anat

last: Gershoni


title: TAZ facilitates breast tumor growth by promoting an immune-suppressive tumor microenvironment


title: Effect of depletion of C17orf80 on mtDNA transcription in HEK-293T cells

first: Xianhua

last: Wang

overall_design:
To investigate the function of C17orf80, we established HEK-293T cell lines in which target gene has been knocked out by CRISPR/Cas9.
We then performed gene expression profiling analysis using data obtained from RNA-seq of wild type and knockout cells.

first: Hao

last: Wu

first: Wanqiu

last: Ding


title: Mutations in the Drosophila melanogaster gene pyruvate kinase interfere with larval development

city: Bloomington

first: Jason

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

institute: Indiana University

summary: Pyruvate kinase (Pyk) is a rate-limiting enzyme that catalyzes the final metabolic reaction in glycolysis. The importance of this enzyme, however, extends far beyond ATP production, as Pyk is also known to regulate tissue growth, cell proliferation, and development. Studies of this enzyme in Drosophila melanogaster, however, are complicated by the fact the fly genome encodes six Pyk paralogs and the function of these individual genes remain poorly defined. To address this issue, we used a phylogenetic approach to demonstrate that the gene Pyk encodes the enzyme most similar to the mammalian Pyk orthologs while the other five Drosophila Pyk have significantly diverged from the canonical enzyme. Consistent with this observation, metabolomic studies of two different Pyk mutant backgrounds revealed that larvae lacking Pyk exhibit a severe block in glycolysis, with a buildup of glycolytic intermediates upstream of pyruvate. However, our analysis also unexpectantly reveals that steady state pyruvate levels are unchanged in Pyk mutants, indicating that larval metabolism maintains pyruvate pool size despite severe metabolic limitations. Consistent with our metabolomics findings, a complementary RNAseq analysis revealed that genes involved in lipid metabolism and peptidase activity are elevated in Pyk mutants, again indicating that loss of this glycolytic enzyme induces compensatory changes in other aspects of metabolism. Overall, our study provides both insight towards understanding how Drosophila larval metabolism adapts to disruption of glycolytic metabolism and immediate clinical relevance considering that Pyk deficiency is the most common congenital enzymatic defect in humans.

overall_design: RNA-seq of Pyk 23/+ heterozygous controls versus Pyk 23/31 CRISPR mutants, three whole-fly biological replicates

first: Yasaman

last: Heidarian

middle: P

last: Tourigny

first: Tess

last: Fasteen

first: Nader

last: Mahmoudzadeh

first: Alexander

last: Hurlburt

first: Julie

last: Reisz

first: Angelo

last: D’Alessandro


title: Carbonyl compounds in the gas phase are critical determinants of wood smoke toxicity

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

institute: IRSN

summary: Epidemiological studies identified air pollution as one of the prime causes for human morbidity and mortality due to harmful effects mainly on the cardiovascular and respiratory system. Damage to the lung leads to several severe diseases such as fibrosis, chronic obstructive pulmonary disease and cancer. Noxious environmental aerosols are comprised of a gas and particulate phase representing highly complex chemical mixtures composed of myriads of compounds. Although some critical pollutants, foremost particulate matter (PM), could be linked to adverse health effects, a comprehensive understanding of relevant biological mechanisms and detrimental aerosol constituents is still lacking. Here, we employed a systems toxicology approach focusing on wood combustion, an important source for air pollution, and demonstrate a key role of the gas phase, specifically carbonyls, to drive adverse effects. Transcriptional profiling and biochemical analysis of human lung cells exposed at the air-liquid-interface determined the DNA damage and stress response as well as perturbation of cellular metabolism as major key events. Connectivity mapping revealed a high similarity of gene expression signatures induced by wood smoke and agents prompting DNA-protein crosslinks (DPCs). Indeed, various gaseous aldehydes were detected in wood smoke, which promote DPCs, initiate similar genomic responses and are responsible for DNA damage provoked by wood smoke.  Hence, systems toxicology enables the discovery of critical constituents of complex mixtures i.e. aerosols and highlights the role of carbonyls on top of particulate matter as important health hazard.

overall_design: Exposure of two human lung cell lines (A549 alveolar epithelial cells, and BEAS-2B bronchial epithelial cells) to three different conditions:  complete wood smoke, filtered wood smoke and control. All conditions were performed in triplicates and analyzed by mRNAseq (Illumina)

first: Olivier

last: Armant

first: Marco

last: Dilger

first: Carsten

last: Weiss


title: Transcriptome and physiological analysis of rapeseed tolerance to post-flowering temperature increase

city: Valdivia

first: Javier

last: Canales

state: Los Ríos

address: Campus Isla Teja s/n

department: Instituto de Bioquimica y Microbiologia

country: Chile

institute: Universidad Austral de Chile

summary: This study investigates the transcriptome and physiological responses of rapeseed to post-flowering temperature increases, providing valuable insights into the molecular mechanisms underlying rapeseed tolerance to heat stress. Two rapeseed genotypes, Lumen and Solar, were assessed under control and heat stress conditions in field experiments conducted in Valdivia, Chile. Results showed that seed yield and seed number were negatively affected by heat stress, with genotype-specific responses. Lumen exhibited a 9.3% average seed yield reduction, while Solar showed a 28.7% reduction. RNA-seq analysis of siliques and seeds revealed tissue-specific responses to heat stress, with siliques being more sensitive to temperature stress. Hierarchical clustering analysis identified distinct gene clusters reflecting different aspects of heat stress adaptation in siliques, with a role for protein folding in maintaining silique development and seed quality under high temperature conditions. In seeds, three distinct patterns of heat-responsive gene expression were observed, with genes involved in protein folding and response to heat showing genotype-specific expression. Gene coexpression network analysis revealed major modules for rapeseed yield and quality, as well as the trade-off between seed number and seed weight. Overall, this study contributes to understanding the molecular mechanisms underlying rapeseed tolerance to heat stress and can inform crop improvement strategies targeting yield optimization under changing environmental conditions.

overall_design: Seed samples for the RNA-seq were collected from 5 plants per plot (25 siliques per plant from the bottom of the main raceme) across treatments in two development stages: 7 and 14 after flowering, i.e. after a one and twice weeks after the beginning of the heat stress treatment.


title: MADS1-regulated lemma and awn development benefits barley yield

city: Shanghai

first: Jin

last: Shi

address: NO 800, Dongchuan Rd

institute: Shanghai Jiaotong University

summary:
Floral organ shape and size in cereal crops can affect grain size and yield, so genes that regulate their development are promising breeding targets. The lemma, which protects inner floral organs, can physically constrain grain growth; while the awn, a needle-like extension of the lemma, creates photosynthates to promote grain fill. Although several genes and modules controlling grain size and awn/lemma growth in rice have been characterized, these processes, and the relationships between them, are not well understood for barley and wheat. Here, we demonstrate that the barley E-class gene HvMADS1 positively regulates awn length and lemma width, leading to increased grain size and weight. Cytological data indicated that MADS1 promotes grain growth by promoting cell proliferation, while multi-omics data revealed MADS1 target genes associated with cell cycle, phytohormone signaling, and developmental processes. We defined two direct targets of MADS1 regulation, HvSHI and HvDL, whose knockout mutants mimic awn and/or lemma phenotypes of mads1 mutants; and demonstrated that MADS1 interacts APETALA2 (A-class) to synergistically activate downstream genes in awn/lemma development. Notably, we found that MADS1 function remains conserved in wheat, promoting cell proliferation to increase awn length. These findings extend our understanding of MADS1 function in floral organ development to inform strategies for Triticeae crop improvement.
Three replicates of barley tissues were collected for RNA extraction: lemma and awn from the central part of lemma and awn from WT and mads1 mutants for RNA-seq and RT-qPCR

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mads1 and wild type barley

first: Yueya

last: Zhang

first: Chaoqun

last: Shen

first: Gang

last: Li


title: Altered cartilage gene expression in Aga2 OI mouse negatively impacts linear growth through Sox9 and FGF signaling

city: Los Angeles

first: Jennifer

last: Zieba

address: 615 Charles E. Young Dr.

institute: University of California, Los Angeles

summary: Osteogenesis Imperfecta is characterized by short stature however the cellular mechanisms behind this phenotype are unclear. We isolated tibial and femoral cartilage growth plate chondrocytes from postnatal day 5 wild type and Aga2 (a model of OI) mice and analyzed differential expression patterns using single cell RNA-seq

overall_design: Growth plate chondrocytes from Wild-type and Aga2 mice were isolated from femoral and tibial cartilage tissue at postnatal day 5 and analyzed using scRNAseq.

first: Lisette

last: Nevarez

first: Davis

last: Wachtell

first: Jorge

last: Martin

last: Kot

first: Sereen

last: Wong

first: Daniel

last: Cohn

first: Deborah

last: Krakow


title: RNA sequencing of mouse basal-derived prostate organoids treated with vehicle, UK5099, Butyrate, or UK5099+Butyrate

first: Andrew

middle: Scott

last: Goldstein

address: 610 Charles E Young Dr East

summary: The goal of this study was to perform transcriptomics on vehicle-, UK5099-, Butyrate-, and UK5099+Butyrate-treated mouse prostate organoids. We used FACS to isolate basal cells from C57BL/6 mouse prostates and treated with small molecules for one week before harvesting for RNA-sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for vehicle-, UK5099-, Butyrate-, and UK5099+Butyrate-treated mouse prostate organoids. UK5099 inhibits the mitochondrial pyruvate carrier and butyrate inhibits histone deacetylases.

first: Jenna

last: Giafaglione


title: Endothelial Cell Senescence Stimulates Amyloid-β Phagocytosis and Barrier Function of Microglia Leading to Attenuation of Cognitive Impairment in the APPswe/PS1dE9 Mouse Model of Alzheimer’s Disease

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

summary: Our results reveal that EC senescence enhances microglial phenotype shift into neuroprotective phenotype with increases in phagocytic and barrier functions, and propose that an apparently paradoxical idea may contribute to the development of a novel therapeutic strategy for AD.

overall_design: 4 samples

first: Yoshiyuki

last: Rikitake


title: IL6R-STAT3 oscillations produce stable heterogeneity of metabolic phenotype in pancreatic ductal adenocarcinoma cells

city: Oxford

first: Pawel

last: Swietach

state: I have read and agree

address: Department of Physiology, Anatomy and Genetics, Parks Road

department: Physiology, Anatomy & Genetics

institute: University of Oxford

summary: Pro-growth mutations enable malignancy but for proliferation to proceed, energy and substrates cannot be limiting. However, unrestricted metabolic activation would be self-terminating if it depletes tumor resources. Cancer cells could avoid this by alternating between basal and activated metabolic states, thereby producing dynamic, population-level metabolic heterogeneity that rations resources. Single-cell metabolic phenotyping of pancreatic ductal adenocarcinoma cells identified MIA-PaCa-2 as having broad heterogeneity of fermentative metabolism. Cells sorted by greater lactic acid efflux capacity had higher fermentative rates when subsequently cultured. However, this phenotype was unrelated to cell-cycling or glycolytic and respiratory gene expression, and persisted for less than a week. Transcriptomics linked the higher fermentation with IL6R-STAT3 signaling.  Accordingly, IL6R-positive cells were more active metabolically. Episodic activation of metabolism arises from delayed negative feedback via SOCS3 on IL6R-STAT3. We propose that switching between metabolic states allows cell-cohorts to take turns in progressing energy-intense processes without over-burdening shared resources.

overall_design: RNAseq analysis of FACS sorted subpopulations of MIA PaCa2 cancer cells, representing two extremes of phenotype (a measure of metabolic rate). Repeated four times (i.e. four paired samples).

first: Wiktoria

last: Blaszczak


title: FOXA1 phosphorylation by CDK4 prevents activation of novel chromatin regions and HER2 expression in breast cancer

city: Salamanca

first: Darek

last: Kedra

state: Castilla y León

address: Campus Miguel de Unamuno

department: Cancer Research Center

country: Spain

institute: University of Salamanca

summary:
Cyclin Dependent Kinase 4/6 inhibitors induce transcription in breast tumors via FOXA1 chromatin binding.
The use of Cyclin Dependent Kinase 4/6 inhibitors (CDK4/6i) induce transcription in breast tumors. The control mechanism of such genomic changes and their physiological relevance are not elucidated yet. Now, we identified chromatin activation of tumors treated with CDK4/6i. These chromatin changes induce an increase of HER2 expression and signaling. Mechanically, our study demonstrates that FOXA1 is a new substrate of CDK4 and that its phosphorylation limits the binding of FOXA1 to conventional chromatin regions. Moreover, when patients are treated with CDK4/6i, a dephosphorylated FOXA1 binds to additional chromatin regions. By doing so, FOXA1 leads to an increase of HER2 expression and of the activation of HER2-MEK-ERK pathway in breast cancer patients. Accordingly, we might envision a clinical benefit of adding antiHER2 therapy to delay development of resistance and therefore, to prolong PFS in patients yet receiving CDK4/6i.

overall_design:
Three (3) ChIP-seq samples all derived from BT474 cell line: 1). wild type; 2) FOXA1_S234A mutation 3) FOXA1_S307A mutation. Two replicates each. 76bp long reads. Replicas were merged after mapping to the genome. Peaks were called using a) each of the mutants versus wild type BAMs (control) and wild type BAM vs each of the mutant BAMs (control) separately.

Patient data: There were two samples taken from each of the patients from the same tumor: 1. sample at the week zero, no treatment/baseline; 2. sample at three weeks, after a 3 weeks treatment Letrozole+Ribociclib. Sample 1 was divided into: 1a: control/input; and 1b: ChIP-seq with anti-H3K4me2 antibody. Sample 2 was used just for the ChIP-seq with anti-H3K4me2 antibody.

clinical_trial_name: CORALLEEN
clinical_trial_id: NCT02513394

***Please note that the raw FASTQ data files were submitted to ENA: PRJEB59327***

first: Shixiong

last: Wang

first: Jose

last: Palomeque

first: Gemma

last: Santacana-Font

first: David

last: Tena-Chaves

first: Alice

last: Galeotti

first: Ioanna

last: Michou

first: Sachin

last: Sighn

first: Neus

last: Daviu

first: Javier

last: Gutiérrez-Fernández

first: Marina

last: Portantier

first: Rosa

last: Aliguè

first: Joaquím

last: Gavilà

first: Fara

last: Brasó

first: Aleix

last: Prat

first: Meritxell

last: Bellet

first: Sandra

last: Lopez-Aviles

first: Antonio

last: Hurtado


title: ATAC-sequencing of primary basal-derived mouse prostate organoids treated with vehicle, the mitochondrial pyruvate carrier inhibitor UK5099, or lactate supplementation

first: Andrew

last: Goldstein

department: Urology

summary: The goal of this study was to understand how the mitochondrial pyruvate carrier inhibitor,UK5099, and lactate supplementation alter chromatin accessibility in primary basal-derived mouse prostate organoids.

overall_design: ATAC-sequencing of primary basal-derived mouse prostate organoids treated with vehicle, 10uM UK5099, or 20mM sodium lactate supplementation

first: Goldstein

last: Andrew

first: Giafaglione

last: Jenna


title: Characterizing gene expression after expressing  genetically encoded tools to change cellular NADH/NAD+ ratio in living cells

city: San Diego

first: Xingxiu

last: Pan

state: California

address: 6868 Nancy Ridge Dr

institute: Scintillon institute

summary: To study the  overabundance of reducing equivalents, termed reductive stress, specifically for NADH reductive stress, we introduce a soluble transhydrogenase from E. coli (EcSTH) as a novel genetically encoded tool to promote NADH overproduction

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hela cells expressing LUC, LbNOX, EcSTH, mitoEcSTH

first: Valentin

last: Cracan


title: RNA sequencing of Mpc1 floxed mouse prostate organoids transduced with RFP control or Cre virus and treated -/+ small molecule MPC inhibitor UK5099

summary: The goal of this study was to determine how knockout or pharmacological inhibition of the mitochondrial pyruvate carrier (MPC) alters lineage identity in the prostate. We isolated basal cells from Mpc1 floxed mouse prostates and transduced with a control RFP virus or Cre recombinase virus. We then plated into organoid culture and treated with either vehicle or the small molecule MPC inhibitor UK5099 for one week.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Mpc1 fl/fl RFP vehicle, Mpc1 fl/fl RFP UK5099, Mpc1 fl/fl Cre vehicle mouse prostate organoids

first: Jenna

last: Giafaglione


title: RNA sequencing of wildtype, PTEN single knockout (SKO), and PTEN;Rb1 double knockout (DKO) mouse prostate organoids

summary: The goal of this study was to perform transcriptomics on wildtype, PTEN single knockout (SKO) and PTEN;Rb1 double knockout (DKO) mouse prostate organoids. We isolated basal cells from PTEN floxed and PTEN;Rb1 floxed mouse prostates and infected with either RFP control or Cre recombinase to establish wildtype, SKO, and DKO mouse prostate organoids.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype, SKO, and DKO mouse prostate organoids


title: FAM120A couples SREBP-dependent transcription and splicing of lipogenesis enzymes downstream of mTORC1

city: Irvine

first: Cholsoon

last: Jang

address: 839 Health Science Rd

department: Biological Chemistry

institute: University of California, Irvine

summary: The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth that stimulates macromolecule synthesis via insulin, growth factors, and oncogenic signals. mTORC1 activates anabolic pathways by inducing posttranslational modifications of metabolic enzymes, and by regulating expression through transcription and mRNA processing. However, mechanisms of how mTORC1 orchestrates these tightly connected processes remain unclear. Here, we identify FAM120A as a transcriptional co-activator that couples transcription and splicing of lipid synthesis enzymes downstream of mTORC1-SRPK2 signaling. Mechanistically, the mTORC1-activated SRPK2 phosphorylates a splicing factor SRSF1, enhancing its binding to FAM120A. FAM120A directly interacts with a lipogenic transcription factor SREBP1 at active promoters, thereby bridging newly transcribed lipogenic genes to the RNA splicing machinery. This multi-protein complex regulated by mTORC1 promotes efficient splicing and stability of lipogenic transcripts, resulting in fatty acid synthesis and cancer cell proliferation. These results elucidate FAM120A as a critical transcription co-factor that connects mTORC1-dependent gene regulation programs for anabolic cell growth.

overall_design: We performed a deep RNA sequencing to determine the effect of FAM120A and SRSF1 knockdown on global gene expression and RNA splicing.

first: Yujin

last: Chun

first: Sungyun

last: Cho

first: Gina

last: Lee

first: John

last: Blenis


title: Multiplex Epigenome Editing of MECP2 to Rescue Rett Syndrome Neurons II

city: New York

first: Xiaonan

last: Guan

state: NY

address: 1150 St Nicholas Ave, 403

institute: Russ Berrie Medical Science Pavillion

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

overall_design: Refer to individual Series


title: MicroRNA profiling of mammary gland and liver tissue of cows under different feeding conditions (control, restricted amount of milk replacer, milk replacer ad libitum)

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

summary: To investigate the influence of the feed additive (milk replacer) on biological processes occuring in cow mammary parenchyma, mammary fat pad and liver via miRNA-mediated regulation. To this end, we performed microRNA expression profiling using next-generation sequencing.

overall_design: Comparative gene expression analysis of miRNA-seq data for the investigated tissues and feeding conditions was performed.

first: Ewelina

last: Semik-Gurgul


title: RNA sequencing of PTEN,Rb1 double knockout (DKO) mouse prostate organoids treated with vehicle or the small molecule mitochondrial pyruvate carrier (MPC) inhibitor UK5099

summary: The goal of this study was to determine how pharmacological inhibition of the mitochondrial pyruvate carrier (MPC) alters lineage identity in transformed prostate organoids. We isolated basal cells from PTEN,Rb1 floxed mouse prostates and infected with Cre recombinase to establish PTEN, Rb1 double knockout (DKO) mouse prostate organoids. We then treated the DKO organoids with vehicle or 10uM UK5099 for five days.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DKO vehicle and DKO 10uM UK5099 mouse prostate organoids. Mice are from a mixed C57BL/6:129/Sv:FVB genetic background.


title: Multiplex Epigenome Editing of MECP2 to Rescue Rett Syndrome Neurons (ChIP-Seq)

summary: Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by loss-of-function heterozygous mutations of MECP2. Reactivation of the silent wild-type MECP2 allele on the inactive X chromosome (Xi) represents a promising therapeutic opportunity for female RTT patients. Here, we applied a multiplex epigenome editing approach to reactivate MECP2 on Xi. Demethylation of the MECP2 promoter by dCas9-Tet1 with target sgRNA reactivated MECP2 on Xi in RTT hESCs without detectable off-target effects at the transcriptome level. Neurons derived from methylation edited RTT hESCs reversed the smaller soma size and electrophysiological abnormalities. Insulation of the methylation edited MECP2 locus in RTT neurons by dCpf1-CTCF with target crRNA stabilized MECP2 reactivation and rescued the RTT-related neuronal defects, providing a proof-of-concept study for multiplex epigenome editing to treat RTT.

overall_design: Evaluation of off-target effects of dCpf1-CTCF with crRNA targeting CTCF binding flanking MECP2 locus

first: Rudolf

last: Jaenisch

first: X

last: Liu


title: Next Generation Sequencing Facilitates Quantitative Analysis of the implication of LAIR-1 in sorted lung macrophage Transcriptomes

first: Georges Doumet

last: HELOU

address: 1450 Biggy St, NRT5505, Keck School of Medicine

department: Molecular Microbiology and Immunology

institute: University of Southern California

summary: Recent studies reported the inhibitory properties of LAIR-1 in different inflammatory diseases, including allergic and viral airway inflammation. However, the implication of LAIR-1 in ALI/ARDS remains unknown. Poly(I:C), a synthetic analog of (ds)RNA was administrated intranasally to mimic acute inflammation in viral infections and therefore induce experimental ALI/ARDS.  RNA sequencing approach was used to explore and compare lung macrophage transcriptomic profiles in wild-type and LAIR-1 knock-out mice.

overall_design: mRNA profiles of sorted pulmonary macrophages from WT and LAIR-1 KO mice were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.

first: D

last: Helou

first: O

last: Akbari


title: Multiplex Epigenome Editing of MECP2 to Rescue Rett Syndrome Neurons (WGBS)

overall_design: Evaluation of off-target effects by WGBS of dCas9-dTet1(dC-dT) and dCas9-Tet1(dC-T) with sgRNA3


title: The CX3CL1-CX3CR1 chemokine axis can contribute to tumor immune evasion and blockade with a novel CX3CR1 monoclonal antibody enhances responses to anti-PD-1 immunotherapy [CT26]

city: Boston

first: Gordon

last: Freeman

address: 450 Brookline Avenue

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

summary: To investigate the imunoresistance programs regulated by the CX3CL1-CX3CR1 axis, we treated CT26 mouse tumor cell line with CX3CL1, CX3CL1 + IFN-γ, IFN-γ, and no treatment

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CT26 tumor cells treated with conditions : CX3CL1, CX3CL1 + IFN-γ, IFN-γ, and no treatment

first: Apoorvi

last: Chaudhri


title: Suppression of Established T Cell Immunity and Disease by Immunotherapy with Synthetically Glycosylated Antigen

city: Chicago

first: Jeffrey

last: Hubbell

state: Illinois

address: 5640 S. Ellis Ave

institute: University of Chicago

summary: The purpose of this study was to conduct an in-depth analysis of the molecular characteristics of both CD4 and CD8 T cells upon encounter of self-associated antigen presented by hepatic APCs, induce therapeutic tolerance in transgenic and  endogenous repertoires of T cells, and discover the mechanisms that mediate pGal-induced tolerance.

overall_design: Prophylactic: Ovalbumin-specific CD4 and CD8 T cell mRNA profiles of WT mice 4 days post antigen treatment. Day 0 mice received adoptive transfer of OTI and OTII cells. At 1 day post transfer mice received either 5ug pGal-OVA, 5ug plain OVA, or saline. At Day 5, secondary lymphoid organs were collected and pooled. Each replicate was generated from fluorescent activated cell sorted OTI and OTII cells pooled from 3 mice. Therapeutic: Mice received adoptive transfer of OTI and OTII cells on Day 0, followed by s.c. immunization with CFA+OVA the next day. One month later mice received either 5ug pGal-OVA, 5ug plain OVA, or saline. 4 days after antigen treatment secondary lymphoid organs were collected and pooled. Each sample consists of one mouse.

first: Andrew

middle: C

last: Tremain

first: Rachel

last: Wallace

first: Kristen

last: Lorentz

first: Thomas

middle: B

last: Thornley

first: Jennifer

middle: T

last: Antane

first: Michal

middle: R

last: Raczy

first: Joseph

middle: W

last: Reda

first: Aaron

last: Alpar

first: Elyse

last: Watkins

first: Chitavi

last: Maulloo

first: Erica

last: Budina

first: Ani

last: Solanki

first: Mindy

last: Nguyen

first: David

last: Bischoff

first: Jamie

last: Harrington

first: Rabinarayan

last: Mishra

first: Gregory

last: Conley

first: Romain

last: Marlin

first: Nathalie

last: Dereuddre-Bosquet

first: Anne-Sophie

last: Galloeut

first: Anna

last: Slezak

first: Roger

last: LeGrand

first: D. Scott

last: Wilson

first: Stephan

last: Kontos


title: RNAseq transcriptomic data of the human mammary cell line MCF10A expressing a shRNA against MME (CD10) or a control shRNA

city: Lyon

first: Véronique

last: Maguer-Satta

address: 28 Rue Laennec, Bat Cheney D, 4ème étage

institute: Centre de Recherche en Cancérologie de Lyon

summary: The immortalized but not transformed human mammary epithelial stem-like cell line MCF10A was stably transfected with a lentiviral vector expressin a shRNA targeting the MME transcript, coding for the CD10 membrane endopeptidase. This study aims to identify genes regulated by the CD10 modulation.

overall_design: mRNA profiles of MCF10A stably transfected with a lentiviral vector expressing a shRNA targeting the MME transcript or a control vector, three replicates for each condition.

first: Boris

last: Guyot


title: RNAseq transcriptomic data of MCF10A cells following long-term exposition to BMP2 and IL6

summary: RNAseq transcriptomic analysis of MCF10A-CT, MC26 and M1B26 cell lines. MCF10A cells are human not transformed mammary stem-like cells that do not form colonies in soft-agar assay and do not engraft in immunocompromised mice. MC26 are MCF10A derivatives that were submitted to long-term culture in presence of human recombinant BMP2 and IL6 for several weeks until colony formation in soft-agar was detected. M1B26 are MCF10A derivatives that were sorted for high expression of the BMPR1b BMP receptor prior to BMP2 and IL6 treatment and expanded from several soft-agar colonies. M1B26 are more transformed than MC26 based on the frequency of soft-agar colonies forming cells and on the ability to engraft in mice. As a control, MCF10A-CT were kept in culture for similar length of time than MC26 and M1B26 but without BMP2 and IL6 and do not generate soft-agar colonies or engraft in mice. This study aims to document the transcriptomic changes associated with early transformation events mediated by abnormal exposure to BMP2 and inflammatory signal.

overall_design: RNA profiles from three independant cultures of MCF10A-CT, MC26 and M1B26 cells.


title: RNAseq transcriptomic data of healthy primary human mammary epithelial cells from WT, BRCA1 mutated or BRCA2 mutated patients

summary: Normal primary epithelial cells from  women following reduction mammoplasty or BRCA1 or 2 mutated women following preventive mastectomy were purified from the mammary tissue and analyzed by RNAseq. Since all samples were certified tumor-free by an anatomo-pathologist prior to processing, this study aims to better understand the transcriptomic alterations inudced by BRCA genes mutations in primary cells prior to any detectable transformation event.

overall_design: mRNA profiles of  WT, BRCA1 mutated and BRCA2 mutated human primary mammary epithelial cells (3 independent samples for each genotype)


title: Comparative analysis of sperm DNA methylation supports evolutionary acquired epigenetic plasticity controlling organ speciation

city: Rodovre

first: Farideh

last: Moharrek

address: Hvidovrevej 22B

country: Denmark

institute: Novo Nordisk Foundation Center for Basic Metabolic Research

summary: Gametic DNA methylation is essential to the viability of the embryo and participates in developmental programming. Here, we performed a comparative epigenomic analysis of DNA methylation in spermatozoa from humans, mice, rats and mini-pigs to get insight into species specificity of the gametic epigenetic blueprint. Using data from whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS), we compared the methylation profiles of orthologous single-CpG sites. Transcription profiles of early embryo development were analyzed to provide insight into the association between sperm methylation and gene expression programming. We identified DNA methylation variation near genes related to the central nervous system and signal transduction. Gene expression dynamics at different time-points of preimplantation stages were modestly associated with spermatozoal DNA methylation at nearest promoters. Our analysis revealed that conserved genomic regions subject to epigenetic variation across different species were associated with specific organ functions, suggesting their potential contribution to organ speciation and long-term adaptation to the environment

overall_design: We performed our analyses on a panel of publically available datasets, generated for different studies. In addition, we performed RRBS on mini-pigs sperm. Sperm samples were collected from four adult mini-pigs.

first: Lars

last: Ingerslev

first: Ali

last: Altıntaş

first: Leonidas

last: Lundell

first: Ann

middle: N

last: Hansen

first: Lewin

last: Small

first: Chistopher

last: Workman

last: Barrès


title: DNA methylation landscape and signature of CD4+ lymphocytes of lamina propria in Crohn's patients by reduced representation and bisulfite sequencing [RNA-seq]

city: ROCHESTER

first: ZHIFU

last: SUN

state: Minnesota

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: A genome-wide DNA methylation study was conducted using base resolution bisulfite sequencing for purified intestinal CD4+ cells (resected or biopsied mucosa of a terminal ileum) from 21 patients with Crohn’s disease and 12 age/sex matched controls. The sequencing data was analyzed for differentially methylated CpGs (DMCs) and differentially methylated regions (DMRs). Integration was performed with RNA-sequencing data for the same set of samples to verify the functional impact of DNA methylation changes.

overall_design:
Crohn’s disease; CD4+ lymphocytes; DNA methylation; reduced representation bisulfite sequencing; differential methylation; Th17 phenotype; ATAC-sq
Case/control study

first: Zhifu

last: Sun

first: Manuel

last: Neto

first: Yuning

last: Xiong

first: Saurabh

last: Baheti

first: Jessica

last: Friton

first: Asha

last: Nair

first: Mary

last: Sagstetter

first: Zheqing

last: Ye

first: William

last: Faubion


title: RNA sequencing of nephron progenitor cells obtained from embryos subjected to either control or 70% daily caloric intake food restriction

city: Jerusalem

first: Morris

last: Nechama

state: Israel

address: Hadassah Medical Center, Ein Karem

department: Pediatric

institute: Hadassah Hebrew University Medical Center

summary: The effect of caloric restriction on the gene expression of Nephron Progenitor Cells (NPC) was studied. Pregnant females were subjected to either a control diet or to 70% daily caloric intake food restriction. At E18.5 the embryo kidneys were extracted and the NPCs were cell sorted and the RNA was extracted for gene expression analysis to identify changes in the gene expression of these NPC

overall_design: CD-1 females were mated with Six2 Cre tg/+ males. After plaque identification, the mice were randomly assigned to either a control diet or 70% daily caloric intake throughout pregnancy.  At E18.5 the embryos were sacrificed and the kidneys were extracted. NPCs were FACS sorted and RNA was extracted for RNA sequencing. Each condition had 3 biological replicates.

first: Oded

last: Volovelsky


title: DNA methylation landscape and signature of CD4+ lymphocytes of lamina propria in Crohn's patients by reduced representation and bisulfite sequencing


title: Salt induces hepatic inflammatory response through epigenetic modulation of SIRT3 [Bisulfite-seq]

city: Chongqing

first: Peng

last: Gao

state: Chongqing

address: 10 Chang Jiang Zhi Lu

institute: Daping hospital, Army Medical University

summary:
Purpose: Our previous study has confirmed that reduction of SIRT3 expression is a main factor contributing to salt-induced hepatic inflammtion. Here we sought to investigate whether salt-induced SIRT3 reduction was related to epigenetic modification.
Methods: 6-week-old male  wild-type mice were fed with high salt diet (HSD, containing 8% NaCl) or normal salt diet (NSD, containing 0.4% NaCl) for 4 months. And then their liver tissues were removed and subjected to bilsulfate-seq.
Results: Through bisulfate-seq, we did not observe any change in DNA methylation in the CpG island of Sirt3 gene promoter region.
Conclusions: Salt-induced SIRT3 reduction is not related to DNA methylation on SIRT3 gene promoter.

overall_design: Including 4 samples, liver DNA methylation profiles of  wild-type (WT) mice fed with high salt diet (HSD) or normal salt diet (NSD) for 4 months.

first: Mei

last: You

first: Zhiming

last: Zhu


title: Salt induces hepatic inflammatory response through epigenetic modulation of SIRT3 [RNA-seq]

summary:
Purpose: Although clinical evidence suggests that high salt intake is associated with NAFLD, the underlying mechanism remains elusive. We sought to investigate whether salt-induced inflammation in liver is dependent on SIRT3 reduction.
Methods: 6-week-old male SIRT3 knockout or their wild-type littermates were fed with high salt diet (HSD, containing 8% NaCl) or normal salt diet (NSD, containing 0.4% NaCl) for 4 months. And then their liver tissues were removed and total RNA was extracted to perform RNA sequencing.
Results: 1850 differentially upregulated expressed genes were identified when comparing HSD group (HSD1, HSD2) to NSD group (NSD WT1, NSD2). Meanwhile, 1246 differentially upregulated expressed genes in response to SIRT3 knockout were determined (each group containing 3 samples). we observed that the common genes upregulated by both HSD and knockout of SIRT3 were enriched in immune system, including Tnf, Ccl2, etc. In addition, the common genes upregulated by knockout of SIRT3 in both NSD and HSD group were still enriched in the immune system.
Conclusions: Through RNA-seq, we determined that HSD-induced hepatic inflammtion was highly similar to the effect of SIRT3 knockout, suggesting that reduction of SIRT3 expression is the main reason leading to salt-induced hepatic inflammation.

overall_design: Including 15 samples, liver mRNA profiles of SIRT3 knockout (KO) or wild-type (WT) mice fed with high salt diet (HSD) or normal salt diet (NSD) for 4 months.


title: Salt induces hepatic inflammatory response through epigenetic modulation of SIRT3


title: The cell-intrinsic role of ANXA1 in human ILC2s

city: Tokyo

first: Hiroki

last: Kabata

address: 35 Shinanomachi, Shinjyuku-ku

institute: Keio University School of Medicine

summary: To investigate the effect of ANXA1, encoding annexin a1, on group 2 innate lymphoid cells (ILC2s), we downregulated the expression using lentiviral vector-based shRNA transfer and performed RNA-seq analysis.

overall_design: Lentiviral vector-based shRNA delivery experiments were performed using human peripheral blood-derived ILC2s. ILC2s transduced with shRNA for ANXA1 or shRNA control under IL-2 stimulation. cDNA libraries were synthesized using SMART-Seq v4 Ultra Low Input RNA Kits (Takara Bio), and libraries were sequenced using 150-bp paired-end sequencing on the NovaSeq 6000 (Illumina).

first: Misato

last: Irie


title: DNA methylation is predominantly stable in mice offspring born after transplantation of long-term cultured spermatogonial stem cells

city: Amsterdam

first: Joana

last: Serrano

address: Meibergdreef 9

institute: Amsterdam UMC - Location AMC

summary: Spermatogonial stem cell transplantation (SSCT) is proposed as a fertility therapy for childhood cancer survivors. SSCT starts with cryopreserving a testicular biopsy prior to gonadotoxic treatments such as cancer treatments. When the childhood cancer survivor reaches adulthood and desires biological children, the biopsy is thawed and SSCs are propagated in vitro and subsequently auto-transplanted back into their testis. However, culturing stress during long-term propagation can result in epigenetic changes in the SSCs, such as DNA methylation alterations, and might be inherited by future generations born after SSCT. Therefore, SSCT requires a detailed preclinical epigenetic assessment of the derived offspring before this novel cell therapy is clinically implemented. With this aim, the DNA methylation status of sperm from SSCT-derived offspring, with in vitro propagated SSCs, was investigated in a multigenerational mouse model using reduced-representation bisulfite sequencing.  Although there were some methylation differences, they represent less than 0.5% of the total CpGs and methylated regions, in all generations. Unsupervised clustering of all samples showed no distinct grouping based on their pattern of methylation differences. After selecting the few single genes that are significantly altered in multiple generations of SSCT offspring compared to control, we validated the results with quantitative Bisulfite Sanger sequencing and RT-qPCRin various organs. Differential methylation was confirmed only for Tal2, being hypo-methylated in sperm of SSCT offspring and presenting higher gene expression in ovaries of SSCT F1 offspring compared to control F1.  We found no major differences in DNA methylation between SSCT-derived offspring and control, both in F1 and F2 sperm.  The reassuring outcomes from our study are a prerequisite for promising translation of SSCT to the human situation and gives confidence to proceed to the first clinical trials.

overall_design: We investigated whether the DNA methylation status is different between sperm from SSCT-derived male offspring (F1 and F2) and control male offspring at three months of age using reduced-representation bisulfite sequencing (RRBS).

first: Nils

last: Tabeling

first: Cindy

last: de Winter-Korver

first: Saskia

middle: K

last: van Daalen

first: Ans

last: van Pelt

first: Callista

last: Mulder


title: Effect of Fumonisin B1 exposure on hepatic gene expression in mice fed a regular diet (CHOW) and in mice fed a High Fat Diet (HFD).

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

institute: INRAE

summary: This experiment was designed to investigate the effect of Fumonisin B1 exposure on liver gene expression in male mice fed a regular diet (Chow group) and in obese mice which were fed a High fat diet (HFD). The Fumonisin B1 was provided through the drinking water.

overall_design: Wild-type male mice (C57BL/6J) were randomly divided into four groups. Two groups were fed a chow diet with 10 kcal% fat (CHOW, D12450J, Research Diets) and the other two groups were fed a high-fat diet with 60 kcal% fat (HFD, D12492, Research Diets) for 15 weeks. After 12 weeks of feeding, half of the CHOW and HFD groups were exposed to FB1 (10 mg/kg bw/day) by adjusting every two days the amount of consumed FB1 in the drinking water during 3 weeks in order to maintain a constant level of exposure. Every week, mice were weighed, and water consumption was measured to adjust the quantity of FB1 in the water. Food intake was also monitored. At the end of the experiment, mice were sacrificed to collect plasma and tissue samples. Liver samples were removed, weighed, snap frozen in liquid nitrogen and stored at −80°C prior to gene expression analysis.

first: Léonie

last: Dopavogui

first: Marion

last: Régnier

first: Claire

last: Naylies

first: Yannick

last: Lippi

first: Nicolas

last: Loiseau


title: Genome-wide adenine N6-methylation map unveils epigenomic regulation of lipid accumulation in Nannochloropsis

city: Qingdao

first: Yanhai

last: Gong

address: No.189 Songling Road

department: single cell center

institute: qibebt, cas

summary: The candidate 6mA methylase and demethylase were knocked out, 6mA distributions were compared with wild-type.

overall_design: The mutants and wild-type were cultivated under high light conditions, sampling were performed at 7 days.

first: Qintao

last: Wang

first: Li

last: Wei

first: Jian

last: Xu


title: Microglia coordinate the anti-tumor immune response to breast cancer brain metastasis [MITRG 10X data]

first: Devon

last: Lawson

address: 839 Health Science Road, Sprague Hall 140

summary: We used single-cell RNA-sequencing to investigate the role of myeloid cells in a humanized mouse model of breast cancer brain metastasis (BCBM). We generated brain metastases with a cardiac-injection of the human triple-negative breast cancer cell line MDA-MB-231BR2 (231BR) into MITRG mice and allowed tumors to grow in the brain for 25 days. We then took all human cells (includes myeloid cells and 231BR) from these mice verses control MITRG brains (only myeloid cells) to find transcriptional changes associated with BCBM.

overall_design:
Single-cell RNA-Seq of human iPSC-derived myeloid cells and MDA-MB-231BR2 from the brains of MITRG mice with and without breast cancer brain metastases.

Please note that, as both BAM and FASTQ are necessary to interpret the data, duplicated sample records are created to link two different raw data type (i.e. BAM containing cDNA reads and fastq containing a set of DNA barcodes from the MULTI-seq element)

first: Kerrigan

last: Blake


title: Microglia coordinate the anti-tumor immune response to breast cancer brain metastasis [Foxn1 nu/nu 10X data]

summary: We used single-cell RNA-sequencing to investigate the role of brain-resident microglia versus infiltrating cells in a mouse model of breast cancer brain metastasis (BCBM). We generated brain metastases with a cardiac-injection of the human triple-negative breast cancer cell line MDA-MB-231BR2 (231BR) into Foxn1 nu/nu mice and allowed tumors to grow in the brain for four weeks. We then compared astrocytes (ASCA2+CD45-) and myeloid cells (CD11b+CD45+) from these mice verses control Foxn1 nu/nu brains to find transcriptional changes associated with BCBM.

overall_design: Single-cell RNA-Seq of myeloid cells, astrocytes, and MDA-MB-231BR2 (231BR) from the brains of Foxn1 nu/nu mice with and without breast cancer brain metastases.


title: Mouse prostate organoid metabolism

city: Los Angeles

first: Andrew

last: Goldstein

address: 610 Charles E Young Dr East

institute: University of California, Los Angeles

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

overall_design: Refer to individual Series


title: Repeat-element-aware profiling of plasma cell-free RNA

city: Santa Cruz

first: Daniel

last: Kim

address: McLaughlin Dr

department: Biomolecular Engineering

institute: UC Santa Cruz

summary: Liquid biopsies provide a means for the profiling of cell-free RNAs secreted by cells throughout the body. Although well-annotated coding and noncoding transcripts in blood are readily detectable and can serve as biomarkers of disease, the overall diagnostic utility of the cell-free transcriptome remains unclear. Here we show that transposable elements and other repeat RNA elements are enriched in the cell-free transcriptome of patients with cancer, and that they serve as signatures for the accurate classification of the disease. We used repeat-element-aware sequencing and analysis technology and single-molecule nanopore sequencing to profile the cell-free transcriptome in plasma from patients with cancer and to examine millions of genomic features comprised of all annotated genes and of repeat elements throughout the genome. By aggregating individual repeat elements to the subfamily level, we found that samples with pancreatic cancer are enriched with specific Alu subfamilies, whereas other cancers exhibit their own characteristic cell-free RNA profile. Our findings show that repetitive RNA sequences are abundant in blood and can be used as disease-specific diagnostic biomarkers.

overall_design: 32 total (N = 10 Pancreatic Cancer, N = 22 Normal healthy donors) blood plasma samples were sequenced to determine the potential for disease classification from cell-free RNA

first: Roman

last: Reggiardo


title: CRISPR-based epigenome editing screens identify transcriptional and epigenetic regulators of human CD8 T cell function [Sorting-based CRISPR screens]

status: Public on Aug 31 2023

city: Durham

first: Sean

last: McCutcheon

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

summary:
All bulk CRISPR based screens
CD2 and B2M CRISPRi tiling screens (primary human CD8 T cells), IL2RA CRISPRa tiling screens (Jurkats), CRISPRi/a TF screens (primary human CD8 T cells), and CRISPR TFome KO (primary human T cells)

overall_design: Bulk CRISPR-based (CRISPRi/a/ko) screens using surface marker readouts in primary human CD8 T cells or Jurkats.

first: Charles

last: Gersbach


title: Salt induces hepatic inflammatory response through epigenetic modulation of SIRT3 [ChIP-seq]

first: Peng

last: Gao

summary:
Purpose: Our previous study has confirmed that reduction of SIRT3 expression is a main factor contributing to salt-induced hepatic inflammtion. Here we sought to investigate whether salt-induced SIRT3 reduction was related to epigenetic modification.
Methods: 6-week-old male SIRT3 knockout or their wild-type littermates were fed with high salt diet (HSD, containing 8% NaCl) or normal salt diet (NSD, containing 0.4% NaCl) for 4 months. And then their liver tissues were removed and subjected to ChIP-seq using antibodies against H3K27ac (ab4729), H3K4me1 (ab8895), H3K9ac (39917) and H3 (ab1791).
Results: Through ChIP-seq, we observed the enrichment of H3K27ac was increased on the promoters of Sirt3 and some pro-inflammatory genes, including Ccl2, Tnf and Il6, after high salt loading. However, neither H3K4me1 nor H3K9ac displayed such phenomunum. In addition, those genes containing increased H3K27ac level in response to high salt were mainly enriched in metabolism and inflammatory pathways. And knockout of SIRT3 mainly affected genes related to AMP-activated protein kinase (AMPK) and insulin signaling pathways.
Conclusions: Salt-induced SIRT3 reduction is related to the epigenetic regulation, especially H3K27ac.

overall_design: Including 5 samples, liver histone modifications profiles of  wild-type (WT) mice fed with high salt diet (HSD) or normal salt diet (NSD) for 4 months. And 6-week-old SIRT3 knockout (KO) and wild-type (WT) mice were also compared.

first: Mei

last: You

first: Zhiming

last: Zhu


title: Cell-in-cell-mediated entosis reveals a progressive mechanism in pancreatic cancer

city: Beijing

first: Jianlu

last: Song

state: Beijing

address: Shuaifuyuan No.1

institute: Peking Union Medical College Hospital

summary: Pancreatic ductal adenocarcinoma (PDAC) is a deadly malignancy with high intratumoral heterogeneity. There is a lack of effective therapeutics for PDAC. Entosis, a form of nonapoptotic regulated cell death mediated by cell-in-cell structures (CICs), has been reported in multiple cancers. However, the role of entosis in PDAC progression remains unclear. In this study, we evaluated CICs using immunohistochemistry and immunofluorescence staining. The formation of CICs was induced by suspension culture. Through fluorescence-activated cell sorting and single-cell RNA sequencing (scRNA-seq), we collected entosis-forming cells and analyzed their differential gene expression. Cell functional assays and mouse models were used to investigate malignant phenotypes. Clinical correlations between entosis and PDAC were established by retrospective analysis. We found that entosis was associated with an unfavorable PDAC patient prognosis and was more prevalent in liver metastases than in primary tumors. The scRNA-seq results revealed that several oncogenes were upregulated in entosis-forming cells compared with parental cells. These highly entotic cells demonstrated higher oncogenic characteristics in vitro and in vivo. NET1, neuroepithelial cell transforming gene 1, is an entosis-related gene that plays a pivotal role in PDAC progression and is correlated with poor outcomes.

overall_design: The formation of CICs was induced by suspension culture. We mixed an equal number of EGFP- and mCherry-stably expressing cancer cells and then induced CIC formation. After CICs induction, we collected the suspended cells and prepared them for FACS. Cells that exhibited both fluorescence signals in the FACS analysis were defined as double-positive (DP; EGFP+/mCherry+ cells), while those exhibiting one fluorescence signal were defined as single-positive (SP; EGFP+/mCherry- or EGFP-/mCherry+ cells). We performed scRNA-seq on DP cells, SP cells, and parental cells (NC).

first: Ruiyuan

first: Hui

last: Zhang

first: Xuemin

last: Xue

first: Rexiati

last: Ruze

first: Yuan

last: Chen

first: Xinpeng

last: Yin

first: Chengcheng

first: Yupei

last: Zhao


title: Identification of exosomal microRNA panel as diagnostic and prognostic biomarker for small cell lung cancer [mRNAseq_BEAS2B]

city: Songpa-gu

first: Dong Ha

state: Seoul

address: 88, Olympic-ro 43-gil

department: Asan institute for life sciences

country: South Korea

institute: ASAN Medical Center

summary: Small cell lung cancer (SCLC) has an exceptionally poor prognosis; as most of the cases are initially diagnosed as extensive disease with hematogenous metastasis. Therefore, the early diagnosis of SCLC is very important and may improve its prognosis. To investigate the feasibility of early diagnosis of SCLC, we examined exosomal microRNAs (miRNAs) present in serum obtained from patients with SCLC. Exosomes were isolated in serum from patients with SCLC and healthy individuals and were characterized using particle size and protein markers. Additionally, miRNA array was performed to define SCLC-specific exosomal miRNAs. The miRNAs identified in the miRNA array results were validated using a large cohort. Gene ontology analysis has revealed that a panel of miRNAs are linked to various oncogene pathways and nervous system development. Changes in mRNA expression when target miRNAs were introduced into BEAS2B cells strongly indicated the presence of lung diseases, including lung cancer. Additionally, miRNA panels are significantly associated with poor prognosis. In conclusion, our study identified SCLC-specific exosomal miRNAs, and the miRNAs panel may serve as a diagnostic and prognostic marker for SCLC.

overall_design: Comparative gene expression profiling of RNA-seq data for mRNA after introducing miR-3124-5p mimic, miR-200b-3p mimic, miR-92b inhibitor, scrambled miRNA control or 3-miRNA mixture (miR-3124-5p mimic, miR-200b-3p mimic and miR-92b inhibitor) into BEAS2B cells analyze.

first: Dong

first: Wonjun

last: Ji

first: Jin

last: Rho


title: DNA methylation landscape and signature of CD4+ lymphocytes of lamina propria in Crohn's patients by reduced representation and bisulfite sequencing [BiSulfite-seq]

first: ZHIFU

last: SUN

first: Zhifu

last: Sun

first: Manuel

last: Neto

first: Yuning

last: Xiong

first: Saurabh

last: Baheti

first: Jessica

last: Friton

first: Asha

last: Nair

first: Mary

last: Sagstetter

first: Zheqing

last: Ye

first: William

last: Faubion


title: Examining SRP pathway function in  mRNA localization to the endoplasmic reticulum

first: Christopher

middle: Vincent

last: Nicchitta

department: Department of Cell Biology

institute: Duke University School of Medicine

summary: Signal recognition particle (SRP) pathway function in secretory/membrane protein translocation across the endoplasmic reticulum (ER) is well-established; its role in mRNA localization to the ER in mammalian cells remains largely unexplored. We address this question in SRP receptor (SR) knockout mammalian cell lines. SRPRB KO cells were generated by CRISPR editing. SRPRB KO resulted in profound destabilization of SRα with siRNA silencing of SRPRA in SRPRB KO cells yielding SR KO. Steady-state mRNA composition and ER-enrichments were not disrupted by loss of SR. SR function in the ER localization of newly exported mRNAs was examined by 4-thiouridine (4SU) pulse-chase/4SU-seq and found to be SR-independent. Under conditions of translation initiation inhibition, the ER was the default localization site for newly exported mRNAs. These data demonstrate that mRNA localization to the ER can be uncoupled from SRP pathway function and reopen questions regarding the mechanism of mRNA localization to the ER.

overall_design: There are two components to this study. In the first component, RNA-seq studies were performed on the cytosolic and ER-bound mRNAs from parental, SRPRB knockout, SRPRB knockout + SRPRA siRNA knockdown HeLa cells, to examine the steady-state transcriptomic response to loss of SRP receptor expression. In a second set of studies, the localization of newly exported mRNAs to the cytosol and ER compartments of HeLa Cas9 and HeLa SRPRB knockout/SRPRA siRNA knockdown cells was study by biosynthetic pulse chase. Here, 4-thiouridine (4SU) transcriptional labeling was used to identify newly transcribed and exported mRNAs. 4SU pulse-chase studies were coupled with cell fractionation to identify the subcellular localization site (cytoplasm or endoplasmic reticulum) of 4SU-labeled mRNAs. 4SU mRNAs were isolated following total RNA isolation, 4SU-directed biotinylation, streptavidin-magnetic bead isolation, and oligo-DT selection of poly(A) mRNAs. Time course studies at five time points (0, 15 min, 30 min, 45 min, 60 min) were performed to determine relative nuclear export rates. Subsequently, 4SU transcriptional pulse-labeling studies were performed to examine the effects of translational inhibition on the localization of newly exported mRNAs. In these experiments, cells were treated with either vehicle (control)), DTT (to activate the UPR), or harringtonine, an inhibitor of translation initiation, and 4SU mRNAs captured at the 45 min time point. In a third set of experiments, the role of the SRP pathway in the trafficking of newly exported mRNAs to the cytosol and ER was examined by 4SU-seq analyses in parental vs SR KO cells. To correct for background, parallel experiments were performed where 4SU was omitted and the samples processed as per the experimental (+4SU) conditions and sequenced. Experiments were performed in biological duplicate or triplicate, 4SU-mRNA distributions were assayed by qRT-PCR of marker genes, and samples processed for deep sequencing. A thiolated spike-in control poly(A) mRNA, comprising a Bacillus subtilis sequence, was included for recovery normalization.

last: Child

first: Alex

last: Hofler

first: Qiang

first: Brenda

last: Yang

first: JohnCarlo

last: Kristofich

first: Tianli

last: Zheng

first: Molly

last: Hannigan

first: Andew

last: Elles

middle: V


title: Identification of exosomal microRNA panel as diagnostic and prognostic biomarker for small cell lung cancer

first: Dong Ha

last: Kim


title: Multiplex Epigenome Editing of MECP2 to Rescue Rett Syndrome Neurons (RNA-Seq)

city: New York

first: Xiaonan

last: Guan

address: 1150 St Nicholas Ave, 403

institute: Russ Berrie Medical Science Pavillion

summary:
Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by loss-of-function heterozygous mutations of MECP2. Reactivation of the silent wild-type MECP2 allele on the inactive X chromosome (Xi) represents a promising therapeutic opportunity for female RTT patients. Here, we applied a multiplex epigenome editing approach to reactivate MECP2 on Xi. Demethylation of the MECP2 promoter by dCas9-Tet1 with target sgRNA reactivated MECP2 on Xi in RTT hESCs without detectable off-target effects at the transcriptome level. Neurons derived from methylation edited RTT hESCs reversed the smaller soma size and electrophysiological abnormalities. Insulation of the methylation edited MECP2 locus in RTT neurons by dCpf1-CTCF with target crRNA stabilized MECP2 reactivation and rescued the RTT-related neuronal defects, providing a proof-of-concept study for multiplex epigenome editing to treat RTT.
Evaluation of off-target effects of dCpf1-CTCF with crRNA targeting CTCF binding flanking MECP2 locus

first: Rudolf

last: Jaenisch

first: X

last: Liu


title: Microglia coordinate the anti-tumor immune response to breast cancer brain metastasis

city: Irvine

first: Devon

last: Lawson

state: CA

institute: University of California, Irvine


title: Identification of exosomal microRNA panel as diagnostic and prognostic biomarker for small cell lung cancer [miRNAseq_exosome]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for serum-derived exosomal miRNAs from 5 patients with SCLC and 5 controls with lung nodules.

first: Dong

first: Wonjun

last: Ji

first: Jin

last: Rho


title: CK1δ and CK1ε Signaling Sustains Mitochondrial Metabolism and Cell Survival in Multiple Myeloma

city: TAmpa

first: Yonghong

last: Zhang

state: FL

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

summary: Multiple myeloma (MM) remains an incurable malignancy due to acquisition of intrinsic programs that drive therapy resistance. Here we report that casein kinase-1δ (CK1δ) and CK1ε are therapeutic targets in MM that are necessary to sustain mitochondrial metabolism. Specifically, the dual CK1δ/CK1ε inhibitor SR-3029 had potent in vivo and ex vivo anti-MM activity, including against primary MM patient specimens. RNA sequencing (RNA-seq) and metabolic analyses revealed inhibiting CK1δ/CK1ε disables MM metabolism by suppressing genes involved in oxidative phosphorylation (OxPhos), reducing citric acid cycle intermediates, and suppressing Complexes I and IV of the electron transport chain. Finally, sensitivity of MM patient specimens to SR-3029 correlated with elevated expression of mitochondrial genes, and RNA-seq from 687 MM patient samples revealed that increased CSNK1D, CSNK1E, and OxPhos genes correlates with disease progression and inferior outcomes. Thus, increases in mitochondrial metabolism are a hallmark of MM progression that can be disabled by targeting CK1δ/CK1ε.

overall_design: Isolated patients samples were treated with vehicle or 250 nM SR-3029 for 24 hours

first: John

middle: L

last: Cleveland

first: Ken

last: Shain

first: Karen

last: Burger

first: Mark

last: Meads


title: CD4 T cell stimulation in the presence or absence of the cell line PGA-1 derived from chronic lymphocytic leukemia

first: Chiara

last: Montironi

department: Experimental Immunology

institute: Amsterdam UMC

summary: PBMCs from healthy donor were co-cultured with the cell line PGA-1 and stimulated with anti-CD3/28 antibodies for 48 hours. CD4 T cells were then FACS sorted for RNA seq analysis

overall_design: 5 biological replicates (different healthy donor PBMCs)

first: Fleur

last: Peters


title: Immune vigilant state in deep cerebellar nuclei is contributed by multiple glial populations and linked to reduced amyloid plaque pathology.

city: Singapore

first: Jessica

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University


title: Single cell RNA sequencing of omental tumors or ascites from KPCA syngeneic cancer cell lines

city: Bosotn

first: Maeva

middle: Yvette

last: Chauvin

address: 55 fruit st

institute: Massachusetts General Hospital

summary: The KPCA ovarian cancer cell line was generated by S. Iyer in the Weinberg lab at the Whitehead Institute (MIT) (S. Iyer et al., 2020). Multiple clones derived from the KPCA cells were established, presenting different level of sensitivity to immunotherapy. To investigate the tumor microenvironment in this syngeneic mouse model, we implanted the different KPCA clones (3.5 × 10^6 cells) into the peritoneal cavity. Ten days after grafting, we performed single-cell RNA sequencing on harvested tumors and cells from the peritoneal fluid.

overall_design: Single-cell RNA sequencing of  KPCA.A, KPCA.B, and KPCA.C tumors and ascites (N=4 pooled tumors per genotype, 5000 cells)

first: M

first: D

last: Pépin

first: R

last: Weinberg

first: S

last: Iyer

first: M-C

last: Meinsohn

first: N

middle: M

last: Nguyen

last: Mishra


title: Expression data from a model of human mammary stem cells at different stages of transformation, sorted or not on the basis of their CD10 expression

city: Lyon

first: Véronique

last: Maguer-Satta

address: 28 Rue Laennec, Bat Cheney D, 4ème étage

institute: Centre de Recherche en Cancérologie de Lyon

summary: This study was designed to follow the transcriptome changes during BMP2 mediated transformation of the MCF10A human mammary stem cell model. We found that long-term BMP2/IL6 exposure of MCF10A cells, human immortalized but non-transformed mammary stem cells and progenitors, led to their luminal transformation. MC26 cells correspond to MCF10A cells transformed by BMP2/IL6 long-term exposure and contrarily to their parental cells, are able to engraft in immunodeficient mice and form colonies in soft-agar. M1B26 cells were obtained after BMP2/IL-6 long-term treatment of MCF10A cells sorted for high BMPR1B expression and subsequent isolation and expansion of 3 soft-agar colonies. M1B26 have an increased ability to engraft in mice and form colonies in soft-agar when compared to MC26 cells. As a non-transformed control, MCF10A-CT cells were kept in culture without BMP2/IL6 for the same length of time than MC26 cells. MCF10A-CT, MC26 and M1B26 cells are  thus a model allowing to follow the molecular events associated with the initiation of a luminal transformation in mammary stem cells. Expression of the CD10 membrane endopeptidase has been associated with cancer although it can be a marker of both good or poor prognosis depending on the stage of the cancer and on the tissue of origin. In addition, we showed that CD10 was a marker of stem cell  containing populations in healthy mammary tissue and that CD10 enzymatic activity was involved in the maintenance of cells immature properties. Having recently shown that CD10 expression was increasing during BMP2 mediated transformation and that CD10 expressing cells were more transformed but that CD10 was not required for transformation, we set out to determine the gene signature associated with CD10 expression.

overall_design: MCF10A-CT, MC26 or M1B26 cell lines, unsorted or flow cytometry sorted on the basis of membrane CD10 expression were used for RNA purification and hybridation on Affymetrix microarray

first: Boris

last: Guyot


title: Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis [scRNA-seq]

city: PARIS

first: Stephane

last: NEDELEC

address: 17 rue du fer a moulin

institute: Institut du Fer à Moulin

summary: Integrated in vitro models of human organogenesis are needed to elucidate the multi-systemic events underlying development and disease. We report the generation of human trunk-like structures that model the co-morphogenesis, patterning, and differentiation of the human spine and spinal cord. We identified differentiation conditions for human pluripotent stem cells favoring the formation of an embryo-like extending antero-posterior (AP) axis. Single cell and spatial transcriptomics show that somitic and spinal cord differentiation trajectories organize along this axis and can self-assemble into neural tubes surrounded by somites upon extracellular matrix addition. Morphogenesis is coupled with AP patterning mechanisms which results, at later stages of organogenesis, in in vivo-like arrays of neural subtypes along a neural tube surrounded by spine and muscle progenitors contacted by neuronal projections. This integrated system of trunk development indicates that in vivo-like multi-tissue morphogenesis and topographic organization of terminal cell types can be achieved in human organoids, opening windows for the development of more complex models of organogenesis.

overall_design: Single-cell RNA-sequencing analyses were performed on 26 pooled trunk organoids at day 7 of differentiation. Libraries were prepared following 10X Chromium Next GEM Single cell 3' v.3.1 manufacturer protocol. For the spatial transcriptomic study (Tomo-sequecing), two human trunk organoids at day 7, were freshly frozen and then sectioned. Each section was sequenced by bulk RNA sequencing. Libraries were prepared using Cel-Seq2 protocol and Illumina TruSeq small RNA adapters (RPI series).

first: Simona

last: Gribaudo

first: Remi

last: Robert

first: Bjorn

last: van Sambeek

first: Camil

last: Mirdass

first: Anna

last: Lyubimova

first: Kamal

last: Bouhali

first: Julien

last: Ferrent

first: Xavier

last: Morin

first: Alexander

last: van Oudenaarden

last: Nedelec


title: Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis [TOMO-seq]

last: Ferent


title: Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis.


title: Transcriptional responses to deep cerebellar nuclei (DCN) and entorhinal cortex (EC) protein homogenates in cultured microglia

first: Jessica

last: Gaunt

summary: We hypothesised that enriched cytokines in the microenvironment of the deep cerebellar nuclei (DCN) contribute to the inflammatory gene expression profiles of DCN microglia and thus might induce a similar response in cultured microglia. To test this hypothesis, we treated BV2 microglia cell lines with DCN or entorhinal cortex (EC) protein homogenates and analysed RNA expression 4h post-stimulation, the peak timepoint of LPS-induced inflammatory gene expression (Das et al, 2016). To enrich for extracellular secreted proteins and to prevent effects of extraction buffer components on cell cultures, proteins were gently homogenised in DPBS on ice in the absence of detergent and protease inhibitors. As a positive control for inflammatory response gene induction, we concurrently treated BV2 cultures with LPS.

overall_design: Gene expression profiling of BV2 microglia 4h after treatment with protein homogenates from the DCN or EC, with LPS, or with D-PBS negative control (N=3)

first: Jia

last: Tan

first: Norliyana

last: Zainolabidin

first: Albert

last: Chen

first: Toh

middle: H

last: Ch'ng