title: Glial translatomes in stroke

status: Public on Feb 14 2023

city: Stanford

first: Marion

last: Buckwalter

state: California

address: 1201 Welch Rd

department: Neurology & Neurological Sciences

institute: Stanford University

summary: Neuroinflammation is a hallmark of ischemic stroke, which is a leading cause of death and longterm disability. Understanding the exact cellular signaling pathways that initiate and propagate neuroinflammation after stroke will be critical for developing immunomodulatory stroke therapies. In particular, the precise mechanisms of inflammatory signaling in the clinically relevant hyperacute period, hours after stroke, have not been elucidated. We used the RiboTag technique to obtain Astrocyte IP and microglia-derived mRNA transcripts in a hyperacute (4 hours) and acute (3 days) period after stroke, as these two cell types are key modulators of acute neuroinflammation. Microglia initiated a rapid response to stroke at 4 hours by adopting an inflammatory profile associated with the recruitment of immune cells. The hyperacute Astrocyte IP profile was marked by stress response genes and transcription factors, such as Fos and Jun, involved in pro-inflammatory pathways such as TNF-α. By 3 days, microglia shift to a proliferative state and Astrocyte IPs strengthen their inflammatory response. The Astrocyte IP pro-inflammatory response at 3 days is partially driven by the upregulation of the transcription factors C/EBPβ, Spi1, and Rel, which comprise 25% of upregulated transcription factor-target interactions. Surprisingly, few sex differences across all groups were observed. Expression and log2 fold data for all sequenced genes are available on a user-friendly website for researchers to examine gene changes and generate hypotheses for stroke targets. Taken together our data comprehensively describe the Astrocyte IP and microglia-specific translatome response in the hyperacute and acute period after stroke and identify pathways critical for initiating neuroinflammation.

overall_design: Comparative gene expression profiling analysis of microglia and Astrocyte IP ribotag RNA-seq data 4 hours and 3 days after stroke in adult, male and female mice.

first: Victoria

middle: G

last: Hernandez

first: Kendra

last: Lechtenberg

first: Todd

middle: C

last: Peterson

first: Li

last: Zhu

first: Tawaun

middle: A

last: Lucas

first: Justice

last: Owah

first: Alanna

last: Dorsey

first: Andrew

last: Gentles


title: RNA sequencing data of Mycobacterium marinum treated with compound 8

city: Amsterdam

first: Vien

last: Ho

state: Noord-Holland

address: De Boelelaan 1108, O2 building

department: Medical Microbiology and Infection Control

country: Netherlands

institute: Amsterdam University Medical Center-location VU

type: Expression profiling by high throughput sequencing

summary: The mechanisms of action of compound 8 in Mycobacterium marinum although it inhibits the secretion of the bacteria. In this experiment, we aim to investigated the effect of compound 8 on the global gene expression of Mycobacterium marinum

overall_design: M. marinum cells were grown treated with compund Compound 8-73 or DMSO  at 10 µM or 20 µM. Bacteria were harvested by centrifugation and flash frozen in liquid nitrogen. The RNA of biological duplicates was isolated using the NucleoSpin RNA kit (Macherey-Nagel). The bacteria were lysed by bead beating with zirconium beads in 500 μL buffer RA1 and 5 μL β-mercaptoethanol for 1 min. The rRNA was depleted and mRNA was enriched using RiboMinus prokaryotic kit (Invitrogen). The mRNA was outsourced to BaseClear (Leiden, The Netherlands) for RNA sequencing analysis. Subsequently, low-quality reads were excluded and the remaining reads were aligned to M. marinum MUSA reference genome (NC_010612.1) by CLC Genomics Workbench 12. Count data were converted to reads per million (rpm) and differential analysis was performed using CLC Genomics Workbench 12 or independently analysed by BaseClear service. Gene function and classification were later determined with  mycobrowser (https://mycobrowser.epfl.ch/).

middle: Q

first: Alexander

last: Speer


title: Identification of m6A-modified YTHDF2 targets by high-throughput m6A-seq and RIP-seq in HBV-infected HepG2 cells [RIP-seq]

status: Public on Feb 15 2023

city: Chongqing

first: Yang

last: Yang

state: Chongqing

address: No. 1, Medical College Road

country: China

institute: Chongqing Medical University

summary: We investigated the role of O-GlcNAcylation of m6A reader YTHDF2 in HBV-related hepatocarcinogenesis and progression. We found that YTHDF2 O-GlcNAcylation was elevated upon HBV infection through upregulated HBP. OGT-mediated YTHDF2 O-GlcNAcylation at Ser263 enhanced its protein stability, and subsequently changed the gene expression profiles. Mechanistically, we identified YTHDF2 stabilized minichromosome maintenance protein 2 (MCM2) and MCM5 mRNAs in an m6A dependent manner by high-throughput profiling of m6A-seq and RIP-seq, thereby promoting HBV-related HCC tumorigenesis. Importantly, our study proposed that targeting OGT-mediated YTHDF2 O-GlcNAcylation may be a novel strategy for potential treatment of HBV-associated liver cancer.

overall_design: Identification of YTHDF2 targets by high-throughput RIP-seq.

first: Yu

last: Yan

first: Jiaxin

last: Yin


title: RNA-Seq-guided triple-combination nano-system of gold nanocluster, quercetin, and docetaxel for ultimate synergistic photothermal-chemotherapy against MDR tumor

city: Seoul

first: Chaemin

last: Lim

address: 221 HeukSuk-Dong DongJak-Gu, 102 dong, 315 ho (Chung-Ang university, R&D center)

department: College of Pharmacy

country: South Korea

institute: Chung-Ang University

summary: For oncological purposes, hyperthermia has increasingly emerged as a good therapeutic option for patients without fitness to undergo surgery, or for those with surgically inaccessible tumors. However, tumor recurrence after photothermal therapy constitutes a significant barrier to achieving good survival outcome. In this study, we used a gold nanocluster (GNC) micelle system capable of multiple NIR laser exposure; RNA-seq analysis revealed that repeated NIR exposure upregulates heat-shock protein and cell-cycle process-related genes that could be associated with tumor recurrence. To prevent recurrence, we presented an RNA-seq-guided drug combination strategy of GNC, docetaxel, and quercetin via a nano-system. Quercetin treatment downregulated heat-shock protein expression and inhibited function of P-gp with mild antitumor activity. Furthermore, docetaxel treatment demonstrated antitumor activity with significant G2-M cell-cycle arrest. When two of GNC, docetaxel, and quercetin were administered together, they showed a synergistic antitumor effect, whereas when the drugs were administered simultaneously in a triple combination, a very strong synergistic effect was achieved, as indicated through increased apoptosis induction and cell-cycle arrest in vitro and in vivo. The data from this study emphasize the benefit of triple combination and outlines potential translational directions for photothermal-chemotherapy.

overall_design: Comparative gene expression profiling analysis of mRNA-seq data for Gold nanocluster treated tumor

first: Kyung

middle: T

last: Oh


title: Epigenome analysis of normal human corneal endothelium and corneal endothelium from FECD patients

city: Umeå

first: Ida Maria

last: Westin

address: NUS, 6M

department: Medical Biosciensces

country: Sweden

institute: Umeå University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal human corneal endothelium and human corneal endothelium from FECD cases. The Illumina Infinium MethylationEPIC 850K BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in genomic DNA from human corneal endothelium samples. Samples included 11 non-FECD donors, 17 FECD cases.

overall_design: Bisulphite converted DNA from the 28 samples were hybridised to the Illumina Infinium MethylationEPIC 850K BeadChip.

first: Mattias

last: Landfors

first: Antonios

last: Giannopoulos

first: Andreas

last: Viberg

first: Pia

last: Osterman

first: Berit

last: Byström

first: Sofie

last: Degerman

first: Irina

last: Golovleva


title: Identification of m6A-modified YTHDF2 targets by high-throughput m6A-seq and RIP-seq in HBV-infected HepG2 cells

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

overall_design: Refer to individual Series


title: CircAkt3 participates in bone cancer pain progression in rats by modulating MAPK signalling pathway

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

institute: Forevergen

type: Non-coding RNA profiling by high throughput sequencing

summary: CircRNA parent genes were mainly enriched in MAPK and neurodevelopmental signalling pathways. CircAkt3 and circMap4k1 were significantly up-regulated in the bone cancer pain group. CircaAkt3 may increase p-ERK expression by upregulating Col8a1, which may further activate the MAPK pathway.

overall_design: We established a bone cancer pain rat model. The top four differentially expressed circRNAs (DECs) in the model were validated by agarose gel electrophoresis and Sanger sequencing between the bone cancer pain group and control group. A circRNA-miRNA-mRNA network was constructed based on the interactions among circRNAs, microRNA (miRNA), and mRNA, which were predicted by TargetScan. mRNA and circRNA expression levels were detected by quantitative RT-PCR. In addition, Western Blot was performed to identify the protein levels of p-ERK, ERK, and Col8a1.

first: Lvlv

last: Chen

first: Xiaoxia

last: Zhang

first: Yuqi

last: Su

first: Yiwen


title: Hypometabolism to survive the long polar night in the diatom Fragilariopsis cylindrus

city: Paris

first: Lorenzo

last: Concia

email: colore@gmail.com, concia@bio.ens.psl.eu

address: 46 Rue d'Ulm

department: Institut de Biologie

country: France

institute: École Normale Supérieure

summary: Diatoms, the major eukaryotic phytoplankton in polar regions, are essential to sustain food webs. As such, it is fundamental to understand the physiological mechanisms and associated molecular basis of resilience to polar night of diatoms. Here, we report an integrative approach that reveals that in prolonged darkness, the cell enters a state of hypometabolism associated with reduced transcriptional activity during which no cell division occurs. Minimal energy is provided by respiration via alternative oxidase and progressive degradation of protein, carbohydrate and lipid stores. We also report internal structural changes that manifest the morphological acclimation of cells to darkness. Our results further indicate that immediately after returning to light, the majority of cells were able to use photoprotective mechanisms and resume photosynthesis. Divisions of surviving cells resumed at rates similar to those before darkness. Our study demonstrates the robustness of this species to prolonged darkness at low temperatures.

overall_design: Examination of gene expression (RNA-seq) from the acclimation phase in full light, in prolonged darkness and upon return to light. We analized two experiments: cells kept in the dark for one month (6 samples) or three months (17 samples). We analyzed three biological replicates per sample.

first: Nathalie

last: Joli

first: Marcel

last: Babin

first: Chris

last: Bowler


title: Characterization of differential gene expression pattern in wild-type and C3 deficient mice during retinal vascular development

city: Boston

first: Gracia

last: Bonilla

state: MA

address: 185 Cambridge Street

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

summary: This study reports the comprehensive gene expression profiling of postnatal day (P) 5 wild-type (WT) and complement component (C) 3 mutant (referred as KO) retinas during development. Further functional enrichment analysis revealed up-regulation of biological processes linked to extracellular matrix organization.

overall_design: Retinal mRNA profiles of P5 WT and C3-KO mice were generated by deep sequencing, n=4/genotype, using Illumina Nextseq 2000, and the sequencing target was 25 million reads per samples.

first: Gopalan

last: Gnanaguru

first: Kip

middle: M

last: Connor

first: Ruslan

last: Sadreyev


title: Early Developmental Deficits in the CF sheep model

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Cystic Fibrosis (CF) is associated with pathology in multiple tissues including the lung, digestive tract and reproductive system. Lung disease is primarily a post-natal event but other organs are affected before birth. Here we use the CF sheep model to investigate the initiation and progression of CF disease through gestation.

overall_design: RNA-seq of sheep (ovis aries) tracheal epithelial tissue

first: Alekh

last: Paranjapye

first: Shih-Hsing

last: Leir

first: Jenny

last: Kerschner

first: Makayla

last: Schacht


title: AP-1 Independent NFAT2 Signaling in Primary CD4+ T Cells

city: New Haven

first: Joe

last: Craft

state: CT

address: 300 Cedar St

department: Internal Medicine

institute: Yale University


title: AP-1 Independent NFAT2 Signaling in Primary CD4+ T Cells [ComboCostim]

summary: To determine effect of ICOS costimulation on CD4+ T Cells

overall_design: Transcriptome analysis of CD4+ T cells transduced with anti-CD3 vs anti-CD3/CD28 vs anti-CD3/CD28/ICOS

first: Abhinav

last: Seth

first: Yoshiyuki

last: Yokukura

first: Jin-Young

last: Choi

first: Justin

last: Shyer

first: Aurobind

last: Vidyarthi


title: Profiling transcriptional heterogeneity of epithelium, fibroblasts and immune cells in esophageal squamous cell carcinoma by single-cell RNA sequencing

city: Zhengzhou

first: Ke

last: Shi

address: No.8, Shuanghu Avenue, Longhu Town, Xinzheng, Zhengzhou, Henan Province

institute: Henan Medical College

summary: We generated single-cell RNA sequencing (scRNA-seq) of 25,796 immune and 8,197 non-immune cells from three primary tumor and paired normal samples in ESCC patients. The results revealed that transcriptional signatures of malignant epithelium could be effectively distinguished from that of non-malignant epithelium by scRNA-seq data. The infiltration of myofibroblasts, one subtype of fibroblasts, might play important roles in the progression of ESCC. Diverse cell subtypes of T cells and myeloid cells were identified, including tumor-enriched HAVCR2+ CD4+ T cells with significantly exhausted signature. We also found that epithelium and myeloid cells had more frequent cell-cell communication compared with epithelium and T cells. Taken together, this study provided in-depth insights into the cellular heterogeneity of TME in ESCC and highlighted potential therapeutic targets including for immunotherapy.

overall_design: Single-cell RNA sequencing was performed from three treatment-naïve ESCC samples and three paired adjacent tissues by using 10x Genomics platform.

first: Jinzhong

last: Zhang

first: Yucheng

last: Lu


title: Genome wide analsis of the chromatin accessibility and gene expression in control and NUDT5 depleted U2OS cells [RNA-seq]

city: BOSTON

first: HONGYUN

last: QI

address: 450 Brookline Ave

institute: RADIATION ONCOLOGY

summary: NUDT5 was reported to generate ATP to support local chromatin remodeling and transcription of hormone-responsive genes. Our research has found that NUDT5 is also required for DNA damage repair by homologous recombination. To investigate how NUDT5 regulates HR, we depleted NUDT5 in U2OS cells by siRNA and compared the transcriptome profiling (RNA-seq) of NUDT5 depleted cells with control cells to investigate whether NUDT5 regulate HR by altering the expression of essential components of the HR machinery. The results suggest that NUDT5 does not regulate HR by altering the expression of essential components of the HR machinery. To investigate whether NUDT5 contributes to chromatin remodeling after DNA damage, we compared the chromatin accessibility profiling (ATAC-seq) in NUDT5 depleted U2OS cells and control cells, either before or after ionizing radiation. The results suggest that NUDT5 silencing blocked most DNA damage-induced changes in chromatin accessibility following radiation exposure and implies that NUDT5 may support the activity of remodeling ATPases during damage repair.

overall_design: RNA-seq analysis of U2OS cells transfected with siCtrl or siNUDT5 (samples in triplicate). ATAC-seq analysis of U2OS cells transfected with siCtrl or siNUDT5, treated with or without ionizing radiation at 5Gy (samples in duplicate).

first: Hongyun

last: Qi

first: Matthew

last: Booker

first: Zach

last: Herbert

first: Brendan

middle: D

last: Price


title: Distinct p53 isoforms code for opposing transcriptional outcomes

city: Richmond

first: Hengbin

last: Wang

state: VA

address: 401 College Street

department: Massey Cancer Institute

institute: Virginia Commonwealth University

summary: p53 genes across species are broadly conserved and encode well-characterized transcriptional activators that specify inductive stress-responses. In some contexts, p53 can also down-regulate genes but the mechanisms involved are not understood and assumed to be indirect. Here we integrate synthetic and native cis-regulatory elements with an imaging platform to examine features of p53-mediated gene control in vivo.

overall_design:
Cut&Run for p53 in Drosophila stage L3 salivary glands.
STI150 is a GFP reporter construct in which GFP expression is under control of the p53 DNA binding motif upstream of the reaper gene (homozygous)
mCh is a fly containing a p53 genomic rescue in with p53 has been tagged with mCherry (homozygous)
K1 is a p53 knockout drosophila allele (homozygous)

first: John

last: Abrams


title: Genome wide analsis of the chromatin accessibility and gene expression in control and NUDT5 depleted U2OS cells

type: Genome binding/occupancy profiling by high throughput sequencing


title: Expression data from nine days differentiated C3H10T1/2 adipocytes exposed to adenovirus-mediated scramble and Zc3h10 shRNA

city: Milan

first: Nico

last: Mitro

state: MI

address: Via Balzaretti 9

department: Pharmacological and biomolecular sciences

country: Italy

institute: Università degli studi di Milano

summary:
Zc3h10 is a RNA binding protein able to control both mRNA and miRNA metabolism. Zc3h10 is ubiquitously expressed and controls both cell differentiation and energy metabolism.
In this dataset, we include the expression data obtained adipocytes differentiated for nine days treated with scramble RNA (control) and a Zc3h10 specific shRNA. This data were used to verify which genes are differentially expressed by lack of Zc3h10 during adipogenesis.

overall_design: 6 total samples were used, 3 biological replicates for controls and 3 biological samples for Zc3h10 shRNA. We performed a padj analysis with a cutoff of 5%.

first: Audano

last: Matteo


title: ZNF827-dependent splicing dynamics are critical for EMT during development and disease [RNA-seq]

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

institute: Karolinska Institutet

summary: Epithelial to mesenchymal transition (EMT) is a multi-step process during which epithelial cells become mesenchymal stem cells. EMT is involved during embryonic development, wound healing, fibrosis and tumor metastasis. Here we show that ZNF827, a C2H2-zinc finger containing protein, is critical for molecular and phenotypic changes underlying EMT. We demonstrate that ZNF827 depletion suppresses tumor metastasis and cortical neurogenesis in vivo by impairing EMT. Further analysis showed that ZNF827 is critical for global alternative splicing (AS) during EMT. We further reveal that ZNF827 interacts with various components of core splicing machinery and directly binds DNA. ZNF827 depletion leads to alteration of epigenetic landscape at its target genomic region which might be important for alternative splicing of these target genes. Our findings established ZNF827 as a novel regulator of AS during development and disease contexts of EMT.

overall_design: 3 replicates each for HMLE cells Untreated, d4 TGF-B treated and transfected with siControl or siZNF827

first: Sanjeeb

middle: K

last: Sahu

first: Mustafa

last: Diken

first: Susanne

last: Strand

first: Reini

middle: F

last: Luco

first: Vijay

last: Tiwari


title: Polyvalent mRNA vaccination elicited potent immune response to monkeypox surface antigens

status: Public on Feb 13 2023

city: West Haven

first: Sidi

last: Chen

address: 850 West Campus Drive

summary: The soaring global monkeypox cases lead to a surge in demand for monkeypox vaccine, which far exceeds the supply. mRNA vaccine has achieved great success in prevention of coronavirus disease and holds promise against diverse pathogens. In this study, we generate a polyvalent lipid nanoparticle (LNP) mRNA vaccine candidate for monkeypox virus (MPXV) and evaluate its immunogenicity in animal models. This polyvalent MPXV mRNA vaccine candidate, MPXVac-097, encodes five 2022 MPXV targets that are important surface antigens. Three-dose (prime-boost-booster) MPXVac-097 vaccination elicits strong antibody response to A35R and E8L antigens, moderate response to M1R, but not B6R or A29, highlighting the differences in immunogenicity. Bulk T cell receptor (TCR) sequencing reveals preferential usage of VJ combinations and clonal expansion of peripheral T cells after MPXVac-097 vaccination. These data demonstrate initial feasibility of developing MPXV mRNA vaccine and pave the way for its future optimization.

overall_design: Mice were immunized with three doses of 8 µg MPXVac-097 LNP mRNA two weeks apart (prime, boost and booster), and the peripheral blood T cell response was profiled from the repertoire of T cell receptors (TCR) in day 20 vs day 0 vaccinated mice via bulk TCR-sequencing (TCR-seq).

first: Paul

last: Renauer

first: Zhenhao

last: Fang


title: Gene expression profile of MANF-deficient Cx3cr1+ macrophages during muscle regeneration

city: Lisboa

first: Pedro

last: Sousa-Victor

address: Avenida Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular (iMM)

summary: RNA sequencing analysis of MANF-deficient macrophages revealed changes in key cellular processes.

overall_design: CD45posF4/80pos macrophages were FACS-isolated from BaCl2-injured skeletal muscles at 3 days post injury. MANF deficiency was induced by tamoxifen treatment of Cx3cr1-CreER, Manffl/fl mice and compared with oil treated mice of the same genotype.

first: Neuza

middle: S

last: Sousa

first: Inês

middle: B

last: Antunes

first: Joana

last: Neves


title: AP-1 Independent NFAT2 Signaling in Primary CD4+ T Cells [NF2_CAvCARIT]

first: Joe

last: Craft

summary: To determine AP-1 Independent Signaling Pathways Controlled by NFAT2 in Primary CD4+ T Cells

overall_design: Transcriptome analysis of CD4+ T cells transduced with Control, NFAT2-CA or NFAT2-CARIT overexpression vectors.

first: Abhinav

last: Seth

first: Yoshiyuki

last: Yokukura

first: Jin-Young

last: Choi

first: Justin

last: Shyer

first: Aurobind

last: Vidyarthi


title: Retinoic acid signaling during priming licenses intestinal CD103+ CD8 TRM cell differentiation

city: Stony Brook

first: Brian

last: Sheridan

state: NY

address: 100 Nicolls Road

department: Microbiology and Immunology

institute: Stony Brook University

summary: CD8 tissue-resident memory T (TRM) cells provide front-line protection at barrier tissues; however, mechanisms regulating TRM cell development are not completely understood. Priming dictates the migration of effector T cells to the tissue, while factors in the tissue induce in situ TRM cell differentiation. Whether priming also regulates in situ TRM cell differentiation uncoupled from migration is unclear. Here, we demonstrate that T cell priming in the mesenteric lymph nodes (MLN) regulates CD103+ TRM cell differentiation in the intestine. In contrast, T cells primed in the spleen were impaired in the ability to differentiate into CD103+ TRM cells after entry into the intestine. MLN priming initiated a CD103+ TRM cell gene signature and licensed rapid CD103+ TRM cell differentiation in response to factors in the intestine. Licensing was regulated by retinoic acid signaling and primarily driven by factors other than CCR9 expression and CCR9-mediated gut homing. Thus, the MLN is specialized to promote intestinal CD103+ CD8 TRM cell development by licensing in situ differentiation.

overall_design: Perform RNA-seq on naïve, spleen-primed and MLN-primed CD8 T cells

first: Zhijuan

last: Qiu

first: Lynn

last: Puddington


title: Retinoic acid treatment suppresses fibrolamellar carcinoma growth

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

summary: Fibrolamellar carcinoma (FLC) is a devastating, early-onset rare cancer for which there is no effective standard of care.  FLC tumors are initiated and likely also maintained by the fusion oncoprotein DNAJ-PKAc (DP).  Strategies to therapeutically target DP are underway but remain challenging.  Alternate therapeutic approaches are needed in order to maximize the potential benefit for patients.  In this study, to identify candidate compounds for drug repurposing, we re-analyzed publicly available RNA-seq data in FLC and non-malignant liver (NML) tissue.  We noted that retinoid metabolism, a normal function of a healthy liver, is strikingly suppressed in FLC, which led to the hypothesis that FLC tumors may be responsive to all-trans retinoic acid (ATRA).  To test this hypothesis, we treated FLC tumor cells in culture, established from a patient-derived xenograft (PDX) mouse model, with ATRA and found by RNA-seq that well-established molecular markers of PKA signaling and FLC tumors are significantly reduced.  Moreover, ATRA treatment markedly diminished cell viability, proliferation, and colony forming capability.  We also demonstrated that ATRA sensitizes FLC cells to apoptotic induction by the TLR3 ligand, poly(I:C).  Next, using patient tissue slices, we confirmed that ATRA reduces cell viability only in tumors and not in adjacent NML tissue.  Finally, we performed in vivo studies in PDX mice to show that ATRA significantly suppresses FLC tumor growth.  These findings motivate a more expansive pre-clinical examination of ATRA, especially in conjunction with TLR3 ligands and possibly other adjuvants, to establish the safety and efficacy of ATRA for FLC clinical trials.

overall_design: RNA- and small RNA-seq comparison between patient-derived fibrolamellar carcinoma (FLC) cells with either 4µM ATRA or vehicle control across two separate trials.

first: Adam

last: Francisco

first: Alexandria

last: Shumway


title: Gene expression profile of old macrophages during muscle regeneration

summary: RNA sequencing analysis of pro-repair macrophages isolated from aged mice revealed changes in key cellular processes.

overall_design: CD11bposF4/80posLy6CLow macrophages were FACS-isolated from BaCl2-injured skeletal muscles of young and aged mice at 3 days post injury.


title: S-adenosylmethionine synthases specify distinct H3K3me3 populations and gene expression patterns during heat stress [CUT&Tag]

city: Worcester

first: Amy

last: Walker

state: Massachusetts

address: Suite 137, Biotech 2, 373 Plantation St

department: Program in Molecular Medicine

institute: UMass Chan Medical School

summary: We find that two SAM synthases in C. elegans, SAMS-1 and SAMS-3/4, contribute differently to modification of H3K4me3, gene expression and survival in the heat stress response. Our data showing differential SAM provisioning to distinct groups of methylated targets based on SAM synthase source suggests that determining how methyl donors are provided will broaden insight into 1CC functions in aging and stress.

overall_design: Examination of differential H3K4me3 enrichment at transcription start sites in C elegans genes under low SAM conditions with and without heat shock.

first: Adwait

last: Godbole

first: Sneha

last: Gopalan

first: Thomas

last: Fazzio


title: Metastatic potential in clonal melanomal cells is driven by a rare, early-invading subpopulation [RNA-Seq]

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building, 415 Curie Boulevard

department: Department of Bioengineering

institute: University of Pennsylvania

summary: To investigate the molecular basis driving a highly invasive phenotype of a rare subpopulation of melanoma cells; The highly invasive phenotype was regulated by the NKX2.2 transcription factor and it was marked by transiently high levels of SEMA3C.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of parental and NKX2.2 knockout FS4 and 1205Lu melanoma cell lines.

first: Amanpreet

last: Kaur

first: Luciann

last: Cuenca

first: Karun

last: Kiani

first: Gianna

last: Busch

first: Dylan

last: Fingerman

first: Margaret

last: Dunagin

first: Jingxin

last: Li

first: Ian

last: Dardani

first: Eric

last: Sandford

first: Jordan

last: Pemberton

first: Yogesh

last: Goyal

first: Ashani

last: Weeraratna

first: Meenhard

last: Herlyn


title: S-adenosylmethionine synthases specify distinct H3K3me3 populations and gene expression patterns during heat stress [RNA-seq: sams RNAi, 20C]

first: Amy

last: Walker

overall_design: Examination of differential gene expression in C. elegans with low SAM at 20C

first: Adwait

last: Godbole


title: Gene expression profile at single cell level of DC from B16F10 tumor with Advs treatment

city: Tampa

first: Amer

last: Beg

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

summary: Towards the goal of developing new therapeutic modalities, we investigated the impact of individual and combined activation of CD40 and type 1 IFN pathways on mouse tumor cDCs. To this end, we utilized replication-deficient adenoviruses expressing a membrane-stable CD40L (MEM40), mouse IFNb (mIFNB) and a control null virus (Ad-Null). Then We used single cell RNA sequencing (scRNA-seq) to analyze the gene expression profile in the advs treated tumors of DCs .

overall_design: C57BL/6 mice were inoculated s.c. with 5*e5 B16-F10 cells. On D12, mice were subjected to an intratumoral injection with adenoviruses (Advs). Each scRNA-seq sample was pooled from 3 different similarly treated tumors, CD11c+ MHC-II+ sorted cells were used for  10x Genomics scRNAseq.

first: Hong

last: Zheng

first: Xiaoqing

last: Yu


title: Metastatic potential in clonal melanomal cells is driven by a rare, early-invading subpopulation [ATAC-Seq]

first: Arjun

last: Raj

overall_design: We performed analysis of chromatin accessibility changes using data obtained from ATAC-seq of FS4 and 1205Lu melanoma cell lines.

first: Amanpreet

last: Kaur

first: Luciann

last: Cuenca


title: Metastatic potential in clonal melanomal cells is driven by a rare, early-invading subpopulation

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

overall_design: Refer to individual Series


title: Impact of MEM40 and IFNB on human DC activation markers

summary: To determine the impact of MEM40 and IFNB on normal human donor monocyte-derived DCs (Mo-DCs) phenotype, we used an experimental design where human A549 lung cancer cells were first infected with Ad-Null or adenoviruses expressing human IFNB, MEM40 or MEM40 + IFNB, followed by removal of virus-containing supernatant and co-culture with Mo-DCs. We used the above design followed by sorting of MHC-II+ CD11c+ cells for bulk RNA-sequencing.

overall_design: A549 were infected with ISF35 or/ and IFNB viruses followed by cocultured with human Mo-DCs (CD14+ PBMC were purified and stimulated by IL-4 and GM-CSF). 2 days later, all cells were collected for cell sorting.  RNA-seq was used to determine changes in gene expression after sorting HLA-DR+CD11c+ DCs derived from monocytes of 3 healthy donors.


title: Genome wide analsis of the chromatin accessibility and gene expression in control and NUDT5 depleted U2OS cells [ATAC-seq]

first: HONGYUN

last: QI

overall_design: RNA-seq analysis of U2OS cells transfected with siCtrl or siNUDT5 (samples in triplicate). ATAC-seq analysis of U2OS cells transfected with siCtrl or siNUDT5, treated with or without ionizing radiation at 5Gy (samples in duplicate).

first: Hongyun

last: Qi

first: Matthew

last: Booker

first: Zach

last: Herbert

first: Brendan

last: Price


title: S-adenosylmethionine synthases specify distinct H3K3me3 populations and gene expression patterns during heat stress [RNA-seq: sams-4 RNAi, Heat shock]

overall_design: Examination of differential gene expression in C. elegans with low SAM at with and without heat shock


title: Memory-like Natural Killer cells become resident in non-lymphoid tissue to maintain tissue health

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

summary: Tissue health is dictated by the capacity to respond to perturbations and then return to homeostasis. Mechanisms that initiate, maintain, and regulate immune responses in tissues are therefore essential. Adaptive immunity plays a key role in these responses, with memory and tissue-residency being cardinal features. A corresponding role for innate cells is unknown. Here we have identified a population of innate lymphocytes that we term tissue-resident memory-like natural killer (NKRM) cells. In response to murine cytomegalovirus infection, we show that circulating NK cells were recruited in a CX3CR1-dependent manner to the salivary glands where they formed NKRM cells, a long-lived tissue-resident population that prevented autoimmunity via TRAIL-dependent elimination of CD4+ T cells. Thus, NK cells develop adaptive-like features, including long-term residency in nonlymphoid tissues, to modulate inflammation, restore immune equilibrium and preserve tissue health. Modulating the functions of NKRM cells may provide additional strategies to treat inflammatory and autoimmune diseases.

overall_design: Salivary gland NK cells (live CD45+TCRb- CD3-CD19-NKp46+CD49b+CD200r- cells) were sorted from a pool of 12 mice at day 120 post murine cytomegalovirus infection for single cell RNA sequencing

first: Iona

last: Schuster

middle: R

first: Mariapia

last: Degli-Esposti


title: S-adenosylmethionine synthases specify distinct H3K3me3 populations and gene expression patterns during heat stress


title: Ribonucleotide Reductase Subunit Switching in Hepatoblastoma Drug Response and Relapse

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

summary: To investigate the effect of RNR subunit switching in relation to Drug Resistance in hepatoblastoma

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cells with RNR genetic manipulation both untreated and treated with Cisplatin

first: Anthony

last: Brown

first: Liqin

last: Zhu


title: Infection induces tissue resident memory NK cells that safeguard tissue

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

summary: Tissue health is dictated by the capacity to respond to perturbations and then return to a homeostatic state. Thus, mechanisms that initiate, maintain and regulate immune responses in tissues are essential. The adaptive immune system has been ascribed a principal role in these responses, with memory and tissue-residency being cardinal features of immune protection in tissues. Whether there is a corresponding role for innate cells is unknown. Here we identify a population of innate lymphocytes that we term tissue-resident memory-like natural killer (NKRM) cells. In response to murine cytomegalovirus infection, we show that circulating NK cells are recruited to the salivary glands where they form NKRM cells, a long-lived tissue-resident population that prevents autoimmunity and safeguards organ function. Thus, NK cells develop adaptive-like features, including long-term residency in nonlymphoid tissues, to modulate inflammation, restore immune equilibrium and preserve tissue health. Modulating the functions of NKRM cells may provide new strategies to treat inflammatory and autoimmune diseases.

overall_design: RNA-seq was performed on ex-vivo group 1 innate lymphocytes cells harvested from liver and salivary gland.


title: Transcriptomics reveals the molecular transcriptional regulatory network of Xinhuitong in the treatment of coronary heart disease with Qi deficiency and blood stasis syndrome

city: Changsha

first: Shiying

last: Zhang

address: Xueshi Road No. 300

institute: Hunan University of Chinese Medicine

summary: Research purpose: To explore the key targets and core signal pathways of XHT (Xinhuitong, XHT) in regulating coronary heart disease with Qi deficiency and blood stasis syndrome through transcriptomics, and reveal the transcriptional regulatory network of XHT in treating coronary heart disease with Qi deficiency and blood stasis syndrome.  Research method: Using transcriptomics RNA-Seq technology, gene sequencing of myocardial tissues in the ischemic marginal zone of the Qi deficiency and blood stasis syndrome model group and the high-dose Yiqi Huoxue prescription group and searching for differential genes, from the perspective of gene regulation and expression patterns To study the possible effective drug targets and effect mechanism pathways of XHT in the treatment of coronary heart disease with Qi deficiency and blood stasis syndrome, and to further explore the treatment of coronary heart disease with Qi deficiency and blood by Chinese medicine compound prescriptions. The possible pharmacological mechanism of blood stasis syndrome, and the key molecular nodes and effect mechanism pathways suggested by it are verified by molecular biology methods.

overall_design: Comparative gene expression profiling analysis of RNA-seq data

first: Yan

last: Song

first: Zhiying

last: Yuan

first: Weiqing

last: Li

first: Liang


title: Single-cell RNAseq of the resident immune cells from Gli1HhipCKO_Tam and Gli1HhipCKO_Oil_Control mice lungs

city: San Francisco

first: Tien

last: Peng

state: CA

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

summary: To study resident immune cells in Hhip-deleted lungs, we conduct single-cell RNAseq of the resident immune cells from Gli1HhipCKO_Tam and Gli1HhipCKO_Oil_Control mice lungs using 10X genomics scRNAseq technique.

overall_design: Resident immune cells were sorted from adult control and Hhip-deleted lungs. Dead cells were excluded using DAPI negative selection.

first: Chaoqun

last: Wang


title: TiSA: TimeSeriesAnalysis – A pipeline for the analysis of longitudinal transcriptomics data

city: Oslo

first: Yohan

last: Lefol

state: Oslo

address: Sognsvannsveien 20 Rikshospitalet

department: Institute of Clinical Medicine

country: Norway

institute: University of Oslo

summary: RNAseq dataset created to evaluate Activation Induced Cytidine Deaminase (AICDA/AID) stimulation cocktails in peripheral blood mononuclear cells (PBMC)

overall_design:
PBMC cells were stimulated with either LPS, TGFb.acD40.IL4, or IgM.acD40.IL4.IL21. We also used had unstimulated (control) replicates. Each stimulation (or control) were done in replicates of two. Each replicate had cells harvested and sequenced at Days 1, 3, and 9.
LEMONAID Consortium (contributor)

first: Tom

last: Korfage

first: Bruno

last: Müller


summary: Investigation of the effects of a AID stimulation cocktail on a murine specimen

overall_design: A longitudinal experiment testing the effects of a AID stimulation cocktail (LPS, IL4, TGFb) on mice. Samples were harvested at 10 time points for two mice, one treated and another un-treated.

first: Robin

last: Mjelle

first: Hans

last: Krokan

first: Antonio

last: Sarno

first: Pål

last: Sætrom


title: The Integrator complex regulates microRNA abundance through RISC loading

city: Miami

first: Felipe

last: Beckedorff

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

summary: MicroRNA (miRNA) homeostasis is crucial for the post-transcriptional regulation of their target genes and miRNA dysregulation has been linked to multiple diseases, including cancer. The mechanistic steps of miRNA biogenesis are well understood at molecular level1,2. Subsequent miRNA duplex loading into members of the Argonaute (Ago) protein family, representing the core of the RNA-induced silencing complex (RISC), is pivotal to miRNA-mediated gene silencing3-5. The Integrator complex has been previously identified as important regulator of RNA maturation, RNA polymerase II pause-release, and premature transcriptional termination, processes dependent on Integrator’s catalytical activity6-9. Here we report that absence of the Integrator complex leads to a global loss of mature miRNAs. By incorporating 4-Thiouridine (s4U) in nascent transcripts, we traced miRNA fate from biogenesis to stabilization and identified Integrator to be essential for proper miRNA assembly into RISC. Indeed, Integrator enhances miRNA-Ago2 interaction in vitro, which functionally translates to amplified miRNA target cleavage. These findings demonstrate for the first time cytoplasmic Integrator complex functions and stress an indirect role of Integrator in transcription regulation through modulation of miRNA abundance and stability.

overall_design: small RNA-seq of HeLa cells depleted for INTS1, INTS3, INTS6, INTS7, or INTS11 and their control using shRNA in duplicates  small RNA-seq of HeLa cells depleted for Drosha and Control using siRNA in duplicates  small RNA-seq of shINTS6, shINTS11, and shControl HeLa cells, RNA extracted from nucleus and cytoplasm in duplicates  SLAM small RNA-seq: 4-Thiouridine kinetic labeling of small RNAs in shINTS6, shINTS11, and shControl HeLa cells at 0, 0.25, 0.5, 1, 3, 6, 12, 24 hours including noS4U and noIAA controls in duplicates    Ago2 RNA Immunoprecipitation (RIP) followed by small RNA-seq from shINTS6, shINTS11, and shControl HeLa cells after 0 or 24h of 4-Thiouridine labeling including noS4U controls in duplicates  Total RNA-seq of HeLa cells depleted for INTS1, INTS3, INTS6, INTS7, INTS11 using shRNA in duplicates  Total RNA-seq of HeLa cells depleted for Drosha and Control using siRNA in duplicates  Enhanced UV crosslinking and immunoprecipitation (eCLIP) of INTS11, CPSF73, IgG and their size-matched input controls in duplicates from HeLa cells. The protocol was optimized for smRNA capture by increased RNase concentrations

first: Nina

last: Kirstein

first: Sadat

last: Dokaneheifard

first: Pradeep

last: Cingaram

first: Ezra

last: Blumenthal

first: Helena

last: Gomes Dos Santos

first: Mina

last: Tayari

first: Monica

last: Valencia

first: Ramin

last: Shiekhattar


title: Bulk RNAseq of the HhipCKO (UBCcreER/Myh11creER/Hhipflox/flox) and control (Hhipflox/flox) adult mouse mesenchymal cells

first: Tien

last: Peng

summary: To test the effect of Hhip deletion on mesenchymal cells. We examined the transcriptome of HhipCKO vs. control by bulk RNAseq.

overall_design: The lung mesenchymal cells from HhipCKO (UBCcreER/Myh11creER/Hhipflox/flox) and control (Hhipflox/flox) adult mouse were FACSorted by negative seletion of CD45/CD31/Epcam. Dead cells were excluded by negative selection of DAPI.

first: Chaoqun

last: Wang


title: Single-cell RNAseq of the human normal and emphysema lung

summary: To study emphysema, we conduct single-cell RNAseq of the human healthy and emphysema lung using 10X genomics scRNAseq technique.

overall_design: Adult human lung cells were sorted from the distal fragments. Dead cells were excluded using DAPI negative selection.


title: Estrogen-induced CircRNA, CircPGR, Functions as a CeRNA to Promote Estrogen Receptor-positive Breast Cancer Progression by Regulating Cell Cycle-related Genes

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

summary: Estrogen and estrogen receptor (ER)-mediated gene transcriptional events have been well known to be involved in ER-positive breast carcinogenesis. Meanwhile, circular RNAs (circRNAs) are emerging as a new family of functional non-coding RNAs (ncRNAs) with implications in a variety of pathological processes, such as cancer. However, the estrogen-regulated circRNA program and the function of such program remain uncharacterized. Here, genome-wide circRNA profiling by circRNA sequencing (circRNA-seq) revealed tens of thousands of circRNAs were induced by estrogen, and further functional screening for the several circRNAs originated from PGR revealed that one of them, which we named as circPGR, was required for ER-positive breast cancer cell growth and tumorigenesis. CircPGR was found to be localized in the cytosol of cells. Mechanistically, circPGR functioned as a competing endogenous RNA (ceRNA) to sponge miR-301a-5p to regulate the expression of multiple cell cycle genes. The clinical relevance of circPGR was underscored by its high and specific expression in ER-positive breast cancer cell lines and clinical breast cancer tissue samples. Accordingly, siRNA targeting circPGR was proven to be effective in suppressing ER-positive breast cancer cell growth. These findings reveled that, besides the well-known mRNA, microRNA (miRNA), long non-coding RNA (lncRNA) and enhancer RNA (eRNA) programs, estrogen also induced a circRNA program, and exemplified by circPGR, these estrogen-induced circRNAs were required for ER-positive breast cancer cell growth, providing a new class of therapeutic targets for ER-positive breast cancer.

overall_design: CircRNA-seq performed in this study was designed to uncover the estrogen-induced circRNA program in MCF7 cells; RNA-seq performed in this study was designed to understand the molecular mechanisms underlying circPGR in gene transcriptional activation.

first: Wen

last: Liu

first: Lei

first: Yi


title: Single cell RNA-seq of cultured mouse brain pericytes

city: Leipzig

first: Bilal

last: Sheikh

state: Sachsen

address: Philipp-Rosenthal-Str. 27

department: HI-MAG

country: Germany

institute: Helmholtz Zentrum München

summary: We compared the transcriptional profile of early and late passage primary mouse brain pericytes.

overall_design: Primary mouse pericytes were isolated from the brain of 6 WT female mice. The cells were cultured for 5 or 20 passages. Later the cells were analysed with scRNA-seq

first: Fabiana

last: Oliveira

first: Olga

last: Bondareva


title: C2-signature in Moricandia under limited soil water availability

city: Sesto Fiorentino

first: Giovanni

last: Emiliani

state: Firenze

address: vai Madonna del Piano, 10

institute: IPSP-CNR

summary: Transcriptome profiling in response to water stress and rewatering of Moricandia species with C3 and C3-C4 intermediate photosynthesis.

sample_organism:
Moricandia arvensis
Moricandia moricandioides
Moricandia suffruticosa

overall_design: Comparative mRNA accumulation profiling of 3 Moricandia species under drought and rewatering. Samplings were performed on the basis of stomatal conductance (Gs) values during the water deficit treatment: T0: 100% Gs; T1: 50% Gs; T2: 10% Gs; RW: 100% Gs after rewatering.

first: Carla

last: Pinheiro

first: Duncan

last: Haworth

last: Marino

first: Mauro

last: Centritto


title: Digital RNA Sequencing of Human Epidermal Keratinocytes carrying HPV 16E7

city: Hangzhou

first: Chunting

last: Hua

state: Zhejiang

address: 3 East Qingchun Road

institute: Sir Run Run Shaw Hospital

summary: We applied digital RNA sequencing to explore the expression profiles of human epidermal keratinocytes carrying HPV 16E7.

overall_design: NHEK cells were transfected with pEGFP-C1 and pEGFP-16E7 in triplicate. NHEK_GFP-C1 cells are HPV-negative control.

first: Hao

last: Cheng


title: Modelling host-Trypanosoma brucei gambiense interactions in vitro using human induced pluripotent stem cell-derived cortical brain organoids

status: Public on Feb 12 2023

city: Manchester

first: Juan

middle: Fernando

last: Quintana

address: 2.18c CTF, Grafton Street

department: Lydia Becker Institute of Immunology and Inflammation

country: United Kingdom

institute: University of Manchester

summary:
To explore whether iPSC-derived human brain organoids can be used to model brain-trypanosoma interactions as alternative models to mice.
We performed gene expression profiling analysis using data obtained from RNA-seq of iPSC-derived human brain organoids co-cultured with T. brucei gambiense for 24 and 72 hours, and included untreated controls.

overall_design: Comparative gene expression profiling analysis of RNA-seq data.

first: Praveena

last: Chandrasegaran

first: Agatha

middle: N

last: Lestari

first: Matthew

last: Sinton

first: Jay

last: Gopalakrishnan


title: Assessing the effects of four two-component system response regulator knockouts in E. coli

city: La Jolla

first: Cameron

last: Lamoureux

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

summary: Escherichia coli use two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts of E. coli’s global transcriptional regulatory network (TRN). Here, we profiled the effects of knockout of 4 TCS regulators: atoC, btsR, cusR, and rcsB. These knockouts were grown in the presence of their typical effector molecules to enable comparison to the intact response of the WT system (K-12 MG1655).

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Growth of E. coli was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation. Cells were grown at 37C at pH 7.

first: Kumari

last: Choudhary


title: RNA seq of liver homogenates collected every 4 hours for one 24 hour cycle from adipocyte knockouts for Bmal1

first: Georgios

last: Paschos

address: 10-102 Translational Research Center, 3400 Civic Center Boulevard, Building 421

department: Pharmacology

institute: University of Pennsylvania, School of Medicine

summary: We used RNA seq to evaluate gene expression oscillations in liver from mice lacking Bmal1 in adipocytes.

overall_design: We collected liver from adipocyte specific Bmal1 knockout mice every 4 hours throughout one 24 hour cycle. Mice were housed at room temperature, 12 hour light, 12 hour dark schedule and were fed ad libitum before the experiment. Mice were kept at constant darkness and were fasted for 24 hours prior tissue collection

first: Eun Ji

last: Kim

first: Gregory

last: Grant

first: Tilo

last: Grosser

first: Garret

last: FitzGerald


title: Identification and characterization of pluripotency associated lncRNAs in human iPS cells

city: Pamplona

first: Juan Roberto

last: Rodriguez-Madoz

state: Navarra

address: PIO XII 55

department: Cell Therapy Program

country: Spain

institute: Foundation For Applied Medical Research

summary: Induced pluripotent stem cells (iPSCs) are an attractive source of stem cells for many applications like patient-specific cell therapy, disease modeling or drug screening. Generation of iPSCs by cellular reprogramming is a complex and highly inefficient process that involves a high number of genetic and epigenetic modifications most of them unknown. Those genetic modifications include both coding and non-coding genes like long non-coding RNAs (lncRNAs). A detailed knowledge of the factors that make a cell to return to its own origin would help to a deeper understanding of the reprogramming process and to address new strategies that solve the current problems within this field.

overall_design: Total RNA was extracted from five human iPSCs generated form adipose derived stem cells (ADSCs) and three parental ADSCs. Then RNA was hybridized to SurePrint G3 Human GE Microarray, Agilent Technologies.

first: Natalia

last: Zapata-Linares

first: Felipe

last: Prosper


title: Dietary polyphenols drive alterations in behavior, transcriptional regulation, and commensal microbiota in models of opioid use

city: New York

first: Aya

last: Osman

address: 109 east 102nd street, apartment 3c

department: Neurology

institute: Icahn School of Medicine Mount Sinai

summary: Opioid Use Disorder (OUD) is a neuropsychiatric condition associated with tremendous medical and social consequences. Despite this burden, current pharmacotherapies for OUD are ineffective or intolerable for many patients. As such, interventions aimed at promoting overall health and resilience against OUD are of immense clinical and societal interest. Recently, treatment with a Bioactive Dietary Polyphenol Preparation (BDPP) was shown to promote behavioral resilience and adaptive neuroplasticity in multiple models of neuropsychiatric disease. Here, we assessed effects of BDPP treatment on behavioral and molecular responses to repeated morphine treatment. We find that BDPP pre-treatment alters responses across the dose range for both locomotor sensitization and conditioned place preference. Most notably, polyphenol treatment consistently reduced formation of preference at low dose (5mg/kg) morphine but enhanced it at high dose (15mg/kg). In parallel, we performed transcriptomic profiling of the nucleus accumbens, which again showed a dose x polyphenol interaction. At high dose morphine, BDPP pre-treatment potentiated gene expression changes induced by morphine particularly for genes related to synaptic function. We also profiled microbiome composition and function, as polyphenols are metabolized by the microbiome and can act as prebiotics. The profile revealed polyphenol treatment markedly altered microbiome composition and function, particularly in the low dose morphine group. Finally, we investigated involvement of the SIRT1 histone deacetylase, and the role of specific polyphenol metabolites in these behavioral phenotypes. Taken together, these results demonstrate that polyphenols have robust dose-dependent effects on behavioral and physiological responses to morphine and lay the foundation for future translational work.

overall_design: Comperative gene expression profiling analysis of RNA-seq data from mice pretreated with water or polyphenol mixture called BDPP for 2 weeks followed by either 5mg/kg or 15mg/kg morphine for 3 days.

first: Drew

last: kiraly

first: Giulio

last: Pasinetti

first: Tatsunori

last: Oguchi

first: Kyle

middle: J

last: Trageser

first: Kelsey

middle: E

last: Lucerne

first: Ava

middle: L

last: Shipman

first: Sharon

last: Zeldin

first: Yesha

last: Dave

first: Katherine

last: Meckel

first: Rebecca

last: Hofford


title: The development of a prediction model using serum microRNAs for evaluating axillary lymph node metastasis in breast cancer

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

country: Japan

institute: Toray Industries, Inc.

summary: The combination of serum miRNAs and clinical factors could be a powerful classifier for evaluating axillary lymph node metastasis in breast cancer.

overall_design: Serum microRNA profiles and clinical characteristics of 921 women with breast cancer and 37 women with benign breast disease.

first: Sho

last: Shiino

first: Juntaro

last: Matsuzaki

first: Akihiko

last: Shimomura

first: Junpei

last: Kawauchi

first: Satoko

last: Takizawa

first: Hiromi

last: Sakamoto

first: Yoshiaki

last: Aoki

first: Masayuki

last: Yoshida

first: Kenji

last: Tamura

first: Ken

last: Kato

first: Takayuki

last: Kinoshita

first: Yuko

last: Kitagawa

first: Takahiro

last: Ochiya


title: HeLa-FLCN KO upon Trametinib treatment [Trametinib_RNAseq]

city: Pozzuoli

first: Francesco

last: Panariello

state: Napoli

address: Via Campi Flegrei 34

institute: TIGEM

summary: Transcriptional regulation of gene expression plays a fundamental role in coordinating molecular and metabolic responses to stress conditions. The stress-responsive Transcription Factor EB (TFEB), the master controller of lysosomal biogenesis and autophagy, is regulated at the post-translational level by the nutrient-sensitive kinase complex TORC1. However, little is known about the transcriptional regulation of TFEB in physiological and pathological conditions. Here, we show that during starvation, the immediate-early gene EGR1 binds to the TFEB promoter and positively regulates TFEB expression. EGR1 depletion dampened TFEB-mediated transcriptional response to starvation and significantly inhibited cell proliferation in cellular and 3D spheroid models of Birt-Hogg-Dube' (BHD) syndrome, a TFEB-driven inherited cancer condition. Consistently, the MEK1/2 inhibitor Trametinib, known to inhibit EGR1 expression, suppressed the proliferation of BHD patient-derived cancer cells, suggesting that pharmacological inhibition of the EGR1-TFEB axis may represent a therapeutic strategy to counteract constitutive TFEB activation in cancer-associated conditions.

overall_design: RNA-seq of HeLa FLCN KO cells treated with Trametinb

first: Marcella

last: Cesana


title: EGR1 ChIPseq in HeLa cells at 6 hours of starvation [ChIPseq_HeLa_STV]

overall_design: ChIP-seq of EGR1, H3K4me3, H3K4me1 and H3K27ac in HeLa cells in fed and starved conditions

first: Margherita

last: Mutarelli

first: Susanna

last: Ambrosio


title: Time course of starvation in HeLa cells [STV_time course_RNAseq]

overall_design: RNA-seq of HeLa cells undergoing starvation


title: siEGR1 in HeLa cells at 6 hours of starvation [siEGR1_6h_RNAseq]

overall_design: RNA-seq of HeLa cells transfected with siRNA against EGR1 undergoing starvation for 6 hours.


title: Expression analysis of C. elegans eat-2; acs-20 and ptr-8 eat-2; acs-20 mutants

status: Public on Feb 11 2023

city: Nanjing

first: Zi

last: Wang

state: Jiangsu

address: 12 Xue-Fu Road, Pukou District , Nanjing, Jiangsu

department: Model Animal Research Center

institute: Nanjing University

summary:
Investigation of whole genome gene expression level changes in C. elegans ptr-8 eat-2; acs-20 compared to the eat-2; acs-20 mutant.
This project contains 6 samples (3 from eat-2; acs-20, 3 from ptr-8 eat-2; acs-20) of RNA-seq data.

overall_design: RNA-Seq analysis of C. elegans eat-2; acs-20 mutant (3 replicates) and ptr-8 eat-2; acs-20 mutant (3 replicates).

first: Di

last: Chen


title: Effect of overexpressing CSTA on gene expression of different nasopharyngeal carcinoma (NPC) cells

city: Guangzhou

first: ZhiJie

last: Liu

address: No. 651 Dongfengdong Road

institute: Sun Yat-sen University Cancer Center

summary: To investigate the function of CSTA, we established CSTA-overexpressing cell lines.We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different  NPC cells .

overall_design: To elucidate the molecular mechanisms of CSTA in suppressing NPC cellular motility, we performed high-throughput sequencing of S18 and 5-8F cells with CSTA overexpression or vector control.

first: LiSheng

last: Zheng

first: ChangZhi

last: Li

first: ChaoNan

last: Qian


title: RNF138 inhibits late inflammatory gene transcription through degradation of SMARCC1 of SWI/SNF complex

city: Beijing

first: Wei

address: 5 Dongdan Santiao Road

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

summary: As one of the core components of the SWI/SNF complex, SMARCC1 (SAF155, SRG3) plays essential role in activation of the late inflammatory genes in response to microbial challenge. However, little is known about the mechanisms how SMARCC1 is regulated in innate response. Here, we identify for the first time that nuclear E3 ubiquitin ligase RNF138 acts as a critical negative regulator in inflammatory responses. RNF138 selectively interacts with SMARCC1 and mediates its K48-linked polyubiquitination at position Lys643 and proteasomal degradation. As a result, catalytic activity of RNF138 fine-tunes the kinetics of late inflammatory gene transcription by inhibiting persistent chromatin remodeling at SWI/SNF regulated gene loci. These results provide mechanistic insight into the interplay among nucleosome remodeling, inflammation and ubiquitylation, and underscore the critical role of the E3 ligases in controlling both extent and duration of inflammatory responses.

overall_design: We analyzed and compared the inflammatory genes expression with results obtained from two RNA-seq data of wild type and RNF138 deficient RAW264.7 cells after LPS treatment (100ng/ml) for 3 hours.

first: Ziqiao

first: Shuo

first: Xuan

last: Zhang

first: Xuetao

last: Cao

first: Minghong

last: Jiang


title: RNAseq anaysis of hippocamal GAD2 cells

first: Marina

last: Schernthanner

address: 1230 York Ave.

institute: The Rockefeller University

summary: Purpose: To identify gene expression in GAD2 neurons of the hippocsmpus   Method: Translating Ribosome Affinity Purification (TRAP) to isolate RNA from GAD2+ cells, cDNA synthesis and next generation RNAseq using Illumina Nextseq sequencer.  Results: GAD2 had ~8000 of enriced genes  as compared to bulk mRNA

overall_design: 2 hippocampi were pooled for one translating ribosome affinity purification sample. We used mice that were GAD2 cre+  crossed with L10-EGFP+ mice.

first: Gali

last: Umschweif


title: Single-cell transcriptomic analysis of mouse liver reveals nonparenchymal cells' intricate responses to PCB126 exposure

first: Fengjun

last: Xu

address: No.866, Yuhangtang Road

department: College of Environmental & Resource Sciences

institute: Zhejiang Univeristy

summary: Polychlorinated biphenyls (PCBs) are ubiquitous and representative pollutants that pose great health risks. While cells' responses to dioxin-like PCBs tend to be studied on a bulk scale, few studies have been made from a single-cell level. Here, by using single-cell RNA sequencing, we depicted a detailed landscape of hepatic nonparenchymal cells' intricate responses to PCB126 exposure. A total of 13 clusters were identified. Notably, PCB126 exposure resulted in cell-type-specific gene expression profiles and genetic pathways. By analyzing genes related to aryl hydrocarbon receptors, we discovered that PCB126 induced the canonical genomic AhR pathway mainly in endothelial cells. In contrast, other cell types showed little induction. Enrichment pathway analysis indicated that immune cells changed their transcriptional patterns in response to PCB126. ScRNA-seq is a powerful tool to dissect underlying mechanisms of chemical toxicity regarding biological heterogeneity. Taken together, our study not only extends our current understanding of PCB126 toxicity, but also emphasizes the importance of in vivo cell heterogeneity in environmental toxicology.

overall_design: Single-cell RNA sequencing data of two mouse livers (vehicle control or PCB126 exposure)

first: Yulong

last: Fu

first: Jiaxuan

last: Yang

first: Chunna

last: Yu

first: Chaofeng

last: Shen


title: RNAseq anaysis of hippocamal cck cells of SMARCA3 cKO mice

summary: Purpose: To identify gene expression changes in CCK neurons of hippocsmpus of SMARCA3 cKO mice  Method: Translating Ribosome Affinity Purification (TRAP) to isolate RNA from CCK+ cells and, cDNA synthesis and next generation RNAseq using Illumina Nextseq sequencer.  Results: Biostatistical analysis identified 1378 genes that were altered by SMARCA3 cKO.

overall_design: 4 hippocampi were pooled for one translating ribosome affinity purification sample. We used mice that were CCK cre+  crossed with L10-EGFP+ mice and SMARCA3 fl/fl and littermates without  SMARCA3 fl/fl  controls.


title: Identification of factors involved in the silencing of germline genes in mouse embryonic cells

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

type: Methylation profiling by high throughput sequencing

summary: In mammals, many germline genes are repressed by epigenetic mechanisms to prevent their illegitimate expression in embryonic and somatic cells. To advance our understanding of the complete mechanisms restricting the expression of germline genes in mammals, we performed a genome-wide CRISPR-Cas9 knock-out screen for genes involved in germline gene repression in mouse embryonic stem cells (ESCs). We identified and validated several novel genes involved in the repression of germline genes, and characterized three of them: Usp7, Shfm1 (also known as Sem1) and Erh. Inactivation of Usp7, Shfm1 or Erh leads to the upregulation of germline genes, as well as retrotransposons for Shfm1, in mouse ESCs.

overall_design:
We performed RNA-seq in mouse ESCs transfected with non-targeting control siRNA and siRNA against Usp7, Dnmt1, Erh or Shfm1. siRNA experiments were performed three times independently.
We also performed RNA-seq in four independent WT and Usp7-KO mouse ESC clones.
To study the role of Usp7 in DNA methylation, we performed RRBS in mouse ESCs transfected with non-targeting control siRNA and siRNA against Usp7 or Dnmt1 (three independent experiments for each condition), as well as in four independent WT and Usp7-KO ESC clones.

first: Hala

last: Al Adhami

first: Sylvain

last: Daujat

last: Dumas


title: EGR1 drives cell proliferation by directly stimulating TFEB transcription in response to starvation

first: Francesco

last: Panariello

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

overall_design: Refer to individual Series


title: Transcriptomic analyses of improved cold tolerance in cucumber (Cucumis sativus L.) caused by Exogenous chitosan oligosaccharide

status: Public on Feb 10 2023

city: shenyang

first: jun

last: zhang

address: liaoning

institute: Shenyang Agricultural University

summary: Purpose: the goals of this study are to provide a theoretical basis for the use of chitosan oligosaccharide  to alleviate the damage caused by cold stress in cucumber growth and development.

overall_design: The transcriptome sequence were generated by deep sequencing with three repeats using Illumina. The sequence reads that passed filters were mapped tocucumber genome (http://cucurbitgenomics.org/organism/18) using HISAT2 software. The differently expressed genes were identify by |log2(FoldChange)| > 0 & p < 0.05, and qRT–PCR validation was performed using SYBR Green assays

first: Xueling

last: Ye

first: Chong

last: Tan


title: Changes in miRNA expression during infection with strong IBDV strains

first: Zixian

last: Chen

address: Wushan Road No.483

institute: South China Agriculture University

summary: In our previous studies, we found that the bursae of Fabricius in chickens infected with IBDV were severely atrophied and resulted in immune suppression in the chickens. Therefore, we decided to detect the differential expression of miRNA in chickens infected with IBDV by RNA-seq. We then used the data obtained from bursa of Fabricius RNA-seq for gene expression profiling. Our ultimate goal is to study the regulatory mechanisms of host mirnas on IBDV viruses or cells.

overall_design: Comparative miRNA expression profiling analysis of miRNA-seq data for bursa of Fabricius.

first: Mei

last: Leng

first: Feng

first: Wencheng

last: Lin


title: Effect of calcipotriol treatment, chaetocin treatment and VDR knockdown on gene expression in BJ cells

first: Xiangyang

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: College of Life Sciences

institute: Peking University

summary: To investigate the effect of calcipotriol treatment, chaetocin treatment and VDR knockdown on gene expression primary normal human fibroblasts, we treated BJ cells with 100 nM calcipotriol for 4 or 24 hours, 50 nM chaetocin for 24 hours, knocked down VDR with si RNA respectively. Then, we performed RNA-seq analysis.

overall_design: Differential expression genes are analyzed by comparing treated group with control group

first: Chuanmao

last: Zhang


title: Epigenetic data during proliferation and differentiation of C2C12 cells

city: Wuhan

first: Mingyang

last: Hu

address: No.1,Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: Hundreds of thousands or even millions active cis-regulatory elements like promoters and enhancers have been provide by different reasearches. But how to understanding the function of these cis-regulatory elements is a big challenge. Using C2C12 cell differentiation as a model, a number of regulatory elements that play an important role in myoblast differentiation were identified depend on ATAC-seq data. Then RNA-seq and Hi-C data was used to reveal how these regulatory elements regulate gene expression and affect the 3D structure of the genome.

overall_design: High-throughput sequencing (RNA-seq, ATAC-seq and Hi-C) of different time point C2C12 cells during C2C12 differentiation

first: Yunxia

last: Zhao

first: Xiaolong

last: Qi

first: Shuhong


title: Extensive sex differences in depression-linked variants functionally assayed in mouse brain [Hippocampus II]

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 660 S Euclid Ave, Campus Box 8232

department: Genetics

institute: Washington University in St. Louis

summary: Here, we selected >1000 variants from over 30 depression-associated loci using brain epigenomic data, and functionally assayed them using in vivo functional assays in the mouse brain to examine sex-by-genotype interactions. We identify extensive sex-by-allele effects in mature hippocampus, suggesting genetic risk and thus disease mechanisms may be distinct between the sexes. Unbiased informatics approaches indicated a role for nuclear hormone receptors, which was supported by .  Further, comparative analysis of allelic function in the neonatal mouse brain, during a key between developmental neonates during the masculinizing testosterone surge, and in the adult hippocampus—a region of interest in depression pathology—but not at 10 days old, a older hormonally quiescent developmental stage juveniles. Our study provides novel insights into depression genetics as influenced by age, biological sex, and cell type, and provides a framework for in vivo parallel assays at a scale not previously shown possible to functionally define interactions between sex and disease variation.

sample_organism:
Mus musculus
Adeno-associated virus 9

platform_organism:
Mus musculus
Adeno-associated virus 9

overall_design:
n=5-6 replicates each of AAV9-transduced adult mouse brain tissues (replication experiment): male total hippocampus, ovaries-intact female total hippocampus, ovariectomized female total hippocampus, male Vglut1+ translating-ribosome affinity purification immunoprecipitated RNA fraction, intact female Vglut1+  translating-ribosome affinity purification immunoprecipitated RNA fraction, ovariectomized female Vglut1+  translating-ribosome affinity purification immunoprecipitated RNA fraction.

Adult mice, all B6 background, were injected with AAV9 28 days before tissue collection for MPRA via TRAP and RNA-sequencing. Female mice also underwent either sham surgery or ovariectomy during the same surgical session as AAV9 administration.

Additional grant information: 571009 - Joseph Dougherty - Simons Foundation

first: Bernard

last: Mulvey

first: Din

last: Selmanovic


title: Single-cell RNA sequencing on the vein wall of mouse deep vein thrombosis

city: Madison

first: Bo

last: Liu

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin - Madison

summary: Deep vein thrombosis (DVT) is a common clinical problem, but its cellular and molecular mechanisms remain incompletely understood. We performed single-cell RNA sequencing (scRNA-seq) on the vein wall of mouse inferior vena cava (IVC) ligation model of deep vein thrombosis (DVT), to analyze the transcriptomic changes in the vein wall during acute venous thrombosis.

overall_design: IVC ligation or sham surgery was performed on 8-week-old male C57BL/6J mice. After 24 hours, mice were euthanized and perfused with PBS, the vein wall was collected and analyzed using scRNAseq.

first: Ting

last: Zhou

first: Huan

last: Yang

first: Elise

last: DeRoo


title: mRNAseq of murine PancOVA tumor cells after coculture with Tc17 conditioned -iCafs or Tc17 cells

city: Marburg

first: Magdalena

last: Huber

address: Hans-Meerweinstr. 02

department: Mikrobiology

institute: University of Marburg

summary: we examined the influence of Tc17 conditioned -iCafs or Tc17 cells on the in vitro differentiation of  murine PancOVA tumor cells

overall_design: PancOVA tumor cells  were seeded for 36 h in matrigel droplets with conditioned cells in quadruplicates.

first: M

first: V

last: Lutz

first: A

last: Brichkina

first: F

last: Neuhaus

first: H

last: Chung

first: T

last: Ruckenbrod

last: Raifer


title: Effects of paternal methionine supplementation on sperm DNA methylation and embryo transcriptome in sheep

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Dr.

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: We examined how a prepubertal methionine-enriched paternal diet affected sperm DNA methylation and its subsequent effects on embryo gene expression.

overall_design: Three treatment and three control rams were bred to seven ewes, and blastocysts were flushed for RNA extraction. Semen was collected from all rams and submitted for reduced representation bisulfite sequencing (RRBS) analysis.

first: Jessica

last: Townsend

first: Camila

last: Urbano Braz

first: Todd

last: Taylor


title: Characterizing role of striated-muscle specific ribosomal protein L3-like (Rpl3L) in mouse hearts

city: Cincinnati

first: Jeffery

last: Molkentin

state: Ohio

address: 240 Albert Sabin Way MLC 7020

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Overall goal: To elucidate the function served by Rpl3L in heart. Purpose of analysis: To determine effects of Rpl3L-deficiency on translational mRNA profile in heart. Experimental structure: Polysomes and monosomes were fractionated from cardiac ventricles and associated RNA extracted for library generation and differential gene expression analyses between wild-type and Rpl3L-null samples, using standard RNAseq pipeline.

overall_design: Whole ventricles from wild-type control and Rlp3L-null experimental hearts were pulverized and subsequently manually homogenized using Dounce homogenizers on ice in polysome lysis buffer (10 mM Tris-HCl at pH 7.5, 100 mM KCl, 5mM MgCl2, 0.5% w/ve sodium deoxycholate, 1% v/v IGEPAL CA-630, 10 mM DTT, 150 µg/ml cycloheximide, 1U/µl SUPERase In RNase inhibitor, and 1X HALT protease inhibitor in UltraPure molecular grade H2O). After serial centrifugation, supernatant from final 5-min spin at 16,000 x g at 4°C was layered on top of a 15 to 60% sucrose gradient column and centrifuged at 38,000 RPM for 125 min in a Optima XPN-90 ultracentrifuge (Beckman Coulter + SW 60 Ti swing bucket rotor). Total RNA from monosomal+polysomal fractions was extracted and subjected to downstream sequencing and bioinformatics analyses.

first: Kelly

last: Grimes

first: Vikram

last: Prasad


title: Defining the effects of Rpl3L-deficiency on transcriptional profiles of mouse hearts

summary:
The ribosomal protein L3-like (RPL3L) is a striated muscle-specific ribosomal protein, and mutations in human RPL3L are linked with childhood cardiomyopathy and age-related atrial fibrillation. However, the function served by this protein, a paralogue of the ubiquitously expressed RPL3 protein, remains poorly characterized in both heart and skeletal muscle. To address this, null mutant mice with the Rpl3L gene deleted were generated and studied. The purpose of this microarray analyses was to compare transcriptional profiles of the null mutant hearts (lacking RPL3L) with wild-type control hearts (expressing RpL3L).
We used microarrays to elucidate effects of Rpl3L deficiency on transcriptional profile of mouse hearts

overall_design: Hearts were harvested from control and experimental mice on the C57/BL6 background. Total RNA was isolated using the Trizol protocol and submitted to Affymetrix Clariom S array pipeline after quality control analysis using Agilent 2100 Bioanalyzer.


title: Thrombin exerts an inflammatory role in chondrocytes through activating the MEK-Erk1/2-Stat3 signaling pathway.

city: shanghai

first: daofang

last: ding

address: 1200 Cai Lun Road,Zhangjiang Hi-TechPark,Pudong New Area

institute: Shanghai University of Traditional Chinese Medicine

summary: Rat chondrocytes were divided into control group (RP), thrombin group (RPT), and thrombin plus inhibitor group (RPTi). The differential genes were identified by RNA-sequencing, and verified by western blot (WB), quantitative polymerase chain reaction (qPCR), cell immunofluorescence (IF), endoplasmic reticulum (ER) staining, functional enrichment analysis, and Gene Ontology (GO).

overall_design: To study the mechanism of thrombin regulating chondrocytes function based on RNA-sequencing and experimental verification.

first: Daofang

last: Ding


title: Transcriptional profiling of prefrontal cortex using single nuclei RNAseq

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

institute: Lund University

summary: This study aims to profile transposable element expression in the different cell types of the prefrontal-cortex in human post-mortem samples

overall_design: We performed 10x single nuclei RNAseq of prefrontal cortex post-mortem tissue to characterize transcriptional changes in gene and transposable elements expression in different cell types of the adult human brain

first: Raquel

last: Garza


title: Transcriptomic and epigenomic analyses of transposable elements in the healthy and diseased human brain


title: Epigenomic profiling of human postmortem cortical samples

summary: CUT&RUN was used to profile the epigenetic status of cells in human adult neurons (n=3) by measuring enirchment of H3K4me3 and H3K9me3 epigenetic marks over a non-targeting (IgG) control.

overall_design: CUT&RUN experiments (IgG, H3K4me3 and H3K9me3) were performed in nuclei of human adult NeuN+ nuclei (n=3)


title: Gene expression in duodenal biopsy samples from CVID enteropathy patients and healthy controls

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: A subgroup of CVID patients presents with gastrointestinal complications (enteropathy), which manifests in the duodenum as celiac like-diese ase. CVID enteropathy patients can present with severe histopathology in form of villous atrophy (CVID VA) or without VA (CVID noVA). RNAseq data from CVID VA and CVID noVA derived duodenal tissues were compared to each other and to healthy controls.

overall_design: Duodenal biopsies  derived from CVID patients and healthy controls during endoscopic procedures were dispersed using a homogenizer (T10, IKA) and total RNA was extracted using Rneasy Plus Mini Kit (Qiagen) according to manufacturer's instructions.

first: Melanie

last: Boerries

first: Valentina

last: Strohmeier

first: Susanne

last: Unger

first: Klaus

last: Warnatz


title: RNA sequencing approaches to identify the differential expression gene in the mPFC with AAV-mediated Npas4 shRNA expression

city: Charleston

first: Makoto

last: Taniguchi

state: SC

address: 173 Ashley ave, BSB410C

institute: Medical University of South Carolina

summary: Chronic social defeat stress induces anhedonia-like behavior deficits. We demonstrated that mPFC NPAS is requred for chronic social defeat stress-induced deficits in the sucrose preference and effort-based reward seeking behavior. We conducted the RNA-seq analysis for differential expression genes in the mouse mPFC samples of AAV-mediated Npas4 shRNA expression tissue.

overall_design: Examination of mRNA expression in the mouse mPFC of AAV-mediated Npas4 shRNA and control scramble shRNA expression.

first: Stefano

last: Berto

first: Brandon

last: Hughes

first: Christopher

last: Cowan


title: Highly synchronized cortical circuit dynamics revealed by a new mouse model of neuropathic pain

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

summary: The cerebral cortex plays a key role in the multi-dimensional human pain experience. However, the neural mechanisms mediating pain-related cortical activity remain largely unknown, particularly in primary somatosensory cortex (S1). We therefore developed a new animal model of trigeminal neuralgia, a prototypical neuropathic pain, which allowed us to evaluate pain-related cortical dynamics with unprecedented translational relevance. Our novel model (FLIT: Foramen Lacerum Impingement of Trigeminal-nerve) displayed robust clinically relevant trigeminal neuralgia-like behaviors, including asymmetric facial grimacing, dental pain-like behaviors, anxiety-like behavior, and sexual dysfunction, capturing many features of the human pain experience. Awake FLIT mice exhibited highly synchronized spontaneous population activity in S1, due to GABAergic interneuron hypoactivity. Remarkably, clinically effective treatments including carbamazepine and trigeminal nerve root decompression abrogated S1 synchronization and alleviated trigeminal neuralgia-like behaviors. These results reveal synchronized S1 activity as a new and important cortical substrate of neuropathic pain, which can be clinically targeted to provide effective therapy.

overall_design:
Mice cortical mRNA of the FLIT pain mouse model at day 3 and day 21 as well as contols at day 0

Mouse models:
FLIT: Foramen Lacerum Impingement of Trigeminal-nerve


title: Janus kinase-Inhibition modulates hepatitis E virus infection

status: Public on Feb 09 2023

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

summary: Background: Human hepatitis E virus (HEV) usually causes a self-limiting disease, but especially immunocompromised individuals are at risk to develop a chronic and severe course of infection. Janus kinase (JAK) inhibitors (JAKi) are a novel drug class for the treatment of autoimmune inflammatory rheumatic disease (AIRD). As JAKs play a key role in innate immunity, viral infections and reactivations are frequently reported during JAKi treatment in AIRD patients. The aim of this study was to characterize the influence of JAKis on HEV replication in vivo and in authentic cell culture models ex vivo.   Methods: We evaluated liver enzymes of an AIRD patient under JAKi therapy with hepatitis E and HEV infections in a cohort of  AIRD patients. Experiments with HEV were performed by infection of primary human hepatocytes (PHHs) followed by immunofluorescence staining of viral markers and transcriptomic analysis.    Results: Acute hepatitis was observed in a patient with AIRD and concomitant HEV infection. No acute infection could be detected in the AIRD cohort.  Infection experiments in PHHs displayed an up to 50-fold increase of progeny virus production during JAKi treatment and transcriptomic analysis revealed induction of antiviral programs  during infection. This induction  was perturbed in the presence of JAKis, concomitant with elevated HEV RNA levels.  Conclusion:  Therapeutic JAK inhibition increases HEV replication by modulating the HEV-triggered immune response. Therefore, clinical monitoring of HEV infection during JAKi treatment and in case of elevated liver enzymes should be considered.

overall_design: Plated primary human hepatocytes (PHH) of one representative donor were inoculated with HEV-3 p6 (MOI=1) and treated with 200 nM or 2 uM baricitinib for 72h.

first: Volker

last: Kinast

first: Ioana

last: Andreica

first: Gerrit

last: Ahrenstorf

first: André

last: Gömer

first: Carina

last: Elsner

first: Sarah

last: Schlienkamp

first: Jil

middle: A

last: Schrader

first: Rainer

middle: G

last: Ulrich

first: Ruth

last: Bröring

first: Florian

middle: W

last: Vondran

first: Patrick

last: Behrendt

first: Ulf

last: Dittmer

first: Axel

last: Hamprecht

first: Torsten

last: Witte

first: Xenofon

last: Baraliakos

first: Eike

last: Steinmann


title: Differential gene expression studies in a TGF beta induced EMT model of lung cancer A549 cell lines

city: Elizabeth City

first: Hirendranath

last: Banerjee

state: North Carolina

address: 1704 Weeksville Rd,

department: Department of Natural, Pharmacy and Health sciences

institute: Elizabeth City State University

summary: Investigate the difference in gene expression in TGFbeta induced EMT in lung cancer cell line A549 in comparison to uninduced A549 cells.

overall_design: Comparative gene expression profiling analysis of RNA Seq data for TGF beta induced A549 VIM RFP cell line.

first: Hirendra

first: Brent

last: Lake

first: Joseph

last: Hedley

first: Soumya

first: Anasua

first: Zahidur

last: Abedin

first: Narendra


title: Adaptive laboratory evolution with heterologous pgi

city: La Jolla

first: Cameron

last: Lamoureux

state: CA

address: 9500 Gilman Drive

institute: University of California San Diego

summary: We used RNA-seq to profile E. coli K-12 MG1655 strains subjected to adaptive laboratory evolution after knockout of endogenous glucose-6-phosphate isomerase (pgi) and subsequent expression of heterologous version of the pgi gene from Pseudomonas aeruginosa and Bacillus megaterium.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Growth of E. coli was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation.

first: Troy

last: Sandberg


title: Transcriptome profiling of  NCI-H2030 cell line treated with adagrasib, K-975 and adagrasib+K-975

city: Chilly Mazarin

first: Veeranagouda

last: Yaligara

address: Sanofi R&D

institute: Sanofi

summary: NCI-H2030 lines were seeded in 6-well plates in complete culture medium and cultured at densities allowing exponential growth: 50000 cells/well. After 24 h, compounds were added (DMOS, adagrasib (30 nM), K-975 (100 nM) and adagrasib (30 nM)+K-975 (100 nM)) at a final percentage of 0.2% DMSO. Twenty-four hours after compounds addition, cells were used for transcriptomic profiling.

overall_design: Transcriptomic proofing of DMOS, adagrasib (30 nM), K-975 (100 nM) and adagrasib (30 nM) + K-975 (100nM) with two technical and three biological replicates (4 conditions X 2 technical replicates X 3 biological replicates =24 samples).

first: S

last: Tammaccaro

first: Y

last: Veerangouda

first: J

middle: C

last: Le Bail

first: M

last: Didier

first: I

last: Valtingojer


title: Identification of the Zdhhc20 KO transcriptome

city: London

first: Goran

last: Tomic

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Metastasis is one of the defining features of pancreatic ductal adenocarcinoma (PDAC) that contributes to poor prognosis. In this study, the palmitoyl transferase ZDHHC20 was identified in an in vivo shRNA screen as critical for metastatic outgrowth, with no effect on proliferation and migration in vitro, or primary PDAC growth in mice. In this experiment, we sought to determine the changes in the transcriptome of Zdhhc20 KO cells that were previously generated using CRISPR/Cas9 and com,pare them with control cells.

overall_design: This experiment comprises three groups, with 3 biologial replicates each. The Zdhhc20 KO cells (clone E4) were generated using CRISPR/Cas9, whereas Control cells (Clone C5, WTCtrl) have also undergone nucleofection with the same gRNAs, but without successful editing and were used as a single-cell cloned control that expresses Zdhhc20. The parental cells (PDA50 Met, WT) were used as an additional control group.

first: Stefan

last: Boeing

first: Cory

last: Ocasio

first: Alice

middle: Y

last: Refermat

first: Edward

last: Tate

first: Julian

last: Downward


title: Resveratrol improves hepatic ischemia-reperfusion injury (HIRI) through inhibiting neutrophils via suppressing ERK signaling pathway

city: Beijing

first: Wang

middle: Ya

last: ning

state: Beijing

address: Yong An Road

department: internation medical center

institute: Beijing Friendship Hospital

summary:
Methods: Methods: To better understand the role of resveratrol in the regulation of neutrophils activation and function, neutrophils with or without resveratrol in the expose of LPS were compared in a transcriptome sequencing study. Total RNA was isolated from bone marrow and FACS-separated neutrophils. Transcriptome sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and sequenced on an Illumina Hiseq platform (Illumina, San Diego, CA). Sequences were aligned to the reference genome with TopHat and processed with Cufflinks, which quantifies each transcript in each sample using reference annotations produced bythe University of California Santa Cruz UCSC. Differentially expressed genes with a fold change of >=2.0 and p value<0.01 between resveratrol treated and control neutrophils were submitted to GO and KEGG enrichment analysis, which uses unbiased methods to assess pathway enrichment.
Results: Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that downregulated genes from resveratrol-stimulated neutrophils are involved in neutrophil migration, neutrophil chemotaxis, TNF signaling pathway and cytokine activity, among other. Compared to control neutrophils, neutrophils with resveratrol exhibited downregulated levels of cell survival related genes (Camkk1, Aqp1, Bcl2a1b, etc), cell cycle related genes (Ccnb1, Ccnb2, Cdc20, Cdk1, etc), adhesion and migration related genes (Cass4, Nectin4, Gp5, Gpr35, etc), and cytokines (Csf1, Csf3, Ccl2, Ccl7, Ccl12).

overall_design: Neutrophils mRNA profiles stimulated by LPS with or with resveratrol were generated by deep sequencing in duplicate, using Illumina HiSeq.

first: Yaning

last: Wang

first: Dong

last: Zhang


title: Impact of aging on meningeal gene expression

city: Basel

first: Albert

last: Neutzner

state: BS

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University Hospital Basel

summary: To investigate age-dependent differences in gene expression in mouse meniges

overall_design: Comparing gene expression between young and aged mice using RNA-seq

first: Melanie

first: Corina

last: Kohler

first: Stephan

last: Frank

first: Hanspeter

last: Killer


title: PP2Ac/STRN4 negatively regulates STING-Type I interferon signaling in tumor associated macrophages

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

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

overall_design: Refer to individual Series


title: Bulk RNA-seq of brain samples from fetuses with Tay-Sachs Disease

status: Public on Feb 08 2023

city: Bethesda

first: Cynthia

last: Tifft

state: MD

address: 10 Center Dr

department: MGB

institute: NIH/NHGRI

summary: Treatment of monogenic disorders has historically relied on symptomatic management with limited ability to target primary molecular deficits. However, recent advances in gene therapy and related technologies aim to correct these underlying deficiencies, raising the possibility of disease management or even prevention for diseases that can be treated pre-symptomatically. Tay–Sachs disease (TSD) would be one such candidate, however very little is known about the presymptomatic stage of TSD. To better understand the effects of TSD on brain development, we evaluated the transcriptomes of human fetal brain samples with biallelic pathogenic variants in HEXA. We identified dramatic changes in the transcriptome, suggesting a perturbation of normal development. We also observed a shift in the expression of the sphingolipid metabolic pathway away from production of the HEXA substrate, GM2 ganglioside, presumptively to compensate for dysfunction of the enzyme. However, we do not observe transcriptomic signatures of end-stage disease, suggesting that developmental perturbations precede neurodegeneration. To our knowledge, this is the first report of the relationship between fetal disease pathology in juvenile onset TSD and the analysis of gene expression in fetal TSD tissues. This study highlights the need to better understand the “pre-symptomatic” stage of disease to set realistic expectations for patients receiving early therapeutic intervention.

overall_design: To better understand the effects of Tay-Sachs disease on brain development, we evaluated the transcriptomes of human fetal brain samples with biallelic pathogenic variants in HEXA. This study is, to our knowledge, the first analysis of fetal tissues with juvenile-onset Tay-Sachs and the first investigation of gene expression in fetal Tay-Sachs tissues.

first: Sangwoo

middle: T

last: Han

first: Ashley

middle: K

last: Hirt

first: Elena-Raluca

last: Nicoli

first: Camilo

last: Toro

first: Richard

last: Proia


title: p53 regulates ethanol metabolism via ALDH2 modulating the development of alcoholic fatty liver disease

city: beijing

first: zhenxi

last: zhang

address: Dongdan Santiao No. 5

institute: PUMC

summary: The tumor suppressor p53 is critical for tumor suppression and other biological events. Yet, the regulatory role of p53 in alcohol-induced fatty liver remains unclear. Here, we show a role for p53 in regulating the ethanol metabolism via acetaldehyde dehydrogenase 2 (ALDH2), a key enzyme responsible for oxidization of alcohol. Through repressing ethanol oxidization, p53 suppresses intracellular levels of acetyl-CoA and histone acetylation, leading to the inhibition of the stearoyl-CoA desaturase-1 (SCD1) gene expression. Mechanistically, p53 directly binds to ALDH2 and prevents the formation of its active tetramer, and indirectly limits the production of pyruvate that promotes the activity of ALDH2. Notably, p53 deficient mice exhibit increased lipid accumulation, which can be reversed by ALDH2 depletion. Moreover, hepatic specific knockdown of SCD1 diminishes ethanol-induced fatty liver caused by p53 loss. By contrast, overexpression of SCD1 in liver promotes ethanol-induced fatty liver development in wildtype mice, while has mild effect on p53-/- or ALDH2-/- mice. Overall, our findings reveal a previously unrecognized function of p53 in alcohol-induced fatty liver, and uncover pyruvate as a natural regulator of ALDH2.

overall_design: This experiment was to detect the acetylation modification of histone in P53 knockout and wild-type mice treated with ethanol.

first: Yao

last: Pengbo

first: Zhang

last: Zhenxi

first: Du

last: Wenjing


title: Functional profiles of curatively treated adenoid cystic carcinoma unveil prognostic features and potentially targetable pathways.

city: Brescia

first: Stefano

last: Calza

state: Brescia

address: Viale Europa 11

department: DMMT

institute: University of Brescia

summary:
Adenoid cystic carcinoma (ACC) of salivary gland is an indolent tumor showing a propensity for delayed recurrence, with decreased survival rates. The identification of poor prognosis patients may help in defining molecular-based targeted strategies in this rare disease orphan of new treatments.
Through a gene expression microarray-based approach followed by GSE functional analysis the expression profile of 46 primary untreated ACC samples and of ACC(h-TERT) tumor cells was analyzed. Patients who experienced early relapse showed enrichment in proliferation-related gene sets, including the G2-M checkpoint, E2F and myc targets, and in gene sets related to IFN signaling and aberrant proteostasis (FDR < 0.1), indicating increased mitotic and transcriptional activity in aggressive ACC. Similar functions were enriched in ACC samples classified by immunohistochemical staining as p63-negative, which exhibited increased protein burden and activation of pro-survival stress response pathways compared to p63-positive tumors. Compared to ACC tissues, ACC(h-TERT) cells share transcriptional features of aggressive p63-negative tumors.
These data suggest association of specific pathway alterations with histopathological features of ACC, as recapitulated by p63 testing in patient prognostic stratification, anticipating new avenues for therapeutic intervention.

overall_design: Expression profiling by micorarray. A total of 46 ACC tissue samples were used. RNA was purified from FFPE sections and used for microarray experiments on Affymetrix platform.

first: Paolo

last: Bossi

first: Chiara

last: Romani