title: Dynamic 3D Genome and Epigenetic Landscapes of Macrophage Cells Reprogramming Gene Expression during Differentiation and Infection [sciDLO Hi-C]

city: Wuhan

first: Ping

last: Hong

state: Hubei

address: No.1,Shizishan Street

department: college of informatics

institute: Huazhong Agricultural University

summary: Next-generation sequencing data of single cell indexed DLO Hi-C library of Thp1-mono, Thp1-macro, and Thp1-M.tb.

overall_design: We constructed in situ DLO Hi-C library of 3 samples (Thp1-mono, Thp1-macro, and Thp1-M.tb), and for each sample we did 14 sub-library.

first: Da

last: Lin

first: Weize

last: Xu


title: Depletion or cleavage of cohesin during anaphase differentially affects chromatin structure and segregation

status: Public on Oct 01 2022

city: London

first: Jonay

last: Garcia-Luis

state: London

address: Du Cane Road

department: London Institute of Medical Sciences

country: United Kingdom

institute: UKRI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromosome segregation requires both the separation of sister chromatids and the sustained condensation of chromatids during anaphase. In yeast cells, cohesin is not only required for sister chromatid cohesion but also plays a major role in determining the structure of individual chromatids in metaphase. Separase cleavage is thought to remove all cohesin complexes from chromosomes to initiate anaphase. It is thus not clear how the length and organisation of segregating chromatids are maintained during anaphase in the absence of cohesin. Here we show that degradation of cohesin at the anaphase onset causes aberrant chromatid segregation. Hi-C analysis on segregating chromatids demonstrates that cohesin depletion causes loss of intrachromatid organisation.  Surprisingly, TEV-mediated cleavage of cohesin does not dramatically disrupt chromatid organisation in anaphase, explaining why bulk segregation is achieved. In addition, we identified a small pool of cohesin complexes bound to telophase chromosomes in wildtype cells and show that they play a role in the organisation of centromeric regions. Our data demonstrate that in yeast cells, cohesin function is not over in metaphase, but extends to the anaphase period when chromatids are segregating.

overall_design: ChIP-seq and HiC

first: Hélène

last: Bordelet

first: Agnès

last: Thierry

first: Romain

last: Koszul

first: Luis

last: Aragon


title: Genome-wide analysis of polyadenylation events in Schmidtea mediterranea (II)

city: Bangalore

first: Dasaradhi

last: Palakodeti

state: Karnataka

address: GKVK Campus, Bellary road

department: TAS

country: India

institute: inStem, NCBS

summary: This study is the first to report genome-scale polyadenylation events in S.mediterranea using poly-A position profiling (3P-Seq).Various cis-acting elements such as hexameric PAS & U/GU enrichment after cleavage site were observed to be conserved in planaria.The cleavage site derived from 3P-Seq could be successfully associated with ~38-60% of transcripts (Makers -38%, oxford- 60% and Dresden- 44%).We also investigated the functional consequences of altered 3’UTRs arising from ApA. Around 97 transcripts were observed to undergo coding region alternate polyadenylation (CR-ApA) that resulted in loss of specific domains from proteins (as inferred from pfam domain search). In this study, we also demonstrated that microRNA-mediated regulation might be one of the key factors playing an important role in selection/evolution of alternate 3’UTRs. The 3’ UTR is one of the key regulatory element that decides the fate of mRNA inside a cell. Switching isoforms according to the need of cell and environmental cues could help the cell to adapt. In this study, we also attempted to study the tissue-specific role of ApA pattern in planaria. Due to the limitations associated with isolation of different tissue-specific cells from planaria, we performed a high-throughput microarray analysis across X1, X2 and Xins cell populations. We were clearly able to identify the differential expression pattern of the ApA events across cell population.

overall_design: Expression pattern of alternate polyadenylated transcripts in planarian stem cells (X1), Progenitor cells (X2) and differentiated cell (Xins) populations. All the samples were done in duplicates

first: Vairavan

last: Lakshmanan

first: Aswin

last: Sai Narain Seshasayee

first: Praveen

last: Anand

first: Dhiru

last: Bansal


title: Pre-Transplant recipients’ gene expression profiles in peripheral blood mononuclear cells correlate with the development of delayed graft function in kidney transplantation

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

summary: Delayed graft function (DGF) is associated with a reduced long-term graft survival. Ischemia-reperfusion damage and donors' features have been always considered as key pathogenic factors in this setting. The aim of our study was to evaluate the role of recipients' characteristics in the development of DGF to discover early genomics biomarkers in peripheral blood mononuclear cells (PBMC) in order to identify patients at risk.  We prospectively enrolled 932 kidney graft recipients from 466 donors for both kidneys. A total of 226 recipients experienced DGF. Among the 466 donors, 290 couples of recipients both patients presented with early graft function (EGF, group A), 50 couples  experienced DGF (group B) and 126 couples of recipients were discordant as one presented DGF and the other promptly recovered graft function (group C). In group C we randomly selected 10 couples of DGF/EGF recipients. Peripheral blood mononuclear cells (PBMC) were harvested before transplantation; their transcriptomic profile was investigated by a microarray approach and microarray results were validated by qPCR in an independent group (DGF n=25; EGF n=25).   In the whole study group, DGF was independently associated with both donors’ and recipient’s features. Moreover, group A, B and C presented significant differences in both donors’ and recipients’ characteristics. In group C of patients, DGF was significantly associated with body mass index, dialysis modality and number of mismatches. Two-hundred and seventy-three genes were differentially expressed before transplantation in discordant EGF/DGF patients of group C. Their main biological functions were immune dysfunction and inflammation. Among the differentially expressed genes, we observed a significant increase in the expression of CCR2, the MCP-1 receptor, in DGF patients. CCR-2 and MCP-1 up-regulation was confirmed in an independent cohort of patients.   Our results suggest that recipients' clinical and immunological features, potentially modulated by dialysis modality, are associated with the development of DGF independently of donors' features.

overall_design: In group C, including couples of discordant recipients from the same donor  as one presented DGF and the other promptly recovered graft function, we randomly selected ten EGF/DGF couples for microarray analysis (training group). Twenty ml of whole blood were harvested from the selected patients at the time of transplantation, before the administration of induction therapy. PBMCs were isolated by density separation over a Ficoll-PaqueTM (GE healthcare, Uppsala, Sweden). Total RNA was extracted using the RNeasy Mini Kit (Qiagen AG, Basel, Switzerland) and qualitatively and quantitatively analyzed through Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only samples with good quality, indicated by a RIN> 8, were used in the microarray experiment.   For the microarray experiments, we used the GeneChip® Human Genome U133A oligonucleotide microarray (Affymetrix, Santa Clara, CA) which contains 22,283 gene probe sets, representing 12,357 human genes, plus approximately 3,800 expressed sequence tag clones (ESTs), according to manufacturer’s instructions. We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.

first: Simona

last: Simone

first: Federica

last: Rascio

first: Francesco

last: Pesce

first: Barbara

last: Infante

first: Giuseppe

last: Castellano

first: Gianluigi

last: Zaza

first: Anna

last: Gallone

first: Michele

last: Battaglia

first: Pasquale

last: Di Tonno

first: Giovanni

last: Stallone

first: Loreto

last: Gesualdo

last: Grandaliano


title: MicroRNA Expression Profiles Analysis in Mouse Pancreatitis Tissue With or Without Hypertriglyceridemia

city: Shanghai

first: Guoyong

last: Hu

state: Shanghai

address: No. 110, Haining Road

country: China

institute: Shanghai General Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: The crucial roles of miRNAs have been implicated in various pathological processes, including pancreatitis. However, roles of miRNAs in hypertriglyceridemia-associated pancreatitis have not been reported. Pancreatitis tissue from mice with or without hypertriglyceridemia were analyzed for microRNA profiling. Using qPCR verification, we  further identified miR-153 as the most upregulated miRNA in mice with hypertriglyceridemia. This work provide potential therapeutic targets for the treatment of hypertriglyceridemia-associated pancreatitis.

overall_design: Pancreatitis tissue from mice with or without hypertriglyceridemia were used for microRNA sequencing.

first: Juanjuan

last: Dai

first: Mingjie

last: Jiang

first: Yangyang

first: Li

last: Wen

first: Xingpeng

last: Wang


title: Gene expression of 50 FFPE tissues of adults with T-cell lymphoblastic lymphoma

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: The current study aimed to establish a discriminative gene-based classifier of survival outcomes of T-cell lymphoblastic lymphoma (T-LBL) patients by exploring global gene-expression profiles of progressive versus progression-free T-LBL patients for differentially expressed candidate genes.

overall_design:
Affymetrix Human Gene 2.0 ST microarray (ThermoFisher Scientific, Waltham, MA, USA) was used to select differentially expressed genes.
Our microarray identified differentially expressed mRNAs between 22 progressive and 28 progression-free T-LBL patients.

first: Xiaopeng


title: Inhibition of TRPV4 rescues impaired excitability and social deficits in NAc-specific Shank3-deficient mice.

city: Lausanne

first: Elia

last: Magrinelli

state: Canto Vaud

address: Rue du Bugnon 9

department: Department of Neuroscience

country: Switzerland

institute: University of Lausanne

type: Expression profiling by high throughput sequencing

summary: We used AAV transfection of Shank3 shRNA to study the effect of Shank3 knock down in Nucleus Accumbens neurons. We find that Shank3 knock down leads to social deficits and hyperexcitability of Nucleus Accumbens D1-MSN. Bulk RNA sequencing shows that D1-MSN with Shank3 knock down upregulate TRPV4 and its subsequent antagonist driven inhibition leads to both a rescue of D1-MSN hyperexcitability and social deficit.

overall_design: Analysis of Nucleus accumbens cells from experiments involving the controls AAV-Scrambled or the AAV-Shank3-Sh Virus isolating in each case 4 different types of samples: Drd1 expressing infected cells, Drd1 expressing non-infected cells, non-Drd1 expressing infected cells and non-Drd1 expressing non-infected cells.

first: Natalia

last: Baumann


title: AOS10-FMT could rescure the adverse effects induced by high fat diet & STZ on the cecum [16S-cecum]

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We reported the side-effects of High fat diet & STZ on the cecum, and found that the AOS10-FMT could rescure the side-effect of High fat diet & STZ in many factors

overall_design: Exploration of the FMT effects on the damaged cecum induced by High fat diet & STZ

first: Yanan

last: Hao


title: Effect of depletion of PTEN on gene expression of GL261 cells

status: Public on Sep 30 2022

city: shenyang

first: Xin

last: Chen

address: No. 36, Sanhao Street

institute: Shengjing Hospital Affiliated to China Medical University

summary:
To predict the COCA subtype by gene expression, we established GL261 cell lines in which PTEN has been knocked out by sgRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells.

overall_design: Prediction of  GL261 cells and SgPTEN one by RNA-seq data.

first: Tianqi

last: Liu

first: Jianqi

last: Wu

first: Chen

last: Zhu

first: Wen

last: Cheng

first: Anhua


title: Carbon ion irradiation plus CTLA4 blockade elicits therapeutic immune responses in a murine tumor model

city: Greifswald

first: Theresa

last: Kordaß

state: Mecklenburg-Vorpommern

address: Ferdinand-Sauerbruch Straße DZ7 5.05

department: Surgical Research Laboratory

country: Germany

institute: Univserity Medicine Greifswald

summary: Radiotherapy can act as in situ vaccine activating preventive tumor-specific immune responses in treated patients. While carbon ion radiotherapy holds superior biophysical properties over conventional photon irradiation, little is known about the immunological effects induced by this radiation type. Multiple strategies combining radiotherapy with immune checkpoint inhibition (radioimmunotherapy) to enhance anti-tumor immunity have been described, however, results on the immune cell composition in tumors following radioimmunotherapy with carbon ions are lacking. Here, we present a bilateral tumor model based on time-shifted transplantation of murine, Her2+ EO771 tumor cells onto the flanks of immune competent mice followed by selective irradiation of the primal tumor. αCTLA4- but not αPD-L1-based radioimmunotherapy induced complete tumor rejection and mediated eradication of even non-irradiated, distant tumors. Cured mice were protected against EO771 rechallenge indicative of long lasting, tumor-specific immunological memory. Single cell RNA-sequencing and flow cytometric analyses of irradiated tumors revealed activation of NK cells and distinct tumor-associated macrophage clusters with upregulated expression of TNF and IL1 responsive genes. Distant tumors of irradiated mice showed higher frequencies of naïve T cells, which were activated upon combination with CTLA4 blockade. Thus, radioimmunotherapy with carbon ions plus CTLA4 inhibition reshapes the tumor-infiltrating immune cell composition and can induce complete rejection even of non-irradiated tumors. Our data suggest to combine radiotherapy approaches with CTLA4 blockade to achieve durable anti-tumor immunity. Furthermore, evaluation of future radioimmunotherapy approaches should not be restricted to immunological impacts at the irradiation site, but should also consider systemic immunological effects on non-irradiated tumors.

overall_design: Library preparation:   Single cells suspensions of eight digested tumors per group were pooled. Afterwards, cells were incubated with LIVE/DEAD® Fixable Dead Cell Stain Kit (Thermo Fisher Scientific) diluted 1:1000 in PBS for 30 min at 4 °C and stained with PE Rat Anti-Mouse CD45 antibody (BD) in FACS buffer for 30 min at 4 °C. Sorting for viable CD45+ cells was performed with a BD FACS Aria III.   The cell suspension of CD45 positive cells was adjusted to a concentration of approximately 1000 cells/μl. The cells were then loaded onto the 10x Genomics Chromium controller for droplet-enabled single cell RNA sequencing according to the manufacturer’s instruction manual. Library generation was performed following the Chromium Single Cell 3′ Reagents Kit version 3.1 user guide. The libraries were sequenced on the Illumina NovaSeq 6000 platform.

first: Laura

last: Hartmann

first: Wolfram

last: Osen

first: Oliver

middle: L

last: Eichmüller

first: Jenniger

last: Furkel

first: Elke

last: Dickes

first: Carissa

last: Reid

first: Jürgen

last: Debus

first: Stephan

last: Brons

first: Amir

last: Abdollahi

first: Mahmoud

last: Moustafa

first: Stefan

last: Rieken

middle: B


title: Reprogramming of root cells during nitrogen-fixing symbiosis entails dynamic polysome association of coding and non-coding RNAs

city: La Plata

first: Soledad

last: Traubenik

state: Buenos Aires

department: Ciencias Biologicas

country: Argentina

institute: Universidad Nacional de La Plata

summary:
GMUCT 2.0 data were analyzed to globally identify 5’ ends differentially accumulated in SKI3 RNAi roots as compared with GUS RNAi, as well as those that change in abundance in response to rhizobia
SUPERKILLER3 (*SKI3),* a member of SKI complex that guides RNAs to the 3 to 5'  exoribonuclease of the exosome complex. In the absence of a functional SKI complex to thread transcripts to the exosome, the bulk of the mRNAs that accumulate in the cytoplasm are diverted to the 5 -to-3  XRN4 pathway for degradation. We explored the function of *SKI3* during root nodule symbiosis using RNA interference to knockdown *SKI3* in *M. truncatula* hairy roots. To evaluate whether silencing of *SKI3* in *M. truncatula* roots altered RNA decay in response to rhizobia, we performed genome-wide mapping of uncapped and cleaved transcripts (GMUCT 2.0) on *GUS* RNA and *SKI3*RNAi roots. This method identifies products of miRNA or siRNA guided-endonucleolytic cleavage as well as decapped mRNAs by selecting for molecules with a free 5    monophosphate (5   P) (Willmann et al., 2014). GMUCT 2.0 data were analyzed to globally identify 5' ends differentially accumulated in *SKI3* RNAi roots as compared with *GUS* RNAi, as well as those that change in abundance in response to rhizobia.

overall_design: GMUCT 2.0 libraries were prepared from RNA samples isolated from GUS RNAi or SKI3 RNAi roots inoculated with water (mock) or S. meliloti for 48 hours. Three biological replicates were conducted.

first: Mauricio

last: Reynoso

first: Karen

last: Hobecker

first: Marcos

last: Lancia

first: Maureen

last: Hummel

first: Benjamine

last: Rosen

first: Christhpher

last: Town

first: Julia

last: Bailey-Serres

first: Flavio

middle: A

last: Blanco

first: Maria

middle: E

last: Zanetti


title: The change of gene expression during light damage of 661W photosensitive cells

city: Chengdu

first: Xiaoping

last: YU

state: State...

address: Chengdu Medical College, 610500, Sichuan Province, China

institute: Chengdu Medical College

summary: The changes of iron regulation, pyroptosis, apoptosis and antioxidant genes in 661W photosensitive cells under photodamage were analyzed by next-generation sequencing technology, and specific biomarkers for targeted treatment of retinal photodamage diseases were obtained.

overall_design: Light group: 661W cells were exposed to 2,000±100 lux cold white fluorescent lamp for 24 hours. Dark group: 661W cells were incubated in the dark for 24 hours. Total RNA was extracted for high-throughput sequencing to detect the expression of each gene.

last: Yu

first: Jiayuan

last: Peng

first: Xiaoying

last: Fu

first: Xiaoming

last: Deng


title: Separating DNA from chromatin damage activities detoxifies the anti-cancer drug doxorubicin

city: Leiden

first: Daniel

middle: M.

last: Borras

address: Einthovenweg 20

department: CI

country: Netherlands

institute: LUMC

summary: The anthracycline doxorubicin (Doxo) is one of the most effective and commonly used anti-cancer drugs. However, its clinical application is limited by severe side effects, such as cardiotoxicity, therapy-related tumors and infertility. Doxo induces both DNA damage through double-strand breaks and chromatin damage through histone eviction. We examined whether separating these activities would detoxify Doxo, while maintaining its chemotherapeutic efficacy. Here we present anthracycline variants harboring the histone eviction activity alone which remain potent anti-cancer drugs, while greatly alleviating cardiotoxicity and therapy-related tumor formation. This suggests that the treatment-limited side effects of Doxo in mice can be strongly reduced by modifying the chemical structure. The modified anthracycline anti-cancer drugs may provide effective chemotherapeutics allowing prolonged treatment and a higher quality of life post-treatment.

overall_design: Comparison of ATAC-seq signal for several anticancer drugs

first: Xiaohang

last: Qiao

first: Sabina

last: van der Zanden

first: Dennis

last: Wander

middle: M

first: Olaf

last: van Tellingen

first: Jeroen

last: Bakker

first: Ji-Ying

last: Song

first: Arjo

last: Rutten

first: Noortje

last: van Gils

first: Charlotte

last: Zuur

first: Baoxu

last: Pang

first: Linda

last: Smit

first: Hermen

last: Overkleeft

first: Jacques

last: Neefjes


title: Hepatic inactivation of murine Surf4 results in marked reduction in plasma cholesterol

city: Ann Arbor

first: Vi

last: Tamg

state: Michigan

address: 210 Washtenaw Ave

department: Molecular and Integrative Physiology

country: USA

institute: University of Michigan

summary: SURF4 is a cargo receptor that has been implicated in the intracellular trafficking of PCSK9 and APOB - proteins involved in cholesterol transport and metabolism. We generated hepatic SURF4-deficient mice (Surf4(fl/fl) Alb-Cre+) to investigate the physiologic role of SURF4 in vivo

overall_design: Anlysis of gene expression profile in livers of Surf4(fl/fl) Alb-Cre+ and Surf4(fl/fl) Alb-Cre- mice (n=3 per group) by RNA-seq

first: Tang

last: Vi T

first: McCormick

last: Joseph

first: Xu

last: Bolin

first: Wang

last: Yawei

first: Fang

last: Huan

last: Xiao

first: Siemieniak

last: David

first: Khoriaty

last: Rami

first: Emmer

last: Brian T

first: Chen

last: Xiao-Wei

first: Ginsburg


title: Rapid genomic changes induced by PTH, SIK-inhibition, FGF23, and 1,25(OH)2D3 in the mouse kidney

city: Madison

first: Mark

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

summary: In vivo ChIP-seq in mouse kidney: we examine the genomic recruitment of VDR, RXR, pCREB, CBP, CRTC2 (TORC2), SRC1, SRC3, BRD4, RNApolII, H3K9ac, H3K27ac, and H3K36me3 after intraperitoneal injection of 10 mg/kg body weight (bw) 1,25(OH)2D3 (in propylene glycol), 230 mg/kg bw PTH (1–84) (in phosphate buffered saline (PBS)), 50 mg/kg bw FGF23 (in PBS + 0.1% BSA), 30 mg/kg YKL-05-099 (PBS + 25mM HCl), 40 mg/kg SK-124 (15% HPBCD (hydroxypropyl β-cyclodextrin)), or vehicle (EtOH, PBS, or HPBCD). YKL-05-099 and SK-124 are salt-inducible kinase inhibitors that liberate CRTC2 from sequestration in the cytoplasm and allow CRTC2 translocation to the nucleus. Our findings show that these TFs and coactivators contribute to transcription of genes in the kidney involved in vitamin D metabolism, demonstrates SIK-inhibition as a key modulator of vitamin D metabolism, and provides molecular insight into the coordinated mechanistic actions of PTH, FGF23, and 1,25(OH)2D3 in the mouse kidney that regulate mineral homeostasis.

overall_design: All samples included were analyzed in biological triplicate (3 individual mice). ChIP assay was performed on mouse kidneys (2 per mouse) after intraperitoneal injection of 10 mg/kg body weight (bw) 1,25(OH)2D3 (in propylene glycol), 230 mg/kg bw PTH (1–84) (in phosphate buffered saline (PBS)), 50 mg/kg bw FGF23 (in PBS + 0.1% BSA), 30 mg/kg YKL-05-099 (PBS + 25mM HCl), 40 mg/kg SK-124 (15% HPBCD (hydroxypropyl β-cyclodextrin)), or vehicle (EtOH, PBS, or HPBCD). All treatements were 1 h unless otherwise indicated in treatment column. ChIP-seq libraries were then prepared for all samples and sequenced paired-end on the Illumina NovaSeq instrument. Input files, pCREB, histones with PTH treatment at 60 min included in GSE133025.

first: Nancy

last: Benkusky

first: Sun-Hee

middle: S

last: Yoon

first: Marc

middle: N

last: Wein

first: J

middle: W

last: Pike


title: A time-resolved transcriptome atlas of maize grain development

city: Yangling

first: Zhou

middle: Jian

last: Qu

state: Shaanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

summary: Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas for seed development of eight maize inbred lines based on 144 samples from the middle to late stages of grain development. A total of 26,747 genes with FPKM value more than 1 at least one sample were found to be involved in programming grain development. Global comparisons of genes expression highlighted the fundamental transcriptomic reprogramming and the phases of development. Coexpression analysis provided further insight into the dynamic reprogramming of the transcriptome by revealing functional transitions during maturation. Combined with grain moisture content and grain dehydration rate of different developmental time points of eight maize inbred lines, we captured a large number of genes related to grain moisture content and grain dehydration rate, which should help elucidate key mechanisms and regulatory networks that underlie grain dehydration during maize grain development. These results provide a comprehensive understanding of which biological processes are involved in the regulation of moisture variety of maize grain, the general principles of which provide a new perspective on improving maize grain dehydration characteristics. Meanwhile, this study provides a valuable resource for understanding the genetic regulation of maize grain development.

overall_design: Global gene expression profiles of kernels of 8 maize inbred lines at 21, 28, 35, 42, 49 and 56 days after pollination

first: Jianzhou

first: Jiquan

last: Xue

first: Shutu

last: Xu


title: Expression data from LINC00958-depleted primary human keratinocytes

city: Uppsala

first: Longlong

last: Luo

state: Sweden

address: BMC Husargatan 3 752 37 UPPSALA

country: Sweden

institute: Uppsala University

summary:
Long non-coding RNAs (lncRNAs) have emerged as important regulators of biological processes and diseases, the function of the majority of epidermal lncRNAs in skin homeostasis and their potential role in psoriasis has remained unknown. We report the identification of lncRNAs with altered expression in psoriasis keratinocytes and identify LINC00958 is overexpressed in psoriasis epidermis.
We used microarrays to detail the global programme of gene expression upon LINC00958 depletion in keratinocytes

overall_design: Human primary keratinocytes were transfected with siLINC00958 or siControl (n=4) for RNA extraction and hybridization on Affymetrix microarrays. We performed transcriptomic analysis to dectect differentially expressed genes on siLINC00958 vs siControl.

first: Lorenzo

last: Pasquali

first: Andor

last: Pivarcsi

first: Enikö

last: Sonkoly


title: High-Throughput Isolation of RNA from Single Cells within Intact Tissue for Spatial and Temporal Sequencing

city: Santa Cruz

first: John

last: Stanley

state: CA

address: 1156 High St

institute: UCSC

summary: Obtaining and performing single-cell RNAseq by aspirating only1-5% of sub-single cell RNA content from individual cells within fresh frozen tissue samples.

overall_design: MISSING

first: Aifua

last: Fu

first: Akshar

last: Lohith


title: Genome-wide analysis of polyadenylation events in Schmidtea mediterranea (I)

first: Dasaradhi

last: Palakodeti

first: Vairavan

last: Lakshmanan

first: Aswin

last: Sai Narain Seshasayee

first: Praveen

last: Anand

first: Dhiru

last: Bansal


title: Genome-wide analysis of polyadenylation events in Schmidtea mediterranea

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

overall_design: Refer to individual Series


title: Gene expression profile in mouse skeletal muscle after Mettl21c deletion

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 270 S Russell St

department: Animal Science

institute: Purdue University

summary: Analysis of soleus (SOL) muscle isolated from wildtype (WT) and Mettl21cLacZ/LacZ mice (KO). Results provide unbiased gene expression profile of SOL muscle after Mettl21c deletion.

overall_design: Two-condition experiment, WT SOL vs. KO SOL. Biological replicates: 3 WT replicates, 3 KO replicates. 3 x 2-color arrays: The experiments were performed technically as dual channel (eg, Cy3-labeled-WT and Cy5-labeled-KO samples hybridized to the same array).

first: Chao

last: Wang

first: Jennifer

last: Freeman


title: Identification of SMXL4- and SMXL5-dependent genes in comparison to the SMAX1-dependent genes

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

institute: Heidelberg University

summary: We used RNA-seq to generate the transcriptional profile of 7 days old WT, smxl5-1, smxl4-1 smxl5-1 and smax1-2 Arabidopsis mutant seedlings. We then used statistical analysis to identify differentially expressed genes that potentially contribute to the smxl5-1, smxl4-1 smxl5-1 and smax1-2 mutant phenotype.

overall_design: RNA from three replicates each of WT and smxl5-1, smxl4-1 smxl5-1 and smax1-2 mutants were sequenced and differentially expressed genes were identified by using the DESeq2 package.

first: Eva-Sophie

last: Wallner

first: Virginie

last: Jouannet


title: Co-expression networks of deacclimation-impaired mutants identified involvement of hypoxia and complex regulation of the cold stress release response

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

institute: MPI of Molecular Plant Physiology

summary: Plants adapt to cold, non-freezing temperatures through cold acclimation and subsequently lose the acquired freezing tolerance in warmer temperatures in a process called deacclimation. By measuring the freezing tolerance of mutant lines, this study identified that the loss of HRA1, LBD41, MBF1c and JUB1 slows the rate of deacclimation in the first four days in Arabidopsis thaliana. Comparative transcriptomic (RNA-Seq) and co-expression analysis of Col-0, mbf1c and jub1 during deacclimation identified an involvement of thermoswitches, cell wall remodeler and transporters in the regulation of the rate of deacclimation. In mbf1c and jub1 a unique increase in stress responsive genes and regulation of the jasmonic acid pathway was detected and linked to the mutants’ retention of freezing tolerance during deacclimation. Hypoxia was observed to be induced in early deacclimation evidenced by an increase in ADH enzyme activity and upregulated gene expression of hypoxia markers (qRT-PCR). This work suggests that the overserved hypoxia response creates hypoxic niches within the plants and supports growth and development during deacclimation.

overall_design: RNA-Sequencing of 28 d old Arabdiopsis thaliana plants of lines Col-0, mbf1c and jub1 at non-acclimated conditions (NonA), 3 days of cold acclimation (ACC), 2 days of deacclimation (Deacc2) and 4 days of deacclimation (Deacc4). For each condition and plant line three biological replicates where measured

first: Kora

last: Vyse

first: Axel

last: Fischer

first: Greta

last: Zajancauskaite

first: Alexander

last: Erban

first: Joachim

last: Kopka

first: Salma

last: Balazadeh


title: Tensile strain and altered synovial tissue metabolism in human knee osteoarthritis

city: London

first: Holly

middle: T

last: Philpott

state: Ontario

address: 1551 Richmond St

country: Canada

institute: Western University

summary:
To investigate the physiologic responses of whole osteoarthritic synovium to cycle tensile strain.
We obtained 3 matched synovial tissue samples from 6 patients undergoing total knee arthroplasty, subjected them to cyclic tensile strain, and then performed gene expression profiling analysis using RNA seq from each cyclic tensile strain protocol.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for whole osteoarthritis synovium subjected to 3 different cyclic tensile strain protocols (control (static), low-frequency (0.3Hz), and high-frequency (1.0Hz)).

first: Trevor

last: Birmingham

first: Benoit

last: Fiset

first: Logan

last: Walsh

first: Mitchell

middle: C

last: Coleman

first: Cheryle

last: Séguin

first: C

last: Appleton


title: Circular RNA expression in tongue squamous cell carcinoma patients

city: Fuzhou

first: Zexi

last: Chen

state: Fujian

address: 1 Xue Yuan Road,University Town

institute: Fujian Medical University

summary: circRNA microarrays were performed with 2 pairs of tongue squamous cell carcinoma and their matched adjacent tissues.  The statistical significance of the difference was estimated by t-test. circRNAs having fold changes 1.5 and p-values 0.05 are selected as the significantly differentially expressed. The data from microarray indicated that there were 54 upregulated and 70 downregulated circRNAs in TSCC tissues.

overall_design: Our work showed that several circRNAs may be promising biomarkers,including has_circ_0125480, hsa_circ_0007443 and hsa_circ_0025202, for tongue squamous cell carcinoma patients.

first: Lingling

last: Liu


title: Development of LncRNAs expression signisure of STZ induced rats skin

status: Public on Sep 29 2022

city: guangzhou

first: Meng

last: Ren

address: 107 Yanjiang West Road

department: endocrinology department

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

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

summary: Impaired wound healing is one of the main reasons that leads to diabetic foot ulcerations. However, the exact mechanism of delayed wound healing in diabetes mellitus is not fully understood. Long non-coding RNAs (lncRNAs) are widely involved in a variety of biological processes and diseases, including diabetes and its associated complications. To further identify the roles of LncRNAs in diabetic wound healing, four STZ induced diabetic rat skin tissues and four control rat skin tissues were prepared for a LncRNAs microarray expression profiling by using rat LncRNA Array (4 x 44K, Arraystar).

overall_design: 4-week old Sprague-Dawley (SD) male rats were intraperitoneally (i.p.) injected with 60 mg/kg streptozotocin (STZ; Sigma-Aldrich, St. Louis, MO) to induce diabetes and four sham-treated SD male rats as control group. Rats were housed for 4 weeks before being anesthetized, and full-thickness skin tissue was harvested for microarray analysis.

first: Qin

last: Tan

first: Yan

last: Li


title: ChIP-seq analysis of subunits of meiotic cohesin complexes (mei-Cohesins) in transgenic human cancer cell lines

city: Guangzhou

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

summary:
The study involved chromatin IP analyzed by high-throughput sequencing analysis using stable transgenic human cancer cell lines, which express Tet-inducible combinations of mei-cohesin subunits.
The following individual genes and combinations of mei-cohesin subunits were expressed in human cells : STAG3, SMC1beta, STAG3+SMC1beta+REC8, and STAG3+SMC1beta+RAD21L
The goal of the study was to investigate the epigenomic properties of somatic cells in response to the induction of mei-cohesin subunits using Tet-on inducible transgenes activated by an rtTA transgene and doxycicline.

overall_design: The K562 (ATCC® CCL-243™), hTERT RPE-1 (ATCC® CRL-4000™), or DLD-1 (ATCC® CCL-221™) cell lines, were first stably infected with rtTA, followed by Tet-On-STAG3,  Tet-On-SMC1beta, Tet-On-REC8, and Tet-On RAD21L lentiviruses. In order to generate multi-transgenic cells that model the 4-subunit mei-cohesin holocomplexes, i.e. REC8 and RAD21L-based, the Tet-On-STAG3+Tet-On-SMC1beta cells were separately infected with Tet-On-REC8 and Tet-On-RAD21L lentiviruses, to generate two triple transgenic cell lines. The populations of transgenic cells selected for marker drug-resistance were cloned to generate single transgenic clones used for ChIP-seq experiments.

first: Abdelhalim

last: Boukaba

first: Jian

first: Qiongfang

last: Wu

first: Jierong

last: Liang


title: RNA-seq analysis of DLD-1 cell lines expressing cDNAs of subunits on human mei-cohesin complexes

first: Alexander

summary:
The study involves trabscriptome analysis using RNA-seq of stable transgenic DLD-1 cancer cell line, which express Tet-inducible combinations of mei-cohesin subunits.
The following combinations of mei-cohesin genes were expressed in DLD-1 : STAG3+SMC1beta, STAG3+SMC1beta+REC8, and STAG3+SMC1beta+RAD21L
The goal of the study was to investigate the RNA transcriptional response to the induction of mei-cohesin subunits in somatic cells using Tet-on inducible transgenes activated by an rtTA transgene and doxyciline.

overall_design: The DLD-1 cell line, which is derived from adult male colorectal adenocarcinoma (ATCC® CCL-221™), were first stably infected with rtTA, Tet-On-STAG3 and Tet-On-SMC1beta lentifiruses This cell line was used as an additional control along with the parent cell line DLD-1.  The SMC3+SMC1b cells were also separately infected with Tet-On-REC8 and Tet-On-RAD21L lentiviruses, to generate two triple transgenic cell lines modeling the somatic expression of two major meiotic cohesin complexes: REC8 and RAD21L-based. Both the drug-selected populations of transgenic cell lines and single clones were used as biological replicates.


title: Gene expression profiling of Arabidopsis arf2-6 mutant compared to Col-0 wildtype during dark-induced senescence

city: York

first: Katherine

last: Denby

address: Department of Biology

institute: University of York

summary: The aim of this experiment was to decipher a transcriptional regulatory code of Arabidopsis Auxin Response Factor 2 (ARF2) and understand the molecular basis of ARF2’s role as a promoter of dark-induced senescence. A combination of computational tools and yeast one-hybrid experiments identified potential direct transcriptional regulators of ARF2 belonging to several TF families including AP2/ERFs and AREB/ABF/ABI5s. Using ARF2 promoter mutants in transcriptional activation and Y1H experiments, the binding sites of these TFs in the ARF2 promoter were identified. AP2/ERFs including ERF1, ERF15 and ORA59 transactivate the ARF2 promoter in Arabidopsis mesophyll protoplasts and this transactivation is positively regulated by ABA. Crucially, the positive effect of ABA on ERF1 transactivation of ARF2 relies on the functional ABRE motif in the ARF2 promoter and the presence of AREB/ABF/ABI5s (ABF3 and ABF4) suggesting the existence of combinatorial regulation of ARF2 by these direct regulators. ABF3 and ABF4 were unable to activate the ARF2 promoter on their own indicating the necessity of ERF1 as a coupling TF for AREB/ABF/ABI5-driven regulation of ARF2. We also show that MED25 (a subunit of the Mediator complex) is required for proper transcriptional regulation of ARF2 during senescence. med25 plants show decreased ARF2 mRNA levels during natural senescence and, similarly to arf2-6 mutants, exhibit a delayed dark-induced senescence phenotype. We show that MED25 is important for ERF1-, ERF15- and ORA59-dependent transactivation of ARF2 in Arabidopsis protoplasts and finally idenitfy genes differentially expressed in arf2-6 mutants compared to wildtype during dark-induced senescence. Hence, we elucidate a regulatory network around ARF2 identifying combinatorial transcriptional regulation of this gene during senescence as well as likely downstream targets. The combinatorial regulation, comprised of AP2/ERFs and AREB/ABF/ABI5s TFs, enables integration of at least two key hormone signaling pathways to drive expression of a key senescence regulator.

middle: J


title: Single cell gene expression profile of CD11c-enriched fraction of dissociated mouse lung immune cells

city: San Francisco

first: Xin-Zi

last: Tang

address: 555 Mission Bay Boulevard S

department: CVRI

institute: UCSF

summary: To identify subsets of antigen presenting cells in the normal healthy mouse lung based on gene expression profiling, lung tissues including airways were enzymatically dissociated, and CD11c+ cells were magnetically enriched and submitted for single cell analysis using the 10x genomics pipeline.

overall_design: Whole lung tissues from healthy untreated mice were excised and enzymatically dissociated into single cell suspension. Cells were partially depleted of B cells and alveolar macrophages and then CD11c+ cells were enriched by labeling with magnetic beads. CD11c+ enriched fractions were submitted for single cell RNA sequencing. Mice used were transgenic MacBlue mice (https://www.jax.org/strain/026051), however, transgenic CFP gene was not added to the mm10 library in these analyses.

first: Christopher

middle: D

last: Allen


title: SARS-CoV-2 infection of Lung Organoids Reveals Conserved Use of Tetraspanin-8 by Ancestral-, Delta-, and Omicron- Variants

first: Arjun

middle: Arkal

last: Rao

address: 505 Parnassus Ave, S-447

department: CoLabs

institute: University of California, San Francisco

summary: Ancestral SARS coronavirus-2 (SARS-CoV-2) and variants of concern (VOC) caused a global pandemic with a spectrum of disease variation linked to immune dysfunction. The mechanistic underpinnings of variation related to lung epithelium are relatively understudied. Here, we biobanked lung organoids by preserving stem cell function. We optimized viral infection with H1N1 swine flu and next comprehensively characterized epithelial responses to SARS-CoV-2 infection in phenotypically stable lung organoids from twenty different subjects. We discovered Tetraspanin 8 (TSPAN8) as a novel mediator of SARS-CoV-2-infection. TSPAN8 facilitates SARS-CoV-2 infection rates but does not via enhanced ACE-2-mediated entry.  In head-to-head comparisons with Ancestral SARS-CoV-2, Delta- and Omicron- VOC displayed lower overall infection rates of organoids but triggered increased epithelial interferon responses. All variants shared highest tropism for ciliated- and goblet- cells. ACE2- and TSPAN8- expression are universal features of infected cells. TSPAN8-blocking antibodies diminish SARS-CoV-2 infection and may spur novel avenues for COVID-19 therapy.

overall_design: 2 multiplexed pools consisting of 8 total Lung organoids tagged with lipid-based Multiseq. Mock and SARS-SoC-2 infected organoids of 2522UL , 2450UL, L7UL, and 2524U

first: Lisiena

last: Hysenaj

first: Lauren

last: Rodriguez

last: Andersen

first: Jeroen

middle: P

last: Roose


title: Chip-seq analysis of meiotic Cohesin complexes  (mei-Cohesins) subunits, CTCF, and BORIS/CTCFL in Macaca fascicularis testis

summary:
The study involved chromatin IP analyzed by high-throughput sequencing analysis using purifird germ cells from M. fascucularis testis
M. fascicularis is a monkey with non-seasonal male germ cells production, and the most popular primate for preclinical animal studies.
The goal of the study was to investigate the epigenome of M. fscicularis testis with respect to mei-Cohesin complexes, CTCF and BORIS

overall_design: The cynomolgus monkeys testis material was collected from six 7-9 years old male monkeys. The testes were placed on ice and germ cells were prepared by passing through two mesh sizes.The cell fraction was fixed according to ChIP-seq protocol and kept frozen

first: AbdelHalim

first: Jinjin


title: Expression of vimentin alters cell mechanics, cell-cell adhesion, and gene expression profiles suggesting the induction of a hybrid EMT in human mammary epithelial cells

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

summary: Vimentin is a Type III intermediate filament (VIF) cytoskeletal protein that regulates the mechanical and migratory behavior of cells. Its expression is considered to be a marker for the epithelial to mesenchymal transition (EMT) that takes place in tumor metastasis. However, the molecular mechanisms regulated by the expression of vimentin in the EMT remain largely unexplored. We created MCF7 epithelial cell lines expressing vimentin from a cumate-inducible promoter to address this question.  When vimentin expression was induced in these cells, extensive cytoplasmic VIF networks were assembled accompanied by changes in the organization of the endogenous keratin intermediate filament (KIF) networks and disruption of desmosomes. Significant reductions in intercellular forces by the cells expressing VIFs were measured by quantitative monolayer traction force and stress microscopy.   In contrast, laser trapping micro-rheology revealed that the cytoplasm of MCF7 cells expressing VIFs was stiffer than the uninduced cells. Vimentin expression activated transcription of genes involved in pathways responsible for cell migration and locomotion. Importantly, the EMT related transcription factor TWIST1 was upregulated only in WT vimentin expressing cells and not in cells expressing a mutant non-polymerized form of vimentin, which only formed unit length filaments (ULF). Taken together, our results suggest that vimentin expression induces a hybrid EMT correlated with the upregulation of genes involved in cell migration.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type MCF7 and the MCF7 cells expressing either wild type filamentous vimentin (WT vimentin) or Unit Length Filament mutant form of vimentin (ULF mutant vimentin)

first: Suganya

last: Sivagurunathan

first: Amir

last: Vahabikashi

first: Haiqian

last: Yang

first: Jun

last: Zhang

first: Kelly

last: Vazquez

first: Yuliya

last: Politanska

first: Hiam

last: Abdala-Valencia

first: Jacob

last: Notbohm

first: Ming

last: Guo

first: Stephen

last: Adam

first: Robert

last: Goldman


title: Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.

first: Friedrich

last: Preusser

address: Hannoversche Str. 26

department: Berlin Institute For Molecular Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary: During their lifetime, animals must adapt their behavior to survive in changing environments. This ability requires the nervous system to adjust through dynamic expression of neurotransmitters and receptors but also through growth, spatial reorganization and connectivity while integrating external stimuli. For instance, despite having a fixed neuronal cell lineage, the nematode Caenorhabditis elegans’ nervous system remains plastic throughout its development. Here, we focus on a specific example of nervous system plasticity, the C. elegans dauer exit decision. Under unfavorable conditions, larvae will enter the non-feeding and non-reproductive dauer stage and adapt their behavior to cope with a new environment. Upon improved conditions, this stress resistant developmental stage is actively reversed to resume reproductive development. However, how different environmental stimuli regulate the exit decision mechanism and thereby drive the larva’s behavioral change is unknown. To fill this gap, we developed a new open hardware method for long-term imaging (12h) of C.elegans larvae. We identified dauer-specific behavioral motifs and characterized the behavioral trajectory of dauer exit in different environments to identify key decision points. Combining long-term behavioral imaging with transcriptomics, we find that bacterial ingestion triggers a change in neuropeptide gene expression to establish post-dauer behavior. Taken together, we show how a developing nervous system can robustly integrate environmental changes, activate a developmental switch and adapt the organism’s behavior to a new environment.

overall_design: Transcriptional analysis at 4 different time points (0h, 3h, 6h, 9h) during dauer exit in 2 different environments (with bacteria & no bacteria)

first: Anika

last: Neuschulz

first: Jan

last: Junker

first: Nikolaus

last: Rajewsky

first: Stephan

last: Preibisch


title: Digital-scRRBS: A cost-effective, highly sensitive and automated single-cell methylome analysis platform via digital microfluidics

city: Xiamen

first: Xi

last: Zeng

address: No.422, Siming South Road

institute: Xiamen University

type: Methylation profiling by high throughput sequencing

summary: Single-cell DNA methylation sequencing is a powerful method for elucidating important physiological and pathological processes, identifying cell subpopulations, and constructing epigenetic regulatory networks. Existing methylome analyses typically require substantial starting materials, complex operations, and high cost and are susceptible to contamination. These problems have impeded the development of single-cell methylome technology for rare cell profiling. In this work, we report Digital Microfluidics-based single-cell Reduced Representation Bisulfite Sequencing (Digital-scRRBS), the first microfluidics-based single-cell methylome library construction platform, which is an automatic, efficient, reproducible, and reagent-economy approach to dissect the single-cell methylome. Taking advantage of our uniquely designed digital microfluidic chip, we realized efficient single-cell isolation in less than 15 seconds. Furthermore, with the advantages of a confined environment, superhydrophobic surface, and nano-scale reaction volume of our digital microfluidic chip, more amplifiable DNA is retained for library construction compared to other approaches. We have successfully constructed single-cell methylation sequencing libraries with a unique genome mapping rate of up to 53.6%, covering up to 2.26 million CpG sites. The application of Digital-scRRBS allows us to discriminate cell identity and dynamically monitor DNA methylation levels during drug administration. Digital-scRRBS provides the technology for widespread application of single-cell methylation methods as a versatile tool for epigenetic analysis in rare cells and highly heterogeneous populations.

overall_design: In total, 25 GM12878 cell line samples and 20 K562 cell line samples were analyzed. We examined genome-wide DNA methylation profiles of GM12878 cells, including 8 low-input samples with starting DNA sample amounts in the range of 0.3-10ng, 8 singe-cell samples, pooled-2, 3, 4, 10, 15, 20 cells samples using Digital-scRRBS, and 3 single-cell samples in the tube. K562 cells were treated with decitabine in a final concentration of 300 nM to induce demethylation, and 8 treated samples and 12 untreated sample were analyzed to reveal the mechanism of demethylation.

first: Xiaoxu

first: Zhi

last: Zhu

first: Jia

last: Song

first: Chaoyong


title: Aberrant lncRNA–mRNA Expression Profile and Function Networks during the Adipogenesis of Mesenchymal Stem Cells from Patients with Ankylosing Spondylitis

first: Zhenhua

last: Liu

address: industry Avenue 253#

department: Spine surgery

institute: Zhujiang Hospital

summary: We have already demonstrated that mesenchymal stem cells from patients with ankylosing spondylitis (ASMSCs) exhibited greater adipogenic differentiation potential than those from healthy donors (HDMSCs). Here, we further investigated the expression profile of long noncoding RNA (lncRNA) and mRNA, aiming to explore the underlying mechanism of abnormal adipogenic differentiation in ASMSCs.

overall_design: HDMSCs and ASMSCs were separately isolated and induced with adipogenic differentiation medium for 10 days. Thereafter, lncRNAs and mRNAs that were differentially expressed (DE) between HDMSCs and ASMSCs were identified via high-throughput sequencing

first: Shuizhong

last: Cen

first: Sujun

last: Qiu

first: Mingxi

last: Cai


title: Inhibition of FOXP3 by Stapled Alpha-Helical Peptides Dampens Regulatory T Cell Function

city: Chicago

first: James

last: LaBelle

state: IL

address: 900 East 57th Street, KCBD 5122

institute: University of Chicago

summary: Despite continuing advances in the development of novel cellular-, antibody-, and chemotherapeutic-based strategies to enhance immune reactivity, the presence of regulatory T cells (Tregs) remains a complicating factor to their clinical efficacy. To overcome dosing limitations and off-target effects from antibody-based Treg deletional strategies, we investigated the ability of hydrocarbon stapled alpha-helical (SAH) peptides to target FOXP3, the master transcription factor regulator of Treg development, maintenance, and suppressive function. Using the crystal structure of the FOXP3 homodimer as a guide, we developed SAHs in the likeness of a portion of the native FOXP3 antiparallel coiled-coil homodimerization domain (SAH-FOXP3) to block this key FOXP3 protein-protein interaction (PPI) through molecular mimicry. We show that lead SAH-FOXP3s bind FOXP3, are cell permeable, non-toxic to T cells, induce dose-dependent transcript and protein level alterations of FOXP3 target genes, impede Treg function, and lead to Treg gene expression changes in vivo consistent with Foxp3 dysfunction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for naïve CD4+ Tcons and CD4+CD25+FOXP3+ Tregs following 2 days of daily treatment with either SAH(229-259)C or vehicle. There are 12 samples total (6 Tcon samples, 6 Treg samples). Within each set of 6 Tcon or Treg samples, there are 2 vehicle-treated controls and 4 SAH-treated controls representing cells from either the lymph nodes or spleen.


title: N6-Methyladenosine Methylomic Landscape of human normal skin and heat-denatured dermis

city: Changsha

first: Ran

middle: Yan

last: qin

address: xiangyalu street

institute: Central south university

summary: Preservation of the denatured dermis can facilitate wound repair as well as restore hand function.Denatured dermis can be reversibly recovered after deep partial thermal injury.  In this dataset, we include the m6A methylated RNA data obtained from normal skin tissues  (C group) and denatured dermis (T group).

overall_design: We generated the following comparisons using Fold-change (FC) ≥ 2 or ≤ 0.5, and p < 0.05 were used to identify the differentially m6A methylated RNAs.The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”.  Two channel arrays were used for these samples but the data were analyzed as single-channel so that each sample  represents either IP or supernatent and the sample table includes the normalized signal values.

first: Yanqin

last: Ran

first: Zhuoxian

last: Yan

first: Fangqin

last: Wu

first: Mitao

last: Huang

first: Pihong

last: Zhang

first: Bimei

last: Jiang

first: Pengfei

last: Liang


title: Progenitor like cell type of an MLL-EDC4 fusion in acute myeloid leukemia

first: Linda

middle: Christina

last: Schuster

address: Im Neuenheimer Feld 280

department: Chromatin Networks

institute: German Cancer Research Center (DKFZ)

summary: Transcriptome analysis by single cell sequencing provides valuable information on intratumor heterogeneity and developmental stages of acute myeloid leukemia (AML) as well as interactions of tumor cells with the microenvironment. However, it has been hardly applied to the subgroup of cases with translocations of the mixed lineage leukemia (MLL) gene for which the enhancer of mRNA decapping 4 (EDC4) gene was recently identified as a novel fusion partner (MLL-EDC4). Here, we compared different MLL translocation by single cell RNA sequencing of cells derived from peripheral blood. The AML MLL-EDC4 patient almost exclusively showed a transcriptional profile of hematopoietic progenitor cells while leukemic cells while the MLLT3-MLL and MLL-ELL fusions exhibited a more differentiated phenotype. The MLL-EDC4 progenitor state was characterized by the upregulation of key transcriptional regulators in AML (RUNX1, SOX4, HOPX), target genes of MYC and interferon signaling as well as other genes known to play a critical role in hematopoiesis or leukemic stem cell activation (CDK6, FLT3, NPM1). In addition, we detected an enrichment of a normal and putatively immunosuppressive monocyte population in the patient with MLL-EDC4. Thus, the MLL-EDC4 translocation was associated with unique transcriptional and microenvironmental features.

overall_design:
The scRNA-seq analysis was performed with peripheral blood mononuclear cells (PBMCs) from four patients for the novel MLL-EDC4 translocation in comparison to MLL-MLLT3 and MLL-ELL fusions
Submitter states that the raw data files will be uploaded to the EGA database due to patient privacy issues.

first: Stephan

last: Tirier

first: Simon

last: Steiger

first: Jan-Philipp

last: Mallm

first: Heiko

last: Becker

first: Jesus

last: Duque-Afonso

first: Tobias

last: Ma

first: Seishi

last: Ogawa

first: Michael

last: Cleary

last: Lübbert

first: Karsten

last: Rippe


title: Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [ATAC-Seq]

city: Berlin

middle: I

last: Robson

address: Max Planck Institut für molekulare Genet, Ihnestrasse 63-73

institute: Max Planck Institute for Molecular Genetics

summary: Cohesin loop extrusion facilitates precise gene expression by continuously driving promoters to sample all enhancers located within the same topologically-associated domain (TAD). However, many TADs contain multiple genes with divergent expression patterns, thereby indicating additional forces further refine how enhancer activities are utilised. Here, we unravel the mechanisms enabling a new gene, Rex1, to emerge with divergent expression within the ancient Fat1 TAD in placental mammals. We show that such divergent expression is not determined by a strict enhancer-promoter compatibility code, intra-TAD position or nuclear envelope-attachment. Instead, TAD-restructuring in embryonic stem cells (ESCs) separates Rex1 and Fat1 with distinct proximal enhancers that independently drive their expression. By contrast, in later embryonic tissues, DNA methylation renders the inactive Rex1 promoter profoundly unresponsive to Fat1 enhancers within the intact TAD. Combined, these features adapted an ancient regulatory landscape during evolution to support two entirely independent Rex1 and Fat1 expression programs. Thus, rather than operating only as rigid blocks of co-regulated genes, TAD-regulatory landscapes can orchestrate complex divergent expression patterns in evolution.

sample_organism:
Gallus gallus
Mus musculus
Monodelphis domestica

overall_design: We mapped accessible chromatin in morphologically stage-matched  limb buds from mouse (E11.5), opossum (Stage 30) and chicken (HH22) embryos using ATAC-seq as described in Paliou et al, 2019.

first: Alessa

middle: R

last: Ringel


title: Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [cHiC]

overall_design: We employed capture HiC to map changes in 3D chromatin structure in mouse ESCs and and E11.5 limb buds harbouring large deletions surrounding the Rex1 and Fat1 genes.


title: Distinct immunological and molecular signatures predict influenza vaccine responsiveness in the elderly (scRNA Seq)

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: The significant economic burden and high mortality rates resulting from seasonal influenza outbreaks, especially in high risk groups such as the elderly, represent an important public health problem. The prevailing  inadequate efficacy of seasonal vaccines, both conventional and elderly-tailored, is a crucial bottleneck. Consequentially, understanding immunological and molecular mechanisms resulting in differential influenza  vaccine responsiveness is a prerequisite for the development of new or improved vaccination strategies. To assess differences within the specific risk group of the elderly, randomly selected individuals (≥ 65 years) were immunized with the adjuvanted influenza vaccine Fluad®. Samples were subjected to single cell transcriptome analysis. The analyses revealed profound features segregating vaccine responders from nonresponders as classified according to their vaccine-induced sero-conversion. Non-responders are characterized by a poorly functional, suppressive phenotype, showing a weaker humoral and cellular immune activation and more suppressive regulatory T and B cells. Triple responders display an efficient immune functionality characterized by the activation of humoral and cellular immunity and the up-regulation of genes related to signaling pathways, including those for anti-viral responses, protein processing and B cell activation. The generated comprehensive high dimensional dataset enables the identification of putative mechanisms and nodes responsible for vaccine non-responsiveness regardless of confounding age-dependent effects.

overall_design: For the single cell transcriptome analysis, PBMCs isolated from whole blood samples  were used. Analysis compares the effect of vaccination among two groups classified as vaccine responders ( R ) and vaccine non responders (NR) after 7 days post vaccination. Each group is  represented by three donors ( NR: I-0845, I-4236, I-4964; R: I-4229, I-5127,I-5402 )

first: Peggy

last: Riese

first: Stephanie

last: Trittel

first: Carlos

middle: A

last: Guzmán


title: Transcriptomic analysis of hippocampus of hACE2 mice with SARS-CoV-2 infection

city: Kunming

first: Deng-Feng

last: Zhang

address: No.32 Jiaochang Donglu Kunming 650223 Yunnan, Chin

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

summary: The goals of this study are to dmonstrate transcriptomic profiling of SARS-CoV-2 infected brain samples. Hippocampal mRNA profiles of hACE2 transgenic mice at 30-day post SARS-CoV-2 infection were generated by bulk RNA sequencing, in 3 samples each group. Sequence reads were mapped to the mouse genome (GRCm38) using STAR. RSEM was used to count aligned reads that mapped to the annotated mouse genes. Gene-level differential expression analyses were performed using R package DESeq2. Results showed that SARS-CoV-2 infection led to long-term effect regarding neuroinflammation and neuronal function.

overall_design: Hippocampal mRNA profiles of three 30-day post SARS-CoV-2 infected hACE2 transgenic mice and three uninfected hACE2 transgenic mice

first: Jianxiong

last: Zeng


title: In vivo G-CSF Treatment Activates GR-SOCS1 Axis Suppressing IFN-γ Secretion by Natural Killer Cells

city: Beijing

first: Ting

last: Peng

address: Beijing haidiang

institute: PKU

summary: By comparing the multi-omics profile of human NK cells before and after G-CSF in vivo treatment, we identified a pathway that was activated in response to G-CSF treatment, which suppressed IFN-γ secretion in NK cells. Specifically, integrative genomic strategy uncovered that glucocorticoid receptor (GR) was activated and mediated the genomic response to G-CSF treatment in NK cells. Activated GR can inhibit secretion of IFN-γ via promoting interactions between suppressor of cytokine signaling 1 (SOCS1) promoter and enhancer and increase the expression of SOCS1.

overall_design:
We performed GR CUT&Tag in NK92 cells to aquire whole genome GR bingding information. Also, H3K27ac CUT&Tag was performed to identify enhancer regions in NK92 cells.
Please note that each processed data was generated from both replicates and is linked to the corresponding rep1 sample records.


title: scRNA-Seq of Mouse Trachea Basal Cells

city: Tucson

first: Hongxu

last: Ding

state: AZ

address: The University of Arizona

institute: University of Arizona

summary: Single cell RNA sequencing of 4209 mouse trachea basal cells.

overall_design: Single cell gene expression profiles of 4209 trachea basal cells from adult p63-CreERT2; Rosa26-tdTomato mouse strain were generated using 10x Genomics scRNA-Seq platform.

first: Ying

last: Yang

first: Wellington

last: Cardoso

first: Andrea

last: Califano


title: ATAC-seq analysis of transgenic human cancer cell line expressing subunits of meiotic cohesin complexes (RAD21L mei-Cohesin)

first: Alexander

last: Strunnikov

summary: The goal of the study was to investigate the epigenomic properties of somatic cells in response to the induction of mei-cohesin subunits using Tet-on inducible transgenes activated by an rtTA transgene and doxycicline. The study involved applying ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) analysis of stable transgenic human cancer cell line DLD-1, which expresed Tet-inducible combinations of mei-cohesin subunits. The ATAC-seq method enables mapping DNA accessibility in chromatin with hyperactive Tn5 transposase inserting specific adapters into genome.

overall_design: The DLD-1 (ATCC® CCL-221™) based cell lines were first stably infected with rtTA, followed by Tet-On-STAG3,  Tet-On-SMC1beta, and Tet-On RAD21L lentiviruses, to generate two multi-transgenic cell lines. The populations of transgenic cells selected for marker drug-resistance were cloned to generate single transgenic clones used for ATAC-seq experiments.

first: Abdelhalim

last: Boukaba

first: Jian

last: Liu

first: Qiongfang

last: Wu

first: Jierong

last: Liang

middle: V


title: Synthetic apomixis transfers stably over multiple generations in hybrid rice

status: Public on Sep 28 2022

city: Nanjing

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

institute: Nanjing Agricultural University

summary: we reproduced the clonal plants of Fix (Fixation of rice heterozygosity) to T4 generation with 1.9~3.2% clonal seeds rate of Fix-T01th, T12th, T23th and T34th. The descendant clonal plants Fix-T0, T1, T2, T3 and T4 exhibited no discernible differences on plant morphology, clonal seeds rate (3.7~4.3%), genome, methylome and transcriptome. Unexpectedly, few aneuploids were identified in each generation. The visible morphology changes of aneuploids might be caused by chromosome segments elimination. Together, the synthetic apomixis was heritable through multiple generations and few aneuploids were induced when using the synthetic apomixis system.

overall_design: Previously, the Fix-T0 plants were generated in the hybrid rice Chunyou84 (CY84) genetic background, an elite inter-subspecific hybrid rice from a cross between the maternal Chunjiang 16 A (16 A), a japonica male-sterile line, and the paternal C84, an indica-japonica intermediate-type line17. The Fix-T0 plants self-pollinated to T3 generation with screening diploids at each generation. The Fix-T0 and CY84 (corresponding control for Fix T0) plants were preserved to next generation via roots. The seeds from Fix offsprings (Fix T01th, T12th, T23th and T34th; Fix T0, T1, T2, T3 and T4), MiMe-T1 and Nipponbare variety (continuous self-pollinated four generations materials, coded as 1th, 2th, 3th and 4th) were soaked in deionized water at 37 °C in the dark for 2 d, and then transferred to a net floating on deionized water for further 5 d. The seedlings were cultured in a half-strength Kimura B nutrient solution (pH 5.4) for 21 d. Plant ploidy of the Fix offspring seedlings were identified using flow cytometry as described followings. All the confirmed seedlings were transferred to paddy field in Hangzhou. Plant growth in the field was managed according to local cultivation practices.

first: Chaolei

first: Kejian

last: Wang

first: Wenli


title: Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [Hi-C]

first: Michael

last: Robson

platform_organism:
Gallus gallus
Mus musculus
Monodelphis domestica

overall_design: We employed HiC to embryonic limbs from stage-matched chicken and opossum embryos to map  alterations to 3D chromatin structure across evolution.

first: Alessa

last: Ringel


title: T-cell responses to a specific antigen

city: Boston

first: Magali

last: Soumillon

state: MA

address: 38 Wareham Street, Fl3

institute: Flexomics

summary: The goal of this study is to demonstrate the ability of a novel platform to screen, identify and characterize neoantigen-specific T-cells and their receptors  by combining targeted RNA-seq data on subset of T-cell specific genes and T-cell Receptor sequencing

overall_design: In this study, we demonstrate the ability to use hybrid-capture based enrichment for a subset of 17 T-cell specific genes on 3' Digital Gene Expression (DGE) RNA-seq libraries. The samples processed were CD8+ T-cells enriched from blood from two independant healthy donors with each pool of CD8+ T-cells being either unstimulated (control) or stimulated with the Cytomegalovirus, Epstein-Barr Virus and Influenza Virus (CEF) control peptide pool overnight to monitor for T-cell activation.


title: Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [ChIP-Seq]

overall_design: We profiled H3K4me1, H3K4me3 and H3K27ac in mouse ESCs and CTCF in opossum embryonic fibroblasts (OEFs) by ChIP-seq.


title: Genome binding pattern of H3K27ac and H3K4me3 in MARCO-TST postive triple-negative breast cancer

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

summary: To investigate the transcription start site of MARCO-TST in triple negative breast cancer, we performed endogenous purification of H3K27ac and H3K4me3 under ChIP conditions, followed by high throughput sequencing.

overall_design: Identifiation of H3K27ac and H3K4me3 binding regions in MARCO-TST positive cells

first: Yun-Song

last: Su

first: Hena

last: Zhang


title: RNF4-RGMb axis  is required for osteogenic differentiation and cancer cell survival

city: Haifa

first: Amir

last: Orian

address: Efron 1

country: Israel

institute: technion

summary: Molecular understanding of osteogenic differentiation (OD) of human bone-marrow derived mesenchymal stem cells (hBMSCs) is important for regenerative medicine and has direct implications to cancer. Here we report that the RNF4 ubiquitin ligase is essential for OD of hBMSCs,  and that RNF4 deficient hBMSCs fail to differentiate and remain as stalled progenitors. Remarkably, addition of media from differentiating hBMSCs to RNF4-deficient MSCs alleviated the block in OD. Transcriptional analysis of RNF4-dependent gene signature identified two secreted factors; BMP6 and the guidance molecule BMP6 co-receptor RGMb (Dragon). Knockdown of either RGMb or BMP6 in hBMSCs inhibit differentiation, and only the combined addition of purified RGMb and BMP6 proteins to RNF4-deficient MSCs fully restored osteogenic differentiation. Moreover, RNF4-RGMb axis is highly relevant cancer cell survival and tumorigenicity, including osteosarcoma and Therapy-resistant melanoma cells. In accordance, in human melanoma biopsies high level of RGMb correlates with high level of RNF4, and is associated with resistance to molecular therapy and poor prognosis of patients. Thus, RNF4~BMP6~RGMb is a molecular axis that is key for OD and  tumorigenesis.

overall_design: To determine a potential transcriptional role for RNF4 in OD, and to identify RNF4-regulated, secreted factors we performed RNA-seq analysis.  We compared the changes in gene signature of scrambled Scr-control hBMSCs to that of hBMSCs where RNF4 was knocked-down using shRNF4 upon OD

first: Rostislav

last: Novak


title: Gene expression profile of patient-derived head and neck squamous carcinoma cells subjected to different treatments.

city: NIJMEGEN

first: Dyah

last: Karjosukarso

address: Geert Grooteplein Zuid 28

institute: Radboud University

summary: In order to investigate the mechanisms underlying response and resistance towards treatment in HNSCC, we used low passage in vitro HNSCC cultures from two patients, namely SJG26 and SJG17. Both cultures were subjected to selection by AG1478-mediated EGFR inhibition, radiation, as well as the combination of both for two weeks, generating presumably tolerant cell populations (AG, R and RAG). These tolerant cell populations and a non-treated population were subjected to bulk RNA-seq to study the overall gene expression profile of the cell populations.

overall_design: The cells were subjected to different treatments (non-treated, AG1478 treatment, radiation and radiation combined with AG1478 treatment) folowed by RNA-seq analysis

first: Alice

last: Dini

first: Klaas

middle: K

last: Mulder


title: Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [WGBS]

overall_design: We performed whole genome bisuphite sequencing on wildtype mouse ESCs and E11.5 limbs and mutant E11.5 limbs with a complete loss of function of DNMT3B.


title: The therapeutic effect of KSP inhibitors in preclinical models of cholangiocarcinoma

first: Yuanyuan

last: Shi

address: changhailu 168

institute: the First Affiliated Hospital of Naval Medical University

summary: Cholangiocarcinoma (CCA) is an epithelial malignancy with a dismal prognosis owing to limited treatment options. Here, we identified several compound candidates against CCA using a high-throughput drug screen with approved or emerging oncology drugs, among which kinesin spindle protein (KSP) inhibitors showed potent cytotoxic effects on CCA cells. Treatment with KSP inhibitors SB743921 and ARRY520 caused significant tumor suppression in CCA xenograft models in vivo. Mechanistically, KSP inhibitors led to the formation of abnormal monopolar spindles, which further resulted in the mitotic arrest and cell death of CCA cells both in vivo and in vitro. KEGG pathway analysis of transcriptional data confirmed this finding. Moreover, our clinical data as well as the TCGA database showed KIF11 expression was abundant in most CCA tumor specimens and associated with poor outcomes of CCA patients. Our results demonstrate that the therapeutic regimen of KSP inhibitors could be a promising treatment strategy in CCA.

overall_design: mRNA profiles of CCLP1 cells treated with SB743921 or vehicle control for 0, 8 and  16 hours

first: Xiaowen

last: Cui

first: Tianyi

last: Jiang

first: Yufei

last: Pan

first: Xiaofan

last: Feng

first: Zhiwen

last: Ding

first: Chun

last: Yang

first: Yexiong

last: Tan

first: Hongyang

first: Liwei

last: Dong


title: scRNA-sequencing of non-neuron cells  from hippocampus (HP) of 7 months old Mr1+/+ and Mr1-/-  mice.

city: New Brunswick, NJ 089

first: Qi

state: New Jersey

address: 89 French St

institute: Rutgers

summary: The purpose of this experiment is to examine the cellular and molecular changes in the microglia and other non-neuron cells in the hippocampus of 7 month old Mr1+/+ and Mr1-/- mice.

overall_design: We used the 10X Genomics platform to prepare scRNA-seq libraries to detail the global programme of different gene expression between each type of cells in the HP of wildtype and MR1-/- mice

first: Yuanyue


title: Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [RNA-Seq]

first: Michael

last: Robson

overall_design: We employed RNA-seq to map gene expression changes in mouse ESCs and and E11.5 limb buds harbouring large deletions surrounding the Rex1 and Fat1 genes.

first: Alessa

last: Ringel


title: Dithranol as novel co-adjuvant for non-invasive dermal vaccination

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: The goal of this study is to compare dithranol or IMI-Sol induced transcriptome profiles in murine skin.

overall_design: Expression profiling by high throughput sequencing of RNA from murine ear skin that was either treated with dithranol-vaseline (1/16%, 25mg) or IMI-Sol (containing 5% Imiquimod, 50mg) for 24 hours.

first: Markus

last: Radsak

first: Stephanie

last: Morales

first: Julian

last: Sohl


title: Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes

summary: Regulatory landscapes drive complex developmental gene expression but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically-associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD-partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1’s intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42’s unresponsiveness. Rather, Zfp42’s promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome-wide, most TADs contain multiple independently-expressed genes.

overall_design: Refer to individual Series


title: Telocytes regulate tissue resident macrophages in periodontal disease

city: london

first: Paul

last: Sharpe

address: Craniofacial Development & Stem cell bio, Guy's Tower Floor 27

institute: King's college London

summary: A small population of telocytes (TC) have been identified in periodontium. They are quiescent in homeostasis, however, in periodontitis, they are activated by LPS via the receptor Lbp, which causes TCs to send HGF signals to the LPS activated iNOS+ (M1) macrophages. Macrophages receive the HGF signals via c-Met, which further causes the expression of M2 marker Arg1, representing in an increase of M2 macrophages. The expression of Arg1 can be inhibited by a HGF/c-Met selective inhibitor Tivantinib.

overall_design: Mouse PDL mRNA profiles during periodontitis.

first: Jing

last: Zhao


title: Comparative analysis of transcriptome remodeling in plaque associated and plaque distant microglia during amyloid-ß pathology progression

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

country: France

institute: university Lyon1

summary: In this study, we combined cell-specific laser capture and RNA-seq analysis to investigate transcriptome changes in both  amyloid-ß plaque-associated and plaque-distant microglia at different stages of the disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for microglia isolated from APP/PS1 AD mice at 4, 8 and 12 months of age.

first: Anne-Laure

last: Hemonnot-Girard

first: Cédric

last: Meersseman

first: Manuela

last: Pastore

first: Valentin

last: Garcia

first: Nathalie

last: Linck

first: Catherine

last: Rey

first: Amine

last: Chebbi

first: Joël

last: Lachuer

first: Christelle

last: Reynes

first: François

last: Rassendren

first: Hirbec

last: Hélène


title: Effect of overexpression of miR-210-3p on gene expression of human umbilical vein endothelial cells in hypoxic conditions

first: Han

last: Tang

address: No. 130, Dong’an Road, Xuhui district

department: Orthopedic Surgery

institute: Zhongshan Hospital, Fudan University, Shanghai, China

summary: To investigate machanism of miR-210-3p regulating angiogenic ability of human umbilical vein endothelial cells (HUVECs) in hypoxic conditions, we transfected miR-210-3p mimic to overexpress miR-210-3p in human umbilical vein endothelial cells. We than performed RNA sequencing of miR-210-3p mimic-transfected and control HUVECs under hypoxic conditions to evaluate the transcriptional changes in the miR-210-3p-overexpressing HUVECs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and miR-210-3p overexpressed HUVECs.

first: Wenrun

last: Zhu

first: Duan

last: Ma

first: Changan

last: Guo


title: scRNA-sequencing of mouse meningeal T cells

first: Qi

last: Yang

summary: The purpose of this experiment is to examine the cellular and molecular differences between MAIT cells  and traditional CD4/CD8 T cells in the meninges of 7 month old C57BL/6 mice.

overall_design: We used the 10X Genomics platform to prepare scRNA-seq libraries to examine the transcriptomes between MAITs and CD4 or CD8 T cells in the meningeal tissue of 7-month old mice.

first: Yuanyue

last: Zhang


title: Sequestration of gut pathobionts in intraluminal casts, a mechanism to avoid dysregulated T cell activation by pathobionts

status: Public on Sep 27 2022

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: T cells that express the transcription factor RORg, regulatory (Treg) or conventional (Th17), are strongly influenced by intestinal symbionts. In a genetic approach to mechanisms underlying this influence, we performed a screen for microbial genes implicated, in germfree mice monocolonized with E.coli Nissle. The loss of capsule-synthesis genes impaired clonal expansion and differentiation of intestinal RORg+ T cells. Mechanistic exploration revealed that the capsule-less mutants remained able to induce specific IgA and were highly IgA-coated. They could still trigger myeloid cells, and more effectively damaged epithelial cells in vitro. Unlike wild-type microbes, capsule-less mutants were mostly engulfed in intraluminal casts, large agglomerates composed of myeloid cells extravasated into the gut lumen. We speculate that sequestration in luminal casts of potentially harmful microbes reduces the immune system’s actual exposure, preserving host-microbe equilibrium. The variable immunostimulation by microbes charted in recent years may not solely be conditioned by triggering molecules or metabolites, but also by physical limits to immunocyte exposure.

overall_design: To study the impact of Escherichia coli Nissle 1917 (EcN) K5 capsule on colonic CD4 T responses and activation we monocolonized Germ-Free (GF) mice with EcN wild-type and mutant lacking the K5 capsule (kfiCD). To assess the transcriptional inductions in colonic CD4 T cells, we flow-cytometrically double-sorted CD4 T cells  (DAPI- CD19- CD4+ TCRβ+) from Germ-free mice (GF), EcN wild-type and EcN kfiCD mutant at day 14 post-monocolonization and performed population-level RNA-seq.

first: Martina

last: Sassone-Corsi

first: Christophe

last: Benoist


title: RNAseq analysis of PM2.5 treated mouse cardiomyocyte cell line

city: Busan

first: Jong-Ho

last: Lee

address: 37 Nakdong-daero 550 Beon-gil

country: South Korea

institute: Dong-A University

summary: We report the gene expression profile in mouse cardiomyocyte cell line after treatment of PM2.5.

overall_design: HL-1 cells were treated with 0.01 and 100 µg/mL PM2.5 for 12 h and then lysed. Total RNA was isolated using QIAzol® (Qiagen, Valencia, CA, USA). Total RNA concentration was quantified using Quant-IT RiboGreen (Invitrogen, Waltham, MA, USA). The integrity of total RNA was determined using TapeStation RNA screentape (Agilent Technologies, Atlanta, GA, USA), and samples with RNA integrity numbers higher than 7 were used for library generation. A library was generated with 1 µg of total RNA from each sample using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina Inc., San Diego, CA, USA). First-strand cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen). Second-strand cDNA was synthesized using DNA polymerase I, RNase H, and dUTP. The cDNA samples were processed via end repair by adding a single “A” base and ligating the adapters. The library samples were analyzed using Illumina NovaSeq (Illumina Inc.). Raw reads from the sequencer were preprocessed to eliminate low-quality and adapter sequences before analysis, and the processed reads were aligned to the Mus musculus (mm10) genome using HISAT v2.1.0. Transcript assembly and abundance estimations were performed using StringTie. The aligned reads were assembled, and gene abundance was determined using StringTie v2.1.3b.

first: Gwang

first: Tae Hwan

last: Shin

first: Seok Gi

last: Kim


title: Global hepatic transcript data from fed male BXD strains on chow or high fat diet

city: Lausanne

first: Kristina

last: Schoonjans

address: Station 15

department: SV IBI GR-SCH

institute: Ecole Polytechnique Fédérale de Lausanne

summary: Gene expression levels assessed by microarray in liver samples collected from the BXD mouse genetic diversity model fed either a standard chow or a high fat diet at a fed state.

overall_design: 36 BXD strains, including parental C57BL/6J and DBA/2J strains are included. At 29 weeks of age, mice were fasted overday and refed with their respective diet for 4 hours before sacrifice, following the physiological eating cycle. Liver samples were collected and the gallbladder was discarded. The samples were immediately frozen in liquid nitrogen for RNA extraction and RNEasy cleanup. Each dietary and strain cohort consisted of ~5 animals which were prepared independently then pooled evenly by µg RNA before the Affymetrix arrays were run.

first: Johan

last: Auwerx

first: Hao

last: Li

first: Alessia

last: Perino


title: Repertoire analysis of the repertoire of insulin-reactive B cells in type 1 diabetes-prone mice

status: Public on Sep 26 2022

city: Aurora

first: John

last: Cambier

state: CO

department: Immunology & Microbiology

institute: University of Colorado

summary: Seropositivity for autoantibodies against islet autoantigens is associated with the development of autoimmune type 1 diabetes and B cell targeted therapies are effective in both mouse models and in patients who are affected by or at risk for autoimmune type 1 diabetes. The role of B cell receptor affinity in autoimmune type 1 diabetes is unclear. Here, we employed single cell RNA sequencing to define the relationship between B cell receptor affinity for insulin and B cell phenotype during disease development using immunoglobulin heavy chain (VH125) transgenic mouse model (VH125.NOD) in which insulin binding B cells lose self-tolerance, becoming activated during development of autoimmmun type 1 diabetes.

overall_design: Splenocytes from VH125.NOD mice were isolated. High affinity insulin-binding cells were enriched by serial incubation with biotinylated insulin, streptavidin-Alexa Fluor 647 and anti-Cy5/anti-Alexa Flour 647 microbeads (Miltenyi) followed by passage through a magnet-mounted LS column (Miltenyi). These cells were then FACS sorted to further enrich insulin binding B cells and these cells were then analyzed via scRNASeq

first: Maureen

last: Banach

first: Isaac

last: Harley


title: FOXA1 regulates splicing-related gene expression and alternative splicing in prostate cancer cells

city: Candiolo

first: Matteo

last: Cereda

institute: Italian Institute for Genomic Medicine

summary: Dysregulation of alternative splicing in prostate cancer is linked to transcriptional programs activated by canonical oncogenic transcription factors. However, the relative contribution of these factors to alternative splicing regulation is yet to be defined. We investigated the role of FOXA1 by performing deep RNA-seq on siRNA-treated (i.e. siFOXA1) and control (i.e. NSI) samples from prostate cancer cell lines. Using this data, we performed canonical parametric differential expression analysis between NSI and siFOXA1 samples to determine the effect of FOXA1 depletion on splicing related gene expression. We also identified FOXA1-regulated differentially alternatively spliced exons between NSI and siFOXA1 samples.

overall_design: 12 total samples, 3 replicates per condition.

first: M

last: Del Giudice

first: J

middle: G

last: Foster

first: S

last: Peirone

first: R

last: Arkell

first: A

last: Rissone

first: F

last: Gaudino

first: C

last: Parlato

last: Guarrera

last: Anselmi

last: Oliviero

first: G

last: Basso

first: P

last: Rajan


title: snRNAseq of human vascular dementia white matter vs control

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Transcriptional profiling of cells in white matter of the brain from cases with vascular dementia vs control cases

overall_design: nuc-seq study of human vascular dementia from corpus callosum white matter above the frontal ventricle in patients and controls. Samples prepared with straight nuc seq protocol, and in parallel sample, first with FACS isolation of ERG+ nuclei to isolate endothelial and microglial poulations

first: Dainel

last: Mitroi

last: Carmichael

first: William

last: Lowry


title: A Neurogenic Signature Involving Monoamine Oxidase-A Controls Human Thermogenic Adipose Tissue Development

city: Worcester

first: Silvia

last: Corvera

address: 373 Platantion Street

department: Molecular Medicine

institute: UMASS Medical School

summary: Mechanisms that control “beige/brite” thermogenic adipose tissue development may be harnessed to improve human metabolic health. To define these mechanisms, we developed a species-hybrid model in which human mesenchymal progenitor cells were used to develop white or thermogenic/beige adipose tissue in mice. The hybrid adipose tissue developed distinctive features of human adipose tissue, such as larger adipocyte size, despite its neurovascular architecture being entirely of murine origin. Thermogenic adipose tissue recruited a denser, qualitatively distinct vascular network, differing in genes mapping to circadian rhythm pathways, and denser sympathetic innervation. The enhanced thermogenic neurovascular network was associated with human adipocyte expression of THBS4, TNC, NTRK3 and SPARCL1, which enhance neurogenesis, and decreased expression of MAOA and ACHE, which control neurotransmitter tone. Systemic inhibition of MAOA, which is present in human but absent in mouse adipocytes, induced browning of human but not mouse adipose tissue, revealing the physiological relevance of this pathway. Our results reveal species-specific cell type dependencies controlling the development of thermogenic adipose tissue and point to human adipocyte MAOA as a potential target for metabolic disease therapy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative gene expression profiling analysis of RNA-seq data for implanted human white or thermogenic adipocytes after 8 weeks of development in vivo.

first: Javier

last: Solivan-Rivera

first: Zinger

last: Yang Loureiro


title: MdMYB52 regulates lignin biosynthesis upon the suberization process in apple.

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

summary: Our previous studies, comparing russeted vs. waxy apple skin, highlighted a MYeloBlastosys (Myb) transcription factor (MdMYB52-like), which displayed a correlation with genes associated to the suberization process. The present article aims to assess its role and function in the suberization process. Phylogenetic analyses and research against Arabidopsis thaliana MYBs database were first performed and the tissue specific expression of MdMYB52-like was investigated using RT-qPCR. The function of MdMYB52-like was further investigated using Agrobacterium-mediated transient overexpression in Nicotiana benthamiana leaves. An RNA-Seq analysis was performed to highlight differentially regulated genes in response MdMYB52-like. Transcriptomic data were supported by analytical chemistry and microscopy. A massive decreased expression of photosynthetic and primary metabolism pathways was observed with a concomitant increased expression of genes associated with phenylpropanoid and lignin biosynthesis, cell wall modification and senescence. Interestingly key genes involved in the synthesis of suberin phenolic components were observed. The analytical chemistry displayed a strong increase in the lignin content in the cell walls during MdMYB52 expression. More specifically, an enrichment in G-Unit lignin residues was observed, supporting transcriptomic data as well as previous work describing the suberin phenolic domain as a G-unit enriched lignin-like polymer. The time-course qPCR analysis revealed that the observed stress response, might be explain by this lignin biosynthesis and by a possible programmed senescence triggered by MdMYB52-like. The present work supports a crucial regulatory role for MdMYB52 in the biosynthesis of the suberin phenolic domain and possibly in the fate of suberized cells in russeted apple skins.

overall_design: In order to draw a consistent picture of the MdMYB52 function, we compared  4 biological replicates of Nicotiana benthamiana leaves infiltrated with Pearleygate103 35S::MdMYB52/pBINP19 and 4 biological replicates of control plants infiltrated with P103empty/pBINP19.

first: Xuan

last: Xu

first: Gea

last: Guerriero

first: Roberto

last: Berni

first: Kjell

last: Sergeant

first: Cédric

last: Guignard

first: Audrey

last: Lenouvel

first: Jean-Francois

last: Hausman


title: RNA sequencing analysis of IECs from WT and RhoB-/- mice

city: Tianjin

first: Jian

middle: ming

last: Yang

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

summary: Purpose: RhoB regulates cell functions, such as vesicular transport, apoptosis, autophagy, DNA repair, angiogenesis, proliferation, migration and invasion. We investigated whether RhoB is involved in the pathogenesis of ulcerative colitis (UC).We performed RNA sequencing analysis in intestinal epithelial cells (IECs) from RhoB-deficient mice and WT mice to study the molecular mechanisms through which RhoB regulates goblet cell numbers and epithelial regeneration and confirmed findings in colonic organoids from RhoB-deficient mice and WT mice and siRhoB transfected SW480 cells.

overall_design: Methods:Gene expression profiles of IECs from WT and RhoB-/- mice were generated by deep sequencing,in quintuplicate, using Illumina Hiseq xten.To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM)method. RSEM was used to quantify gene abundances.

first: Quan

last: Wang

first: Zhi

last: Yao

first: Jianming

first: Geng

last: Pei


title: Iron deprivation enhances transcriptional responses to growth arrest of Mycobacterium tuberculosis

city: Madrid

first: Maria Jesus

last: Garcia Garcia

state: Madrid

address: Arzobispo Morcillo, sn

country: Spain

institute: Autonoma University of Madrid

summary: The establishment of Mycobacterium tuberculosis (Mtb) long-term infection in vivo depends on several factors, one of which is bacterial availability of key nutrients such as iron. The relation between Fe deprivation inside the granuloma and the capacity of Mtb to accumulate lipids and persist in the absence of growth is not well understood. In this context, current knowledge of how Mtb modifies its lipid composition in response to iron starvation is scarce.

overall_design: In this work we have compared genome-wide transcriptomic and lipidomic profiles of Mtb at exponential and stationary growth phases using axenic cultures with glycerol as a carbon source, in the presence or absence of iron.

first: Sogol

last: Alebouyeh

first: Jorge

last: Cárdenas-Pestana

first: Lucía

last: Vázquez

first: Rafael

last: Prados-Rosales

first: Patricia

last: Del Portillo

first: Joaquín

last: Sanz

first: M

last: Menéndez

first: María

last: García


title: Analyses of the transcriptional and alternative splicing changes in mdf-1 in comparison to WT via RNA sequencing

city: Hamburg

first: Cloe

last: de Luxán-Hernández

state: Hamburg

address: Ohnhorststraße 18

department: Molecular Plant Physiology

institute: University Hamburg

summary: Purpose: Understand the transcriptional changes and alternative splicing defects associated to the pleiotropic defects observed in mdf-1 mutants. Methods: Total RNA was extracted from 3 different biological replicates containing 12-day-old seedlings of WT and mdf-1 using the innuPREP Plant RNA kit (Analytik Jena Bio solutions). RNA quality assessment, library preparation, sequencing and bioinformatic analyses were performed by Novogene Co. Integrity and quantitation of the extracted RNA were measured using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). With 1 µg RNA per sample as input material, sequencing libraries were subsequently generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) following the manufacturer’s recommendations. Index codes were also added to attribute sequences to each sample. Clustering of the index-coded samples was carried out on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) following manufacturer’s instructions. Afterwards, library preparations were sequenced on an Illumina NovaSeq 6000 platform and approximately 50 million 150 paired end reads per sample were generated. To ensure the high quality of the samples, only clean data was used for subsequent analyses. This was achieved after the removal of reads containing adapter and poly-N sequences and reads with low quality from the raw data. Mapping against the Arabidopsis TAIR10 reference genome was performed using the HISAT2 software. Reads Per Kilobase of exon model per Million mapped reads (RPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analyses between mdf-1 and WT were carried out using the DESeq2 R package with the Benjamini and Hochberg’s approach for adjusting P values according to the False Discovery Rate (FDR). Genes with adjusted p-value < 0.05 were considered as differentially expressed. Alternative splicing (AS) analysis was performed with the rMATS software. Events with adjusted p-value < 0.05 were considered as alternatively spliced. Results: Loss of MDF function is associated with growth defects, impaired transition to mitosis, increased endoreduplication and spontaneous cell death in meristems.  This was associated with strong upregulation of stress-induced genes and down-regulation of mitotic regulators and a subset of genes required for essential developmental processes. MDF is also required for the correct splicing of numerous transcripts including transcription factors and cell cycle associated genes.

overall_design: mRNA and AS profile of 12 day old mdf-1 mutants and Col-0 WT plants

first: Magdalena

last: Weingartner