title: Circulating microRNAs in young individuals with long-duration type 1 diabetes in comparison with healthy controls

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

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

summary: MicroRNAs (miRNAs) are short non-coding RNAs that are involved in post-transcriptional control of gene expression. The objective of this case-control study was to explore circulating miRNAs in young individuals with long-duration type 1 diabetes (T1D) and healthy controls. Twelve adolescents, age 15.0–17.9 years, with T1D duration of more than 8 years (mean 11.1 years), were enrolled from the Swedish diabetes quality registry. An age-matched control group (n = 12) was recruited. Circulating miRNAs (n = 187) were analyzed by quantitative PCR.  We observed that 27 miRNAs were upregulated and one was downregulated in T1D. Six of these miRNAs were tissue-enriched (blood cells, gastrointestinal, nerve, and thyroid tissues). Six miRNAs with the largest difference in plasma, five up-regulated (hsa-miR-101-3p, hsa-miR-135a-5p, hsa-miR-143-3p, hsa-miR-223-3p and hsa-miR-410-3p (novel for T1D)) and one down-regulated (hsa-miR-495-3p), with P-values below 0.01, were selected for further in-silico analyses. AKT1, VEGFA and IGF-1 were identified as common targets.  In conclusion, 28 of the investigated miRNAs were differently regulated in long-duration T1D in comparison with controls. Several associations with cancer were found for the six miRNAs with the largest difference in plasma. Circulating miRNAs are potential biomarkers and treatment targets with clinical implications for diabetes-related complications.

overall_design: A total of 24 samples grouped into 12 controls and 12 young adolescents with type-1 diabetes were analyzed using a custom microRNA qPCR panel including 187 targets and 5 quality controls.

first: Diana

last: Swolin-Eide

first: Gun

last: Forsander

first: Auste

last: Lycka

last: Novak

first: Johannes

last: Grillari

first: Matthias

last: Hackl

first: Per

last: Magnusson


title: DNA methylation profile discriminates sporadic giant cell granulomas of the jaws and cherubism from their giant cell-rich histological mimics

status: Public on Oct 18 2023

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

summary: Giant cell granulomas of the jaws often occur sporadically as single central or peripheral lesions. They are characterized by KRAS, FGFR1, or TRPV4 somatic mutations, the latter occurring exclusively in the central form. Less commonly, multiple giant cell lesions can develop in the context of syndromes such as cherubism, which is an autosomal dominant bone disease. Morphologically, giant cell granulomas can closely resemble other giant cell-rich lesions such as non-ossifying fibroma and aneurysmal bone cyst, and to a minor extent giant cell tumour of bone and chondroblastoma. The epigenetic basis of these giant cell-rich tumours is unclear and, recently, DNA methylation profile has been shown to be clinically useful for the diagnosis of other tumour types, including brain tumours as well as bone and soft tissue sarcomas. Therefore, we aimed to assess the DNA methylation profile of central and peripheral sporadic giant cell granulomas of the jaws and cherubism to test whether DNA methylation patterns can help to distinguish these entities. Additionally, we further compared the DNA methylation profile of these lesions with those of other giant cell-rich mimics to investigate if the microscopic similarities extend to the epigenetic level. Our results showed that central and peripheral sporadic giant cell granulomas of the jaws and cherubism share a related DNA methylation pattern with that of peripheral sporadic giant cell granulomas and cherubism appearing slightly distinct, while central sporadic giant cell granulomas show overlap with both of the former. Non-ossifying fibroma, aneurysmal bone cyst, giant cell tumour of bone, and chondroblastoma, on the other hand, have distinct methylation patterns. Therefore, DNA methylation profiling is currently not capable of clearly distinguishing sporadic and cherubism-associated giant cell lesions of the jaws. Conversely, it could discriminate sporadic giant cell granulomas from their giant cell-rich mimics.

overall_design: retrospective study of archival FFPE tissues

last: von Deimling

first: Carolina

middle: C

last: Gomes


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Set1 S228A S228E mutant Transcriptomes

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

country: China

institute: Hubei university

type: Expression profiling by high throughput sequencing

summary: Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. However, how cells transduce nutrient availability to appropriate gene expression response via histone modifications remains poorly understood. Here,we reported cla4 catalyzed Set1 phosphorylaton regulates cell cycle and histone gene transcription.

overall_design: Total RNA was isolated from exponential growing yeast cells by standard phenol-chloroform extraction procedures and the quality of RNA was examined using Agilent Bioanalyzer according to the manufacturer’s instructions. Library construction, sequencing and bioinformatics analysis were performed . There are three biological replicates for WT  and Set1 S228A, Set1 S228E mutants. Differential expression levels of aligned sequences were calculated using significant thresholds set at fold change over 1.5 and adjusted P-value < 0.05

first: Duan

last: Kai


title: Effect of inhibition of VCP on gene expression during colorectal cancer progression of HCT116 cells

city: Guangzhou

first: Fang

last: Wang

state: None Selected

address: 601 Huangpu Avenue West

institute: Jinan university

summary: To investigate the signaling patheway of  VCP regulation PD-L1 in colorectal cancer cells, HCT116 cells were treated with CB-5083. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells CB-5083 treatment and untreatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells treated CB-5083 and untreated

first: Haipeng

last: Zhang


title: Methylation-mediated retuning on the enhancer-to-silencer activity scale of networked regulatory elements guides driver-gene misregulation

city: Jerusalem

first: Yifat

last: Edrei

address: Ein Karem Cmpus

country: Israel

institute: The Hebrew University of Jerusalem

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Scalable production oftissue-like vascularised liver organoids from human PSCs.

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

summary: Organoid models have been developed for a number of tissues including the liver. Currenthepatic organoid models are generally simplistic, composed of hepatocytes orcholangiocytes, rendering them less physiologically relevant when compared to nativetissue. To address this we have developed an approach that does not require 2Dpatterning, which is ECM independent and growth factor free, to mimic embryonic liverdevelopment that produces massive quantities of liver like organoids. Using single-cell RNAsequencing and immunofluorescence we demonstrate a liver-like cellular repertoire,presenting with vascular luminal structures,and a population of resident macrophage – theKupffer cells. The organoids exhibit key liver functions including drug metabolism, serumprotein production, urea synthesis and coagulation factor production, which preservedpost-translational modifications such as N-glycosylation and functionality. The organoidscan be transplanted and maintained inmice producing human albumin long term.Theorganoids exhibit a complex cellular repertoire reflective of the organ, havede novovascularization, and liver like function. This isa pre-requisite for a myriad of applicationsfrom cellular therapy, tissue engineering, drug toxicity assessment, disease modeling, tobasic developmental biology.

overall_design: Liver organoids differentiated from human pluripotent stem cells

first: Sean

middle: P

last: Harrison

first: Richard

last: Siller

first: Gareth

middle: J

last: Sullivan


title: Small RNA profiles of Sri Lankan Cassava Mosaic Virus (SLCMV) infected Cassava plants

city: Thiruvananthapuram

first: Makeshkumar

last: T

state: Kerala

address: Sreekaryam

department: Division of Crop Protection

country: India

institute: ICAR CTCRI

type: Non-coding RNA profiling by high throughput sequencing

summary: We reported the small RNA profiles of disease free and SLCMV infected leaves of susceptible and tolerant genotypes of cassava. The sRNA data generated through high throughput small RNA sequencing revealed critical regulatory role of host and pathogen derived small RNAs during SLCMV infection.

overall_design: Field-grown cassava plants were screened for SriLankan Cassava Mosaic Virus (SLCMV) infection. The SLCMV positive plants belonging to the susceptible and tolerant genotypes were used for RNA isolation and small RNAs were sequenced using HiSeq 2500 platform.

first: T

last: Makeshkumar

first: Asha

last: Srinivasan

first: Sumayya

last: Mohammad


summary: Cancers arise when particular disease-driving genes adopt abnormal functions, but sequence analyses of coding and regulatory elements leave many of these abnormalities unexplained. We developed a strategy to explore the activities of silencers and enhancers in cancer tumors. Applying the method to human glioblastomas, we produced a driver-gene wide dataset of regulatory elements. Many genes were associated with multiple silencers and enhancers, which cooperatively controlled their expression. Surprisingly, DNA methylation induces enhancers and silencers to acquire new activity setpoints, ranging between strong transcriptional enhancing to strong silencing. Integration of these effects into mathematical models of gene expression resolved the molecular events underlying cancer-genes misregulation in hitherto unexplained tumors. Gene-malfunctioning events due to epigenetically-retuned enhancers or silencers outnumbered causative coding or regulatory sequence alterations, hence dominated driver-genes mutagenesis. The elucidation of this principal gene-transformation mechanism may open the way for methodological disclosing of the driving forces behind cancers and other diseases

overall_design: Regulatory functions of captured cis-regulatory elements were analyzed through massively parallel functional assays under complete de-methylation versus complete re-methylation conditions.

first: Asaf

last: Hellman

first: Revital

last: Levy


title: A cell atlas of the adult Aedes aegypti midgut revealed by single nucleus RNA-Seq

status: Public on Oct 17 2023

city: columbia

first: Alexander

last: Franz

state: MO

address: 303 Connaway Hall

department: Department of Veterinary Pathology

country: USA

institute: University of Missouri

summary: Mosquitoes are the most notorious hematophagous insects and due to their blood feeding behavior and genetic compatibility, numerous mosquito species are highly efficient vectors for certain human pathogenic parasites and viruses. The mosquito midgut is the principal organ of blood meal digestion and nutrient absorption. It is also the initial site of infection with blood meal acquired parasites and viruses. We conducted an analysis based on single-nucleus RNA sequencing(snRNA-Seq) to assess the cellular diversity of the midgut and how individual cells respond to blood meal ingestion to facilitate its digestion.

overall_design: We dissected about 30 midguts from unfed and blood-fed Aedes aegypti mosquitoes, and isolated single nuclei, constructed two libraries, we analyzed the data with R package Seurat, the formed clusters were annotated. We further compared the cellular composition and gene expression between midguts from unfed and blood-fed mosquitoes.

first: Yingjun

last: Cui

middle: W


title: Targeting doublecortin-like kinase 1 reveals a novel strategy to circumvent chemoresistance and metastasis in ovarian cancer

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

summary: Targeted mRNA expression profiling was performed using nCounter® Tumor Signaling 360™ Panel (NanoString Technologies) composed of 780 genes (including internal reference genes) involved in cellular energetics, sustained proliferation, evasion of growth suppression, genomic instability, resistance to cell death, epithelial to mesenchymal transition (EMT), and metastasis. Normalization of housekeeping genes for the quantification of gene expression levels, normalization of the positive control for background correction, and data analysis were performed using the nSolverTM analysis software (NanoString Technologies).

overall_design: Total RNA was extracted from OVCAR-8 CPR sgCtrl and DCLK1 KO spheroids (3 resplicates/ sample). Transcripts with an RNA count < 20 for all samples were excluded because they were considered unexpressed. The mean and standard deviation (SD) were calculated for each group. Only genes with significant (p < 0.05) fold changes (< –2 or > +2) were considered differentially expressed.

first: Samrita

last: Dogra


title: The effect of epigenetics on diapause of Asian corn borer larvae [WGBS]

city: Beijing

first: Pengfei

last: Lv

address: No. 2, Old Summer Palace West Road

institute: China agricultural university

summary: H3K9me3 and H3K27me3 were involved in diapause regulation of O. furnacalis larvae

overall_design: The newly molted fourth instar larvae were collected and maintained at 20 °C under a photoperiod of 12L: 12D for at least 30 days to achieve diapause (Guo et al, 2013). The newly molted fourth instar larvae maintained for 20 days at a photoperiod of 20 ° C and 12L: 12D were in a pre-diapause state. CHIP-seq was performed on the heads of diapause, pre-diapause and  non-diapause Asian corn borer larvae using antibodies H3K9me3 and H3K27me3 .


title: Effects of ibudilast treatment on hippocampal gene expression in Female Fisher transgenic 344-AD rats.

city: New York

first: Kelechi

last: Ndukwe

state: NY

address: 695 Park Ave, New York, NY 10065

department: Biology

institute: Hunter College City University of New York Graduate Center

summary: 5 month old Female Fisher transgenic 344-AD (Tg-AD) rats expressing humanSwedishamyloid precursor protein (APPsw) and Δ exon 9 presenelin-1 (PS1ΔE9) were treated with Ibudilast  (cat. no. HY-B0763, MCE) at 10 mg/kg body weight administered in rodent chow. Following 6 months of Ibudilast  treatment, rats (11 months of age) were tested for cognitive behaviour prior to sacrificing. Hippocampal Brain region were dissected and  RNA sequencing (RNAseq) analyses was done on the Isolated sample. Taken together we showed that Ibudilast  treatment: (i) reduces inflammation by decreasing the levels of the pro inflammatory cytokine IL6, interferon receptor 1, the macrophage migration inhibitory factor (MIF), microglial associated proteins such as transmembrane protein 119 (TMEM119), arachidonate 5-lipoxygenase activating protein (Alox5ap), toll like receptor 7 (TLR7), lysosomal protein transmembrane 5 (LAPTM5) and triggering receptor expressed on myeloid cells 2 (TREM2); (ii) increases expression of synaptic proteins such as synaptotagmin 2 (SYT2), which regulates vesicular transport, syntaxins (STX), which participates in neurotransmitter release, and cadherin (CDH1), which maintains synapse structure; and (iii) reduces the expression of the neurotrophic factor BDNF by 2-fold in both male and female treated rats.

overall_design:
To show the effects of ibudilast-treatment on gene expression levels, Hippocampi of 5 Ibudilast -treated and 5 untreated transgenic rats of Female rats were analysed for gene expression by RNAseq
At 11 months of age, the rats were anaesthetized intraperitoneally with ketamine (100 mg/kg) and xylazine (10 mg/kg) and transcardially perfused with cold RNAse-free 1× PBS. Left hippocampi were removed and snap frozen for RNAseq analysis.
Left hemisphere of the hippocampus. F1 – F5 (untreated transgenic rats), FIB1 – FIB5 (transgenic AD rats treated with the drug ibudilast).
Female Rats started ibudilast treatments at 5-months of age and were treated for 6 months until they were 11 months old. ). For this experiment, the gene expression for the drug treated transgenic rats will be compared to that of the untreated transgenic group (FIB1-5/F1-5)
Male and Female Data uploaded separately. Male data have been assigned GEO accession numbers (GSE245214)

first: Giovanni

last: Oliveros

first: Charles

middle: H

last: Wallace

first: Osama

last: Chaudry

first: Qiao

last: Liu

first: Yue

last: Qiu

first: Lei

last: Xie

first: Patricia

last: Rockwell

first: Maria

middle: E

last: Figueiredo-Pereira

first: Peter

middle: A

last: Serrano


title: The effect of epigenetics on diapause of Asian corn borer larvae [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing


first: Yifat

last: Edrei

overall_design: A new strategy for methylation-centered interrogations of functional gene-associated regulatory elements was applied to H3K4me1-marked chromatin within the regulatory domains of 125 pan-cancer and/or glioblastoma (GBM) driver genes, and 52 reference cancer genes. The effect of DNA methylation on gene transcription was analyzed for 38,050 targeted methylation sites in experimental massively paralleled reporter assay as well as in 24 GBM tumors. Technical and biological replicates provided as well.

first: Asaf

last: Hellman

first: Bernhard

last: Radlwimmer


title: The effect of epigenetics on diapause of Asian corn borer larvae


title: Transcriptional profiling of Tumour and normal intestinal tissue from mice with a Kras G12D mutation and loss of the second WT allele.

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

summary: A profile of gene expression in Tumour and normal intestinal tissue from mice with Kras G12D mutation and loss of the WT Kras allele.

overall_design: Tumour and normal tissue was taken from the small intestine of mice with Kras G12D mutation and loss of the second WT Kras allele. Transcriptomic data was obtained for each sample.

first: Arafath

last: Kaja Najumudeen

first: Owen

last: Sansom


title: Transcriptional profiling of intestinal Tumour tissue from mice with combinations of Apc, Kras G12D, p53, Notch1, Tgfbr1 and Tgfbr2 mutations.

summary: A profile of gene expression in Tumours from the small intestine of mice with a variety of mutations.

overall_design: Tumour tissue was taken from the small intestine of mice with Apc, Kras G12D, p53, Notch1, Tgfbr1 and/or Tgfbr2 mutation, and transcriptomic data was obtained for each sample.

first: David

last: Lewis


title: Transcriptional profiling of Tumour and normal intestinal tissue


title: Effects of ibudilast treatment on hippocampal gene expression in Male Fisher transgenic 344-AD rats.

first: Kelechi

last: Ndukwe

summary: 5 month old Male Fisher transgenic 344-AD (Tg-AD) rats expressing humanSwedishamyloid precursor protein (APPsw) and Δ exon 9 presenelin-1 (PS1ΔE9) were treated with Ibudilast  (cat. no. HY-B0763, MCE) at 10 mg/kg body weight administered in rodent chow. Following 6 months of Ibudilast  treatment, rats (11 months of age) were tested for cognitive behaviour prior to sacrificing. Hippocampal Brain region were dissected and  RNA sequencing (RNAseq) analyses was done on the Isolated sample. Taken together we showed that Ibudilast  treatment: (i) reduces inflammation by decreasing the levels of the pro inflammatory cytokine IL6, interferon receptor 1, the macrophage migration inhibitory factor (MIF), microglial associated proteins such as transmembrane protein 119 (TMEM119), arachidonate 5-lipoxygenase activating protein (Alox5ap), toll like receptor 7 (TLR7), lysosomal protein transmembrane 5 (LAPTM5) and triggering receptor expressed on myeloid cells 2 (TREM2); (ii) increases expression of synaptic proteins such as synaptotagmin 2 (SYT2), which regulates vesicular transport, syntaxins (STX), which participates in neurotransmitter release, and cadherin (CDH1), which maintains synapse structure; and (iii) reduces the expression of the neurotrophic factor BDNF by 2-fold in both male and female treated rats.

overall_design:
To show the effects of ibudilast-treatment on gene expression levels, Hippocampi of 5 Ibudilast -treated and 5 untreated transgenic rats of male rats were analyzed for gene expression by RNAseq
At 11 months of age, the rats were anaesthetized intraperitoneally with ketamine (100 mg/kg) and xylazine (10 mg/kg) and transcardially perfused with cold RNAse-free 1× PBS. Left hippocampi were removed and snap frozen for RNAseq analysis.
Left hemisphere of the hippocampus. M1 – M5 (untreated transgenic rats), MIB1 – MIB5 (transgenic AD rats treated with the drug ibudilast).
*The MIB1 – MIB5 samples have been stored in a solution called RNAlater®-ICE Frozen Tissue Transition Solution. The reagent has a blue dye so the tissues are blue. This reagent is compatible with most RNA isolation procedures including that sold by Qiagen.
Male Rats started ibudilast treatments at 5-months of age and were treated for 6 months until they were 11 months old. ). For this experiment, the gene expression for the drug treated transgenic rats will be compared to that of the untreated transgenic group (MIB/M). Male and Female Data uploaded separately. Female data have been assigned GEO accession numbers (GSE245623)


title: A distal lung organoid model to study interstitial lung disease, viral infection and human lung development.

first: Hans-Willem

last: Snoeck

address: 650 west 168th street

institute: Columbia University Irving Medical Centre

summary: Organoid models have been one of the most exciting advancements in stem cell research of the past decade. Here we describe a strategy for directed differentiation of human pluripotent stem cells into distal lung organoids that can be used to model interstitial lung disease, viral infection and human endoderm and lung development. This protocol entails five stages that recapitulate lung development. hPSCs are sequentially specified to definitive endoderm, anterior foregut endoderm, ventral anterior foregut endoderm, lung bud organoids, and finally branching lung organoids that can be maintained, while progressively maturing up to the a stage consistent with the second trimester of human gestation, for more than 180 days. This protocol is conducted in defined, serum-free conditions and does not require lineage-specific reporters or cell purification. We also provide a protocol for the generation of single cell suspensions for single cell RNAseq, and for clearing and 3D light sheet fluorescence imaging.

overall_design: We performed single cell RNA sequencing analysis across four developmental stages  (day25/40/60 and 80) of our organoid model. All organoids at each stage were dissociated to single cell suspension and resuspended to a concentration of 5000cells /ul for sequencing.

first: Ivana

last: Matkovic-Leko

first: Remy

middle: T

last: Schneider

first: Tania

last: Thimraj

first: Nadine

last: Schrode

first: Daniel

last: Beitler

first: Hsiao-Yun

first: Kristin

last: Beaumont

first: Ya-Wen

last: Chen


title: Transcriptome networks identify susceptibility to frequent asthma exacerbations

city: Cincinnati

first: Kieran

last: Phelan

state: Ohio

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: To investigate mechanisms underlying frequent asthma exacerbation, we profiled the nasal transcriptome of both frequent and non-frequent asthma exacerbators.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for frequent and non-frequent asthma exacerbators

first: Kim

last: Dill-McFarland

first: Arjun

last: Kothari

first: R

middle: M

last: Segnitz

last: Spagna

first: Seth

last: Jenkins

first: Britanny

last: Grashel

first: Jeff

last: Burkle

first: Lisa

last: Martin

middle: B

last: Haslam

first: Jocelyn

last: Biagini

first: Maninder

last: Kalra

first: Kristie

last: Ross

first: Karen

middle: S

last: McCoy

last: Jackson

first: Tesfaye

last: Mersha

first: Matthew

last: Altman

first: Gurjit

middle: K

last: Hershey


title: Genome wide N-MYC binding in human inv(16) AML cells

city: Wauwatosa

first: John

middle: Anto

last: Pulikkan

state: WI

address: 8727 W Watertown Plank Rd

institute: Versiti

summary: To identify the role of N-MYC in transcriptional regulation in human inv(16) AML, we conducted conducted CUT&Tag analysis for N-MYC and H3K27AC in ME-1 cells

overall_design: Chromatin was immunoprecipitated with N-Myc, H3K27ac and IgG antibodies. Sequencing was performed on an Illumina NextSeq500 (paired-end).

first: Sridevi

last: Surapally


title: Nicotine exposure declines quality of early embryos and disrupts placental structure by destabilizing Notch signaling pathway

city: Wuhan

first: Jing-Jing

last: Zhang

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

summary: Nicotine is a common environmental pollution which is diffused into the air in the form of cigarette smoke fumes. Due to its lipophilic nature, nicotine can rapidly transport through membrane barriers and spread throughout the body which leads to abnormalities in the human brain, heart and even the fatal. However, the effects of nicotine on early embryonic development remains elusive. In this study, we found that nicotine significantly affected early embryonic development with decreased blastocyst formation. In addition, embryos treated with nicotine caused increased level of ROS, DNA damage and cell apoptosis. By RNA sequencing analysis, we demonstrated that nicotine affected the expression of placental development genes. Consistently, we found that the placental development at E17.5 was impaired by nicotine exposure, with increased placental weight and disrupted placental structure. This was due to excessive activation of the Notch signaling pathway, since blocking Notch signal by DAPT treatment recovered abnormal placental weight and structure induced by nicotine exposure. We also observed that nicotine exposure could specifically cause promoter hypermethylation of Phlda2 (a maternally expressed imprinted gene associated with placental development) and lead to its abnormal expression. Overall, this study provides evidence that nicotine causes the declining quality of early embryo and leads to placental abnormalities related with over-activation of the Notch signaling pathway.

overall_design: The RNA-Seq experiments of the control and nicotine treated embryos at the morula, ICM and TE stage.

first: Qiao-Ran

last: Sun

first: Jilong

last: Zhou

first: Yi-Liang

last: Miao


title: Generation of off-the-shelf CAR-NKT cells for cancer immunotherapy with genetically engineered HSCs and feeder-free differentiation culture

status: Public on Oct 16 2023

city: Los Angeles

first: Wenbin

last: Guo

state: CA

address: 610 Charles E. Young Drive, TLSB 5000

institute: UCLA

summary: Current CAR-T cell therapy's clinical potential is hampered by its autologous nature that poses significant challenges in manufacturing, costs, and patient selection. This spurs demand for off-the-shelf therapies. Here we introduce an ex vivo feeder-free culture to differentiate gene-engineered HSCs into allogeneic NKT cells and their CAR-armed derivatives (AlloCAR-NKT cells). The AlloCAR-NKT cells are generated at high yield, purity, and robustness. These cells exhibit potent antitumor efficacy, showing effective tumor homing, clonal expansion, and persistence In vivo. Impressively, AlloCAR-NKT cells can alter the tumor microenvironment by selectively depleting immunosuppressive TAMs and MDSCs, and can antagonize tumor immune evasion by deploying CAR/TCR/NKR triple-targeting mechanisms. AlloCAR-NKT cells also demonstrate an appealing safety profile with low GvHD and CRS risks, and exhibit a stable “hypoimmunogenic” phenotype attributed to epigenetic and signaling regulations. The reported technology presents a scalable strategy for diverse allogeneic CAR-NKT cell products, with potential for clinical translation and commercialization against various cancers.

overall_design: A total of 24 cell samples were analyzed, including 3 AlloNKT (6B11+TCRαβ+), 3 AlloBCAR-NKT (6B11+TCRαβ+), 3 Allo15BCAR-NKT (6B11+TCRαβ+), 2 Allo15CAR19-NKT (6B11+TCRαβ+), 3 PBMC-NKT (6B11+TCRαβ+CD4-), 8 PBMC-Tc (6B11-TCRαβ+CD4-), and 2 PBMC-NK (CD56+TCRαβ-) cell samples.  Note that Allo/15(CAR)-NKT cells displayed a CD4-CD8+/- phenotype, therefore the CD4- populations of PBMC-NKT and PBMC-Tc cells were used in this study. Among the 24 cell samples, 11 samples were newly sequenced in this study, and the remaining 13 samples were sequenced in our previous study (GEO Accession: GSE164425). We downloaded the raw sequencing data of these 13 samples and reanalyzed them. All the samples were subject to the same data processing and analysis procedure as denoted in the protocols fields.

first: Yan-Ruide

last: Li

first: Yang

first: Jiaji

last: Yu

first: Lili

last: Yang


title: Chromatin Profiling of CBFA2T3-GLIS2 AMLs Identifies Key Transcription Factor Dependencies and BRG1 Inhibition as a Novel Therapeutic Strategy

city: Seattle

first: Brandon

last: Hadland

state: WA

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Center

summary: Oncogenic fusions involving transcription factors are present in the majority of pediatric leukemias; however, the context-specific mechanisms they employ to drive cancer remain poorly understood. CBFA2T3-GLIS2 (C/G) fusions occur in treatment-refractory acute myeloid leukemias and are restricted to young children. To understand how the C/G fusion drives oncogenesis we applied CUT&RUN chromatin profiling to an umbilical cord blood/endothelial cell (EC) co-culture model of C/G AML that recapitulates the biology of this malignancy. We find C/G fusion binding is mediated by its zinc finger domains. Integration of fusion binding sites in C/G- transduced cells with Polycomb Repressive Complex 2 (PRC2) sites in control cord blood cells identifies MYCN, ZFPM1, ZBTB16 and LMO2 as direct C/G targets. Transcriptomic analysis of a large pediatric AML cohort shows that these genes are upregulated in C/G patient samples. Single cell RNA-sequencing of umbilical cord blood identifies a population of megakaryocyte precursors that already express many of these genes despite lacking the fusion. By integrating CUT&RUN data with CRISPR dependency screens we identify BRG1/SMARCA4 as a vulnerability in C/G AML. BRG1 profiling in C/G patient-derived cell lines shows that the CBFA2T3 locus is a binding site, and treatment with clinically-available BRG1 inhibitors reduces fusion levels and downstream C/G targets including N-MYC, resulting in C/G leukemia cell death and extending survival in a murine xenograft model.

overall_design: Single cell RNA-sequencing (10X Genomics platform) of human cord blood hematopoietic stem cells. Baseline were fresh FACS-isolated cord blood cells, Control were transduced with a control lentiviral vector and cultured for 4 days.

first: Jay

last: Sarthy


title: NK92 cells and peripheral blood NK cells respond oppositely upon dasatinib treatment

city: Tianjin

first: Fengqi

state: Tianjin

address: No. 92, Weijin Road, Xuefu Street, Nankai District

department: School of Pharmaceutical Science and Technology

institute: Tianjin university

summary: Natural Killer (NK) cell is a valuable tool for immunotherapy in cancer treatment, both the cultured cell line NK92 and primary NK cells are widely studied and used in the research and clinical trials. Clinical observations witnessed the improvement of patients’ NK cells in terms of cell counts and cytotoxic activity upon dasatinib treatment, an approved drug against CML and Ph+ ALL. Several studies supported the clinical observations, yet others argued a detrimental effect of dasatinib on NK cells. Due to the complex conditions in different studies, the definite influence of dasatinib on NK92 and primary NK cells remains to be settled. Here, we used a well-defined in vitro system to evaluate the effects of dasatinib on NK92 cells and peripheral blood (PB)-NK cells. By coculturing NK cells with dasatinib to test the cell counts and target cell killing activities, we surprisingly found that the chemical influenced oppositely on these two types of NK cells. While dasatinib suppressed NK92 cell proliferation and cytotoxic activity, it improved PB-NK killing tumor cells. RNA-seq analysis further supported this finding, uncovering several proliferating and cytotoxic pathways were responding invertedly between them. Our results highlighted an intrinsic difference between NK92 and PB-NK cells and may build clues to understand how dasatinib interacts with NK cells in vivo.

overall_design: To explore the functional effects of dasatinib on PBNK and NK92 NK cells, we treated two cells at a concentration of 50 nM for three days, extracted total RNA, and performed RNAseq analysis in both cells compared to DMSO

first: Zhongyi

last: Wang

first: Dongpeng

last: Zheng

first: Zhaojun

last: Pang

first: Chunjing

last: Feng

first: Yue

last: Ma

first: Ce

first: Xueren

first: Shouchun

last: Peng

first: Zichuan

last: Liu

first: Xin

last: Mu


title: Pro-survival A1 is induced by pathogen ligands to limit myeloid cell death and NLRP3 inflammasome activation

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Despite the importance of cell death in pathogen-induced innate immune responses, comparatively little is known about the regulation of intrinsic apoptosis during infection, nor how pathogens may subvert this pathway for their own benefit. Here, we identify that the pro-survival BCL-2 family member, A1, controls activation of the essential intrinsic apoptotic effectors, BAX/BAK, in macrophages and monocytes following bacterial lipopolysaccharide (LPS) sensing. We show that, due to its tight transcriptional and post-translational regulation, A1 acts as a molecular rheostat to regulate BAX/BAK-dependent apoptosis and the subsequent NLRP3 inflammasome-dependent and -independent maturation of pro-IL-1b. Furthermore, induction of A1 expression in inflammatory monocytes limits cell death modalities and IL-1b activation triggered by Neisseria gonorrhoeae-derived outer membrane vesicles (NOMVs). Consequently, A1-deficient mice exhibit heightened IL-1b production in response to NOMV injection. These findings reveal that bacteria can induce A1 expression to delay myeloid cell death and inflammatory responses, which has implications for the development of host-directed antimicrobial therapeutics.

overall_design: BMDMs isolated from three separate Wildtype C57BL/6J mice housed at WEHI were treated with LPS.

first: Daniel

last: Simpson

first: James

last: Vince

first: Kathryn

last: Lawlor


title: RBM6 promotes tumor cell apoptosis and disrupts the alternative splicing of related genes in HeLa cells

first: Dong

last: Chen

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: RNA binding proteins have important functions in tumorigenesis; therefore, their regulatory mechanisms should be further explored. The present study aimed to determine the regulatory roles of RNA binding motif protein 6 (RBM6) in transcription and alternative splicing in Hela cells. RBM6 expression levels and its effect on the prognosis of different tumors in The Cancer Genome Atlas database were analyzed using TIMER2.0. Short hairpin RNA was used to ablate RBM6 expression in HeLa cells. Differentially expressed genes and alternative splicing events in Hela cells were assessed using RNA sequencing and quantitative real-time reverse transcription polymerase chain reaction. RBM6 was identified as a prognostic marker for  bladder urothelial carcinoma, kidney renal clear cell carcinoma, mesothelioma, and pancreatic adenocarcinoma. Knockdown of RBM6 promoted cell proliferation. In Hela cells, RMB6 regulated the expression and alternative splicing of many genes involved in tumorigenesis_x001E_related pathways, including ‘apoptotic process’, ‘mitotic cell cycle’, and ‘RNA splicing’. RBM6-regulated alternatively spliced genes (DIABLO (Diablo IAP-binding mitochondrial protein), PAK4 (P21 (RAC1) activated kinase 4) and ERCC2 (ERCC excision repair 2, TFIIH core complex helicase subunit)) were subjected to quantitative real-time reverse transcription polymerase chain reaction validation, which demonstrated the same expression trends as the RNA sequencing results. Our findings showed that RBM6 affects tumorigenesis and cancer progression by disrupting  alternative splicing in HeLa cells.

overall_design: Short hairpin RNA was used to ablate RBM6 expression to study its effect on cell proliferation in Hela cells

first: Danqing

last: Li

first: Yuankun

last: Qin

first: Ya

last: Zhang

first: Yanli


title: Eosinophils promote lung emphysema via CTSL

summary: Patients with chronic obstructive pulmonary disease (COPD) having higher blood eosinophil levels exhibit worse lung function and more severe emphysema, implying the potential role of eosinophils in emphysema development. However, the specific mechanism underlying eosinophil-mediated emphysema development is not fully elucidated. In this study, single-cell RNA sequencing was used to identify eosinophil subgroups in mouse models of asthma and emphysema and analyze their functions. Analysis of the accumulated eosinophils revealed differential transcriptomes between the mouse lungs of elastase-induced emphysema and ovalbumin-induced asthma., Eosinophil depletion alleviated elastase-induced emphysema. Notably, eosinophil-derived cathepsin L (CTSL) degraded the extracellular matrix (ECM), causing emphysema in the pulmonary tissue. Eosinophils were positively correlated with serum CTSL levels, which were increased in patients with emphysema than in those without emphysema. Collectively, these results suggest that CTSL expression in eosinophils plays an important role in ECM degradation and remodeling and is related to emphysema in patients with COPD. Therefore, eosinophil-derived CTSL may serve as a potential therapeutic target for patients with emphysema.

overall_design: 13 sample from lung tissue

first: Xia

last: Xu


title: Reorganization of pancreas circadian transcriptome with aging

city: Chicago

first: Deepak

last: Sharma

state: Illinois

address: 1653 W Congress Pkwy #12

institute: Rush University Medical Center

summary: The evolutionarily conserved circadian system allows organisms to synchronize internal processes with 24-h cycling environmental timing cues, ensuring optimal adaptation. Like other organs, the pancreas function is under circadian control. Recent evidence suggests that aging by itself is associated with altered circadian homeostasis in different tissues which could affect the organ’s resiliency to aging-related pathologies. Pancreas pathologies of either endocrine or exocrine components are age-related. Whether pancreas circadian transcriptome output is affected by age is still unknown. To address this, here we profiled the impact of age on the pancreatic transcriptome over a full circadian cycle and elucidated a circadian transcriptome reorganization of pancreas by aging. Our study highlights gain of rhythms in the extrinsic cellular pathways in the aged pancreas and extends a potential role to fibroblast-associated mechanisms.

overall_design: Here we carried out a 24-h circadian transcriptomic analysis of pancreas from male mice at young and old ages. We define a comprehensive circadian transcriptome landscape and identify biological pathways that are reflective of aging pancreas. Additionally, analysis of pancreatic microenvironment revealed novel mechanistic insights into the fibroblast mediated regulation of rhythmicity in aged pancreas. We suggest that circadian transcriptome in aging pancreas re-organizes in response to age-specific signals from the cellular microenvironment, primarily modulated by fibroblasts.

first: Caitlin

middle: R

last: Wessel

first: Mahboobeh

last: Mahdavinia

first: Fabian

last: Preuss

first: Faraz

last: Bishehsari


title: Dietary ligands diindolylmethane and resveratrol result in diverse ERα signaling not seen after E2 and a subset of diindolylmethane mediated signaling needs concurrent AHR activation. [ChIP-Seq]

city: Oslo

first: Jason

last: Matthews

address: Sognsvannsveien 9

department: Nutrition

country: Norway

institute: University of Oslo

summary: Background: Estrogen receptor (ERα) and aryl hydrocarbon receptor (AHR) are two nuclear receptors involved in regulating gene expression. ERα and AHR are regulated by estradiol(E2) and TCDD respectively. They are also regulated by dietary ligands including 3,3´diindolylmethane (DIM) and resveratrol (RES). DIM is an ERα and AHR agonist, while RES is an ERα agonist and AHR antagonist. Few studies have investigated the impact of RES and DIM on ERα and AHR signaling at a genome-wide level. This study assessed ERα and AHR binding and associated gene expression changes after treatment of MCF-7 human breast cancer cells with DIM, RES, E2, TCDD, and E2+TCDD for 1 hour and 6 hours before ChIP and RNA sequencing respectively.   Results: 88% and 86% of the ERα bound sites after RES and DIM overlapped with E2 ERα sites. RES and DIM resulted in 577 and 446 differentially expressed genes (DEGs) respectively compared to 866 after E2. 68% and 62.3% of the DEGs after RES and DIM were closest to an ERα binding site. Motif analysis indicated enrichment for AHRE motif among DIM ERα sites but not among E2 or RES ERα sites. Both DIM and E2+TCDD resulted in greater genome wide binding of AHR than TCDD. DIM and E2+TCDD resulted in 10546 and 8904 AHR and ERα co-occupied sites respectively. While co-occupied sites for both enriched for the AHR and ERE motif among others, DIM mediated co-occupied sites enriched for Tcfcp2l1, Tgif1, Gata3 motifs while E2+TCDD mediated ones enriched for the NF1 and Ppara motifs. Overlap of coregulated DEGs after DIM and E2+TCDD indicated 123 were the same among both with 81 and 85 unique coregulated DEGs respectively. Enrichment analysis indicated that more enrichment terms were different than similar for coregulated genes after E2+TCDD and DIM.  Conclusions: AHR activation is responsible for DIM mediated reduced regulation of gene expression by ERα relative to E2 and only a subset of the DEG’s after DIM and RES are ERα targets indicating future studies into other transcription factors regulated by DIM and RES are needed for insights into the regulation of gene expression by these ligands.

overall_design: MCF-7 human breast cancer cells (HTB-22, ATCC) were cultured in low-glucose (1 g/L) DMEM (Dulbecco’s modified Eagle’s media) supplemented with 1% (v/v) penicillin/streptomycin (P/S) either 10% (v/v) fetal bovine serum (FBS) or 5% dextran coated charcoal (DCC)-treated FBS. They were then treated with activated charcoal and subject to various ligands or DMSO for 1 hour and the ChIP sequencing experiment was done in triplicates.

first: Siddhartha

last: Das

first: Stine

last: Ulven


title: A chromatin-regulated biphasic circuit coordinates IL1B-mediated inflammation

city: Nijmegen

first: Ezio

last: Fok

state: Gelderland

address: Geert Grooteplein

department: Cell biology

country: Netherlands

institute: Radboud University

summary: Inflammation is characterized by a biphasic cycle consisting initially of a pro-inflammatory phase which is subsequently resolved by anti-inflammatory processes. The coordination of these two disparate states needs to be highly controlled, suggesting that the regulation of the cytokines that drive these processes are intimately linked. Interleukin-1 beta (IL1B) is a master regulator of pro-inflammation and is encoded within the same topologically associated domain (TAD) as interleukin-37 (IL37). IL37 has recently emerged as a powerful anti-inflammatory cytokine which diametrically opposes the function of IL1B. Within this TAD, we identified a novel long non-coding RNA called AMANZI which negatively regulates IL1B expression and trained immunity through the induction of IL37 transcription. We found that the activation of IL37 occurs through the formation of a dynamic long-range chromatin contact that leads to the temporal delay of anti-inflammatory responses. The common variant rs16944 present in AMANZI augments this regulatory circuit, predisposing individuals to enhanced pro-inflammation or immunosuppression. Our work illuminates a chromatin-mediated biphasic circuit coordinating expression of IL1B and IL37, thereby regulating two functionally opposed states of inflammation from within a single TAD.

overall_design: In order to investigate the functional role of the long noncoding RNA AMANZI, we depleted AMANZI RNA in THP-1 monocyte-like cells using locked nucleic acids (LNAs) in the gapmer configuration. THP-1 monocytes were activated by exposure to 10ng/ml of LPS for 24 hours prior to RNA extraction and library preparation.  The transcriptional profile of AMANZI knockdown were compared to a control LNA conditions in duplicate.

first: Simone

last: Moorlag

first: Yutaka

last: Negishi

first: Laszlo

last: Groh

first: Jéssica

last: dos Santos

first: Cathrin

last: Grawe

first: Valerie

middle: V

last: Monge

first: Daphne

middle: D

last: Craenmehr

first: Mellanie

last: van Roosmalen

first: David

last: da Cunha Jolvino

first: Letícia

last: Migliorini

first: Ary

last: Neto

first: Patricia

last: Severino

first: Michiel

last: Vermuelen

first: Leo

last: Joosten

first: Mihai

middle: G

last: Netea

first: Stephanie

last: Fanucchi

first: Musa

last: Mhlanga


title: Exploring the Mechanism of TACSTD2 Causing Cisplatin Resistance

first: Xiaoyang

last: Han

address: Qihelou

department: Beijing Obstetrics and Gynecology Hospital

institute: Capital Medical University

summary: TACSTD2 has been confirmed to be highly expressed in various cancers, but the mechanism has not been explored in ovarian cancer

overall_design: SKOV3 cells were sequenced by knocking out TACSTD2, divided into shNC, sh (sh TACSTD2), shNCDDP (cisplatin), shDDP (shTACSTD2+cisplatin).


title: Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma [Bulk RNA-seq]

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

summary: Pediatric malignancies, including neuroblastoma, are best understood as disorders of development. Neuroblastoma explicitly represents a failure of sympathoadrenal development. Yet, its molecular pathogenesis remains elusive. The application of an in vitro model of human sympathoadrenal development would allow for studying the normal developmental trajectory. Such a model could also interrogate the early steps toward neuroblastoma transformation utilizing genetic manipulation. However, in vitro models have thus far been unable to generate the cells of interest reliably. We developed and characterized a human in vitro pluripotent stem cell-based model via sequential single-cell RNA sequencing throughout sympathoadrenal development. We demonstrate the power of our model to study early events of the development of human neuroblastoma. We do so by identifying the differences between normal and patient-specific induced pluripotent stem cells, derived from a child with familial neuroblastoma, harboring a germline mutation in the Anaplastic Lymphoma Kinase (ALK) gene.

overall_design: Induced pluripotent stem cells (iPSC) were differentiated along the sympathoadrenergic precursor (SAP) development during a 40 day long differentiation process. We performed bulk RNA sequencing on selected time-points (D0/Start, D3, D7, D11, D16, D21, D23, D25, D27, D29, D31, D35, D40) covering the entire differentiation process. The experiments were repeated four times, twice with a human induced pluripotent stem cell line (J2) and twice with a human embryonic stem cell line (H9) for a total of four biological replicates.

first: Stéphane

last: Van Haver

first: Frank

last: Speleman

first: Stephen

last: Roberts


title: SERPINE1 and SERPINB7 as potential biomarkers for intravenous vitamin C treatment in non-small-cell lung cancer

city: Guangzhou

first: Junwen

last: Ou

address: 3 Hongfu Road, Panyu District

institute: Clifford Hospital, Jinan University

summary: High dose intravenous vitamin C (IVC) has been proposed as a pro-oxidant anticancer agent. However, there lack biomarkers that are specific for this treatment. Here we explored profiles of gene expression responding to IVC treatment in non-small cell lung cancer (NSCLC) cells as an effort for potential biomarker discovery. Genome-wide RNA-seq was performed in human NSCLC cell lines treated with pharmacological concentrations of vitamin C（VitC） for differential expression of genes. The identified genes were analyzed for correlations with patient prognosis using data from the Kaplan-Meier Plotter and the Human Protein Atlas databases. Further, tumor samples from a retrospective study of 153 NSCLC patients were analyzed with immunohistochemistry for expression of targeted genes, and patient prognosis was correlated to these genes. Two genes, namely SERPINE1 and SERPINB7 were found to be downregulated in NSCLC cells following VitC treatment. Combined patient data from the cohort analysis and online databases revealed that these 2 genes presented an unfavorable prognostic prediction of overall survival (OS) in NSCLC patients receiving standard of care. However, high expression level of these 2 genes were associated with prolonged OS in NSCLC patients receiving IVC in addition to standard of care. These data revealed that SERPINE1 and SERPINB7 have the potential to serve as predictive factors indicating favorable responses to IVC treatment in patients with NSCLC. Further validations are warranted.

overall_design: To investigate the differential gene expression profiles of NSCLC cells under VitC treatment. H1299 and PC9 treated or untreated with IC50 concentrations of VitC were collected at 24 hours, and then gene expression profiles were performed by RNA-seq analysis.

first: Yanping

last: Du

first: Wentao

last: Xi


title: The effect of Sulfonulyrea short form (SUR2A-55) overexpression on cardiac gene expression

city: Madison

first: Mohun

last: Ramratnam

address: 600 HIGHLAND AVE

institute: University of Wisconsin

summary: The small splice variant of the sulfonylurea receptor protein isoform 2A (SUR2A-55) targets mitochondria and enhances mitoKATP activity. In male mice the overexpression of this protein promotes cardioprotection protecting hearts from ischemia reperfusion injury. However, it is unclear what impact this has on the female myocardium as SUR2A and KATP channels are known to be differentially expressed in male and female hearts. To define the impact of SU2R2A-55 on the female heart, RNA seq was performed on hearts from mice with cardiac specific transgenic overexpression of SUR2A-55 (TGSUR2A-55). RNA seq analysis found 227 differnetial expressed genes between WT and TGSUR2A-55 female mouse hearts that were enriched in pathways of cellular metabolism. This was in direct contrast to male mice that had only three differentially expressed genes. Future research directed at the expression and activity of mitoKATP subunits according to sex may elucidate gender specific treatments.

overall_design:
Hearts from male and female mice that were previously created with cardiac specific overexpression of the short form sulfonylurea receptor protein (TGSUR2A-55) were used. We performed gene expression profile analysis on 4 male and 4 female transgenic and WT mouse hearts from data obtained after RNA -seq.
[contributor] University of Wisconsin – Madison Biotechnology Center Gene Expression Center (Research Resource Identifier – RRID:SCR_017757)
[contributor] University of Wisconsin-Madison Biotechnology Center Bioinformatics Core Facility (Research Resource Identifier – RRID:SCR_017799)

first: Sarah

last: El-Meanawy


title: Cell type-specificity of mosaic chromosome 1q gain resolved by single-nucleus RNA-seq in a case of pharmacoresistant epilepsy associated with hyaline protoplasmic astrocytopathy

city: San Francisco

first: Kun

last: Leng

state: Calfironia

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California San Francisco

summary:
Introduction:
Mosaic gain of chromosome 1q (chr1q) is a recently described driver of malformation of cortical development (MCD) and pharmacoresistant epilepsy. Hyaline protoplasmic astrocytopathy of the neocortex is a rare neuropathological finding seen in cases of pharmacoresistant epilepsy with focal cortical dysplasia or other MCD. The cell-type specificity of mosaic chr1q gain in the brain is unknown, and no data exists on the molecular signatures of hyaline protoplasmic astrocytopathy.
Methods:
We present a child with pharmacoresistant epilepsy who underwent epileptic focus resections at age 3 and 5 years and was found to have mosaic chr1q gain and hyaline protoplasmic astrocytopathy with partial reduction in seizure burden after the second surgery. We performed single-nucleus RNA-sequencing (snRNA-seq) of brain tissue from the second resection.
Results:
Remarkably, snRNA-seq showed increased expression of chr1q genes only in select populations of neurons and astrocytes. Differentially expressed genes correlating with inferred chr1q gain included AKT3 and genes associated with cell adhesion or migration. A subcluster of astrocytes demonstrated enrichment for synapse-associated transcripts, possibly linked to the astrocytic inclusions observed in hyaline protoplasmic astrocytopathy.
Discussion:
snRNA-seq may be used to infer the cell type-specificity of mosaic chromosomal copy number variations and identify associated gene expression alterations, which in the case of chr1q gain may involve aberrations in cell migration. Future studies using spatial profiling could yield further insights on the molecular signatures of hyaline protoplasmic astrocytopathy.

overall_design: Single-nucleus RNA-seq using the 10x platform (v3 chemistry) of a single sample of fresh frozen surgically resected brain tissue from the right frontal lobe

first: Erron

last: Titus

first: Vaibhav

last: Upadhyay

first: Mercedes

last: Paredes


title: Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma

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

overall_design: Refer to individual Series


title: Transcriptional activity of a T-ALL PDX line following in vitro treatment with idasanutlin, navitoclax (ABT-263), or combination therapy

city: St. Louis

first: Daniel

middle: C

last: Link

address: 660 South Euclid Avenue

department: Medicine/Oncology

institute: Washington University School of Medicine in St. Louis

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with an umet need for improved therapies. We explored the potentially synergic combination of MDM2 inhibition and Bcl-2, Bcl-xL inhibition through cotreatment of T-ALL models with idasanutlin and navitoclax. In order to understand the early transcriptional changes induced by this combination therapy, we performed RNA sequencing on drug treated cells.

overall_design: T-ALL PDX line was cultured with cytokine support and treated for 16 hours. Confirmation of cell viability was performed via Annexin V flow cytometric assay (>80% not yet apoptotic). Cells were treated with DMSO, 300nM navitoclax, 1.5uM idasanutlin, or combination therapy.

first: Kimberly

last: Johansson

first: Iryna

last: Dmytrenko

first: Megan

last: Zimmerman

first: Feng

last: Gao


title: Genome-Wide Characterization of TAZ Binding Sites in Mammary Epithelial Cells

city: Buffalo

first: Tao

last: Liu

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute


title: Dietary ligands diindolylmethane and resveratrol result in diverse ERα signaling not seen after E2 and a subset of diindolylmethane mediated signaling needs concurrent AHR activation.

first: Jason

last: Matthews

summary:
Inhibitory crosstalk between estrogen receptor alpha (ER alpha ) and aryl hydrocarbon receptor (AHR) regulates 17-estradiol (E2)-dependent breast cancer cell signaling. ER alpha and AHR are transcription factors activated by E2 and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), respectively.
Dietary ligands resveratrol (RES) and 3,30diindolylmethane (DIM) also activate ER alpha while only DIM activates AHR and RES represses it. DIM and RES are reported to have anti-cancer and antiinflammatory
properties. Studies with genome-wide targets and AHR- and ER alpha-regulated genes after DIM and RES are unknown. We used chromatin immunoprecipitation with high-throughput sequencing and transcriptomics to study ER alpha as well as AHR coregulation in MCF-7 human breast cancer cells treated with DIM, RES, E2, or TCDD alone or E2+TCDD for 1 and 6 h, respectively. ER alpha bound sites after being DIM enriched for the AHR motif but not after E2 or RES while AHR bound sites after being DIM and E2+TCDD enriched for the ERE motif but not after TCDD. More than 90% of the differentially expressed genes closest to an AHR binding site after DIM or E2+TCDD also had an ER alpha site, and 60% of the coregulated genes between DIM and E2+TCDD were common. Collectively, our data show that RES and DIM differentially regulate multiple transcriptomic targets via ER alpha and ER alpha /AHR coactivity, respectively, which need to be considered to properly interpret their cellular and biological responses. These novel data also suggest that, when both receptors are activated, ER alpha  dominates with preferential recruitment of AHR to ER alpha  target genes.

overall_design: MCF-7 human breast cancer cells treated with DIM, RES, E2, or TCDD alone or E2+TCDD for 1 and 6 h and assayed for ERa and AHR binding via ChIP sequencing and gene expresison changes via RNA sequencing respectively.


title: Dietary ligands diindolylmethane and resveratrol result in diverse ERα signaling not seen after E2 and a subset of diindolylmethane mediated signaling needs concurrent AHR activation. [RNA-Seq]

summary: Abstract: Inhibitory crosstalk between estrogen receptor alpha (ERalpha) and aryl hydrocarbon receptor (AHR) regulates 17β-estradiol (E2)-dependent breast cancer cell signalling. ERalpha and AHR are transcription factors activated by E2 and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) respectively. Dietary ligands resveratrol (RES) and 3,3´diindolylmethane (DIM) also activate ERalpha while only DIM activates AHR and RES represses it. DIM and RES are reported to have anti-cancer and anti-inflammatory properties. Studies with genome wide targets and AHR and ERalpha regulated genes after DIM and RES are unknown. We used chromatin immunoprecipitation with high-throughput sequencing and transcriptomics to study ERalpha as well as AHR coregulation in MCF-7 human breast cancer cells treated with DIM, RES, E2 or TCDD alone or E2+TCDD for 1 and 6 hours respectively. ERalpha bound sites after DIM enriched for the AHR motif but not after E2 or RES while AHR bound sites after DIM and E2+TCDD enriched for the ERE motif but not after TCDD. More than 90% of the differentially expressed genes closest to an AHR binding site after DIM or E2+TCDD also had an ERalpha site and 60% of coregulated genes between DIM and E2+TCDD were common. Collectively our data shows that RES and DIM differentially regulate multiple transcriptomic targets via ERalpha and ERalpha/AHR coactivity respectively, which need to be considered to properly interpret their cellular and biological responses. These novel data also suggest that when both receptors are activated, ERalpha dominates with preferential recruitment of AHR to ERalpha target genes.

overall_design: The MCF-7 cells were treated with 10 nM or 10uM of various ligands for 6 hours or DMSO in triplicate. Total RNA was isolated with the Aurum™ total RNA mini kit (BioRad, Hercules, CA, USA), following the manufacturer’s protocol. The RNA yield was assessed with NanoDrop™ 1000 from Thermo Fisher Scientific. The RNA quality was evaluated using the Agilent 2100 bioanalyzer from Agilent (Palo Alto, California, USA) with the RNA 6000 Nano LabChip kit and subjected to RNA sequencing. They were multiplexed and sequenced using strand specific TruSeq RNA sequencing library prep as single end reads on a NextSeq 500 machine using 75 base reads.

first: Siddhartha

last: Das

first: Stine

last: Ulven


title: Massively parallel functional dissection of schizophrenia associated non-coding genetic variants [ATAC-seq]

city: Muenster

first: Michael

last: Ziller

address: Busso-Peus-Str. 10

institute: University of Muenster

summary: Schizophrenia (SCZ) is a highly polygenic disease and genome wide association studies have identified thousands of genetic variants that are statistically associated with this psychiatric disorder. However, our ability to translate these associations into insights on the disease mechanisms has been challenging since the causal genetic variants, their molecular function and their target genes remain largely unknown. In order to address these questions, we established a functional genomics pipeline in combination with induced pluripotent stem cell technology to functionally characterize 35,000 non-coding genetic variants associated with schizophrenia along with their target genes. This analysis identified a set of 620 (1.7%) single nucleotide polymorphisms as functional on a molecular level in a highly cell type and condition specific fashion. These results provide a high-resolution map of functional variant-gene combinations and offer comprehensive biological insights into the developmental context and stimulation dependent molecular processes modulated by SCZ associated genetic variation.

overall_design:
We performed ATAC-Seq on iPSC derived neurons under baseline and Kcl treatment conditions
Sumitter declares that raw data will be deposited in EGA.


title: RNA-sequencing of patients with hypertrophic cardiomyopathy or patients with aortic stenosis compared to heart healthy donors

city: Hannover

first: Valentin

last: Burkart

state: Lower Saxony

address: Carl-Neuberg-Strasse 1

department: Institute for Molecular and Cell Physiology

institute: Hannover Medical School

summary: Hypertrophic cardiomyopathy (HCM) is often associated with heterozygous mutations in sarcomeric genes. One of the most commonly affected genes encodes for myosin binding protein C (cMyBP-C, MYBPC3). Interestingly, most mutations in MYBPC3 lead to premature termination codons which could result in truncated fragments of cMyBP-C. However, truncated cMyBP-C has not been detect, but rather a reduction of total wildtype cMyBP-C. Nonsense mediated mRNA decay of mutated MYBPC3-mRNA was often hypothesized as cause for the reduced MYBPC3-expression, however it has not been shown in human patients. Therefore, we performed RNA-sequencing of MYBPC3trunc patients, AS-patients and donors, to detect if expression of regulatory proteins of the NMD is altered in the MYBPC3trunc patients. By gene set enrichment analysis (GSEA) of the presented data, we found expression of NMD components to be enriched in the MYBPC3trunc patients, which was furthermore associated with upregulation of UP-frameshift protein (UPF3B, UPF3B) which is a regulator of NMD.

overall_design: We analyzed patients with hypertrophic cardiomyopathy due to truncation mutations in myosin binding protein C (cMyBP-C, MYBPC3, MYBPC3trunc, n=6) or left verntricular hypertrophy due to aortic stenosis (AS-patients, n=5) and heart healthy donors (Donor, n=5). Total RNA was extracted from left ventricular cardiac tissue ground in a cryomortar. Gene expression of the MYBPC3trunc patients was either compared to donors or to AS-patients.

first: Judith

last: Montag

first: Maike

last: Kosanke

first: Oliver

last: Dittrich-Breiholz


title: Massively parallel functional dissection of schizophrenia associated non-coding genetic variants [MPRA]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We performed massively parallel reporter assay (MPRA) experiments in human iPSC derived cell types as well as mouse primary cultures in vitro under baseline and stimulation conditions


title: Massively parallel functional dissection of schizophrenia associated non-coding genetic variants [scRNA-seq]

overall_design: We performed a CROP-Seq screen for gene regulatory elements in iPSC derived neurons using an engineered dCas9-KRAB cell line and a guide RNA library followed by scRNA-Seq


title: Massively parallel functional dissection of schizophrenia associated non-coding genetic variants


title: Transcriptomic changes driving pulmonary fibrosis resolution in young and old Bleomycin-treated mice

city: Biberach

first: Katrin

last: Fundel-Clemens

address: Birkendorfer 65

institute: Boehringer Ingelheim

summary: Bleomycin-induced pulmonary fibrosis in mice mimics major hallmarks of idiopathic pulmonary fibrosis, yet in this model it spontaneously resolves over time. We studied molecular mechanisms of fibrosis resolution and lung repair, focusing on transcriptional and proteomic signatures and the effect of aging. Old mice showed delayed and incomplete lung function recovery 8 weeks after Bleomycin instillation. This shift in structural and functional repair in old Bleomycin-treated mice was reflected in a temporal shift in gene and protein expression. We reveal gene signatures and signaling pathways which underpin the lung repair process.

overall_design: Male mice (Mus musculus), strain C57BL/6J, age 8 – 12 weeks (young) and 21 months (old) were subjected to Bleomycin intratracheal instillation or control saline (NaCl) treatment, sacrificed on days 0, 14, 21, 28, 35, 42 and 56. Subsequently, lungs were dissected flash frozen in liquid nitrogen, homogenized, and upon RNA-isolation and library preparation, RNA-seq was performed. Transcriptomics and proteomics data were analysed in order to follow resolution of pulmonary fibrosis and lung repair over time and to elucidate age-related differences.

first: Jelena

last: Weckerle

first: Stephan

last: Klee

first: Karsten

last: Quast

first: Coralie

last: Viollet

first: Marc

last: Kaestle


title: Transcriptomic analysis of leaves and leaf cells from the medicinal plant Catharanthus roseus

city: Vairao

first: Mariana

last: Sottomayor

state: Select:

address: Rua Padre Armando Quintas, No. 7

department: PLANTBIO

country: Portugal

institute: CIBIO, Research Centre in Biodiversity and Genetic Resources

summary: The goal of this study is to investigate differential transcription profiles of leaf material/cells accumulating different levels of alkaloids in the anticancer plant Catharanthus roseus.

overall_design: Gene expression profiling was performed for three biological replicates of: i) protoplasts of specific leaf cells specialized in alkaloid accumulation (idioblasts) and their control mesophyll protoplasts, total leaf protoplasts, and origin leaves; ii) 4 different developmental stages of leaves from plants growing in two different conditions leading to differential accumulation of alkaloids.

first: Rogério

last: Ribeiro

first: Joana

last: Guedes

first: Nuno

last: Fonseca


title: Human iPSC modeling recapitulates in vivo sympathoadrenal development and reveals an aberrant developmental subpopulation in familial neuroblastoma [scRNA-seq]

first: Sarah-Lee

last: Bekaert

overall_design: Induced pluripotent stem cells (iPSC) were differentiated along the sympathoadrenergic precursor (SAP) development during a 40 day long differentiation process. We performed single cell RNA sequencing (scRNAseq) on eight subsequent time-points to characterize the normal SAP development. We further investigated the effect of the ALK R1275Q mutation on the sympathoadrenergic developmental process by performing serial scRNAseq at four time points between days 25 and 32 using an ALKR1275Q patient-specific iPSC line. Prior to scRNAseq the cells of selected time-points were hashed and pooled together for scRNAseq analysis. The time-points D25-26, D27-28, D29-30 and D31-32 were hashed for the WT cells. For the ALK mutant cells time-points D25-27-29-32 were hashed. The single-cell RNA-Seq was performed on Chromium instrument (10X genomics).

first: Stéphane

last: Van Haver

first: Frank

last: Speleman

first: Stephen

last: Roberts


title: Spatial sequencing of young and aged lungs following influenza A virus infection

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: Aging is known to alter the host repsonse to influenza infection. Here, we use 10x Visium spatial sequencing to identify spatial changes in mRNA expression of left lungs of young (16-week-old) and aged (80-week-old) mice following influenza infection.

overall_design: Mice were infected with influenza A/PR8/34 (~50 PFU/mouse) to establish acute infection. Infections were performed by intranasal (i.n.) administration under anesthesia as described before (Sun et al., 2009). Mice were then euthanized and the right ventricle was perfused with 10 mL cold DPBS (Corning). For Visium spatial sequencing, mice were euthanized and lungs were inflated with 500 μL of 50% v/v OCT/PBS (Fisher Healthcare) via an intratracheal catheter. The left lung was excised and the caudal half was placed in a cryomold containing OCT. The mold was frozen in an isopentane (Fisher Scientific) bath chilled by liquid nitrogen. 10 μm sections were generated from frozen inflated left lungs using a cryostat and placed on barcoded slides (10x Genomics). The Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics) was used to generate barcoded cDNA libraries. H&E stained tissues on Visium slides were imaged using a Nikon Eclipse Ti2 inverted microscope. Lung tissue on Visium slides was permeabilized for 14 minutes to extract mRNA. Barcoded cDNA libraries were sequenced on an Illumina NextSeq 500 instrument using a NextSeq 500/550 High Output Kit v2 (150 cycles) (20024907, Illumina) with the following cycle counts: 28 (read 1), 10 (index 1), 10 (index 2), 90 (read 2). Loupe Browser (v5.0, 10x Genomics) was used to identify which spatial sequencing capture area spots were in contact with tissue. Demultiplexing and alignment was performed with Space Ranger (v2.1, 10x Genomics) and the mm10 2020-A reference transcriptome (10x Genomics). Analysis was mainly performed in R using Seurat (v4.0). Visium datasets were integrated using the SCTransform pipeline, and PCA and UMAP were performed using the top 30 principal components. SPOTlight (Elosua-Bayes et al., 2021) was used to demultiplex Visium data with our integrated scRNA-seq data used as a reference.

first: Moujtaba

last: Kasmani


title: m6A Demethylase FTO Stabilizes LINK-A to Exert Oncogenic Roles via MCM3-Mediated Cell Cycle Progression and HIF-1α Activation

status: Public on Oct 15 2023

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences

summary: We identified that the m6A demethylase FTO demethylates and stabilizes a lncRNA long intergenic noncoding RNA for kinase activation (LINK-A) during ESCC chemoresistance. LINK-A directly interacts with minichromosome maintenance complex component 3 (MCM3) and increases the phosphorylation of MCM3 at Ser112 by cyclin-dependent kinase 1 (CDK1), which facilitates MCM3 incorporation into the MCM2-7 complex and subsequent chromatin loading, promoting cell cycle progression. On the other hand, LINK-A insulates the interaction between MCM3 and HIF-1α to free HIF-1α. The enhancement of HIF-1α transcriptional activity reprograms metabolic status from OXPHOS to glycolysis. Additionally, targeting LINK-A substantially sensitized ESCC patient-derived xenografts (PDXs) to first-line chemotherapy, thus indicating LINK-A is a promising target for cancer treatment.

overall_design: RNA-seq of LINK-A knockdown (SH2, SH4) and control (SHC) KYSE450 cells

first: Yabing

first: Shi

last: Liu


title: Dormancy heterogeneity among Arabidopsis thaliana seeds is linked to individual seed size

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

summary: Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops yield visually homogenous seeds. Using automated phenotype analysis, we observed that in Arabidopsis small seeds tend to have higher primary and secondary dormancy levels when compared to large ones. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds had higher expression of translation-related genes implicated in germination competence. In contrast, small seeds showed elevated expression of many positive regulators of dormancy, including a key regulator of this process – the DOG1 gene. Differences in DOG1 expression were associated with differential production of its alternative cleavage and polyadenylation isoforms where in small seeds proximal poly(A) site is selected resulting in a short mRNA isoform. Furthermore, single-seed RNA-seq analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single seed level, the expression of genes affected by seed size was correlated with the expression of genes positioning seeds on the path towards germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species producing highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.

overall_design: 1) Single seed RNA-seq: three libraries, each consisting of 32 seeds were prepared for two time points of secondary dormancy induction (3d, 7d+24h) and two seed sizes (small and large). 2) 3'RNA-seq: comparison of transcriptomes of Col-0 small, medium and large dry seeds (four biological replicas).

first: Szymon

last: Swiezewski


title: Massively parallel functional dissection of schizophrenia associated non-coding genetic variants [RNA-seq]

first: Michael

last: Ziller

overall_design:
We performed RNA-seq on iPSC derived neurons under baseline and Kcl treatment conditions
Sumitter declares that raw data will be deposited in EGA.


title: Comparing the microbiota composition between HPV positive and negative patients with CRC

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Total DNA was extracted from the stool of the patients, amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

sample_organism:
Homo sapiens
unidentified

platform_organism:
Homo sapiens
unidentified

first: Amedeo

last: Amedei

first: Elena

last: Niccolai

first: Leandro

last: Di Gloria


title: GsMTx4 suppresses pro-inflammatory gene expression in DSS-induced colitis in mice.

city: Jinan

first: Xiuli

last: Zuo

address: 107 Wenhuaxi Road

institute: Shandong University

summary: The spider venom-derived peptide GsMTx4 specifically inhibits mechanosensory ion channels. It has been reported that GsMTx4 plays an immunoregulatory role in several inflammatory conditions. Therefore, we administrated GsMTx4 to mice with dextran sodium sulfate (DSS)-induced acute colitis, to explore whether it regulates inflammatory responses in colitis.

overall_design: 8-week-old mice were administered 2.5% DSS (MP Biologicals) in drinking water for 7 consecutive days, with intravenous injection of GsMTx4 (10 mg/kg, Alomone Labs) or solvent on days 2, 4, and 6. Mice given normal drinking water were used as Control group.

first: Chang


title: USP28 Serves as A Key Suppressor of Mitochondrial Morphofunctional Defects and Cardiac Dysfunction in the Diabetic Heart [RNA-seq]

city: Wuhan

first: Saiyang

last: Xie

address: Jiefang Road 238

institute: Wuhan university

summary: The majority of diabetics are susceptible to cardiac dysfunction and heart failure, while conventional drug therapy cannot correct diabetic cardiomyopathy (DCM) progression. Herein, we assessed the potential role and therapeutic value of ubiquitin-specific protease 28 (USP28) on the metabolic vulnerability of DCM. cardiac USP28 deficient diabetic mice showed cardiac dysfunction, lipid accumulation, and mitochondrial disarrangement, compared to their controls. Conversely, USP28 overexpression improved systolic and diastolic dysfunction and ameliorated cardiac hypertrophy and fibrosis in the diabetic heart. Mechanistically, USP28 directly interacted with peroxisome proliferator-activated receptor α (PPARα), deubiquitinating and stabilizing PPARα (Lys152) to promote mitofusin 2 (Mfn2) transcription, thereby impeding mitochondrial morphofunctional defects.

overall_design: To evaluate function of USP28 overexpression in diabetic heart failure and cardiac remodeling, recombinant adeno-associated virus serotype 9 carrying USP28 under cTnT promoter (rAAV9-cTnT-USP28) was injected into db/db mice to evaluate the effects of USP28 overexpression on DCM.

first: Qizhu

last: Tang


title: USP28-regulated mitochondrial homeostasis mechanism that involves the PPARα-Mfn2 axis in diabetic hearts [ChIP-seq]

summary: The majority of diabetics are susceptible to cardiac dysfunction and heart failure, while conventional drug therapy cannot correct diabetic cardiomyopathy (DCM) progression. Herein, we assessed the potential role and therapeutic value of ubiquitin-specific protease 28 (USP28) on the metabolic vulnerability of DCM. PPARα-/- in the db/db background mice were constructed to check the mechanism of USP28 in vivo. Inducible cardiac-specific deletion of Mfn2 in the db/db background mice was utilized to evaluate USP28-mediated cardioprotection. chromatin immunoprecipitation (ChIP) assays revealed that PPARα promote mitofusin 2 (Mfn2) transcription, thereby impeding mitochondrial morphofunctional defects.

overall_design: The interaction of PPARα and Mfn2 promoter was verified by chromatin immunoprecipitation (ChIP) assay in hiPSC-CMs


title: CHD1 Alters Sensitivity to Aurora Kinase A Inhibitors

city: Houston

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

institute: MD Anderson Cancer Center

summary: In this study, we sought to understand the impact of CHD1 on sensitivity to Aurora A inhibitors in prostate and other cancers and underlying mechanisms

overall_design: WT and CHD1 KO BPH1 cells were treated with DMSO or Alisertib (10μM) for 24 hours. Then, cells were lysed with TRIzol, followed by RNA extraction. Experiment was performed in triplicate. RNA-Sequencing was performed by UT MD Anderson Science Park NGS Core.

first: Haoyan

last: Li

first: Yue

last: Lu

first: Kevin

last: Lin


title: Transcriptomic changes in Arabidopsis thaliana seedlings in response to traffic noise exposure

city: Daejeon

first: Seyun

last: Kim

address: Daehak-ro 291

country: South Korea

institute: KAIST

summary: Seeds in the experimental group were exposed to 48 h of traffic noise recorded in a highly congested area of the city, while the control group was kept under background white noise. While traffic noise exposure made no effects on seed germination, noise treatment significantly increased the growth of seedlings by 39%. By employing RNA-sequencing profiling, we further investigated the noise-induced molecular changes in the A. thaliana seedlings. The aberrant expression of 690 genes was detected in the noise-exposed seedlings.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for arabidopsis thaliana seedlings exposed to either control background noise (10 dB) or traffic noise (average 75 dB) for 48 h

first: Wooseok

last: Jeong

first: John


title: Corticosteroid-induced chromatin loop dynamics at the FKBP5 gene

city: Nijmegen

first: Cheng

last: Wang

address: Geert Grooteplein 28

department: Molecular biology

institute: Radboud Institute for Molecular Life Sciences

summary: FKBP5 is a long glucocorticoid-inducible gene implicated in psychiatric disorders. To investigate the complexities of chromatin interaction frequencies at the FKBP5 topologically associated domain (TAD), we deployed fifteen one-to-all chromatin capture viewpoints near gene promoters, enhancers, introns, and CTCF-loop anchors. This revealed a ‘one-TAD-one-gene’ structure encompassing the FKBP5 promoter and its enhancers. The FKBP5 promoter and its two glucocorticoid-stimulated enhancers roam the entire TAD while displaying subtle cell type-specific interactomes. The FKBP5 TAD consists of two nested CTCF loops that are coordinated by one CTCF site beyond the FKBP5 polyadenylation site and another in its 8th intron, 61 kb further. Loop extension correlates with transcription increases through the intronic CTCF site. This is efficiently compensated for, since the short loop is restored even under high transcription regimes. The boundaries of the FKBP5 TAD consist of divergent CTCF sites, harbor multiple smaller genes and are resilient to glucocorticoid stimulation. Interestingly, both FKBP5 TAD boundaries harbor H3K27me3-marked heterochromatin blocks that may reinforce them. We propose that cis-acting genetic and epigenetic polymorphisms underlying FKBP5 expression variation are likely to reside within a 240 kb region that consists of the FKBP5 TAD, its left sub-TAD, and both its boundaries.

overall_design: The cells were cultured in the presence of 100 nM triamcinolone acetonide(TA). Cells were then collected for 4C-seq.

first: Colin

last: Logie

first: Freek

last: Manders

first: Laszlo

last: Groh

first: Roel

last: Oldenkamp


title: Colon macrophage transcriptomes reveals the impact of mitochondrial dysfunction in ulcerative colitis

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

summary: we use ulcerative colitis macrophage RNAseq to show the critical role of mitochondria dysfunction in a mouse model with reduced mitochondrial electron transport chain Complex I activity due to MCJ deficiency.

overall_design: Genome-wide changes in gene Expression of macrophages isolated from mice colon suffering from experimental colitis were generated by RNAseq.

first: Leticia

last: Abecia

middle: L


title: RNase H2 degrades toxic RNA:DNA hybrids behind stalled forks to promote replication restart

status: Public on Oct 14 2023

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

summary: R-loops represent a major source of replication stress but the mechanism by which these structures impede fork progression remains unclear. To address this question, we monitored fork progression, arrest and restart in S. cerevisiae cells lacking RNase H1 and H2, two enzymes responsible for degrading RNA:DNA hybrids. We found that while RNase H-deficient cells could replicate normally their chromosomes under unchallenged growth conditions, their replication was impaired when exposed to hydroxyurea (HU) or methyl methanesulfonate (MMS). Indeed, these cells exhibited increased levels of RNA:DNA hybrids at stalled forks and were unable to generate RPA-coated single-stranded (ssDNA), an important postreplicative step in resuming replication. Similar impairments in nascent DNA resection at HU-arrested forks were observed in human cells lacking RNase H2. However, the addition of triptolide, an inhibitor of transcription that induces RNA polymerase degradation, fully restored fork resection. Taken together, these data indicate that RNA:DNA hybrids not only act as barriers to replication forks, but also interfere with postreplicative fork repair mechanisms if not promptly degraded by RNase H.

overall_design: To investigate the profil of origin firing in rnh1delta rnh201delta cells, we measured DNA Copy Number across the genome of S. cerevisiae wild-type strains and rnh1delta rnh201delta cells that were synchronised in G1 and released into S-phase + 0.2M hydroxyurea.

first: Jonathan

last: Heuzé

first: Samira

last: Kemiha

first: Antoine

last: Barthe

first: Alba

last: Toran

first: Umberto

last: Aiello

first: Yea-Lih

first: Armelle

last: Lengronne

first: Jérôme

last: Poli

first: Philippe

last: Pasero


title: Transcriptome analysis of MET-constitutively active versus MET-silenced colorectal cancer cells

city: Bologna

first: Mattia

last: Lauriola

address: Via Belmeloro 8

institute: University of Bologna

summary:
To investigate the expression patterns driven by hyperactivated MET in MET-dependent cells, we employed LoVo colon adenocarcinoma cell line, harbouring a post-translational modification of MET that leads to its constitutive activation.
We then silenced MET in LoVo cells using CRISPR/Cas9 knock-out (KO) protocol, and performed gene expression profiling analysis using data obtained from RNA-seq of cells with hyperactivated-MET versus MET-KO.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LoVo cells and its KO derivative (LoVo MET KO)

first: Lauriola

last: Mattia


title: Inactivating Negative Regulators of Cortical Branched Actin Enhances Persistence of Single Cell Migration.

city: Paris

first: Laura

last: Courtois

address: 25 rue d'Ulm

institute: Institut Curie

summary: Here we show that enhancing polymerization of branched actin at the cell cortex by removing as many as 3 negative regulators promotes single cell migration, but not collective migration of mammary epithelial cells

overall_design: fastq of parental MCF10A cells and their kOs that we combined

first: Artem

middle: I

last: Fokin

first: Arthur

last: Boutillon

first: John

last: James

first: Sophie

last: Vacher

first: Gleb

last: Simanov

first: Yanan

last: Wang

first: Anna

last: Polesskaya

first: Ivan

last: Bièche

first: Nicolas

last: David

first: Alexis

last: Gautreau


title: TRPV3 mediates Propionibacterium acnes-induced chemotaxis and inflammation in sebocytes

status: Public on Oct 13 2023

city: Nanjing

first: Ziyu

last: Wei

state: Jiangsu

address: Pujian Road 160, Shanghai

department: Genetic Skin Disease Center

institute: Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: TRPV3 is highly expressed in human skin and is involved in the development of inflammatory dermatoses. However, it remains unclear whether TRPV3 influences inflammation in human sebaceous glands and its role in the pathogenesis of acne. Here, we showed that TRPV3 expression was increased in the sebaceous glands of facial acne lesions and acne-like mice. TRPV3 increased the secretion of pro-inflammatory cytokines and chemokines in human SZ95 sebocytes, as well as the chemotaxis of neutrophils, which were the major immune cells found in acne lesions. We demonstrated that P.acnes promoted TRPV3 expression through regulating lipid profile especially upregulated arachidonic acid levels in human sebocytes. TRPV3 further upregulated TLR2 expression by promoting transcriptional factor p-FOSL1 expression and its binding to the TLR2 promoter, leading to downstream NF-κB signaling activation. Importantly, either genetic silencing or pharmacological inhibition of TRPV3 alleviated acne-like inflammation in mice, showing reduced acne-characteristic cytokines and chemokines production and neutrophil infiltration by inhibiting the TLR2-NF-κB axis. Thus, our study revealed the critical role of TRPV3 in sebocytes inflammation, which was involved in the development of acne, indicating that TRPV3 is a potential therapeutic target for acne and other disorders of the pilosebaceous unit.

overall_design: To investigate the role of TRPV3 in the inflammation of human sebocytes, we established TRPV3-overexpressed human sebocytes by transfecting either Mock or TRPV3-overexpression plasmids into human SZ95 sebocytes. Three biological replicates were used for each group.

first: Yong

last: Yang


title: RNA catabolism restricts ERV expression and functionalization [EU-RNA-Seq]

city: New York

first: Robert

last: Sebra

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: Endogenous retroviruses (ERVs) are remnants of ancient parasitic viral integrations and comprise a sizable portion of the genome in most organisms. Deregulated expression of ERVs in human is associated with a plethora of disease conditions, such as cancer and neurodegeneration. Epigenetic mechanisms silence most ERVs by generating a local repressive environment (heterochromatin) to prevent their expression. However, the mechanisms controlling the fate of ERVs residing in euchromatic regions of the genome (e.g. MERVL elements) are not well understood. Here, by integrating multidimensional epigenetic and genomic analyses, we demonstrate that silencing of euchromatic MERVL elements is achieved via transcription-coupled RNA degradation. Disrupting RNA catabolism promotes RNAPII elongation from MERVL promoters, increases MERVL expression and exonization, creating novel chimeric gene isoforms, and directing embryonic stem (ES) cells toward a terminal undifferentiated state.  Our results indicate that RNA catabolism is a core regulatory module of gene networks that safeguards cell identity and potency, restricts MERVL functionalization and suppresses gene birth.

overall_design: EU-Seq of WT and Exosc3 cKO mESCs, including total and labeled (10min) RNA samples each. N=2 replicates per condition, 8 samples total.

first: D

last: Torre

first: Y

last: Fstkchyan

first: I

last: Marazzi


title: Deciphering disease signatures and molecular targets in vascular Ehlers-Danlos syndrome through transcriptome sequencing of a large cohort of patients’ dermal fibroblasts

city: Brescia

first: Nicola

last: Chiarelli

state: Lombardy

address: Viale Europa 11

department: Molecular and Translational Medicine

institute: University of Brescia

summary:
Vascular Ehlers-Danlos syndrome (vEDS) is a severe connective tissue disorder caused by dominant mutations in the COL3A1 gene, which encodes type III collagen (COLLIII). COLLIII is primarily found in blood vessels and hollow organs, and its deficiency causes fragile soft connective tissues, with life-threatening arterial and organ ruptures. There are currently no targeted therapies available. Although disease results from COLLIII misfolding caused by triple helix structure disruption, the underlying pathomechanisms are largely unknown. To address this knowledge gap, we conducted a comprehensive transcriptome analysis using RNA-seq on a large cohort of dermal fibroblasts from vEDS patients and healthy donors. Our investigation revealed an intricate interplay between proteostasis abnormalities, inefficient endoplasmic reticulum (ER) stress response, and compromised autophagy, which may significantly impact the molecular pathology. We reported the first comprehensive map of complex gene expression networks, which may provide significant molecular insights into intricate interactions within cellular signaling pathways. the current RNA-seq data not only confirm these initial findings but also provide convincing evidence that ineffective proteostasis, unbalanced ER homeostasis, and compromised autophagy could substantially impact the molecular pathology driving the disease. aken together, or findings suggest that the accumulation of these misfolded aggregates can impair critical cellular functions such as ER proteostasis, adaptative responses to counteract ER stress (UPR and ERAD pathways), autophagy, mTOR pathway, and lysosome function. Perturbation of these key biological processes can have an impact on a range of cell activities, including differentiation, proliferation, and apoptosis, all of which are associated with the pathophysiology of vEDS.

This work was supported by Fondazione Telethon and the “Associazione con Giacomo contro vEDS”, (Grant number: GSA21F001, Seed Grant Fall 2021 vEDS) to Nicola Chiarelli.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of fibroblast cell strains derived from 18 vEDS  patients and 36 healthy donors


title: miRNome sequencing  of a large cohort of vascular Ehlers-Danlos syndrome patients' dermal fibroblasts reveals aberrantly expressed miRNAs involved in pathways relevant for the disease pathophysiology

summary:
To investigate the potential role of miRNAs in disease mechanisms, we conducted a thorough analysis by comparing the entire miRNome of 18 vEDS dermal fibroblasts to those of 18 control cells. To improve statistical reliability, we sequenced each sample from both groups as biological replicates. By applying a log2 fold change threshold of greater than 1 or less than -1, and an adjusted p-value of less than 0.05, we identified 137 DE-miRNAs in patient vs. control fibroblasts. Among these, 71 miRNAs exhibited decreased expression, while 66 miRNAs were upregulated. To explore the functional relationship between DE-miRNAs and the altered gene expression profile of vEDS cells, we conducted an extensive review of the literature and consulted several bioinformatics databases. Our search involved utilizing data from four miRNA-target prediction databases (microT-CDS, Targetscan, miRTarBase, and miRwalk) in addition to relevant literature sources providing information on the functional roles of these miRNAs. We thus focused our research on a specific subset of DE-miRNAs, known as miR-15b-5p, miR-16-5p, miR-21-3p, miR-24-3p, miR-29a-3p, miR-29b-3p, miR-138-5p, miR-145-5p, and miR-195-5p, which may play a biological role in dysregulated molecular mechanisms underlying disease pathogenesis. Our initial emphasis was on miR-29a-3p and miR-29b-3p due to their involvement in regulating critical cellular processes such as ECM remodeling into the vascular network, autophagy, cell proliferation, and apoptosis. To study how miR-29a-3p and miR-29b-3p contribute to the dysregulated cellular processes observed in patient cells, we performed GO and pathway enrichment analyses on their predicted target DEGs. GO analysis revealed that both these miRNAs may disturb fundamental biological functions, such as regulation of transcription by RNA polymerase II, negative gene expression regulation, miRNA-mediated gene silencing, translation regulation, heterochromatin organization, and ECM organization. This comphrensive transcriptome analysis of a large cohort of dermal fibroblasts from patients with vEDS reveals deregulated biological functions potentially involved in the disease pathogenesis. Taken together, the abnormal expression of several miRNAs suggests the presence of epigenetic control in vEDS cells, which could influence the transcriptional regulation of numerous target DEGs and related biological processes, potentially influencing disease mechanisms.

This work was supported by Fondazione Telethon and the “Associazione con Giacomo contro vEDS”, (Grant number: GSA21F001, Seed Grant Fall 2021 vEDS) to Nicola Chiarelli.

overall_design: Comparative gene expression profiling analysis of miRNome sequencing data of fibroblast cell strains derived from 18 vEDS  patients and 18 healthy donors


title: Total and chromatin-associated RNA (totalRNA and chRNA) sequencing experiments upon rapid depletion of endogenous DHX15 or DHX38

city: Cambridge

first: Qing

last: Feng

state: MA

address: 31 Ames St, Building 68, 68-265

department: Biology

institute: MIT

summary: To investigate DHX15's functions in splicing QC in human cells, we induced rapid proteolysis-mediated depletion of endogenous DHX15 and DHX38 and performed high-throughput sequencing of totalRNA and chRNA.

overall_design: We generated two degron cell lines, HEK.dDHX15 and HEK.dDHX38 cells, tagging endogenous DHX15 or DHX38 gene copies with degron tags, and performed total- and chromatin-associated RNA-seq following 2 hours of DMSO or dTAG13 treatment.

first: Keegan

last: Krick

first: Jennifer

last: Chu

first: Christopher

last: Burge