title: Effect of PGE2 pathway antagonists on APCmin/+ small intestine polyps

city: South San Francisco

first: Brian

last: Francica

state: CA

address: 2000 Sierra Point Hwy

institute: Tempest Therapeutics

summary: While the role of prostaglandin E2 (PGE2) in promoting malignant progression is well-established, how to optimally block the activity of PGE2 signaling remains to be demonstrated. Clinical trials with prostaglandin pathway targeted agents have shown activity but without sufficient significance or dose-limiting toxicities that have prevented approval. PGE2 signals through four receptors (EP1-4) to modulate tumor progression. EP2 and EP4 signaling exacerbates tumor pathology and is immunosuppressive through potentiating cAMP production. EP1 and EP3 signaling has the opposite effect through increasing IP3 and decreasing cAMP. Using available small molecule antagonists of single EP receptors, the COX-2 inhibitor celecoxib, or a novel dual EP2/EP4 antagonist generated in this investigation, we tested which approach to block PGE2 signaling optimally restored immunologic activity in mouse and human immune cells and antitumor activity in syngeneic, spontaneous and xenograft tumor models. We found that dual antagonism of EP2 and EP4 together significantly enhanced the activation of PGE2-suppressed mouse and human monocytes and CD8+ T cells in vitro as compared to single EP antagonists. CD8+ T cell activation was dampened by single EP1 and EP3 antagonists. Dual EP2/EP4 PGE2 receptor antagonists increased TME lymphocyte infiltration and significantly reduced disease burden in multiple tumor models, including in the adenomatous polyposis coli (APC)min+/- spontaneous colorectal tumor model, compared to celecoxib. These results support a hypothesis that redundancy of EP2 and EP4 receptor signaling necessitates a therapeutic strategy of dual blockade of EP2 and EP4. Here we describe TPST-1495, a first-in-class orally available small molecule dual EP2/EP4 antagonist.

overall_design: Animals were treated starting at 13 weeks of age for 3 weeks with TPST-1495 (100mg/kg BID, orally), E7046 (150mg/kg QD, orally), PF04418948 (100mg/kg QD, orally), or Celecoxib (60mg/kg QD, orally). After 3 weeks of treatment, small intestines were removed and polyps were resected and frozen at -80°C until seqencing.

first: Thomas

last: Dubensky


title: RNA-Seq analysis LEF1 or KDM4A knockdown effect on CAL-27 cells

status: Public on Aug 21 2023

city: Jinan

first: Lei

last: Chen

address: No.44-1 Wenhua Road West

department: Department of Orthodontics

country: China

institute: School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University

type: Expression profiling by high throughput sequencing

summary: To investigate the carcinogenesis function LEF1 or KDM4A in the regulation of oral squamous cell carcinoma, we used siRNA knockdown of LEF1 or KDM4A in CAL-27 cells.

overall_design: CAL-27 cells were transfected with  siLEF1, siKDM4A or control (n=3 for each group) for 48 hours. Total RNA was isolated using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality.

first: Yiming

last: Hou

first: Wenqian

last: Yu

last: Li


title: BS-seq and H3K9me2 ChIP-seq in Arabidopsis after flavopiridol (FLA) treatment

city: Beijing

first: Jincong

last: Zhou

address: Tsinghua Yuan

institute: Tsinghua University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Programmed constitutive heterochromatin silencing is essential for eukaryotic genome regulation, yet the initial step of this process is ambiguous. A large proportion of R-loops (RNA:DNA hybrids) had been unexpectedly identified within Arabidopsis pericentromeric heterochromatin with unknown functions. Through a genome-wide R-loop profiling screen, we find DDM1 (Decrease in DNA Methylation 1) is the primary restrictor of pericentromeric R-loops via its RNA:DNA helicase activity. Low levels of pericentromeric R-loops resolved by DDM1 co-transcriptionally can prime constitutive heterochromatin silencing. Furthermore, we demonstrate that DDM1 physically excludes histone H2A variant H2A.Z, and promotes H2A.W deposition for faithful heterochromatin initiation soon after R-loop clearance. The dual functions of DDM1 in R-loop resolution and H2A.Z eviction are essential for sperm nuclei structure maintenance in mature pollen. Our work unravels the co-transcriptional R-loop resolution coupled with accurate H2A variants deposition is the primary step of constitutive heterochromatin silencing in Arabidopsis, which might be conserved across eukaryotes.

overall_design: To test the impact of R-loop on pericentromeric heterochromain formation, we prevent directly the formation of R-loops with the transcriptional inhibitor in ddm1 and then profile the genome-wide DNA methylation with bisulfite sequencing (BS-seq) and H3K9me2 ChIP-seq.


title: Single-cell transcriptome atlas of Moso bamboo

first: Jian

last: Gao

address: No.8 Futong East Street, Chaoyang District, Beijing 100102, China

institute: International Center for Bamboo and Rattan

summary: Bamboo is a large Poaceae perennial with 1,642 species worldwide. We reported single-cell transcriptomes of 14,279 filtered single cells derived from the basal root tips of Moso bamboo.

overall_design: Protoplasts of basal root tips were isolated and used for scRNA-seq.

first: Zhanchao

last: Cheng


title: Extracellular vesicle-based cancer panels diagnose glioblastomas with high sensitivity and specificity

city: Minneapolis

first: Charles

middle: Scott

last: Cameron

state: Minnesota

address: 420 Delaware St SE

department: Pediatrics

country: USA

institute: University of Minnesota-Twin Cities,

summary: This study focused on the development of serum extracellular vesicle (EV)-based glioblastoma tumor marker panels that can be used in the clinic to diagnose glioblastomas.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for serum samples from glioblastoma and control patients.

first: Saydam

last: Okay

first: Melike

last: Mut

first: Zelal

last: Adiguzel

first: Henzler

last: Christine


title: The m6A reader YTHDF1 attenuates fulminant hepatitis via MFG-E8 translation in an m6A dependent manner [RNA-seq]

city: xi'an

first: mengyun

last: ke

address: No 277 west yanta road

institute: the first affiliated hospital of xi'an jiaotong university

summary: We report the application of RNA-Seq, m6A-Seq and RIP-Seq to find out YTHDF1 regulate the target genes.

overall_design: Construction of YTHDF1 gene knockdown cell line by using lentivirus infection.

first: Mengyun

last: Ke


title: The m6A reader YTHDF1 attenuates fulminant hepatitis via MFG-E8 translation in an m6A dependent manner

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

overall_design: Refer to individual Series


title: Targeting ITGB4/SOX2-driven cancer stem cells using proteasome inhibitors

city: Duarte

middle: David

last: Warden

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

institute: City of Hope

summary: The transcription factor SOX2 required for pluripotency, is amplified in 40% of the lung squamous cell carcinoma (LUSC) cases. However, a long-term survival analysis using TCGA cohorts of LUSC patients revealed no significant differences between high versus low SOX2 expressing cases. The treatment options for irresectable LUSC are limited to chemotherapy where carboplatin or cisplatin is given in combination with gemcitabine. However, drug resistance remains a serious concern. We previously showed integrin β4 (ITGB4) and paxillin (PXN) play a critical role in platinum resistance in LUAD. Heterogenous NSCLC cells that up-regulate ITGB4 and PXN epigenetically, can switch phenotypes from cisplatin sensitive to tolerant. However, the significance of ITGB4 expression in SOX2 driven cancer stem cells (CSCs) in NSCLC remains unappreciated. In this study, we isolated CSCs from LUSC patients and characterized them. We elucidated the significance of ITGB4 and SOX2 expression in maintaining the stemness of CSCs and their response to cisplatin treatment. Finally, we showed that the proteasome inhibitor carfilzomib (CFZ) targets SOX2 dependent CSCs and this function of CFZ is independent of its proteasome inhibitory function.

overall_design:
Triplicates are provided for Control, Actinomycin D, and Carfilzomib (CFZ) in 3 Cell Lines (H520, SBC5, and COH2)
>>>Raw data for human samples not available due to either unknown consent or lack of explicit consent<<<

first: Atish

last: Mohanty

first: Ravi

last: Salgia


title: The m6A reader YTHDF1 attenuates fulminant hepatitis via MFG-E8 translation in an m6A dependent manner [m6a-seq]


title: scRNA-Seq analysis of unperturbed and perturbed HSC, MPP1 and MPP2 cells of miR-221/222-proficient and deficient mice.

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

country: Germany

summary: We have studied the effect of miR-221/222-deficiency on early hematopoietic stem and progenitor cell quiescence activation in unperturbed and after short-term perturbed hematopoiesis.

overall_design: Comparative gene expression profiling analysis on unperturbed and perturbed HSC, MPP1 and MPP2 cell populations of miR-221/222-proficient and deficient mice  using single-cell RNA-Seq.

first: Peter

middle: K

last: Jani

first: Georg

last: Petkau

first: Yohei

last: Kawano

first: Uwe

last: Klemm

first: Gabriela

last: Guerra

first: Gitta

middle: A

last: Heinz

first: Pawel

last: Durek

first: Mir-Farzin

last: Mashreghi

first: Fritz

last: Melchers


title: scRNA-Seq analysis of lineage negative compartments of miR-221/222-proficient and deficient mice.

summary: To study the effect of miR-221/222-deficiency on early hematopoietic lineage differentiation pathways on sorted multipotent progenitor (MPP), common lymphoid progenitor (CLP),  lineage-ckit+Sca1- and lineage-ckit-Sca1- populations of miRNA-proficient and deficient mice.

overall_design: Comparative gene expression profiling analysis on MPP, CLP, lineage-ckit+Sca1- and lineage-ckit-Sca1- cell populations of miR-221/222-proficient and deficient mice  using single-cell RNA-Seq.


title: Development of a glucoamylase hyper-production platform in thermophilic fungus Myceliophthora thermophila via the rational redesigning and engineering manipulation

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

institute: TIB CAS

summary: The development of proteins hyper-production platform in thermophilic fungus Myceliophthora thermophila is essential for both molecular basis understanding and industrial process. Herein the glucoamylase hyper-production strain MtGM12 was generated from our previously strain MtYM6 via genetically engineering. Transcriptional profiling analyses revealed that the amylolytic gene expression levels were significantly up-regulated in the MtGM12 than in MtWT.

overall_design: mRNA profiles of Myceliophthora thermophila cells exposed to 1d starch and 2d starch.

first: Qian

last: Liu

first: Defei

first: Zhijian

last: Zhu

first: Chaoguang

last: Tian


title: Characterization of miR-34 effectors in colorectal cancer cells.

city: Munich

first: Markus

last: Kaller

address: Thalkirchner Str. 36

institute: LMU Munich

summary: MiR-34a and miR-34b/c encoding genes represent direct targets of the p53 tumor suppressor. MiR-34a/b/c mediate tumor suppression by p53 via down-regulation of the expression of specific target mRNAs. Here, we characterized the miR-34 effectors using a CRISPR/Cas9-approach in HCT116 cells with or without 5-FU treatment.

overall_design: HCT116 wildtype cells and HCT116 miR-34a/b/c-KO cells were treated with DMSO or 5-FU for 48 hours. For each group, RNAs from three biological replicates were obtained.

first: Heiko

last: Hermeking


title: The m6A reader YTHDF1 attenuates fulminant hepatitis via MFG-E8 translation in an m6A dependent manner [RIP-seq]

first: mengyun

last: ke

first: Mengyun

last: Ke


title: scRNA-Seq analysis of HSC, MPP1 and MPP2 cells after serial transplantation of miR-221/222-proficient and deficient HSC.

first: Frederik

last: Heinrich

summary: We have studied the effect of miR-221/222-deficiency on early hematopoietic stem and progenitor compartments after serial transplantation of miRNA-proficient and deficient HSC.

overall_design: Comparative gene expression profiling analysis on HSC, MPP1 and MPP2 cell populations after serial transplantation of miR-221/222-proficient and deficient HSC  using single-cell RNA-Seq.

first: Peter

last: Jani

first: Georg


title: SREBP2 regulates endothelial response to inflammation via direct transcriptional activation of KLF6

city: Tucson

first: Casey

last: Romanoski

state: AZ

address: 1230 N Cherry Ave

institute: U. Arizona

summary: Cholesterol homeostasis plays a central role in disease pathogenesis in chronic disorders such as cardiovascular and kidney diseases. The transcription factor SREBP2 is the main regulator of cholesterol metabolism and is central to the mechanism of action of lipid lowering drugs, such as statins, that are responsible for the largest overall reduction in cardiovascular risk and mortality in humans with atherosclerotic cardiovascular disease. Recently, SREBP2 has been implicated in both the innate and adaptive immune responses by upregulation of cholesterol flux or via direct transcriptional activation of pro-inflammatory genes in leukocytes. Here, we investigate the role of SREBP2 in endothelial cells (ECs), since ECs are at the interface of circulating lipids with tissues and are activated in response to damage and inflammation. The loss of SREBP2 in cultured human ECs results in significant alterations of the transcriptional response to inflammatory cytokines whereas SREBF2 knockdown inhibits the transcription and secretion of pro-inflammatory chemokines but amplifies type I interferon response genes. Furthermore, we show that SREBP2 regulates chemokine expression not through enhancement of endogenous cholesterol synthesis or lipoprotein uptake, but partially through direct transcriptional activation. Chromatin immunoprecipitation sequencing (ChIP-seq) of endogenous SREBP2 reveals the SREBP2 bound to the promoter regions of classical response genes as well as two non-classical sterol responsive genes involved in immune modulation, BHLHE40 and KLF6. Overexpression of SREBP2 upregulated both BHLHE40 and KLF6 transcripts independent of inflammatory stress and the transcription of these genes were found to be sensitive to cellular cholesterol levels. Of these two targets, we found that KLF6 was responsible for the amplification of chemokine expression highlighting a tight relationship between cholesterol homeostasis and inflammatory phenotypes in ECs.

overall_design: SREBP2 ChIP-seq was performed on 3 separate donor lines of HUVEC treated with or without TNF alpha

first: Joseph

middle: M

last: Fowler

first: Nabil

middle: E

last: Boutagy

first: Rong

last: Zhang

first: Daiki

last: Horikami

first: Michael

middle: B

last: Whalen

first: William

middle: C

last: Sessa


title: SRSF3/AMOTL1 Splicing Axis Promotes the Tumorigenesis of Nasopharyngeal Carcinoma through Regulating the Nucleus Translocation of YAP1

city: Guangzhou

first: Jin-Xin

last: Bei

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District, Guanzhou, P.R. China

institute: Sun Yat-sen University Cancer Center

summary: Dysregulation of serine/arginine splicing factors (SRSFs) and thereby the abnormal alternative splicing (AS) has been widely implicated in the development of multiple cancers, but scarcely investigated in nasopharyngeal carcinoma (NPC). Here we examine the expression of 12 classical SRSFs between 87 NPC and 10 control samples, revealing a significant upregulation of SRSF3 and its association with worse prognosis in NPC. Functional assays demonstrate that SRSF3 knockdown markedly inhibits the proliferation, migration, tumorigenesis and induces apoptosis in NPC cells, suggesting its oncogenic role in NPC progression. Transcriptome analysis reveals 1 934 SRSF3-regulated AS events in genes involved in cell cycle and mRNA metabolism, among which the generation of a long isoform of AMOTL1 (AMOTL1-L) is further verified through a direct bond of SRSF3 RRM domain with the exon 12 of AMOTL1 to promote the exon inclusion. Functional studies reveal that AMOTL1-L could promote the proliferation and migration of NPC cells, nor did AMOTL1-S. Moreover, overexpression of AMOTL1-L significantly rescues the abovementioned inhibitory effects of SRSF3 knockdown, nor did AMOTL1-S. Furthermore, compared with AMOTL1-S, AMOTL1-L has a localization preference in the intracellular than the cell membrane, leading to a stronger interaction with YAP1 to promote its translocation to nucleus. Taken together, our findings identify SRSF3/AMOTL1 as a novel alternative splicing axis with pivotal roles in NPC development, which could be served as promising prognostic biomarkers and therapeutic targets of NPC.

overall_design: We performed transcriptome sequencing to explore SRSF3-regulated  alternative splicing events in NPC.

first: Xiaochen

last: Xu

first: Jiaxin

last: Jiang

first: Yaqing

last: Zhou

first: Shuai

last: He

first: Yang

first: Panpan

last: Wei

first: Jian

last: Sun

first: Chunling

last: Luo


title: The specific DNA methylation landscape in Focal Cortical Dysplasia ILAE Type 3D

city: Erlangen

first: Katja

last: Kobow

state: Bavaria

address: Schwabachanlage 6

department: Neuropathology

institute: Universitätsklinikum Erlangen

type: Methylation profiling by genome tiling array

summary: Focal Cortical Dysplasia (FCD) is a frequent cause of drug-resistant focal epilepsy in children and young adults. The international FCD classifications of 2011 and 2022 have identified several clinico-pathological subtypes, either occurring isolated, i.e., FCD ILAE Type 1 or 2, or in association with a principal cortical lesion, i.e., FCD Type 3. Here, we addressed the DNA methylation signature of a previously described new subtype of FCD 3D occurring in the occipital lobe of very young children and microscopically defined by neuronal cell loss in cortical layer 4. We studied the DNA methylation profile using 850K BeadChip arrays in a retrospective cohort of 104 patients with FCD 1A, 2A, 2B, 3D, TLE without FCD, and 16 postmortem specimens without neurological disorders as controls, operated in China or in Germany. DNA was extracted from formalin-fixed paraffin-embedded tissue blocks with microscopically confirmed lesions, and DNA methylation profiles were bioinformatically analyzed with a recently developed deep learning algorithm. Our results revealed a distinct position of FCD 3D in the DNA methylation map of common FCD subtypes, also different from non-FCD epilepsy surgery controls or non-epileptic postmortem controls. Within the FCD 3D cohort, the DNA methylation signature separated three histopathology subtypes, i.e., fibrotic scarring around porencephalic cysts, loss of layer 4, and Rasmussen encephalitis. Differential methylation in FCD 3D with loss of layer 4 specifically mapped to biological pathways related to neurodegeneration, biogenesis of ECM components, axon guidance, and regulation of the actin cytoskeleton. Our data suggest that DNA methylation signatures in cortical malformations are not only of diagnostic value but also phenotypically relevant, providing the molecular underpinnings of structural and histopathological features associated with epilepsy. Further studies will be necessary to confirm these results and clarify their functional relevance and epileptogenic potential in these difficult-to-treat children.

overall_design:
Bisulphite converted DNA from 7 samples was hybridised to Illumina Infinium 850K Human Methylation Beadchip arrays

Please note that this records represent control samples only. The FCD 3D samples and all other samples were published previously in the OMIX (https://ngdc.cncb.ac.cn/omix, under the accession number PRJCA009245 and GEO under accession number: GSE185090 and GSE156374).

first: Dan-Dan

last: Wang

first: Mitali

last: Katoch

first: Samir

last: Jabari

first: Ingmar

last: Blumcke

first: David

last: Blumenthal

first: De-Hong

last: Lu

first: Roland

last: Coras

first: Yu

middle: J

first: Jie

last: Shi

first: Wen-Jing

first: Ji-Dong

first: Yue-Shan

last: Piao


title: Transcriptomic profile of blood cells exposed to particulate matter

city: Botucatu

first: Geysson Javier

middle: Fernandez

last: Garcia

state: Sao Paulo

address: Departamento morfologia IBB UNESPRubiao Junior

country: Brazil

institute: UNESP

summary: Here we used next generation sequencing (NGS), to determine the transcriptional profile of blood cells exposed to particulate matter to contribute to the clarification of the importance of deregulated molecules in the molecular pathways involved in the inflammation. For this, blood cells from six adult healthy donors were treated with particulate matter.

overall_design: Samples we in vitro exposed to particulate matter for 48 hours. RNA was extracted from each sample and forming two groups (treated vs untreated control). Each sample was used to build the sequencing libraries. The cDNA libraries were built with the Kapa Stranded mRNA Sample Preparation Kit and sequencing took place on the NextSeq 500 System platform (Illumina, USA)

first: Geysson

last: Fernandez

first: Marin-Palma

last: Damariz

first: Juan

last: Hernandez

first: Natalia

last: Taborda


title: DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis

first: Jincong

last: Zhou


title: DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis [ssDRIP-seq, WGBS-seq, ChIP-seq]

overall_design: We conducted ssDRIP-seq, BS-seq and ChIP-seq with Arabidopsis seedlings to reveal genome-wide relationship among R-loops, H2A.Z and heterchromatin formation.


title: Adult-onset loss of hepatocyte growth hormone receptor (GHR) signaling increases steatosis, associated with enhanced glucokinase activity, de novo lipogenesis (DNL) and pathway selective hepatic insulin resistance

city: Boston

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: RNA-seq analysis of livers from control mice, mice with adult onset, hepatocyte-specific GH receptor (GHR) deficiency, and GHR-deficient mice combined with IGF1 expression or expression of constitutively active ('CA') STAT5b. This dataset is part of a large study showing that adult-onset loss of hepatocyte GHR signaling increases steatosis, associated with enhanced glucokinase activity, de novo lipogenesis (DNL) and pathway selective hepatic insulin resistance.

overall_design: We analyzed total RNA from male livers (6 mice/group) from GHR intact-control mice and adult-onset, specific GHR knockdown mice, without (aHepGHRkd) or with hepatic reconstitution of IGF1 (aHepGHRkd + 2.0*E11 AAV8-TBGp-rIGF1) or STAT5bCA (aHepGHRkd + 0.75*E11 AAV8-TBGp-STAT5bCA)

first: Rhonda

middle: D

last: Kineman

first: Mari

last: Vázquez Borrego

first: Mercedes

last: Del Rio Moreno

first: Maxim

last: Pyatkov


title: Gene expression profile at single cell level of cells from healthy and BV-induced murine liver.

first: Pan

last: Shen

address: Courtyard 27, Taiping Road

institute: BIRM

summary:
Bavachin (BV), a therapeutic phytoestrogen in Fructus Psoraleae (FP), has been used in various diseases. However, the molecular mechanism of BV hepatotoxicity reported by many studies remains unclear.
Here, we used single cell RNA sequencing (scRNA-seq) to explore the early cytotoxicity induced by BV in the liver.

overall_design: Liver cells from healthy and BV-induced mice were isolated and analyzed using scRNAseq.

first: Zhi-jie

last: Bai

first: Ning-ning

last: Wang

first: Lei

first: Zhe-xin

last: Ni

first: De-zhi

last: Sun

first: Cong-shu

last: Huang

first: Wei

first: Bo-li

last: Zhang

first: Yue

last: Gao


title: DDM1-facilitated R-loop resolution and H2A.Z exclusion primes heterochromatin formation in Arabidopsis [ssDRIP-seq, ChIP-seq, pNET-seq, ATAC-seq]

summary: Programmed constitutive heterochromatin silencing is essential for eukaryotic genome regulation, yet the initial step of this process is ambiguous. A large proportion of R-loops (RNA:DNA hybrids) had been unexpectedly identified within Arabidopsis pericentromeric heterochromatin with unknown functions. Through a genome-wide R-loop profiling screen, we find DDM1 (Decrease in DNA Methylation 1) is the primary restrictor of pericentromeric R-loops via its RNA:DNA helicase activity. Low levels of pericentromeric R-loops resolved by DDM1 co-transcriptionally can prime constitutive heterochromatin silencing. Furthermore, we demonstrate that DDM1 physically excludes histone H2A variant H2A.Z, and promotes H2A.W deposition for faithful heterochromatin initiation soon after R-loop clearance. The dual functions of DDM1 in R-loop resolution and H2A.Z eviction are essential for sperm nuclei structure maintenance in mature pollen. Our work unravels the co-transcriptional R-loop resolution coupled with accurate H2A variants deposition is the primary step of constitutive heterochromatin silencing in Arabidopsis, which might be conserved across eukaryotes.

overall_design: To compare the genome-wide R-loop levels among different genotypes , ssDRIP-seq was conducted using 12-day-old seedlings under long day conditions.  Native ChIP (see details in extract protocol) -seqs were conducted to examine the enrichment levels of H2A.W-Flag, H2A.Z, H3K27me1 and H3K9me2 in wide-type and ddm1 mutant (12-day-old seedlings under long day conditions). To test the nascent RNA abundance in wide-type and ddm1 mutant, pNET-seq was conducted using 12-day-old seedlings under long day conditions. And ATAC-seq was used to compare the chromatin condensation state between wide-type and ddm1 mutant.


title: WGBS-seq, CUTANDRUN, ATAC-seq of urothelial stem cells isolated from Juvenile Naïve C3H/HeN mice

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: To study epigenetic changes in mouse bladder urothelial cells with different infection histories, urothelial stem cells (USCs) isolated from C3H/HeN mice with different infection histories (Adult Naive, Resolved, and Sensitized) were used to perform WGBS , ATAC, and CUT&RUN for comparison.

overall_design: USCs isolated from mice with various infection histories were characterized using ATAC-seq, WGBS-seq and cutandrun for active and repressive histone modifications

first: Seongmi

last: Russell

first: Jessica

last: Harrison

first: Xiaoyun

last: Xing

first: Ting

first: Scott

last: Hulgren


title: LINE1 TGS mechanism mediated by SETDB1-AGO2 complex in human somatic cells [RNA-seq]

city: Daejeon

first: Kyuheum

last: Jeon

address: 125 Gwahak-ro

country: South Korea

institute: KRIBB

summary: LINE1s are abundant retroelements comprising 17% of human genome. Naturally, genomic LINE1s are tightly repressed by epigenetic mechanism; however, if relieved, they can be detrimental to genome stability by their transposition capability. So, a supervising mechanism that quickly re-represses the leaky LINE1s is demanded. Here we show that de-repressed LINE1s generate small RNAs, L1-siRNAs, which SETDB1 and AGO2 recognize, then move into searching for a transcript with sequence complementarity, and ultimately re-install a repression mechanism at LINE1 5’-untranslated region (5’UTR) by depositing trimethyl-H3K9 (H3K9me3). Immunoprecipitation (IP) results showed that SETDB1, AGO2, and L1-siRNA bound to each other and Chromatin-IP-seq and small-RNA-seq results demonstrated that they sat at the same locus within the 5’UTR. SETDB1, AGO2, and L1-siRNA all were necessary for LINE1 repression, particularly the evolutionary young and transposition-competent families such as L1HS/L1PA1 and L1PA2. KAP1, which frequently partners with SETDB1 for silencing local chromatin, was dispensible for the repression of young L1PAs. Our findings indicate that, as a surveillance mechanism, the L1-siRNA-triggered, SETDB1-AGO2-effected repair of epigenetic errors at the 5’UTR establishes a homeostatic re-repression mechanism on inadvertently de-repressed LINE1 copies over the genome.

overall_design: Comparative gene expression profiling analysis of HAP1 cells and its SETDB1 KO derivative.

first: Byungkuk

last: Min

first: Jung

middle: S

last: Park

first: Yong-Kook

last: Kang


title: LINE1 TGS mechanism mediated by SETDB1-AGO2 complex in human somatic cells

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Refer to individual Series


title: LINE1 TGS mechanism mediated by SETDB1-AGO2 complex in human somatic cells [ChIP-seq]

overall_design: Genome binding/occupancy profiling of SETDB1, AGO2, KAP1 and H3K9me3.


title: Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [ChIPmentation]

city: Randwick

first: Julie

last: Thoms

state: NSW

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

department: Adult Cancer Program

country: Australia

institute: UNSW Sydney

summary: Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay of transcription factors (TFs) to regulate their differentiation into mature blood cells. A heptad of TFs - FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2 - has been shown to bind to regulatory elements in bulk CD34+ HSPCs. However, whether specific combinations of these TFs have distinct roles in regulating hematopoietic differentiation remained unknown. In this study, we mapped the genome-wide binding profiles of these TFs and other chromatin-associated markers in distinct HSPC subsets (HSC, CMP, GMP, MEP). We found that the heptad occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type specific gene expression. Moreover, we observed distinct regulatory elements that were enriched with specific combinations of TFs, such as stem-cell specific elements with ERG, and myeloid and megakaryocyte-erythroid specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. These findings suggest that specific combinations of TFs play critical roles in the regulation of hematopoietic differentiation, and provide a valuable resource for the development of targeted therapies to manipulate specific HSPC subsets.

overall_design: ChIPmentation

first: Shruthi

last: Subramanian

first: John

last: Pimanda


title: N6-methyladenosine circRNA Epitranscriptomic Microarray of  human nucleus pulposus in  intervertebral disc degeneration

city: Shanghai

first: Zhenhao

last: Chen

address: 12 Mid- Wulumuqi Road

department: Department of Orthopedics

institute: Huashan Hospital, Fudan university

summary: It is well documented that low back pain is a common condition and the leading cause of disability globally. A widely recognised contributor to low back pain is intervertebral disc degeneration (IVDD), which is the major cause of a series of degenerative disc diseases. Recently, it has been reported that circRNAs are involved in the development of IVDD. However, the mechanisms by which m6A modifies circRNA in nucleus pulposus cells remain poorly understood. Here, we aim to identify differentially expressed m6A circRNAs in degenerative nucleus pulposus cells and figure out how the circRNAs regulate IVDD progression and the m6A methylation functions.

overall_design: 4 degenerative human  nucleus pulposus and 4 healthy  human  nucleus pulposus

first: Hongli

last: Wang

first: Jianyuan

last: Jiang

first: Fei

last: Zou

first: Jian

last: Song


title: Gene expression changes induced by SFRP2 silencing in RB383 retinoblastoma cells

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: To gain insight into signaling downstream of SFRP2 in retinoblastoma,  we used siRNA to silence SFRP2 in RB383 retinoblastoma cells and assessed the resulting gene expression changes at 24 hours and 48 hours after siRNA transfection.

overall_design: RB383 cells were were transfected with either scrambled-siRNA or SFRP2-siRNA (Dharmacon) for 24 and 48 hours. Transfection was carried out using Lipofectamine™ RNAiMAX Transfection Reagent (Thermo Fisher) according to the manufacturer’s protocol. After 24 and 48 hours, cells were harvested and total RNA was extracted using TRIzol reagent (Invitrogen). For whole-genome transcriptome profiling, four libraries were generated from total RNA using a TruSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol (Illumina Inc.). Samples were sequenced on the Illumina HiSeq 3000 platform (Illumina Inc.) using the 51 base-pair single-read (50SR) sequencing module.

first: Panneerselvam

last: Jayabal

first: Fuchun

last: Zhou

first: Yuzuru

last: Shiio

first: Zhao

last: Lai


title: Co-condensation with photoexcited Cryptochromes facilitates MOS4-associated complex subunits 3A/3B to antagonize HY5 activities during photomorphogenesis in Arabidopsis

city: Chicago

first: Bochen

address: Department of Chemistry

institute: The University of Chicago

summary: Cryptochromes (CRYs) is known as the key blue light receptors that promote photomorphogenesis in Arabidopsis, but to date, the underlying mechanisms are still not fully understood. Through interrogating the CRY2 interactome, we identified MOS4-ASSOCIATED COMPLEX subunits 3A and 3B (MAC3A and MAC3B) as blue light-independent CRY2 interacting partners. MAC3A/B proteins could be assembled into liquid nuclear condensates of CRYs in a blue light-dependent manner. Hypocotyl elongation is markedly repressed in mac3ab double knock-out mutants under various light conditions, which uncovers a previously unknown role of MAC3A/B as negative regulators in plant photomorphogenesis. Our results also uncover the noncanonical activities of MAC3A as the DNA-binding proteins that regulate transcription. Genome-wide mapping of MAC3A-binding sites reveals that blue light facilitates the binding of MAC3A to its targets, which is weakened in cry1cry2 mutants, suggesting that CRYs may enhance MAC3A activities in blue light to negatively influence photomorphogenesis. Interestingly, we observe that the genomic binding sites of MAC3A and HY5 are largely overlapped, and physical interactions between MAC3A and HY5 are detected as well. In addition, the in vitro DNA-binding assay shows that both proteins compete for the same DNA probe. These results indicate that MAC3A may antagonize the function of HY5 by competing for the common binding sites across the genome. Taken together, we propose that cryptochromes may fine-tune Arabidopsis photomorphogenesis by balancing the positive and negative effects on HY5 activities.

overall_design: Charaterize genome-wide distribution of MAC3A in Arabidopsis.


title: LINE1 TGS mechanism mediated by SETDB1-AGO2 complex in human somatic cells [small RNA-seq]

first: Kyuheum

overall_design: Comparative small RNA expression profiling analysis for HAP1 cells and its SETDB1 KO derivative.

first: Byungkuk


title: Transcriptional activity of genes in yellow lupine seeds, cultivar Taper

city: Piotrków Trybunalski

first: Waldemar

last: Wojciechowski

address: ul. Gliniana 14

country: Poland

institute: Generiks Sp. z o.o. Sp. k.

summary: Obtaining large amounts of protein of plant origin is an indispensable prospect from the perspective of environmental changes taking place on earth. However, it is extremely important to be able to diversify the sources of plant proteins, which is affected, among other things, by their local availability, sensitivity to specific climatic conditions of the region, and the qualitative differentiation of amino acids. A lot of data show that higher amounts of protein with improved properties can be obtained from species native to a specific climate zone. In Europe, such species include yellow lupine (Lupinus luteus L.), narrow-leaved lupine (Lupinus angustifolius) and white lupine (Lupinus albus L.). In the case of yellow lupine, the amount may be up to 40% of the dry weight of the seeds. Additionally, these proteins have a favorable amino acid composition. Detailed understanding of the mechanisms and the process of accumulating storage proteins is invaluable for the study of the use of this species to increase the production of plant proteins. In the presented work, yellow lupine seeds cultivar Taper, which were cultivated in the field, were used for the research. Therefore, the aim of the research was to identify genes encoding storage proteins (conglutins) and genes regulating the process of accumulation of storage proteins in the seeds of yellow lupine cultivar Taper in the following days of their development.

overall_design: The research material consisted of seeds of the yellow lupine cultivar Taper collected at 10, 20 and 30 DAA (Day After Anthesis). For each variant, about 250 seeds were collected from about 50 pods of ten plants. Three biological replicates were performed for each variant. The obtained results were compared between the analyzed variants.

first: Natalia

last: Klajn

first: Paulina

last: Glazińska


title: Fetal hematopoietic stem cells subjected to vitamin D deficiency in utero, conferred permanent insulin resistance to vitamin D-sufficient mice

first: Daofeng

last: Li

summary: genome wide methylation data include: MeDIP-seq and MRE-seq in Vitamin D deficient and sufficient bone marrow cells

overall_design: J, Oh

first: C

last: Bernal-Mizrachi

first: Xiaoyun

last: Xing

first: Ting


title: LncRNA and mRNA expression data from Control or IL-8 overexpressed MCF7 cells

first: Yu

address: No 58, Zhongshan 2nd street

department: Division of Vascular Surgery

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

summary: Metastasis is one of the pivotal causes of high breast cancer mortality, which is consist of epithelial-to-mesenchymal transition (EMT), migration, invasion. While long noncoding RNAs (lncRNAs) are implicated in a variety of diseases, their role in breast cancer is not well understood. IL-8 has been reported to induce EMT of breast cancer cell. In this study, we used microarrays to identify dysregulated  lncRNAs and mRNAs underlying IL-8-induced EMT.

overall_design: The differentially expressed lncRNAs and mRNAs between control MCF7 cells and  IL-8 overexpressed MCF7 cells were examined using Agilent Human lncRNA 4*180K

first: Duanyang

last: Zhai

last: Shao

first: Ying

last: Lin


title: WT mouse transcriptome changes with age

city: San Francisco

first: Tom

last: McMahon

address: 1550 4th Street

department: Neurology

institute: University of California San Francisco

summary: We collected the hypothalamus of mice of different ages to ascertain the biomarkers of aging via comparing the transcriptome changes between old and young WT (C57BL/6J) mice.

overall_design: Hypothalamus of three P5 old, three 3-week old, four 4-week old, four 5-week old, three 2-month old, three 6-month old, three 12-month old, three 18-month old and three 24-month old mice.

last: Mcmahon

first: Zenghua

last: Fan

first: Qing

last: Dong

middle: H

last: Fu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Canine Cytotoxic T Cells Transcriptome

city: Taipei

first: Chen-Si

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Veterinary Medicine

country: Taiwan

institute: Nationwide Taiwan University

summary: This study aims to investigate the functions of cDLBCL-derived exosomes on cytotoxic T cells among peripheral blood mononuclear cells (PBMCs) in healthy dogs. Through RNA next-generation sequencing (NGS) and bioinformatics. Reveal the differences between the two groups with or without exosomes treatment. It includes the gene function list, protein profiles, the differentially expressed genes, the biological pathways, and the analysis of networks.

overall_design: Harvested canine CD8+ T cells to perform Transcriptome Next Generation Sequencing after co-culturing with 50 ug/ mL lymphoma exosomes for 48 hours. And vehicle controls were parallel treated with PBS. The results include two independent repeated experiments (N=2, N means the numbers of the samples from healthy dogs).

first: Che-Si

first: Hsin-Pei

last: Weng


title: LINE1 TGS mechanism mediated by SETDB1-AGO2 complex in human somatic cells [MBD-seq]

first: Kyuheum

last: Jeon

overall_design: Methylation profiling for comparative DNA methylation analysis in HAP1 WT and SETDB1 KO cells.

first: Byungkuk

last: Min

first: Jung

last: Park

first: Yong-Kook

last: Kang


title: Expression data from primary murine CD8+ T cells incubated in AML cell or dendritic cell conditioned medium

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary:
During activation T cells need to undergo metabolic reprogramming for proper effector function. Disturbances in metabolic pathways lead to impaired T cell function. Active metabolic evasion of cancer cells lead to less immunosurveillance and uncontrolled tumor growth.
We used microarrays to investigate the expression changes in T cells challenged with AML supernatants shedding light on the underlying mechanisms of metabolic evasion in leukemia.

overall_design: Primary murine T cells isolated from the spleen were activated and cultured in fresh medium (Tc.Tc) as a control, medium conditioned by WEHI 3B murine AML cells (Tc.WEHI) or bone marrow derived dendritic cells (Tc.Dc). CD8+ T cells were reisolated after 48 hrs for RNA extraction and hybridization on Affymetrix microarrays. Seven biological replicates per condition were analyzed.

first: Franziska

last: Uhl

first: Robert

last: Zeiser

first: Melanie

last: Boerries


title: Ddx10 functions as a positive regulator of somatic cell reprogramming

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: RNA-binding proteins (RBPs) function in all steps of cellular RNA metabolism. Here, we find that Ddx10 gain-of-function promotes but loss-of-function impedes somatic cell reprogramming. Ddx10 loss-of-function results in significantly abnormal expression of innate immune response genes at the late stage of reprogramming. Knockdown of interferon transcription factor Irf1 or its downstream targets, Igtp and Tgtp2, respectively, obviously inhibited reprogramming. This study revealed that Ddx10 regulated reprogramming through modulating innate immune network.

overall_design: Gene expression profiling of reprogrammed cells with OSKM plus control shRNA or Ddx10 shRNAs at different time points. Each experiment was done in biological replicates.

last: Xia

first: Gongcheng


title: Tumor fibroblast-derived FGF2 regulates SPRY1 expression in esophageal tumor-infiltrating T cells and plays a role in T cell exhaustion

first: Qing-yun

last: Chen

state: -- None selected --

address: State Key Laboratory of Oncology in South China

institute: Sun-Yat Sen University Cancer Center

summary: Using single-cell RNA sequencing, we found that exhausted T cells in esophageal cancer were more heterogeneous than previously clarified. We discovered that SPRY1 was notably enriched in two subsets of exhausted CD8+ T cells. When overexpressed, SPRY1 impaired T cell activation by interacting with CBL, which is a negative regulator of ZAP-70 tyrosine phosphorylation.

overall_design: In this study, we provided a landscape of esophageal tumor-infiltrating T cells using 10x scRNA-seq. We identified a novel exhausted T cell marker gene-SPRY1, which especially upregulated in two subsets of exhausted T cells. We then investigated the biological effect of SPRY1 on TCR signaling and the potential inducement of its upregulation.

first: Yi-ni

last: Li

first: Xin-yue

last: Wang

first: Xu

last: Zhang

first: Yi

first: Lei

first: Da-qin

last: Suo

first: Ke

last: Ni

first: Zhuo

first: Jia-rong

last: Zhan

first: Ting-ting

last: Zeng

first: Ying-hui

last: Zhu

first: Yan

first: Li-jia

last: Ma

first: Xin-Yuan

last: Guan


title: cGAS/STING drives ageing-related inflammation and neurodegeneration III

status: Public on Aug 20 2023

city: Lausanne

first: Andrea

last: Ablasser

address: route Cantonale

country: Switzerland

institute: EPFL

summary: Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated impairment and disease. Multiple factors can contribute to ageing-associated inflammation, however the molecular pathways transducing aberrant inflammatory signalling and their impact in natural ageing remain poorly understood. Here we show that the cGAS-STING signalling pathway, mediating immune sensing of DNA, is a critical driver of chronic inflammation and functional decline during ageing. Blockade of STING suppresses the inflammatory phenotypes of senescent human cells and tissues, attenuates ageing-related inflammation in multiple peripheral organs and the brain in mice, and leads to an improvement in tissue function. Focusing on the ageing brain, we reveal that activation of STING triggers reactive microglia transcriptional states, neurodegeneration and cognitive decline. Cytosolic DNA released from perturbed mitochondria elicits cGAS activity in old microglia defining a mechanism by which cGAS-STING signalling is engaged in the ageing brain. Single-nuclei RNA-sequencing (snRNA-seq) of microglia and hippocampi of a newly developed cGAS gain-of-function mouse model demonstrates that engagement of cGAS in microglia is sufficient to direct ageing-associated transcriptional microglia states leading to bystander cell inflammation, neurotoxicity and impaired memory capacity. Our findings establish the cGAS-STING pathway as a critical driver of ageing-related inflammation in peripheral organs and the brain, and reveal blockade of cGAS-STING signalling as a potential strategy to halt (neuro)degenerative processes during old age.

overall_design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Hippocampus were collected and compared to the hippocampus of 10w young mice

first: Muhammet

middle: F

last: Gulen

first: Natasha

last: Samson

first: Alexander

last: Keller

first: Marius

last: Schwabenland

first: Chong

last: Liu

first: Sélène

last: Glück

first: Vivek

middle: V

last: Thacker

first: Lucie

last: Favre

first: Bastien

last: Mangeat

first: Lona

last: Kroese

first: Paul

last: Krimpenfort

first: Marco

last: Prinz


title: Reduced transformation of intestinal smooth muscle cells into fibroblasts inhibit intestinal wound healing and colitis-associated cancer in ageing mice

city: Chengdu

first: Yi

state: Sichuan Province

address: No. 4 keyuan road, gaopeng avenue

institute: Sichuan University

summary: Although ageing is usually regarded as a high risk of cancer, the relationship between ageing stromal microenvironment and spontaneous cancer initiation is poorly understood. In murine models of DSS-induced colitis and AOM/DSS-induced colitis-associated cancer (CAC), we found ageing significantly inhibit both intestinal wound healing and simultaneous CAC initiation. In young mice, through conditional lineage tracing, a novel and important source of fibroblasts transformed from intestinal smooth muscle cells (ISMCs) was identified during intestinal wound healing, which existed persistently in CAC. We further found that activation of YAP/TAZ in ISMCs is required for their transformation into fibroblasts. However, in ageing intestinal microenvironment, the failure of YAP/TAZ activation in ISMCs led to reduced fibroblast numbers, orchestrating the inhibition of wound healing and simultaneous inhibition of CAC initiation. Collectively, our work revealed an important role of ageing stromal microenvironment in intestinal wound healing and CAC development. Meanwhile, our work also discovered an important source of fibroblasts involved in colitis and CAC.

overall_design: AOM/DSS induced gene expression in young and old murine colorectum was measured at 0, 10 and 21 days. Three independent experiments were performed at each time (0, 10 or 21 days).

first: Hongxin

last: Deng


title: Evaluating Detection of small RNA derived fragments from small RNA-seq data

city: Honolulu

first: Ken

middle: M.

last: Nakatsu

state: Hawaii

address: Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Biosciences Building 325B, 651 IIalo Street

department: Quantitative Health Sciences

institute: John A. Burns School of Medicine

summary: An increasing amount of evidence indicates that fragments derived from longer small RNAs such as snoRNAs, snRNAs, and rRNAs may hold functions relevant to biology and disease. However, they remain poorly understood. Few pipelines exist to analyze the fragmentation of small RNAs, and even fewer take users from raw reads to processed results. Every decision that a user makes when processing small RNA-seq data can greatly impact downstream results. Thus, we sought to develop sRNAfrag, a standardized workflow that can accurately quantify and describe the presence of sRNA fragments, with three inputs: run data, a reference genome, and an annotation file.

overall_design: Nine total cell lines were sequenced, including HMEC (n = 1), SK-N-SH (n = 2), IMR32 (n = 2), T47D (n = 2), and HCC1143 (n = 2) to evaluate the detection of small RNA derived fragments with our new pipeline, sRNAfrag. Here we report the results of counts obtaned from snoRNA fragments (sd).

first: Mayumi

last: Jijiwa

first: Vedbar

last: Khadka

first: Youping


title: Gefitinib induced liver damage+liver Transcriptome sequencing

city: 郑州

first: yucheng

last: li

state: 河南省

address: 河南省郑州市金水区博学路街道金水东路156号

institute: Henan University of Chinese Medicine

summary: The liver genome was sequenced by gene set enrichment analysis to see the difference before and after administration and detect the damage of Gefitinib to the liver

overall_design: 9 samples; triplicates


title: Investigating the effect of HIV-1 Coat proteins on Primary Bovine Muller glia

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: We have employed microarray expression profiling to investigate and study the potential gene expression and signaling pathways in HIV-1 TAT and HIV-1 gp120 treated primary bovine muller glia. Exposure of HIV and its coat protein affects ocular tissue and enters Central nervous system. Our group focuses on investing and understanding the various mechnism of inflammation and aging.

overall_design: Agilent Bovine Microarray Gene expression 8x60k  AMADID: 029411

first: K

last: Kamini

first: Nivedita

last: Chatterjee


title: Profiling of cold exposure induced browning of white fat

first: Yu

last: Li

address: Minhang Dongchuan Road No.500

institute: East China Normal University

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

overall_design: Refer to individual Series


title: cGAS/STING drives ageing-related inflammation and neurodegeneration

first: Andrea

last: Ablasser

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Mouse HP1γ regulates TRF1 expression and telomere stability

status: Public on Aug 19 2023

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Telomeric Repeat-containing RNA are long non-coding RNAs generated from the telomeres. TERRAs are essential for the establishment of heterochromatin marks at telomeres, which serve for the binding of members of the Heterochromatin Protein 1protein family of epigenetic modifiers involved with chromatin compaction and gene silencing. While HP1γ is enriched on gene bodies of actively transcribed mammalian genes, it is unclear if its transcriptional role is important for HP1γ function in telomere cohesion and telomere maintenance. We aimed to study the effect of mouse HP1γ on the transcription of telomere factors and molecules that can affect telomere maintenance. We investigated the telomere function of HP1γ by using HP1γ deficient mouse embryonic fibroblastsderiving from 13.5 embryonic day embryos compared to their littermate controls. We used gene expression analysis of HP1γ deficient MEFs and validated the molecular and mechanistic consequences of HP1γ loss by telomere FISH, immunofluorescence, RT-qPCR and DNA-RNA Immunoprecipitation. Loss of HP1γ in primary MEFs led to a downregulation of various telomere and telomere-accessory transcripts, including the shelterin protein TRF1. Its downregulation is associated with increased telomere replication stress and DNA damage (γH2AX), effects more profound in females. We suggest that the source for the impaired telomere maintenance is a consequence of increased telomeric DNARNA hybrids and TERRAs arising at and from mouse chromosomes 18 and X. Our results suggest an important transcriptional control by mouse HP1γ of various telomere factors including TRF1 protein and TERRAs that has profound consequences on telomere stability, with a potential sexually dimorphic nature.

overall_design: Cleavage Under Targets & Release Using Nuclease (CUT & RUN) for chromatin binding protein HP1γ, histone modification H3K27me3 and IgG (negative control) in primary Mouse Embryonic Fibroblast (MEFs) deriving from E13.5 embryos.

first: Emmanouil

last: Stylianakis

first: Jackson

middle: P

last: Chan

first: Sanjay

last: Khadayate

first: Mohammad

last: Karimi

first: Jean-Baptiste

last: Vannier


title: cGAS/STING drives ageing-related inflammation and neurodegeneration IV

overall_design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer.

first: Muhammet

last: Gulen

first: Natasha

last: Samson

first: Alexander

last: Keller

first: Marius

last: Schwabenland

first: Chong

last: Liu

first: Sélène

last: Glück

first: Vivek

last: Thacker

first: Lucie

last: Favre

first: Bastien

last: Mangeat

first: Lona

last: Kroese

first: Paul

last: Krimpenfort

first: Marco

last: Prinz


title: Tanscriptome profiling of cold exposure induced browning of white fat

first: Yu

last: Li

summary: We set two groups of 2-month-old C57BL6/J male mice at either thermoneutral temperature of 30℃ or under cold stimulation at 4℃ for one week. To identify events vital to beige fat activation, we performed RNA-seq using mice subcutaneous adipose tissue (iWAT) and focused on differentially-expressed genes characterized significant upregulation.

overall_design: The biege fat obtained from the mice with housed at either 30℃ or 4℃ for 7 days in a temperature-controlled incubator

first: Yankang

last: Zhang


title: cGAS/STING drives ageing-related inflammation and neurodegeneration II

first: Andrea

last: Ablasser

overall_design: 20m old aged mice were treated for 16w with DMSO or H151 over 24w. Aged mice were injected intraperitoneally with 750 nmol H151 per mouse five days a week for 8 weeks. The mice were rested for 8 weeks, and 8 weeks of treatment were repeated one more time. Nuclei from mouse brain were extracted by homogenizing mouse brain tissues in Nuclei EZ Lysis Buffer using a douncer. Nuclei were labelled with DAPI and sorted for sequencing. To enrich microglial cells, in addition to DAPI staining, nuclei were stained with anti-RBFOX3/NeuN-647.


title: Microarray analysis of lung cancer cells gene expression in overexpressing different semaphorin 5a domains

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

institute: National Taiwan University

summary: Semaphorin 5A (SEMA5A) is one member of semaphorin family, which was identified as an axon guidance molecule in nervous systems. In our previous studies, SEMA5A was identified as a prognostic biomarker for lung cancer in nonsmoking women and acted as a tumor suppressor gene in inhibiting the proliferation and migration of lung cancer cells. Yet, the regulatory mechanism of SEMA5A was not clear. Therefore, the purpose of this study was to explore the roles of different domains of SEMA5A on the tumor suppressive effects in lung cancer cell lines.

overall_design: Total RNA was extracted 24 h after the transfection of different SEMA5A domains plasmids, including SEMA5A full length (5A-Full), SEMA5A extracellular domain (5A-ECD) and intracellular domain (5A-ICD) and control plasmid

first: Liang-Chan


title: Bromodomain member BRD4 is required for hematopoietic stem cell functions (scRNA-Seq)

first: Hui

last: Yang

address: 5114 medical dr.

institute: UTHSCSA

summary: To investigate the role of BRD4 in normal hematopoiesis, Brd4 conditional KO mouse model was generated. We purified the cKit+ and LSK cells from bone marrow of WT and Brd4 KO mice and performed the single cell RNA-seq to study the molecular changes in each cell population.

overall_design: Single cell RNA-seq for bone marrow cKit+ and LSK cells from WT (n=2) and Brd4 conditional KO (n=2) mice.

first: Feng-Chun

first: Pinpin

last: Sui


title: Methylation profiling of cold exposure induced browning of white fat

summary: We set two groups of 2-month-old C57BL6/J male mice at either thermoneutral temperature of 30℃ or under cold stimulation at 4℃ for one week. To identify events vital to beige fat activation, we performed MeRIP-seq using mice subcutaneous adipose tissue (iWAT) and focused on differentially-expressed genes characterized significant upregulation.


title: cGAS/STING drives ageing-related inflammation and neurodegeneration I

overall_design: WI-38 fibroblasts were irradiated (12 Gy, IR) or maintained at 5%O2(CTRL), and treated with H-151 (daily, 0.5μM) or DMSO for 10 days and collected when senescent (day 10 to 20).

first: Muhammet

last: Gulen

first: Natasha

last: Samson

first: Alexander

first: Marius


title: Nuclear transport surveillance of p53 by nuclear pores in glioblastoma

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

summary: Nuclear pore complexes (NPCs) are the central apparatus of nucleocytoplasmic transport. Disease-specific alterations of NPCs contribute to the pathogenesis of many cancers; however, the roles of NPCs in glioblastoma (GBM) are unknown. In this study, we report genomic amplification of NUP107, a component of NPCs, in GBM and show that NUP107 is overexpressed simultaneously with MDM2, a critical E3 ligase that mediates p53 degradation. Depletion of NUP107 inhibits the growth of GBM cell lines through p53 protein stabilization. Mechanistically, NPCs establish a p53 degradation platform via an export pathway coupled with 26S proteasome tethering. NUP107 is the keystone for NPC assembly; the loss of NUP107 affects the integrity of the NPC structure, and thus the proportion of 26S proteasome in the vicinity of nuclear pores significantly decreases. Together, our findings establish roles of NPCs in transport surveillance and provide insights into p53 inactivation in GBM.

overall_design: Comparison between negative control cells and NUP107 knocked down cells. There are two biological replicates for each conditions.

first: Dini

last: Kurnia Ikliptikawati

first: Nozomi

last: Hirai

first: Kei

last: Makiyama

first: Hemragul

last: Sabit

first: Masashi

last: Kinoshita

first: Keesiang

last: Lim

first: Makiko

last: Meguro-Horike

first: Masaharu

last: Hazawa

first: Mitsutoshi

last: Nakada

first: Richard

middle: W

last: Wong


title: Bromodomain member BRD4 is required for hematopoietic stem cell functions (RNA-Seq)

first: Hui

summary: To investigate the role of BRD4 in normal hematopoiesis, Brd4 conditional KO mouse model was generated. We purified the Lin-cKit+ cells from bone marrow of WT and Brd4 KO mice and performed the RNA-seq to study the molecular changes in each cell population.

overall_design: RNA-seq for bone marrow Lin-cKit+ cells from WT (n=4) and Brd4 conditional KO (n=4) mice.

first: Feng-Chun


title: Bromodomain member BRD4 is required for hematopoietic stem cell functions (ATAC-Seq)

summary: To investigate the role of BRD4 in normal hematopoiesis, Brd4 conditional KO mouse model was generated. We purified the Lin-cKit+ cells from bone marrow of WT and Brd4 KO mice and performed the ATACseq to study the chromatin accessibility in each cell population.

overall_design: ATAC-seq for bone marrow Lin-cKit+ cells from WT (n=2) and Brd4 conditional KO (n=2) mice.

first: Pinpin


title: Bromodomain member BRD4 is required for hematopoietic stem cell functions (CUT&RUN)

summary: To investigate the role of BRD4 in normal hematopoiesis, Brd4 conditional KO mouse model was generated. We purified the Lin-cKit+ cells from bone marrow of WT and Brd4 KO mice and performed the CUT&RUN to study the histone modification and Brd4 occupancy around genome in HSC/HPCs population.

overall_design: Brd4, H3K27Ac, H3K122Ac, H3K4me3, Clipping H3 in WT (n=2) and Brd4 KO (n=2) Lin-Ckit+ cells


title: Cytochrome c-Peroxidase Modulates ROS Homeostasis to Regulate the Sexual Mating of Sporisorium scitamineum

city: Guangzhou

first: Enping

last: Cai

address: Wushan Road, Tianhe District

department: College of Plant Protection

institute: South China Agricultural University

summary: we identified a cytochrome c-peroxidase encoding gene SsCCP1 that is essential for oxidative stress resistance. We further found that absence of SsCcp1 leads to defects in mating/filamentation and imbalance of intracellular ROS homeostasis. To further elucidate the effect of SsCcp1 on intracellular ROS homeostasis, we performed comparative transcriptome analysis with the ssccp1Δ-1 and the wild-type MAT-1 sporidia grown in YePSA medium.

overall_design: comparative gene expression profiling analysis of RNA-seq data for the wild-type MAT-1 sporidia cells and its ssccp1Δ-1 derivatives

first: Huan

last: Jia

first: Ruqing

last: Feng

first: Wenqiang

last: Zheng

first: Lei

last: Li

first: Li

last: Zhang

first: Zide

last: Jiang

first: Changqing

last: Chang


title: Thrombospondin-1 promotes fibro-adipogenic stromal expansion and contractile dysfunction of the diaphragm in obesity II

status: Public on Aug 18 2023

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: This study defines the impact of in vivo thrombospondin-1 (THBS1) ablation on diaphram stromal cell profile, histology and contractile funciton in a mosue model of diet-induced obesity

overall_design: Bulk RNA sequencing performed on tissue samples of daiphragms from wild type C57 mice and thrombospondin-1 knockout mice fed high fat diet (45% kcal from lipid) for 6 months

first: Eric

last: Buras

first: Tae-Hwa

last: Chun


title: Bromodomain member BRD4 is required for hematopoietic stem cell functions

last: Yang


title: Circular RNA TMEM87A promotes cell proliferation and metastasis of gastric cancer by elevating ULK1 via sponging miR-142-5p (circRNA)

city: huai’an

first: haixiao

last: wang

state: Jiangsu

address: No 1,  The Yellow River West Road

department: Department of General Surgery

institute: The Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University

summary:
Background:Circular RNAs (circRNAs) act as vital regulators of gene expression in a variety of cancers. However, the role of circRNAs in gastric cancer (GC) remains largely unexplored. Herein, we identified that circTMEM87A sponges miR-142-5p to promote GC progression through up-regulating ULK1 expression.
Methods:The expression of circTMEM87A in GC was determined by RNA sequencing and quantitative real-time PCR (qRT-PCR). The effects of knockdown or exogenous expression of circTMEM87A on GC cell phenotypes were evaluated both in vitro and in vivo. The interacting miRNA of circTMEM87A was predicted by bioinformatics and confirmed by RNA pull-down, dual-luciferase reporter assay and fluorescence in situ hybridization (FISH). The mechanism by which circTMEM87A/miR-142-5p/ULK1 axis promotes GC was determined by western blot, GFP/mRFP-LC3 puncta analysis, transmission electron microscope (TEM).
Results:CircTMEM87A was dramatically elevated in GC tissues and cell lines, and high circTMEM87A expression was closely correlated with poor prognosis of GC patients. Knockdown of circTMEM87A suppressed cell growth, migration, invasion and induced apoptosis in vitro, as well as inhibited GC tumorigenicity and lung metastasis potential in vivo. Meanwhile, circTMEM87A overexpression had the opposite effects. Furthermore, we demonstrated that circTMEM87A could act as a sponge of miR-142-5p to regulate ULK1 expression and GC progression.
Conclusions:Our findings suggest that circTMEM87A functions as an oncogene through the miR-142-5p/ULK1 axis in GC. CircTMEM87A might be a prognostic biomarker as well as a promising therapeutic target for GC.

overall_design: circRNA  expression profiles involved in Gastric cancer progression

first: Zekuan

last: Xu

first: Haixiao

last: Wang


title: RNA BS-seq of Nocodazole treated HeLa cells with NSUN family member deficiency

first: Rui

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

summary: m5C accumulates on mRNAs in Nocodazole (Noc) treated cells. To figure out which m5C writer is responsible for these m5C sites, we generated three KO cell lines  (NSUN2, NSUN5, and NSUN6) with CRISPR induced mutagenesis. We also used siRNA to suppress the expression of Nop2 (NSUN1) in wild-type HeLa cells. Then we performed mRNA BS-seq on the cells harvested after 48 hours Noc-treatment (for siRNA experiments, cells were treated with siRNA for 48 hours first).

overall_design: RNA BS-seq of mRNA from human cell lines (NSUN2 KO, NSUN5 KO, NSUN6 KO, Nop1 KD). For each type of cells, one biological replicate was performed.

first: Tao

last: Huang

first: Jianheng

last: Liu


title: cAMP response element-binding protein mediates immune-evasion of KRAS-mutant lung adenocarcinomas

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

summary: We discovered that KRAS-mutant lung adenocarcinomas (LADC) co-opt CREB in order to evade the innate immune system: KRAS-driven CREB activation in LADC suppresses the expression of CXCR1 ligands that would otherwise recruit neutrophils to the tumor site. CREB was overexpressed in murine KRAS-mutant LADC, pulmonary Creb1-deletion inhibited disease development, and Creb1-overexpression boosted the tumorigenicity of KRAS-mutant cells. Conditional Creb1 deletion in Kras-mutant LADC cells caused overexpression of CXCR1/2 ligands, and lung tumor-bearing Creb1-deleted mice displayed increased pulmonary neutrophils. Cxcr1-deficient mice were selectively permissive to KRAS-mutant tumor growth and showed defective neutrophil recruitment. The pro-tumor effects of CREB required intact host-Cxcr1 and those of host-Cxcr1 necessitated mutant KRAS in cancer cells. Pharmacologic CREB blockade prevented tumor growth and restored neutrophil recruitment only when initiated before immune evasion of KRAS-mutant LADC cells. CREB and CXCR1 expression were respectively restricted to tumor and stromal cells of human LADC, while CREB-controlled genes profoundly impacted survival. In summary, CREB-mediated immune evasion of KRAS-mutant LADC rests on signaling to myeloid CXCR1 and is actionable.

overall_design: Compare differential gene expression between murine urethane-induced lung adenocarcinoma cells expressing or silenced for Creb1

first: G

last: Giotopoulou


title: Circular RNA TMEM87A promotes cell proliferation and metastasis of gastric cancer by elevating ULK1 via sponging miR-142-5p (miRNA)

overall_design: microRNA  expression profiles involved in Gastric cancer progression


title: Transcriptome analysis provides insights into the skeletal malformation induced by dietary phospholipids deficiency in largemouth bass (Micropterus salmoides) larvae

city: 上海

first: Zishuo

last: Fang

state: 上海

address: 沪城环路999号

institute: Shanghai Ocean University

summary: Largemouth bass is one of the most important freshwater aquaculture species in China. However, the mechanisms underlying the development of skeleton in the fish are unclear. High-throughput RNA-Seq was used to analyze the transcriptome of largemouth bass skeleton between high-phospholipids and low-phospholipids groups. Thirty individuals each from 3 high-phospholipids families and 3 low-phospholipids families were used to reduce inaccuracies. The results indicated that 255 up-regulated and 329 down-regulated genes were identified in the differentially expressed genes (DEGs). GO and KEGG enrichment analyses revealed the DEGs were involved in the MAPK signaling pathway, phosphatidylinositol signaling system, glycosphingolipid biosynthesis-lacto and neolacto series and fatty acid degradation. Twist2 and Daam1, genes related to osteoblast development, were up-regulated in high-phospholipids group. BGLAP, gene associated with the skeletal development and osteohormatology, was also up-regulated in high-phospholipids group. PCOLCE b, a gene related to the development of gristle, was up-regulated in high-phospholipids group. Higher expression of SCPP1 and SCPP7 in high-phospholipids group was associated with tooth and bone development. The trend changes in the above genes all indicate that the lack of phospholipids may affect the skeletal development through the above genes, increasing malformations. In summary, these results provide valuable information about the reduction of deformity rates in largemouth bass and contribute to our understanding of the molecular mechanisms and regulative pathways regulating skeletal growth in teleosts.

overall_design: The largemouth bass larvae were collected from the feeding trail of (Wang et al. 2022). Briefly, after 12 days’ feeding trial, larvae fed the diet without phospholipid inclusion resulted in skeletal malformation at high proportion. The visual deformity rate was decreased with the increase of dietary phospholipids in a dose dependent manner, and only sporadic malformed fish was observed in the larvae fed the diet with 8% phospholipids inclusion. Therefore, three replicates of 30 deformity larvae per tank fed the diet without phospholipids supplementation were pooled after being measured for the body weight and body length for transcriptome analysis and gene expression analysis, and named as SP_L. Equivalent normal larvae per tank fed the diet with 8% phospholipids supplementation were sampled and named as SP_H.

first: Ye

last: Ge

first: Songlin


title: Gene expression profiling in salivary glands by BMP-2.

city: Shinagawa

first: Atsushi

last: Yamada

state: Tokyo

address: 1-5-8 Hatanodai

department: School of Dentistry

institute: Showa University

summary: Bone Morphogenetic Protein (BMP), a bone induction factor, belongs to the TGF-β superfamily, and more than 15 types of BMP family molecules have been reported in mammals. They are known to enhance osteoblast differentiation and their osteogenic effects, and also promote differentiation into chondrocytes. While the effects of BMPs on hard tissues are varied and numerous reports have been reported, only a few have reported the effects of BMPs on salivary glands. The aim of this study was to investigate the function of BMP-2 in the formation of salivary glands.

overall_design: To investigate the function of BMP-2 on the formation of salivary glands, we treated 300 ng/ml of BMP-2 with salivary gland primordia of Embryonic day 13.5, and

first: Shinnosuke

last: Ono

first: Takahiro

last: Funatsu

first: Ryutaro

last: Kamijo


title: Single cell transcriptomics analysis of young Ncstnfl/fl (control), middle-aged Ncstnfl/fl (control) and middle-aged LeprCre; Ncstnfl/fl (cKO) bone and bone marrow

city: New York

first: Ziyan

last: Lin

state: NY

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

summary: Skeletal stem and progenitor cells (SSPCs) perform bone maintenance and repair. With age, they produce fewer osteoblasts and more adipocytes leading to a loss of skeletal integrity. The molecular mechanisms that underlie this detrimental transformation are largely unknown. Single-cell RNA sequencing revealed that Notch signaling becomes elevated in SSPCs during aging. To examine the role of increased Notch activity, we deleted Nicastrin, an essential Notch pathway component, in SSPCs in vivo. Middle-aged conditional knockout mice displayed elevated SSPC osteo-lineage gene expression, increased trabecular bone mass, reduced bone marrow adiposity, and enhanced bone repair. Thus, Notch regulates SSPC cell fate decisions, and moderating Notch signaling ameliorates the skeletal aging phenotype, increasing bone mass even beyond that of young mice. Finally, we identified the transcription factor Ebf3 as a downstream mediator of Notch signaling in SSPCs that is dysregulated with aging, highlighting it as a promising therapeutic target to rejuvenate the aged skeleton.

overall_design: 5 mice per condition pooled.Hindlimbs were isolated with subsequent bone and bone marrow isolation with fluorescence-activated cell sorting to isolate hematopoietic and endothelial cells (CD45+CD31+TER-119-) and skeletal and stromal lineages (CD45-CD31-TER-119-). Hematopoietic/endothelial and osteolineage/stromal compartments were then mixed at a 1:1 ratio to allow for enrichment of the rarer osteolineage/stromal cells.

first: Philipp

last: Leucht

first: Lindsey

last: Remark


title: ATAC-sequencing of young and middle-aged SSPCs from mouse bone

summary: Skeletal stem and progenitor cells (SSPCs) perform bone maintenance and repair. With age, they produce fewer osteoblasts and more adipocytes leading to a loss of skeletal integrity. The molecular mechanisms that underlie this detrimental transformation are largely unknown. To identify transcriptional changes that occur with aging we performed bulk RNA sequencing on young (3 month) and middle-aged (12 month) SSPCs.

overall_design: Tibial and femoral SSPCs were isolated by centrifugation. Bone marrow was resuspended in growth media (GM) [DMEM containing 10% FBS and 1% penicillin/streptomycin;  and then plated in 150cm2 tissue- culture flasks. Media changed the following day and then every two days. All cellular assays were performed with SSPCs at passage one from at least three different mice and young and middle-aged SSPCs for ATAC-sequencing.

first: Anne

last: Josephson


title: Bulk RNA sequencing of  LEPR+CD45-CD31-TER-119– skeletal stem cells from middle-aged Ncstnfl/fl (control) and LeprCre; Ncstnfl/fl (cKO) mouse bone

overall_design: Hindlimbs were isolated with subsequent bone and bone marrow isolation with fluorescence-activated cell sorting to isolate LEPR+CD45-CD31-TER-119– skeletal stem cells from middle-aged control and cKO mice. N=4 mice per group.


title: Young and middle-aged SSPCs from mouse bone

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

overall_design: Refer to individual Series


title: Single-Cell Sequencing Reveals the Existence of Fetal Vascular Endothelial Stem Cell-Like Cells in the Liver

first: Tomohiro

last: Iba

address: 13-1, Takara-machi

institute: Kanazawa University School of Medicine

summary: A resident vascular endothelial stem cell (VESC) population expressing CD157 and CD200 has been identified recently in the adult mouse. However, the origin of this population and how it develops has not been characterized, nor has it been determined whether VESC-like cells are present during the perinatal period. Here, we investigated the presence of perinatal VESC-like cells and their relationship with the adult VESC-like cell population. We applied single-cell RNA sequencing of endothelial cells (ECs) from embryonic stage liver and investigated transcriptomic changes during liver EC development. We performed flow cytometry, immunofluorescence, colony formation assays and transplantation assays to validate the presence of and to assess the function of CD157+ and CD200+ endothelial cells (ECs) in the perinatal period. We identified CD200-expressing VESC-like cells in the perinatal period. These cells formed colonies in vitro and had high proliferative ability. The RNA Velocity tool and transplantation assay results indicated that the projected fate of this population was towards adult VESC-like cells expressing CD157 and CD200 one week after birth. Our study provides a comprehensive atlas of liver EC development and documents VESC-like cell lineage commitment at single-cell resolution.

overall_design: Single cell RNA sequencing of liver endothelial cells along from Embrionic Stage

first: Fitriana

middle: N

last: Rahmawati

first: Hisamichi

last: Naito

first: Shota

last: Shimizu

first: Hirotaka

last: Konishi

first: Weizhen

last: Jia

first: Nobuyuki

last: Takakura


title: Sciatic nerve injury-responsive differential CSDE1 association efficiency of ribosomal protein coding mRNAs

city: Dalseonggun, Daegu

first: Yongcheol

last: Cho

state: Daegu

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Department of Brain Sciences

institute: DGIST

summary: Gpr151 is an injury-responsive gene that promotes axon regeneration through its interaction with the 5'UTR region of its mRNA transcripts and the RNA-binding protein CSDE1. We found that knocking down or overexpressing the 5'UTR of Gpr151 changes the ribosomal protein mRNA regulon regulated by CSDE1. After the sciatic nerve injury, the association between the ribosomal protein mRNA regulon and CSDE1 was enhanced at dorsal root ganglions(DRGs), but this enhancement was not observed in the AAV-shGpr151 injected mice. Overexpression of 5'UTRmut, which has increased binding affinity to CSDE1, enhanced the ribosomal protein mRNA regulon and its association with CSDE1 in embryonic DRG neurons.

overall_design:
Wild type or AAV-shGpr151 injected mice were subjected to sciatic nerve injury in order to profile the injury-responsive changes in CSDE1 binding RNA pools at DRGs. The DRG tissues were collected 72 hours after the injury, and the RNAs were extracted from the anti-CSDE1 immunoprecipitated lysates.
Primary DRG neurons were spot cultured and infected with LV-control or LV-5'UTRmut at DIV6. Neurons were collected at DIV6, and their RNAs were extracted from the anti-CSDE1 immunoprecipitated lysates.
Adult DRG neurons from the wild type or RiboTag+/+;Advillin-Cre+ mice were cultured after giving the pre-conditioning effects induced by sciatic nerve injury 24 hours prior to DRG tissue dissection, and infected with AAV-control or AAV-shGpr151 four hours after cell culture. Neurons were collected at DIV6, and their RNAs were extracted from the anti-CSDE1 or anti-HA immunoprecipitated lysates.
In vivo gene delivery of control, shGpr151 or 5'UTRmut, packaged in the AAV9 viral vectors, was conducted through the facial vein injection at P1.
In vitro gene delivery of control, shGpr151 or 5'UTRmut, packaged in the AAV9 or lentiviral vectors, was conducted through the infection to cultured neurons.

first: Eunsu

last: Jang

first: Yeonsoo

last: Oh

first: Hoyong

last: Jin

first: Bohm

last: Lee

first: Jinyoung

first: Yewon

last: Jeon

first: Hyemin

last: Kim

first: Minjae

last: Kwon

first: Jung

last: Shin


title: Overexpression of TMEM213, 207, 116, 72 and 30B in HEK293 cell line

city: Poznań

first: Joanna

last: Wesoly

address: Uniwersytetu Poznańskiego 6

institute: Adam Mickiewicz University

summary: TMEM213, 207, 116, 72 and 30B were found to be deregulated in ccRCC tumors, but their function in the epithelium remains unclear. To obtain an insight into their role in cellular processes the five TMEM genes were overexpressed in HEK293 cell line

overall_design: Expression profiling by high throughput sequencing. 3 biological replicates were prepared for overexpression of each TMEM. Controls included non-transfected samples and samples transfected with an empty vector


title: Sympathetic nerves regulate intestinal regeneration through IL22 signaling

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

summary: The intestine is a barrier tissue whose epithelium has high intrinsic turnover rate; intestinal stem cells, in response to signals from the niche, self-renew and produce progeny that differentiate to fulfill the continuous demand for new epithelial cells that are continuously shed into the lumen. The intestine is innervated by a dense network of peripheral nerves that controls nutrient absorption, intestinal motility, and visceral pain sensation. However, the roles of neurons in regulating epithelial cell homeostasis or regeneration remain as yet undiscovered. Here we investigate the effects of gut-innervating sympathetic neurons on epithelial cell repair following irradiation (IR)-induced gut injury. We observed that sympathetic innervation density in the gut increases post IR, while chemical sympathetic denervation impairs gut regeneration. Combining single cell RNA-sequencing and in vivo experiments, we discovered that sympathetic neurons regulate gut regeneration through modulation of IL22 production in type 3 innate lymphoid cells (ILC3) downstream of 2-adrenergic receptor signaling. These results define a novel neuroimmune axis important for intestinal regeneration.

overall_design: scRNA sequenced from disscoiated intestine of 13 control and 4 denervated (6-OHDA treated) animals at time points following irradiation

first: P

last: Wang

first: F

last: de Sauvage

first: R


title: Gene expression of breast tumors with mutant p53 or mutant p53 deleted [RNA-seq]

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: We conducted gene expression analysis from total tumor treated with AAV-Control or AAV-mut-p53 deleted.

overall_design: RNA sequencing analysis was conducted in AAV-Control (N=3) or AAV-mut-p53 deleted (N=6).

first: Denada

last: Dibra

first: Guillermina

last: Lozano


title: Molecular typing and functional profiling of acne-derived Cutibacterium acnes isolates reveal determinants of skin inflammation

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: Cutibacterium acnes (C. acnes) is a ubiquitous skin commensal bacterium that is generally well tolerated by the immune system. Different strain-types of C. acnes have been reported to be enriched on patients with acne. To understand if these strain-types contribute to skin inflammation, we generated a library of over 200 C. acnes isolates from skin swabs of healthy and acne subjects and assessed their strain-level identity and inflammatory potential. Phylotype II K-type strains were more frequent on healthy and acne non-lesional skin compared to lesional. Phylotype IA-1 C-type strains were dominant on acne lesional skin but absent from healthy. Measurement of host cytokine responses from C. acnes supernatant revealed neither strain-type nor skin-type association predicted inflammatory potential. However, differential proinflammatory responses were induced from identical strain-types, but these differences were not attributable to protease, short chain fatty acid or porphyrin production. Instead, whole genome sequencing revealed the presence of a linear plasmid in high inflammatory strain-types. Intradermal injection of C. acnes in mouse skin revealed a plasmid-associated inflammatory response in dermal fibroblasts, revealed by single-cell RNA sequencing. We conclude that C. acnes strain-type is not sufficient to predict inflammation but other virulence factors including a plasmid may contribute to disease.

overall_design: Single-cell RNA-seq of skin biopsies from mice intradermally infected with C acnes

first: Alan

middle: M

last: O'Neill

first: Richard

middle: L

last: Gallo


title: Ribosomal protein S3 mediates drug resistance of proteasome inhibitor: therapeutic application in multiple myeloma

city: Shanghai

first: Jumei

last: Shi

address: 150 Jimo Road

department: Department of Hematology

institute: Shanghai East Hospital

summary: Multiple myeloma (MM) remains incurable due to drug resistance. Ribosomal protein S3 (RPS3) has been identified as a non-Rel subunit of NF-κB. However, the detailed biological roles of RPS3 remain unclear. Here, we report for the first time that RPS3 is necessary for MM survival and drug resistance. RPS3 was highly expressed in MM, and knockout of RPS3 in MM inhibited cell growth and induced cell apoptosis both in vitro and in vivo. Overexpression of RPS3 mediated the proteasome inhibitor resistance of MM and delayed the survival of MM tumour-bearing animals. Moreover, our present study found an interaction between RPS3 and the thyroid hormone receptor interactor 13 (TRIP13), an oncogene related to MM tumorigenesis and drug resistance. We demonstrated that the phosphorylation of RPS3 was mediated by TRIP13 via PKCδ, which played an important role in activating the canonical NF-κB signalling and inducing cell survival and drug resistance in MM. Notably, the inhibition of NF-κB signalling by the small-molecule inhibitor targeting TRIP13, DCZ0415, was capable of triggering synergistic cytotoxicity when combined with bortezomib in drug-resistant MM. This study identifies RPS3 as a novel biomarker and therapeutic target in MM.

overall_design: To investigate the mechanism of TRIP13 in multiple myeloma (MM), we established ARP-1 MM cells stably transfected with TRIP13 overexpression (TRIP13-OE) and empty vector (EV).We then performed RNA-seq analysis on three independent groups of TRIP13 OE ARP-1 cells and corresponding EV cells. Comparative gene expression profiling analysis of RNA-seq data for TRIP13-OE and its corresponding EV ARP-1 MM cells.

first: Weiliang

last: Zhu

first: Gege

last: Chen

first: Xuejie

last: Gao


title: Study of the protective effect of D-Lactate-producing probiotics on CNS pathology

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: Dendritic cells (DCs) control the generation of self-reactive pathogenic T cells. Thus, DCs are attractive therapeutic targets for autoimmune diseases. Using single-cell and bulk transcriptional and metabolic analyses in combination with cell-specific gene perturbation studies we identified a negative feedback regulatory pathway that operates in DCs to limit immunopathology. Specifically, we found that lactate, produced by activated DCs and other immune cells, boosts NDUFA4L2 expression through a mechanism mediated by HIF-1a. NDUFA4L2 promotes mitochondrial fitness in DCs, limiting the production of mitochondrial reactive oxygen species that activate XBP1-driven transcriptional modules involved in the control of pathogenic autoimmune T cells. Moreover, we engineered a probiotic that produces lactate and suppresses T-cell autoimmunity in the central nervous system via the activation of HIF-1a/NDUFA4L2 signaling in DCs. In summary, we identified a novel immunometabolic pathway that regulates DC function, and developed a synthetic probiotic for its therapeutic activation via the gut-brain axis.

overall_design: WT and Itgax Cre HIF1a flox mice were treated with D-Lactate-producing bacteria starting 3 days before EAE induction and DCs were sorted at endpoint

first: Liliana

last: Sanmarco

first: Francisco

last: Quintana


title: Engineered probiotics limit T-cell driven CNS autoimmunity by promoting mitochondrial fitness in dendritic cells


title: Bulk RNA sequencing of young and middle-aged SSPCs from mouse bone

first: Ziyan

last: Lin

overall_design: Tibial and femoral SSPCs were isolated by centrifugation. Bone marrow was resuspended in growth media (GM) [DMEM containing 10% FBS and 1% penicillin/streptomycin;  and then plated in 150cm2 tissue- culture flasks. Media changed the following day and then every two days. All cellular assays were performed with SSPCs at passage one from at least three different mice and young and middle-aged SSPCs subjected to bulk RNA sequencing.

first: Philipp

last: Leucht

first: Anne

last: Josephson

first: Lindsey

last: Remark


title: Analyses of HIF-1a-deficient DCs in the context of pre-clinical model of Multiple Sclerosis, Experimental Autoimmune Encephalomielitis (EAE)

overall_design: DCs from WT or Itgax Cre HIF1a flox mice were sorted from Central Nervous system (CNS) or spleen during EAE


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to carbon black (Printex 90)

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

country: France

institute: Université de lorraine

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 0.9 cm²/cm² of carbon black (Printex 90). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (0.9 cm²/cm²) of carbon black (Printex 90) for 4 h were measured. For each condition, four biological replicates were performed.

first: Sara

last: Nahlé

first: Romain

last: Schmitt

first: Bertrand

last: Rihn

first: Luc

last: Ferrari


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to  ZnO 4 µg/mL and ZnO 16 µg/mL

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 4 µg/mL and 16 µg/mL of ZnO. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (4 µg/mL or 16 µg/mL) of ZnO for 4 h were measured. For each condition, four biological replicates were performed.

first: Zahra

last: Doumandji


title: Effect of XBP1-deficiency in DCs on CNS pathology

overall_design: Experimental autoimmune encephalomyelitis was induced in Itgax Cre Xbp1 flox and WT mice and dendritic cells were sorted from Central Nervous System and spleen.


title: Effect of free D-Lactate in CNS pathology

overall_design: WT mice were treated with D-lactate by intraperitoneal injections starting 3 days before experimental autoimmune encephalomyelitis induction. DCs were sorted from Central Nervous system and spleen at endpoint.


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to pristine single-walled carbon nanotubes (NRCWE055)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 11 cm²/cm² of pristine single-walled carbon nanotubes (NRCWE055). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (11 cm²/cm²) of pristine single-walled carbon nanotubes (NRCWE055) for 4 h were measured. For each condition, four biological replicates were performed.


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to NH2-functionalized carbon nanotubes (NRCWE049)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 1.2 cm²/cm² of NH2-functionalized carbon nanotubes (NRCWE049). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (1.2 cm²/cm²) of NH2-functionalized carbon nanotubes (NRCWE049) for 4 h were measured. For each condition, four biological replicates were performed.


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to  zinc iron oxide (ZnFe2O4, NRCWE021)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 17 µg/mL of zinc iron oxide (ZnFe2O4, NRCWE021). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (17 µg/mL) of zinc iron oxide (ZnFe2O4, NRCWE021) for 4 h were measured. For each condition, four biological replicates were performed.


title: Transcriptional regulation of ES cell by FGF signalling

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

institute: The Francis Crick Institute

summary: FGF4 paracrine signaling through FGF receptors is believed to induce Erk activity and promotes the exit from pluripotency. However,  we have recently observed that FGF4 and FGF2 have opposing effects on mES cell fate. The aim of this study was to understand the underlying transcriptional changes associated with these opposing actions.

overall_design: Mouse embryonic stem cells were grown in a naïve state of pluripotency using 2iLIF media and subsequently stimulated with FGF2 in N2B27 media for 24hrs and 48hrs.

first: Borzo

last: Gharibi

first: Stephanie

last: Strohbuecker


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to  Fe2O3 (NRCWE018)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 2 µg/mL of Fe2O3 (NRCWE018). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (2 µg/mL) of Fe2O3 (NRCWE018) for 4 h were measured. For each condition, four biological replicates were performed.


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to NiZnFe2O4

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 9.25 µg/mL of NiZnFe2O4. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (9.25 µg/mL) of NiZnFe2O4 for 4 h were measured. For each condition, four biological replicates were performed.


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to COOH-functionalized carbon nanotubes (NRCWE042)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 6.8 cm²/cm² of COOH-functionalized carbon nanotubes (NRCWE042). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (6.8 cm²/cm²) of COOH-functionalized carbon nanotubes (NRCWE042) for 4 h were measured. For each condition, four biological replicates were performed.


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to multi-walled carbon nanotubes (NRCWE006)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 1 cm²/cm² of multi-walled carbon nanotubes (NRCWE006 - Mitsui-7). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (1 cm²/cm²) of multi-walled carbon nanotubes (NRCWE006) for 4 h were measured. For each condition, four biological replicates were performed.


title: Transcriptomic study of NR8383 rat macrophages cells following exposure to  TiO2 (NRCWE001)

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 3 cm²/cm² of rutile TiO2 (NRCWE001). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (3 cm²/cm²) of TiO2 (NRCWE001) for 4 h were measured. For each condition, four biological replicates were performed.