title: Transcriptomic analysis of Pseudomonas aeruginosa in response to host antimicrobial peptide S100A12

status: Public on Jan 31 2022

city: Hyderabad

first: Sanhita

last: Roy

state: Telangana

address: Banjara Hills Road no2

department: BHERC

country: India

institute: L V Prasad Eye Institute

type: Expression profiling by high throughput sequencing

summary: Pseudomonas aeruginosa is a gram negative, opportunistic pathogen, which is the major cause of corneal infections in India and worldwide. Being categorised in the critical group of antibiotic resistant species, it has prompted significance rise in research to develop alternative therapeutics. One such alternative to combat bacterial infections is antimicrobial peptides (AMPs). This study aims to investigate the role of S100A12, a host defence peptide against PAO1. It was also seen to inhibit the bacterial growth of PAO1 in vitro as seen from the colony forming units. Our study sheds light on how S100A12 impacts Pseudomonas and that it might have the potential to be used as therapeutic intervention in addition to antibiotics in future.

overall_design: 200 μl of overnight culture of PAO1 was grown for 2 hours to get an OD600 of 0.2 and then 106 cfu was incubated with 500 μg/ml of S100A12 for 6 hours in 37°C.

first: Priyasha

last: Mishra


title: Analyses of translatome combined with transcriptome in Arabidopsis shoot and root reveals new players responding to magnesium deficiency.

status: Public on Jan 30 2022

city: Urbana

first: Liqing

last: Chen

state: IL

address: 1201 W Gregory Dr

department: Plant Biology

country: USA

institute: University of Illinois at Urbana Champaign

summary: Translational control of gene expression, including recruitment of ribosome to mRNA, is particularly important for stress responses. Translating Ribosome Affinity Purification (TRAP)-based RNA-sequencing offers a tool to study ribosome-associated mRNAs, which better proxies protein levels via the levels of transcripts to be translated into proteins. Magnesium (Mg) greatly inhibits plant growth and affects crop productivity. To identify new players for better understanding plants in response to Mg deficiency at the translational level, we combined the transcriptome with translatome analyses. We revealed that 26 previously unreported Mg responsive genes, which were only regulated at the translational level, not transcriptional level at an early stage upon Mg deficiency. Among six mutants analyzed, we found that mutants of the transcriptional factor of ELONGATED HYPOCOTYL 5 (HY5), H+/cation exchanger 1 and 3 and UBIQUITIN 14 exhibited early chlorosis phenotype under Mg deficiency. UBIQUITIN 14 is the first UBIQUITIN protein reported to be functionally involved in ion homeostasis. Overall, our study demonstrates that there is a strong correlation between ribosome-associated mRNA abundance and mutant phenotypes, strongly supporting that TRAP-seq combined with RNA-seq followed by phenotype screening could serve as a valuable tool to identify novel players during stress responses.

overall_design: 24 samples from shoot and root under normal growth condition (CK) and Mg deficiency (MgD) condition are analyzed, including three independent replicates.

first: Yaxin

last: Li

first: Qianqian

first: Gabriel

last: Beuchat

first: Houqing

last: Zeng

first: Cankui

last: Zhang

first: Li-Qing


title: Circular RNA YPEL2 promotes cell proliferation, migration and invasion as a biomaker in cervical cancer

city: Wuhan

first: Chunjiang

last: He

address: Donghu Road 185

department: School of Basic Medical Sciences

country: China

institute: Wuhan University

summary: Circular RNA (circRNA) is newly type of noncoding RNA that are formed by back-splicing of exon and play the important functions in tumorigenesis. However, the research of circRNA is deficient in cervical cancer (CC). We performed high-throughput sequencing on cervical cancer tissues and normal cervical control samples. We discovered the up-regulated circYPEL2 (has_circ_0005400) in cervical cancer and used this as a potential research object through bioinformatics analysis. Finally, through RNA sequencing and bioinformatics technology, we analyzed the downstream targeted genes that may be affected by circYPEL2.

overall_design:
Cervical cancer tissues and normal cervical control samples were collected from 3 cervical cancer patients and 3 normal patients. Total RNA was extracted from these samples, and the RNA was reverse transcribed to cDNA and constructed into a strand-specific library. Illumina HiSeq2000 was performed for sequencing.
We designed short interfering RNAs (si-NC, si-circYPEL2-1, si-circYPEL2-2) to transfect into HeLa and SiHa cell lines. After verifying by qRT-PCR, we found the si-circYPEL2-2 is the most efficient. So we used it for three independent replicates to knock down circYPEL2. Total RNA was extracted, and the RNA was reverse transcribed to cDNA and constructed into a strand-specific library. Illumina HiSeq2000 was performed for sequencing.

first: Xinyang

first: Siqi

last: Yang

first: Yu

last: Fang

first: Xiangfei

last: Mei

first: Wenbo

first: Xin

last: Dong

first: Jin

last: Deng


title: The use of a complex tetra-culture alveolar model to study the toxicological effects of gold nanoparticles with different physicochemical properties

city: Belvaux

first: Sebastien

last: Cambier

state: - select a state -

address: 41 rue du brill

department: ERIN

country: Luxembourg

institute: LIST - Luxembourg Institute of Science and Technology

summary:
Purpose: In the last decades, the advancements of nanotechnologies lead to a massive increase of engineered nanoparticles in consumer products, which translates in an increased human and environmental exposure to nanomaterials. For humans, inhalation is considered as the main exposure route to nanomaterials, which is the reason why lung toxicity studies should be considered as a priority. Inhalation studies are often performed in vivo in rodents. Therefore, in vitro models may represent a valid and efficient alternative to predict the acute toxicity effects of inhaled NPs on human health.  The model used in this study represents the human alveolar barrier; it is constituted by four different human pulmonary cell lines (EA.hy 296 on the basolateral side; A549, HMC-1 and macrophage-like cells in the apical side). The cells in the apical side were cultivated at the air-liquid-interface (ALI) and they have been exposed to AuNPs with the VitroCell® Cloud System.
Results: We describe the effects after 24 hours of exposure to three different gold nanoparticles (AuNPs) in order to evaluate the suitability of our model to assess the toxicological effects of particles. The set of PEGylated AuNPs used included spheres (GNPs), rods (GNRs) and stars (GNSs). The exposure did not cause any significant decrease of viability; all the AuNPs caused cytotoxicity and increase of IL-8 levels at the highest dose. The AuNP were up-taken by the cells in the apical side and they also translocated in the basolateral side. Regarding the global transcript, among differentially expressed genes (DEG) were found genes related to the enhancement of immune cells.
Conclusion: AuNPs in the used range of concentrations did not cause severe effects on the co-culture, but different effects were observed for the different types of AuNPs supporting the role of the physico-chemical NP parameters in NP-cell interactions. In addition, our model resulted perfectly suitable to investigate the biological effects of particles especially in terms of inflammatory response and translocation.

overall_design: Epithelial and endothelial mRNA profiles of 24h exposed complex lung alveoli in vitro models to 3 different type of Au NPs in comparison to a negative control all in three biological replicates.

first: Melissa

last: Saibene

first: Tommaso

last: Serchi

first: Patrizia

last: Bonfanti

first: Anita

last: Colombo

first: Inge

last: Nelissen

first: Rashi

last: Halder

first: Jean-Nicolas

last: Audinot

first: Beatriz

last: Pelaz

first: Mahmoud

middle: G

last: Soliman

first: Wolfgang

middle: J

last: Parak

first: Paride

last: Mantecca

first: Arno

middle: C

last: Gutleb


title: Vitamin D modulates cortical transcriptome in an Mecp2 heterozygous Rett syndrome mouse model

city: Syracuse

first: Jessica

last: MacDonald

state: NY

address: 107 College Place

department: Biology

institute: Syracuse University

summary: We investigated whether dietary vitamin D supplementation can rescue the expression of genes that are dysregulated within the neocortex of Mecp2+/- mice, and whether vitamin D deficiency further exacerbates transcriptome disruptions in these mice. We found that dietary vitamin D modification has a profound impact on the transcriptome of the neocortex. We identified more than 200 differentially expressed genes whose expression is normalized with vitamin D supplementation, many of which are associated with neuronal morphology. Dietary vitamin D deficiency exacerbated the dysregulation of many of these genes in the Mecp2+/- cortex, but, strikingly, it normalized the expression of many other dysregulated genes, similar to the effect of supplementation.

overall_design: Total cortical RNA-seq profiles of 7 month-old Mecp2+/+ and Mecp2+/- mice on diets with defined vitamin D concentrations.

middle: L

first: Mayara

last: Ribeiro


title: Small RNA sequencing of small extracellular vesicles secreted by nonsenescent vs. senescent human umbilical cord mesenchymal stem cells

city: Seoul

first: Ok Sarah

last: Shin

address: 148, Gurodongro, Gurogu

country: South Korea

institute: Korea Univ.

type: Non-coding RNA profiling by high throughput sequencing

summary: We report small RNA sequencing technology for high-throughput profiling of microRNA content within small extracellular vesicles isolated from nonsenescent and senescent human umbilical cord mesenchymal stem cells (hUCMSCs)

overall_design: Comparison of microRNA profiles of small extracellular vesicles isolated from senescent vs. nonsenescent human umbilical cord mesenchymal stem cells

first: Ok

middle: S

first: Jae

middle: K

last: Lee

first: Chris

last: Kim


title: Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells [Kinetics RNA-seq]

city: New Haven

first: Tomokazu

last: Sumida

state: CT

address: 300 George St,, 3rd floor room349

department: Neurology

institute: Neurology, Yale School of Medicine

summary: While inhibition of T cell co-inhibitory receptors has revolutionized cancer therapy, the mechanisms governing their expression on human T cells have not been elucidated. Type 1 interferon (IFN-I) modulates T cell immunity in viral infection, autoimmunity, and cancer, and may facilitate induction of T cell exhaustion in chronic viral infection. Here we show that IFN-I regulates co-inhibitory receptor expression on human T cells, inducing PD-1/TIM-3/LAG-3 while surprisingly inhibiting TIGIT expression. High-temporal-resolution mRNA profiling of IFN-I responses enabled the construction of dynamic transcriptional regulatory networks uncovering three temporal transcriptional waves. Perturbation of key transcription factors on human primary T cells revealed unique regulators that control expression of co-inhibitory receptors. We found that the dynamic IFN-I response in vitro closely mirrored T cell features with IFN-I linked acute SARS-CoV-2 infection in human, with high LAG3 and decreased TIGIT expression. Finally, our gene regulatory network identified SP140 as a key regulator for differential LAG3 and TIGIT expression, which were validated at the level of protein expression. The construction of IFN-I regulatory networks with identification of unique transcription factors controlling co-inhibitory receptor expression may provide targets for enhancement of immunotherapy in cancer, infectious diseases, and autoimmunity.

overall_design: Human naïve CD4+/CD8+ T cells were stimulated with anti-CD3/CD28 w/wo IFN-b (500U/ml). Gene expression kinetics were assessed by mRNA-seq with 9 different time points.

first: Asaf

last: Madi

first: David

middle: A

last: Hafler


title: miRNA expression of Pinus pinaster roots under ammonium nutrition

city: Malaga

first: Rafael

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

summary: In the present study, the miRNA expression changes in the maritime pine roots from seedlings of one-month old under different levels of ammonium nutrition was analyzed.

overall_design: Pine seedlings were subdivided into three different groups. The control group was irrigated with 80 mL of water (C), the second group was supplied with 80 mL of 0.1 mM NH4Cl and the third group was supplied with 80 mL of 3 mM NH4Cl. Root samples were collected before the irrigation and at two different time points after the treatments (2 and 24 hours). Ten seedlings were collected and pooled per each sample. The 21 samples were sequenced on an Illumina HiSeq 4000 as single-end reads of 50 bp length.

first: Francisco

last: Ortigosa

first: César

last: Lobato-Fernández

first: José

middle: M

last: Valderrama-Martín

last: Urbano-Gámez

middle: R

last: Cantón


title: Identification and characterization analysis of the different  genes in primary mouse microglia response to circDYM using RNA-seq.

city: Nanjing

first: Xiaoyu

last: Yu

state: Jiangsu

address: Dingjiaqiao 87

institute: Southeast univeristy

summary: Whole RNA-sequencing analysis was performed and analyzed by Lc. Biotech Co. Ltd. (Hangzhou, China). Primary mouse microglia from the Con + circCon group, Con + circDYM group, LPS + circCon group, and LPS + circDYM group were collected in TRIzol. Total RNAs were extracted from Trizol. UMI technology was used to label each sequence fragment with sequence tags, which minimized the interference of duplication caused by PCR amplification on the quantitative accuracy of the transcriptome. RNA sequencing reads were aligned to the mouse genome (GRCh37/hg19) using the software Hisat2 (2.0.4). Transcript abundance was evaluated by calculating fragments per kilo base of exon per million fragments mapped (FPKM).

overall_design: Examination of different genes by Over-expressed circDYM in primary mouse microglia in presence of LPS by RNA-seq.

first: Honghong

last: Yao


title: mNET sequencing facilitates identification of native elongating transcripts in control and Carm1 KO melanoma cells

city: Boston

first: Matthew

last: Booker

state: MA

address: 21-27 Burlington Ave.

department: Informatics

institute: Dana Farber Cancer Institute

summary: We investigated whether RNA Pol II mediated transcription was altered in Carm1 KO compared to control KO tumor cells. We examined p-Ser2 CTD Pol II relative to total CTD Pol II using mammalian native elongating transcript sequencing (mNET-Seq) (Nojima et al., 2016). Inactivation of the Carm1 gene substantially increased the normalized read density of p-Ser2 CTD Pol II tags relative total Pol II tags. These data provide evidence for altered transcriptional regulation in Carm1 deficient cells.

overall_design: Examination of transcripts associated with Ser2 phosphorylated RNA Pol II in control and Carm1 KO melanoma cells.

first: Sushil

last: Kumar

first: Kai

last: Wucherpfennig


title: Diet steatosis in commercial crossbreed swine

city: Zaragoza

first: Luis

middle: Vicente

last: Herrera-Marcos

state: Zaragoza

address: C/Miguel servet nº177

department: Bioquimica y biologia molecular y celular

institute: Universidad de Zaragoza. Facultad de Veterinaria

summary: This study aims to fully characterize the changes taht undergoes hepatic transcriptome due to dietically induced steatosis in commercial crossbreed pigs

overall_design:
8 Landrace x Large White pigs recieved a steatotic diet during two months, sampling took place before and after the intervention.
Liver biopsies were immediately removed and frozen in liquid nitrogen. RNA from each liver was isolated using Tri-reagent (Ambion). DNA contaminants were removed by TURBO DNAse treatment using the DNA removal kit from Ambion. RNA was quantified by absorbance at A260/280. The integrity, concentration and purity of RNA was verified by a Biorad experion chip (Hercules, CA, USA)
Finally, 4 pools (2 animal samples in each pool) for each condition (initial state (non-steatosis) and final state (steatosis)) were prepared and studied by RNAseq. Results of RNAseq were verified by qPCR.

first: Jesús

last: Osada García

first: Carmen

last: Arnal Atarés

first: Antonio

middle: T

last: Güemes-Sánchez

first: Agustín

last: García-Gil

first: Joaquin

last: Surra-Muñoz

first: Roberto

last: Martinez-Beamonte

middle: V


title: STK25 in iPS Cardiomyocytes

status: Public on Jan 29 2022

city: NEW YORK

first: Barry

last: Fine

address: 622 West 168th Street, PH8-406

department: Medicine

institute: Columbia University

summary: We report the effect of the deletion of STK25 kinase on the transcriptomes of induced pluripotent stem cell derived cardiomyocytes (iPS-CM).

overall_design: STK25 homozygous knockout induced pluripotent stem cells were derived with CRISPR/Cas9 in a wild-type background (WTC11 cell line). This isogenic pair of cell lines  were differentiated to cardiomyocytes (Burridge et al, Nature Methods 2014). Three biological replicates of cardiomyocytes per genotype were processed for sequencing on day 15 post differentiation.

first: Xiaokan

last: Zhang

first: Bryan

middle: Z

last: Wang


title: Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells [shRNA RNA-seq]

first: Tomokazu

last: Sumida

overall_design: Human naïve CD4+ T cells were transduced lentiviral shRNAs, followed by stimulation with anti-CD3/CD28 w/wo IFN-b (500U/ml). GFP+ lentiviral transduced cells were sorted by FACS and proceeded to RNA extraction. Gene expression profiles were assessed by mRNA-seq.

first: Asaf

last: Madi

first: David

last: Hafler


title: Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The Plasmodium falciparum protein PfMRP1 functions as an influx ABC transporter

city: Braga

first: Nuno

middle: S.

last: Osório

address: Campus de Gualtar

country: Portugal

institute: ICVS

summary: Adenosine triphosphate (ATP)-binding cassette (ABC) transporters play an important role in mediating solute or drug transport across cellular membranes. Although this class of transporters has been well characterized in diverse organisms little is known about the physiological roles in Plasmodium falciparum, the deadliest malaria parasite species. We studied the Plasmodium falciparum Multidrug Resistance-associated Protein 1 (PfMRP1; PF3D7_0112200), an ABC transporter localized to the parasite plasma membrane, generating genetic disrupted parasites. We demonstrate that parasites with disrupted pfmrp1 are resistant to folate analogs, methotrexate and aminopterin, with antimalarial activity. This phenotype occurs due to reduction in compound accumulation in the parasite cytoplasm. Phylogenetic analysis supports pfmrp1 being distantly related to ABC transporters in other eukaryotes, suggesting an unusual function. We propose that PfMRP1 can act as a solute importer, a function not previously observed in this organism.

sample_organism:
Plasmodium falciparum 3D7
Plasmodium falciparum Dd2

overall_design: Study focused on the impact of truncating the PfMRP1 transporter on P. falciparum physiology and drug response. RNA was extrated after tighly synchronization of parasites of estimatly 28-32h after cycle initiation. One sample was colected for wild-type and knock-out for the two strains in study the 3D7 and Dd2.

first: Miguel

last: Silva

first: Carla

last: Calçada

first: Vitória

last: Baptista

first: Vandana

last: Thathy

last: Teixeira

first: Adam

last: Reid

first: Pedro

middle: F

last: Ferreira

last: Fidock

first: Maria

middle: I

last: Veiga


title: Transcriptomic analysis of HCV+ vs HCV- hepatocytes  and tumoral cells

city: Montpellier

first: Damien

last: Grégoire

address: 1919, route de Mende

country: France

institute: CNRS

summary: HCV+ cells were detected by smiFISH on liver section of a patient with hepatocellular carcinoma. Clusters of HCV+ and HCV- cells were captured by laser microdissection and transriptomes analysed by RNA sequening. Highly sensitive single molecule fluorescent in situ hybridization applied to frozen tissue sections of a hepatitis C patient allowed the delineation of clusters of infected hepatocytes. Laser micro-dissection followed by RNAseq analysis of HCV-positive and -negative regions from the tumoral and non-tumoral tissues from the same patient revealed HCV-related deregulation of expression of genes in the tumor and in the non-tumoral tissue.

overall_design: mRNA profiles of clusters of cells HCV+ or HCV- from one patient were generated by deep sequencing using Illumina HiSeq2000.

first: Jacqueline

last: Butterworth

first: Amal

last: Zine El Aabidine

first: Guillaume

last: Desandré

first: Urszula

last: Hibner


title: Single cell RNA-seq analysis of CNCCs at embryonic E9.5

first: Arya

last: Mani

address: 300 George Street

department: Internal Medicine

institute: Yale University

summary: Cardiac NCC were extracted by dissecting out Prdm6f/f; Wnt1-Cre2; ZsGreen1 embryos and their wildtype littermates (Prdm6+/+; Wnt1-Cre2; ZsGreen1) from mid otic placode to the posterior edge of the 4th somite. The ScRNA-seq was carried out using the 10X Genomics Chromium system. There was an average of 2,742 and 3,102 counts per cell or an average of 1,294 and 1,432 unique genes detected in respectively WT and KO conditions. In our models we show that the absence of Prdm6 tips the balance in favor of Wnt1 by reducing Bmp4 and increasing Wnt1 transcripts in several clusters, leading to impaired CNCC migration.

overall_design: Single cell RNA-seq analysis of E9.5 embryos from the mid otic placode to the posterior edge of the 4th somite.

first: Lingjuan

last: Hong

first: Victor

last: Gasque


title: Bulk RNA-sequencing analysis of E17.5 DA from Prdm6f/f; SM22-Cre mice and wildtype littermates

summary: RNA-sequencing analysis of E17.5 DA from Prdm6f/f; SM22-Cre mice and wildtype littermates identified contractile proteins such as Tagln and Myh11 as the most downregulated genes in the DA of Prdm6f/f; SM22-Cre mice vs. wildtype littermates from 280 differentially exressed genes. Strikingly, the expression levels of the Tfap2b and Sox9, which also function as NCC specifiers were significantly reduced at in DA of Prdm6f/f; SM22-Cre vs. wildtype littermates

overall_design: RNA-sequencing analysis of E17.5 DA from WT and Prdm6f/f; SM22-Cre mice.

first: Sameet

last: Mehta

first: Li


title: Genome-wide screening of IKZF1 binding in multiple myeloma cells.

city: Yakushiji

first: NAOKI

last: OSADA

address: Tochigi

department: Center for Molecular Medicine

country: Japan

institute: Jichi Medical University

summary: We analyzed genome-wide distribution of IKZF1 binding in multiple myeloma using ChIP-seq.

overall_design: We isolated fixed chromatin from MM.1S cells and performed immunoprecipitation with anti-IKZF1 antibody, followed by deep sequencing.

first: Naoki

last: Osada

first: Jiro

last: Kikuchi


title: Functions of  OGDH in primed human embryonic stem cells.

city: shanghai

first: Liu

last: Yujie

address: South Chongqing Road

institute: Shanghai Jiao Tong Univeraity School of Medicine

summary: Human embryonic stem cells (hESCs) can self-renew infinitely, or differentiate into the three germ layer lineages in vitro with certain cues, holding great promise to model early human embryo development ex vivo.It is wildly accepted that hESCs take advantage of both glycolysis and mitochondrial respiration to favor the naïve pluripotency, while prefer glycolysis to support the primed pluripotency. Thus, the function of mitochondrial respiration in primed hESCs has been underestimated for a long time, and has not been fully understood yet. Herein, we report that the adenosine triphosphate (ATP) production rate is comparable between mitochondrial respiration and glycolysis, suggesting that mitoATP serves as one of the major sources of the ATP pool in primed hESCs. Next, we constructed a OGDH knockdown cell line whose ability of mitochondrial respiration was impired. Of note, OGDH deficiency led to the exit of primed pluripotency accompanied by cell death.Collectively, the current study unveils that OGDH acts as a key regulator to fine-tune the abundance of TCA cycle metabolites to ensure the mitochondrial respiration activity in primed hESCs, and highlights the pivotal roles of mitochondrial respiration in terms of ATP production and the maintenance of primed pluripotency.

overall_design: There are 9 samples which are WT and OGDH knockdown cell samples upon Dox induction for 4 days as well as 5 days.These group of samples all have three replicates.

first: Yujie

last: Liu

first: Han

last: Wang

first: Min

last: Shao


title: Chromatin remodeler Brahma safeguards canalization of a labile epigenomic state in precardiac mesoderm[scRNA-Seq]

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens Street

institute: Gladstone Institute of Cardiovascular Disease

summary: We perfromed single cell RNA Seq of WT and BRM KO cells at mesoderma nd cardiac myocyte stages of cardiac differentiation

overall_design: Cells isolated at each of these stages were processed according to 10x genomics V2 chemistry manufactures protocols. Libraies were sequenced in a HiSeq4000 sequencer. Reads were alligned with CellRanger and analysed on Seurat R package

first: Swetansu

last: Hota


title: Genome-wide effect of ZBP1-mediated inflammatory response to LPS

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

summary: We report the role of ZBP1 in mediating responses to LPS in the mouse macrophages.

overall_design: Primary macrophages from wild type and ZBP1-deficient mice were activated for 4 hours with TNF.

first: Hayley

last: Muendlein


title: Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells [ATAC-seq]

first: Tomokazu

last: Sumida

overall_design: Human naïve CD4+/CD8+ T cells were stimulated with anti-CD3/CD28 w/wo IFN-b (500U/ml). ATAC-seq samples were collected from 2h, 8h, 72h timepoints.

first: Asaf

last: Madi

first: David

last: Hafler


title: Next Generation Sequencing Facilitates Quantitative Analysis of control, NDEA,  NDEA + CFT-1 and NDEA+FYT Transcriptomes

city: Fuzhou

first: Sufeng

last: Liao

state: Fujian

address: No.15 Shangxiadian Road, Cang Shan Distrit,

institute: Fujian Agriculture and Forestry University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) between treatment and control model samples.

Results: Using the RNA-seq  analysis workflow, we mapped about an average of  80 million sequence reads per sample to the rat genome (Rnor_6.0) and identified 34,194  transcripts.

Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design:
Male Wistar rats (N = 48, 140-160 g) were housed in a specific pathogen-free animal room and maintained under standard experimental conditions: temperature 22 ± 1 °C, relative humidity 50±10% with a 12 h light/dark cycle.
After 1 week quarantine, the rats were randomized into 4 groups (N = 12/group): normal control group (Control group, intraperitoneal injection of 0.9% saline solution twice a week from 2-9th weeks and drink water), model controls group (NDEA group, intraperitoneal injection of 25 mg/kg N-nitrosodiethylamine twice a week from 2-9th weeks and drink water), CFT-1-treated group (NDEA + CFT-1, treated with Camellia sinensis (L.) O. Kuntze cv. CFT-1 tea infusion rich in epigallocatechin-3-gallate for 20 weeks and intraperitoneal injection of 25 mg/kg N-nitrosodiethylamine twice a week from 2-9th weeks), FYT-treated group (NDEA + FYT, treated with common tea Fuyun6 green tea infusion for 20 weeks and intraperitoneal injection of 25 mg/kg N-nitrosodiethylamine twice a week from 2-9th weeks). The feed, water, tea infusion intake and body weights were measured weekly.
After 20 weeks, the rats were anesthetized by intraperitoneal injection of pentobarbital sodium (40 mg/kg) for collection of liver samples. Three liver samples were randomly selected from each group and stored at -80C for RNA sequencing.


title: GSDMB is increased in IBD and regulates epithelial restitution/repair independent of pyroptosis

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: Gasdermins are a family of structurally-related proteins originally described for their role in pyroptosis. Gasdermin B (GSDMB) is currently the least studied, and while its association with genetic susceptibility to chronic, mucosal inflammatory disorders is well-established, little is known of its functional relevance during active disease states. Herein, we report increased GSDMB in inflammatory bowel disease, with single-cell analysis identifying epithelial specificity to inflamed colonocytes/crypt top colonocytes. Surprisingly, mechanistic experiments and transcriptome profiling reveal lack of inherent GSDMB-dependent pyroptosis in activated epithelial cells and organoids, but instead, point to increased proliferation and migration during in vitro wound closure, which arrests in GSDMB-deficient cells that display hyper-adhesiveness and enhanced formation of vinculin-based actomyosin stress fibers dependent on PDGF-A-mediated FAK phosphorylation. Importantly, carriage of disease-associated GSDMB SNPs confers functional defects disrupting epithelial restitution/repair, which altogether, establishes GSDMB as a critical factor for restoration of epithelial barrier function and the resolution of inflammation.

overall_design: Colonic epithelial cell line, HT-29, were CRISPR cas9 targetted for GSDMB deletion: GSDMB-KO cells. GSDMB-KO cells were then rescued with overexpression of either canonical GSDMB or mutant, IBD-associated GSDMB containing 2 SNPs: glycine to arginine at position 299 and from proline to serine at position 306.

first: Nitish

last: Rana

first: Hannah

last: Kondolf

first: E

first: Theresa

last: Pizarro


title: Prdm6 controls heart development by regulating neural crest cell differentiation and migration

first: Arya

last: Mani


title: Multiple Myeloma cells

first: NAOKI

last: OSADA

summary: Multiple Myeloma cell line MM.1S  performed ChIP-seq analysis using anti-c-Fos antibody.

overall_design: We isolated fixed chromatin from MM.1S cells  performed immunoprecipitation with anti-c-Fos antibody, followed by deep sequencing.

first: Yusuke

last: Furukawa

first: Jiro

last: Kikuchi


title: Transcriptomes of lung adenocarcinomas

city: Kashiwa

first: Shogo

last: Kumagai

state: Chiba

address: 6-5-1 Kashiwanoha

institute: National Cancer Center

summary: We performed RNA-seq using 23 human surgically-resected gastric adenocarcinomas.

overall_design: Examination of 23 gastric adenocarcinomas by RNA-seq.

first: Hiroyoshi

last: Nishikawa


title: Screening and verification of differentially expressed long non-coding RNAs in the peripheral blood of patients with asthma

city: Shanghai

first: Shiyuan

last: Wang

state: Shanghai

address: 12 Middle Urumqi Road

department: Department of Integrative Medicine

institute: Huashan Hospital, Fudan University

summary:
Purpose: The goals of this study are to explore the differentially expressed long non-coding RNAs in the peripheral blood of patients with asthma.
Methods: lncRNA and mRNA profiles of peripheral blood (human) were generated by deep sequencing.
Results: There were 1137 differentially expressed lncRNAs in the asthma patients compared to in the healthy controls, of which 485 were upregulated and 652 were downregulated.

overall_design: Second-generation high-throughput sequencing was performed on 4 patients and 3 healthy subjects' peripheral blood samples.

first: Cheng

last: Ma

first: Ying

last: Wei

first: Jingcheng

last: Dong


title: MYCL-mediated in vivo reprogramming expands pancreatic insulin-producing cells to reverse diabetes

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

summary: β cell proliferation rates decline with age and adult β cells have limited self-duplicating activity for regeneration, which predisposes to diabetes. Here we show that, among MYC family members, Mycl was expressed preferentially in proliferating immature endocrine cells. Genetic ablation of Mycl caused a modest reduction in cell proliferation of pancreatic endocrine cells in neonatal mice. By contrast, systemic expression of Mycl in mice stimulated proliferation in pancreatic islet cells and resulted in expansion of pancreatic islets without forming tumors in other organs. Single-cell RNA sequencing and genetic tracing experiments revealed that the expression of Mycl provoked transcription signatures associated with immature proliferating endocrine cells and stimulated self-duplication in adult hormone-expressing cells. The expanded hormone-expressing cells ceased proliferation but persisted after withdrawal of Mycl expression. Remarkably, a subset of the expanded α cells gave rise to insulin-producing cells after the withdrawal. Moreover, transient Mycl expression in vivo was sufficient to normalize increased blood glucose levels in diabetic mice evoked by chemical ablation of β cells. In vitro expression of Mycl similarly provoked active replication without inducing apoptosis in adult hormone-expressing islet cells, even those from aged mice. Furthermore, the expanded islet cells functioned in diabetic mice after transplantation. Finally, we show that MYCL stimulated self-duplication of human adult cadaveric islet cells. Collectively, these results demonstrate that sole induction of Mycl expands adult β cells both in vivo and in vitro. Moreover, islet cell-specific reprogramming via transient Mycl transduction elicits endogenous expansion of insulin-producing cells in adult pancreas through both self-duplication of β cells and transdifferentiation ofα cells into insulin-producing cells, which may provide a regenerative strategy of β cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For scRNAseq in chimeric mouse islets, we transduced Mycl in 8-week-old adult chimeric mice for 8 weeks by drinking Dox-containing water (Dox: 2.0mg/mL). After dissociation of the islets into single cells in TrypLE, we generated chromium single cell 3′ v1 libraries and sequenced them using Illumina Novaseq 6000. We profiled 7,001 cells (ex1: 4,307 cells; ex2: 2,694 cells).For scRNAseq in mouse islets, we transduced Mycl in 8-week-old adult mice for 8 weeks by drinking Dox-containing water (Mycl ON, Dox: 2.0mg/mL) and ceased Mycl expression for 4 weeks (Mycl ON-OFF). For the control, islet cells were harvested from no treatment Mycl inducible mice at 20wks(WT). After dissociation of the islets into single cells, we generated chromium single cell 3′ v1 libraries and sequenced them using Illumina Novaseq 6000. We profiled 6,394 cells (Mycl ON: 3,513 cells; Mycl ON-OFF: 1,560 cells; WT: 1321 cells).

first: Michitada

last: Hirano

first: Mio

last: Kabata

first: Takuya

last: Yamamoto


title: Oncogenic mutation BRAF V600E changes phenotypic behavior of THLE-2 liver cells through alteration of gene expression

status: Public on Jan 28 2022

city: Little Rock

first: Christopher

middle: Paul

last: Wardell

state: AR

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: The accumulation of mutations in cancer driver genes such as tumor suppressors or pro-to-oncogenes affects cellular homeostasis. Disturbances in the mechanism controlling prolifera-tion causes significant augmentation of cell growth and division due to the loss of sensitivity to the regulatory signals. Nowadays, an increasing number of cases of liver cancer are observed worldwide. Data provided by the International Cancer Genome Consortium (ICGC) have indi-cated many alterations within gene sequences, whose roles in tumor development are not well understood. A comprehensive analysis of liver cancer (hepatocellular carcinoma-virus associated) samples has identified new and rare mutations in B-Raf proto-oncogene (BRAF) in Japanese HCC patients, as well as BRAF V600E mutations in French HCC patients. However, their function on liver cancer has never been investigated. Here, using tests for functional analysis and next gen-eration sequencing we demonstrate the tumorigenic effect of BRAF V600E on hepatocytes (THLE-2 cell line). Moreover, we identified genes such as BMP6, CXCL11, IL1B, TBX21, RSAD2, MMP10, SERPIND1, which are possibly regulated by BRAF V600E-mediated mitogen-activated protein kinases/extracellular signal-regulated kinases (MAPK/ERK) signaling pathway. Through several functional assays, we demonstrated that BRAF L537M, D594A, and E648G mutations by its own are not pathogenic in liver cancer. The investigation of genome mutations and the de-termination of their impact on cellular processes and functions are crucial to unraveling the mo-lecular mechanisms of liver cancer development.

overall_design: Investigation of phenotypes of THLE-2 liver cells with BRAF mutations

first: Hiroaki

last: Taniguchi

middle: P


title: MYCL-mediated in vivo reprogramming expands pancreatic insulin-producing cells to reverse diabetes - RNA-Seq

overall_design: For RNAseq in mouse liver, we transduced c-Myc or Mycl in 4-week-old adult mice for 48 hrs by intraperitoneal injection of Dox (0.2 ml; 2.0mg/mL). For the control, liver were harvested from no treatment Mycl inducible mice at 4wks(WT).


title: Comparative analysis of human brain tissue preprocessing methods for single-nucleus chromatin accessibility profiling

city: New York

first: Shan

last: Jiang

department: Taub Institute for Research on Alzheimer’s Disease and the Aging Brain

institute: Columbia University Irving Medical Center

summary: The ability to analyze chromatin accessibility at the single-nucleus level is a critical step towards capturing the highly complex mechanisms that regulate gene expression in the human brain, and to functionally characterize the genetic architecture of neuropsychiatric traits. The assay for transposase accessible chromatin (ATAC-seq) has rapidly established itself as a robust means of studying epigenome regulation in bulk tissues and, more recently, at the single-cell level. To facilitate optimal preparation of frozen archival human brain tissue samples for single-nuclear ATAC-seq (snATAC-seq), we assessed the impact of different sample preparation approaches on the quality of snATAC-seq libraries. We tested six conditions, including different fluorescent activated nuclear sorting (FANS) strategies, from nuclei isolated from a sample of human cortical tissue. Using an unbiased computational approach, we were able to identify major cell populations in all snATAC-seq libraries, including those not subjected to FANS. When FANS was used, we observed that the choice of DNA stain impacts the quality of ATAC-seq libraries. Staining samples with DAPI can lead to insufficient detection of open chromatin regions, whereas 7aad provides improved identification of some nuclear sub-populations. We also observed that use of fluorescent dyes (in particular, DAPI) can lead to under-sampling of excitatory neurons. Our work provides guidelines on the trade-offs associated with different nuclear isolation strategies when preparing samples for snATAC-seq.

overall_design: Single-nucleus ATAC-seq samples from 6 different experiment settings

first: Panos

last: Roussos

first: John

last: Fullard

first: Hao-Chih

last: Lee


title: SOX4 facilitates PGR protein stability and FOXO1 expression conducive for human primary endometrial decidualization

city: Xiamen

first: Wenbo

last: Deng

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

summary: To detect the direct target genes of SOX4 in differentiated human primary endometrial stromal cells, differentiated  human primary endometrial stromal cells  cells at the presence of MPA, E2 and cAMP are collected and subjected to ChIP-Seq. After aligned to human Hg38 by STAR, peaks are called by MACS2. Our results show that SOX4 is the key regulator for decidualization by regulating FOXO1, STAT3, PRL and FOSL2. This specific enrichment is confirmed by ChIP-qPCR. Additionally, there are also some other direct genes of SOX4, indicating the essential role of SOX4 in decidualization. This ChIP-Seq data provides fundamental information for our further physiological study of SOX4.

overall_design: ChIP was performed according to the reported previousl with slight modification. Briefly, about 2x106 human primary endometrial cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified. The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150.


title: Tubastatin A maintains skeletal muscle stem cell (MuSC) quiescence

city: Palo Alto

first: Jamie

middle: O.

last: Brett

address: 3801 Miranda Avenue, Building 100, Room E4-216

department: Neurology and Neurological Sciences

institute: Stanford University

summary: We show that Tubastatin A (TubA) preserves MuSC quiescence and stem cell potency ex vivo, by inhibiting HDAC6 and, consequently, primary cilium resorption. Treatment with TubA improves MuSC engraftment potential and induces a return to quiescence in cycling MuSCs, revealing a potentially valuable approach to enhancing the therapeutic potential of MuSCs. To examine the state of quiescence preserved by TubA at the transcriptome level, we performed RNA-Seq and we found that TubA-treated MuSCs exhibit a quiescent transcriptome. The molecular mechanisms involved in the maintenance of quiescence by TubA were ribosome- and oxidative phosphorylation-related genes as well as low expression levels of cell cycle genes and Hh signaling genes.

overall_design: Young C57BL/6 male mice were used. Quiescent muscle stem cells were isolated from limb muscles by FACS (CD45- CD31- Sca1- VCAM+) and either immediately used for analysis or cultured ex vivo for 24h in the presence or abscence of Tubastatin A. Each replicate represents the muscle stem cells from a single animal. There are 4 replicates for Tubastatin A-treated cells and 3 replicates in the other two conditions.

first: Marina

last: Arjona

first: Thomas

last: Rando

middle: O


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Poststroke Anxiety and General Anxiety Transcriptomes and Predictive Description of Downstream Transcriptional Differences with HDAC3 Inhibitor Treatment or not.

first: Hongrui

last: Zhu

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District, Xiamen, Fujian Province, China

summary: Our study represents the first detailed analysis of transcriptomes between poststroke anxiety and General Anxiety by RNA-seq technology. We founded that: compared with pure restraint stress, stroke plus restraint stress leaded to other pathways: 1) Oxidative stress and redox pathways are out-of-balance; 2). Production of nitric oxide is disordered; 3). Mitochondrial ATP synthesis is coupled with electron transport pathway dysfunction. These upregulated genes analyzed integrally were greatly enriched in the regulation of cytokine production, inflammatory response and leukocyte infiltration. And our results detailly predicted downstream transcriptional differences with HDAC3 inhibitor treatment or not in poststroke anxiety. We concluded that HDAC3-regulated PGE2 production by microglia constitutes phobic anxiety susceptibility after stroke.

overall_design: 1. Damaged cortex tissue of photothrombotic stroke mice with plus restraint stress (PTS + RS) and generalized anxiety disorder (restraint stress, RS) was extracted RNA for detection. 2. RNA profiles from HDAC3 treatment or not in PTS + RS model.

first: Bin

first: Yi

last: Guo


title: δ-cell conversion to insulin+ bihormonal cells in zebrafish

city: Concepción

first: Claudio

last: Carril Pardo

state: Biobío

address: Lientur 1457

country: Chile

institute: Universidad San Sebastian

summary: Restoring damaged b-cells in diabetic patients by harnessing the plasticity of other pancreatic cells raises the questions of the efficiency of the process and of the functionality of the new Insulin-expressing cells. To overcome the weak regenerative capacity of mammals, we used regeneration-prone zebrafish to study b-cells arising following destruction. We show that most new insulin cells differ from the original b-cells as they coexpress Somatostatin and Insulin. These bihormonal cells are abundant, functional and able to normalize glycemia. Their formation in response to b-cell destruction is fast, efficient and age-independent. Bihormonal cells are transcriptionally close to a subset of d-cells that we identified in control islets and which are characterized by the expression of somatostatin 1.1 (sst1.1) and by genes essential for glucose-induced Insulin secretion in β-cells such as pdx1, slc2a2 and gck. We observed in vivo the conversion of monohormonal sst1.1-expressing cells to sst1.1+ ins+ bihormonal cells following b-cell destruction. Our findings support the conclusion that sst1.1 d-cells possess a pro-b identity enabling them to contribute to the neogenesis of Insulin-producing cells during regeneration. This work unveils that abundant and functional bihormonal cells benefit to diabetes recovery in zebrafish.

overall_design: RNA-sequencing of 19 samples from adult fish 6–10 months old. δ-cells (sst1.1:GFP +), β-cells (ins:mCherry +) and Bi hormonal cells (sst1.1:GFP/ins:mCherry +). Transcriptomic profiles of 20 dpt (days post-treatment) control zebrafish sst1.1:GFP high and low 3 replicates for each one.  And ins:mCherry + 7 replicates. Regenerated zebrafish sst1.1:GFP/ins:mCherry + bi-hormonal cells 6 replicates were generated

first: Arnaud

last: Lavergne


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Sirt3K223R Bone-Marrow derived Macrophages Transcriptomes

first: Wei

last: Zhou

address: N0.280 South Chongqing Road

institute: Shanghai Jiao Tong University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare Transcriptomes of Sirt3 WT and KR macrophages with high-throughput data analysis
Methods: Macrophages' mRNA profiles of 8 weeks-old wild-type (WT) and Sirt3 K223R mice were generated by deep sequencing, in quadruplicate, using Total RNA from each sample was quantified using a NanoDrop ND-1000 instrument. 1μg total RNA  was used to prepare the sequencing library in the following steps: 1. Total RNA is enriched by oligo (dT) magnetic beads (rRNA removed); 2. RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method. To sequence the libraries on the Illumina HiSeq 4000 instrument, the barcoded  libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified in situ, and subsequently sequenced for 150 cycles for both ends on Illumina HiSeq instrument.
Results: Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequence quality was examined using the FastQC  software. The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software. The transcript abundances for each sample was estimated with StringTie , and the FPKM value for gene and transcript level were calculated with R package Ballgown. The differentially expressed genes and transcripts were filtered using R package Ballgown. The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown, then use CPAT to assess the coding potential of those sequences. Then use rMATS  to detecting alternative splicing events and plots. Principle Component Analysis (PCA) and correlation analysis were based on gene expression level, Hierarchical Clustering, Gene  Ontology, Pathway analysis, Gene Ontology, Pathway analysis, scatter plots and volcano plots were performed with the differentially expressed genes in R, Python or shell environment for statistical computing and graphics.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with 4 biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results offer a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Macrophages mRNA profiles of 8-week-old wild type (WT) and Sirt3K223R(KR) mice

first: Zhou

last: Wei

first: Cheng

last: Jinke


title: Impact of small molecule and genetic inhibition of PKM2 in muscle progenitor cells

city: Birmingham

first: Anna

last: Thalacker-Mercer

state: Alabama

address: 1900 University Blvd

institute: University of Alabama at Birmingham

summary: Cultured, proliferating C2C12 cells were treated with a short hairpin RNA (shRNA) targeting PKM2 or small molecules that selectively impact canonical and non-canonical PKM2 activity (shikonin and TEPP-46).

overall_design: n=1 sample each: shPKM2, shControl, Vehicle Control, Shikonin, TEPP-46

middle: E

last: Blum

first: Brandon

middle: J

last: Gheller

first: Abby

last: Benvie

first: Martha

last: Field

first: Elena

last: Panizza

first: Nathaniel

last: Vacanti

first: Daniel

last: Berry


title: Thymic epithelial cell alterations and defective thymopoiesis lead to central and peripheral tolerance perturbation in MHCII deficiency

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

summary: Major Histocompatibility Complex (MHC) class II (MHCII) deficiency, also known as Bare Lymphocyte Syndrome (BLS), is a rare combined immunodeficiency due to mutations in genes regulating expression of MHCII molecules. MHCII deficiency results in impaired cellular and humoral immune responses, leading to severe infections and autoimmunity. The contribution of thymic epithelial cell (TEC) defects to the pathogenesis of this primary immunodeficiency has not been well characterized to date, in particular in regard to immune dysregulation. To this aim, we have performed an in-depth cellular and molecular characterization of TEC alterations in this disease. We observed an overall perturbation of thymic structure and function in both MHCII-/- mice and patients. Transcriptomic and proteomic profiling of murine TEC revealed several alterations. In particular, in MHCII-/- mice, impaired cross-talk and mTEC maturation resulted in altered promiscuous gene expression and leaky central tolerance. Furthermore, we observed peripheral tolerance impairment, likely due to defective Treg cell generation and/or function and B cell tolerance breakdown. Overall, our findings reveal disease-specific TEC defects resulting in perturbation of central tolerance and limiting the potential effect of hematopoietic stem cell transplantation in MHCII deficiency.

overall_design: mRNA sequencing of sorted cTEC and mTEC from pooled WT and Aβ0/0 mice, with three replicates per condition.

first: Francesca

last: Ferrua

last: Villa

first: Marita

last: Bosticardo


title: Multi-omics characterization of a diet-induced obese model of non-alcoholic steatohepatitis

city: Hørsholm

first: Martin

middle: Rønn

last: Madsen

state: Please Select

address: Hørsholm Kongevej 11

department: Computation Biology

country: Denmark

institute: Gubra

summary: To improve the understanding of the complex biological processes underlying the development of non-alcoholic steatohepatitis (NASH), a multi-omics approach combining bulk RNA-sequencing based transcriptomics, quantitative proteomics and single-cell RNA-sequencing was used to characterize tissue biopsies from histologically validated diet-induced obese (DIO) NASH mice compared to chow-fed controls. Bulk RNA-sequencing and proteomics showed a clear distinction between phenotypes and a good correspondence between mRNA and protein level regulations, apart from specific regulatory events discovered by each technology. Transcriptomics-based gene set enrichment analysis revealed changes associated with key clinical manifestations of NASH, including impaired lipid metabolism, increased extracellular matrix formation/remodeling and pro-inflammatory responses, whereas proteomics-based gene set enrichment analysis pinpointed metabolic pathway perturbations. Integration with single-cell RNA-sequencing data identified key regulated cell types involved in development of NASH demonstrating the cellular heterogeneity and complexity of NASH pathogenesis.

overall_design: Liver RNAseq of DIO-NASH and Lean-Chow mice

first: Helene

last: Ægidius

first: Kristoffer

last: Rigbolt


title: Identification of HOXB13 binding sites in metastatic PC treated with Enzalutamide

city: gainesville

first: jiqiang

last: yao

state: United States

address: 9453 nw 24th rd

institute: moffitt cancer center

summary: HOXB13 is a developmentally regulated transcription factor, co-expressed along with the   Androgen receptor (AR) in a majority of PCs. Previous studies have indicated context dependent   roles of HOXB13 in the functional regulation of AR and enrichment of HOXB13 motifs in the AR   cistrome. Our studies showed that genetic or pharmacological blockade of HOXB13   sensitized mCRPCs to Enzalutamide (ENZ, Xtandi), an anti-androgen that is currently   deployed to treat mCRPC patients. To identify HOXB13-mediated mechanism of   castration-resistance ChIP-sequencing was  performed with the HOXB13-K13ac,  or IgG antibodies   in the metastatic prostate cancer cell line, C4-2B in vehicle treated as well as Enzalutamide  treated cell lines. We demonstrated for the first time  that BRD4, epigenetically regulates HOXB13  gene expression in PCs. Consistently, JQ1 the prototype BET inhibitor suppresses   HOXB13 expression and inhibit mCRPC growth. ChIP-sequence analysis reveals that  HOXB13 recruitment to the chromatin is not completely abrogated in Enzalutamide treated  cells identify a subset of genes that may have potential role in CRPC proliferation, anti-androgen   resistance and metastasis.

overall_design:
Six samples were analyzed. These samples included Vehicle control for the inhibitor treatments and IgG  for antibody control.
treaan be targeted with MA4--022-1

first: Kiran

last: Mahajan

first: Jiqiang

last: Yao


title: A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis [RNA-seq EZH2i]

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: Multiple sclerosis (MS) is a disease characterized by a targeted immune attack on myelin in the central nervous system (CNS). We have previously shown that oligodendrocytes (OLs), myelin producing cells in the CNS, and their precursors (OPCs), acquire disease-specific transcriptional states in MS. To understand how these alternative transcriptional programs are activated in disease, we performed single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) on the OL lineage in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. We identified regulatory regions with increased accessibility in oligodendroglia (OLG) in EAE, some of which in the proximity of immune genes. A similar remodeling of chromatin accessibility was observed upon treatment of postnatal OPCs with interferon-gamma (IFNg), but not with dexamethasone. These changes in accessibility were not exclusive to distal enhancers, but also occurred at promoter regions, suggesting a role for promoters in mediating cell-state transitions. Notably, we found that a subset of immune genes already exhibited chromatin accessibility in OPCs ex vivo and in vivo, suggesting a primed chromatin state in OLG compatible with rapid transitions to an immune-competent state. Several primed genes presented bivalency of H3K4me3 and H3K27me3 at promoters in OPCs, with loss of H3K27me3 upon IFNg treatment. Inhibition of JMJD3/KDM6B, mediating removal of H3K27me3, led to the inability to activate these genes upon IFNg treatment. Importantly, OLGs from the adult human brain showed chromatin accessibility at immune gene loci, particularly at MHC-I pathway genes. A subset of single-nucleotide polymorphisms (SNPs) associated with MS susceptibility overlapped with these primed regulatory regions in OLG from both mouse and human CNS. Our data suggest that susceptibility for MS may involve activation of immune gene programs in OLG. These programs are under tight control at the chromatin level in OLG and may therefore constitute novel targets for immunological-based therapies for MS.

overall_design: We have performed bulk paired-end RNA-seq from FACS sorted Sox10GFP+ oligodendrocyte precursor cells and treat them with EZH2 inhibitor for 4 days.

first: Mandy

last: Meijer

first: Mukund

last: Kabbe

first: Cassandra

middle: A

last: van Tuijn

first: Abeer

last: Heskol

first: Ana

last: Falcao

first: M

last: Corces

first: Thomas

last: Montine

first: Xingqi

last: Chen

first: Howard

middle: Y

last: Chang

first: Gonçalo

last: Castelo-Branco


title: A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis [RNA-seq IFNg_vs_Dexa_vs_Ctr]

overall_design: We have performed bulk paired-end RNA-seq from FACS sorted Sox10GFP+ oligodendrocyte precursor cells and treat them with Dexamethasone and IFNg.

middle: M

middle: R


title: Therapeutic efficacy of FASN inhibition in preclinical models of HCC

first: Xin

address: 513 Parnassus St.

department: Bioengineering and Therapeutic Sciences

institute: UCSF

summary: Background & Aims: Aberrant activation of fatty acid synthase (FASN) is a major metabolic event during the development of HCC. We evaluated the therapeutic efficacy of TVB3664, a novel FASN inhibitor, either alone or in combination, for HCC treatment.  Approach & Results: The therapeutic efficacy and the molecular pathways targeted by TVB3664, either alone or with tyrosine kinase inhibitors or the checkpoint inhibitor anti-PD-L1 antibody, were assessed in human HCC cell lines and multiple oncogene-driven HCC mouse models. RNAseq was performed to characterize the global gene expression and metabolic profiles. TVB3664 effectively ameliorated the fatty liver phenotype in the aged mice and AKT activation-induced hepatic steatosis. TVB3664 monotherapy showed moderate efficacy in NASH-related murine HCCs, induced by loss of PTEN and c-MET overexpression. TVB3664, in combination with cabozantinib, triggered tumor regression in this mouse HCC model but did not improve the responsiveness to immunotherapy. Global gene expression revealed that TVB3664 predominantly modulated metabolic processes, while TVB3664 synergized with cabozantinib to downregulate multiple cancer-related pathways, especially the AKT/mTOR pathway and cell proliferation genes. TVB3664 also improved the therapeutic efficacy of sorafenib and cabozantinib in the FASN-dependent c-MYC HCC model. However, TVB3664 had no efficacy nor synergistic effects in FASN-independent mouse HCC models.   Conclusions: This preclinical study suggests the limited efficacy of targeting FASN as monotherapy for HCC treatment. However, FASN inhibitors could be combined with other drugs for improved effectiveness. These combination therapies could be developed based on the driver oncogenes, supporting precision medicine approaches for HCC treatment.

overall_design: mRNA profiles of FVB/N wildtype mice and c-Met/sgPTEN induced HCC tumors treated with vehicle, TVB3664, Cabozantinib or TVB3664/Cabozantinb

first: Haichuan

last: Wang

first: Hongwei

last: Xu

first: Carsten

last: Sticht


title: Excitatory SST neurons in the medial paralemniscal nucleus control repetitive self-grooming and encode reward

first: Bing

last: Liu

address: No. 280, South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: We revealed that the MPLSST neurons are excitatory neurons releasing neurotransmitter  glutamate,and reveal that more than half of these neurons corelease neuropeptides SST and PTH2

overall_design: We performed a spatial transcriptomics analysis using the 10x Genomics Visium platform seeking to profile potentially informative markers in the MPL from a coronal section (close to bregma -4.72 mm) from post-natal day 60 (P60) male mice

first: Huang

last: Ju


title: ZNF676 ChIP-seq in HEK293T and H1 cells

city: Lausanne

first: Delphine

last: Grun

address: route Cantonale

country: Switzerland

institute: EPFL

summary: Genome-wide binding profile of the primate-specific KRAB zinc finger protein ZNF676 in cell lines overexpressing the protein.

overall_design: Stable cell lines overexpressing ZNF676 were made by lentiviral vector transduction and selection. They were then fixed with formaldehyde and immunoprecipitation was performed with an anti-HA antibody.

first: Alexandra

last: Iouranova


title: RNA-seq of differentiated primary normal human bronchoepithelial (NHBE) cells overexpressing ZNF676.

summary: RNA-seq of primary normal human bronchoepithelial (NHBE) cells differentiated to have cilia. They express either ZNF676 (experiment), either LacZ (control).

overall_design: Primary NHBE cells transduced with lentiviral vectors coding for ZNF676-3HA and LacZ-3HA followed by differentiation. Experiment performed in triplicates.


title: ZNF728 ChIP-seq in HEK293T cells

summary: Genome-wide binding profile of the primate-specific KRAB zinc finger protein ZNF728 in a HEK293T cell line overexpressing the protein.

overall_design: A stable cell line overexpressing ZNF728 was made by lentiviral vector transduction and selection. Overexpression of the HA-tagged protein was induced with doxycycline. Cells were then fixed with formaldehyde and immunoprecipitation was performed with an anti-HA antibody.

first: Jonas

last: de Tribolet-Hardy


title: IL-17B/IL-17RB signaling cascade contributes to self-renewal and tumorigenesis of cancer stem cells by regulating Beclin-1 ubiquitination

city: Jining

first: Qingli

last: Bie

state: Sandong

address: 89 Guhuai Road

department: Department of Laboratory Medicine

institute: Affiliated Hospital of Jining Medical University

summary: Recombinant IL-17B (rIL-17B) promoted the sphere formation ability of CSCs in vitro and enhanced tumor growth and metastasis in vivo. Furthermore, the activation of autophagy was critically involved in IL-17B/IL-17RB-mediated regulation of CSC functions.

overall_design: HGC-27 GC cells were treated with PBS or 200ng/ml rIL-17B for 48 h, then collected RNA to analyze Transcriptome-sequencing

first: Hui

last: Song

first: Xinke

first: Xiao

last: Yang


title: A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis [ATAC-seq]

first: Eneritz

last: Agirre

overall_design: We have performed bulk ATAC-seq from FACS sorted Sox10GFP+ oligodendrocyte precursor cells and treat them with Dexamethasone and IFNg.

first: Mandy

last: Meijer

first: Mukund

last: Kabbe

first: Cassandra

last: van Tuijn

first: Abeer

last: Heskol

first: Ana

last: Falcao

first: M

first: Thomas


title: A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis [HiChIP]

overall_design: We have performed H3K27ac-directed HiChIP in cultured primary mOPCs in control and IFNg treated conditions.

last: Corces

last: Montine

first: Xingqi

last: Chen

first: Howard

last: Chang

first: Gonçalo

last: Castelo-Branco


title: RNA-seq of ZNF676 KD Win1 naive embryonic stem cells and control cells

first: Delphine

last: Grun

summary: RNA-seq analysis of Win1 naive embryonic stem cells carrying an shRNA against ZNF676 and a control shRNA

overall_design: Embryo-derived Win1 naive embryonic stem cells maintained in naive culture conditions were transduced with a lentiviral construct coding for an shRNA against ZNF676 to reduce its expression in biological triplicates and selected with puromycin. A control shRNA (shScramble) was also used.

first: Iouranova

last: Alexandra


title: A primed immune transcriptional programme is activated in oligodendroglia in multiple sclerosis [ATAC-Seq and RNA-Seq II]

summary: Multiple sclerosis (MS) is characterized by a targeted attack on oligodendroglia (OLG) and myelin by immune cells, which are thought to be the main drivers of MS susceptibility. We found that immune genes exhibit a primed chromatin state in single mouse and human OLG in a non-disease context, compatible with transitions to immune-competent states in MS. We identified transcription factors as BACH1 and STAT1 involved in immune gene regulation in oligodendrocyte precursor cells (OPCs). A subset of immune genes present bivalency of H3K4me3/H3K27me3 in OPCs, with Polycomb inhibition leading to their increased activation upon interferon-gamma (IFN) treatment. Some MS susceptibility single-nucleotide polymorphisms (SNPs) overlap with these regulatory regions in mouse and human OLG. Treatment of mouse OPCs with IFN leads to chromatin architecture remodeling at these loci and altered expression of interacting genes. Thus, susceptibility for MS may involve OLG, which therefore constitute novel targets for immunological-based therapies for MS.

overall_design:
Two 10X Genomics single cell multiomics Grey matter brain control samples one from 2 donors.
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Access to raw fastq and bam files through https://ega-archive.org/ portal, accession ID EGAD00001008457 .

last: van Tuijin

last: Mendanha Falcao

first: Goncalo


title: A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis [CUT&Tag]

overall_design: We have performed Stat1 CUT&Tag from FACS sorted Sox10GFP+ oligodendrocyte precursor cells and treated with IFNg for 48hs.


title: Hominoid-restricted ZNF676 influences transcriptional activation and transgenerational inheritance of epigenetic marks at LTR12C loci

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

overall_design: Refer to individual Series


title: A primed immune transcriptional programme is activated in oligodendroglia in multiple sclerosis [ATAC-Seq and RNA-Seq]

overall_design: Two 10X Genomics single cell multiomics samples one from  Multiple Sclerosis mouse model, EAE (at the peak of the disease)  and a control sample. From Sox10GFP+ sorted cells from adult mice spinal cords.


title: A primed immune transcriptional programme is activated in oligodendroglia in multiple sclerosisn [RNA-Seq]

overall_design: We have performed bulk RNA-seq of Stat1 and Bach1 transcription factors knockdown upon IFNG treatment in primary OPCs.


title: ZNF676 and ZNF728 ChIP-exo in HEK293T cells

summary: Genome-wide binding profile of the primate-specific KRAB zinc finger proteins ZNF676 and ZNF728 in cell lines overexpressing the proteins.

overall_design: Stable HEK293T cell lines overexpressing ZNF676 and ZNF728 were made by lentiviral vector transduction and selection. They were then fixed with formaldehyde and immunoprecipitation was performed with an anti-HA antibody. An exonuclease treatment was performed according to ChIP-exo protocol.

first: Alexandra

last: Iouranova

first: Michael

last: Imbeault

first: Julien

last: Duc


title: ChIP-seq for transcriptional regulator CodY of Lactococcus lactis

city: Tianjin

first: Hao

last: Wu

address: Jinnan District ,Yaguan Road No.135

institute: Tianjin University

summary: CodY is a widely conserved global regulator, regulating nitrogen metabolism, virulence, and stress response in Gram-positive bacteria. Here, we performed ChIP-seq to define the CodY regulon in L. lactis, and found that CodY served either as an activator or as a repressor of hundreds of genes. The genes involved in amino acid biosynthesis and transport, cell wall synthesis, nisin synthesis and immunity, and several transcription regulators were identified regulated by CodY for the first time. Intriguingly, CodY could directly bind to the downstream of codY. This study gives new insights into the function of CodY controlling cell wall synthesis, nisin synthesis and immunity, as well as self-regulation in L. lactis.

overall_design: ChIP-seq for CodY

first: Jianjun

last: Qiao


title: Exploring the downstream genes of HDAC4

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

summary: To explore the downstream genes of HDAC4, we performed RNA-seq to screen after knocking down HDAC4 in 5-8F cells, a nasopharyngeal carcinoma cell line.

overall_design: We used two shRNA to knock down HDAC4 in 5-8F cells.

first: Chun

last: Cheng


title: MAT2A expression and methionine dependency in Diffuse Midline Gliomas creates a distinct metabolic and epi-genetic sensitivity

city: Pittsburgh

first: Sameer

last: Agnihotri

state: PENNSYLVANIA

address: 530 45TH ST, 7TH FL BAY 20 RANGOS RESEARCH

department: Neurosurgery

institute: University of Pittsburgh

summary: We generated a syngeneic H3K27M diffuse midline glioma (DMG) mouse model and performed total RNA seq on  H3K27MPP cells and control cell lines H3wtMPP and Normal Neural stem cells. Aditionally we generate a Dox Inducible Mat2A Knockdown in that human DIPG cell line DIPG04 and performed RNA sequencing on cells treated with 2ug/ml Doxycyclin and no treatment

overall_design: Samples werer analyzed in triplicate

first: Brian

last: golbourn

first: Matt

last: Habert


title: Epithelial miR-215 negatively modulates Th17-dominant inflammation by inhibiting CXCL12 production in the small intestine

status: Public on Jan 27 2022

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: MicroRNAs are a class of non-coding short-chained RNAs that control cellular functions by downregulating their target genes. Recent research indicates that microRNAs play a role in the maintenance of gut homeostasis. miR-215 was found to be highly expressed in epithelial cells of the small intestine; however, the involvement of miR-215 in gut immunity remains unknown. Here, we show that miR-215 negatively regulates inflammation in the small intestine by inhibiting CXCL12 production. Mice lacking miR-215 showed high susceptibility to inflammation induced by indomethacin, accompanied by an increased number of Th17 cells in the lamina propria of the small intestine. Our findings support a promising perspective of targeting miR-215 to treat inflammatory conditions in the small intestine.

overall_design: We compared gene expression profiles of the small intestinal epithelia between wild-type and miR-215−/− mice by RNA-Seq analysis.

first: Siddhika

last: Pareek

first: Taiki

last: Sakaguchi


title: Kinetics of Tbet+ B cells during LCMV infection

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: Inflammatory (B220+ CD19+ CD44+ CD11c+ Tbet-AmCyanhi) B cells were sorted from female Tbet-AmCyan reporter mice at day 8, 10, and 15 post infection with LCMV-Armstrong. RNA-seq was employed to assess transcriptional changes in inflammatory B cells throughout the infection.

overall_design: Mice were infected i.p. with 2 × 10^5 pfu LCMV Armstrong and inflammatory B cells were sorted from Tbet-AmCyan reporter mice at various day post LCMV infection

first: Jason

last: Weinstein

first: Alex

first: Wenzhi

last: Song


title: Microglia contribute to the propagation of Abeta pathology into healthy brain tissue

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

summary: The extracellular accumulation of amyloid-beta (A) peptides is a major hallmark of Alzheimer’s disease (AD). It is widely accepted that microglia associate with A plaques and appear morphologically activated especially in their immediate vicinity. Whether microglia play a role in A plaque formation and contribute to the propagation of A pathology remains however unknown. We therefore investigated the characteristics of microglia during neural transplantation experiments where wild-type neurons are grafted into the cortex of AD mouse models. Here, we demonstrate that A from the transgenic host tissue is able to enter and deposit within wild-type (WT) grafts, a process that is accompanied by massive microglia infiltration. Notably, manipulation of microglia function or microglia elimination significantly reduced A deposition within the grafts. Similarly, time-lapse in vivo two-photon imaging revealed that microglia transport A to the site of injury thereby identifying microglia as cellular carrier of A that propagate A pathology in previously unaffected CNS tissue. Our data thus argue for a hitherto unexplored mechanism of A propagation.

overall_design: examination of gene profile of microglia isolated from cortical grafts and non-grafted tissue

first: Charlotte

last: Mezö


title: Single-cell RNA-sequencing reveals the heterogeneity of microglia in fibrous membrane derived from proliferative diabetic retinopathy and proliferative vitreoretinopathy

city: Nanjing

first: Songtao

last: Yuan

address: 300 Guangzhou Road

institute: First Affiliated Hospital of Nanjing Medical University

summary: Fibrous membrane (FM), the hallmark for proliferative diabetic retinopathy (PDR) and proliferative vitreoretinopathy (PVR), can cause hemorrhages and retinal detachment, which may lead to blindness if not properly treated. However, little is known about the pathophysiology of FM. In this study, we successfully employed single-cell RNA sequencing on the small-sized vitreous FMs, and generated a comprehensive cell atlas of FMs derived from PVR and PDR. Distinct cell compositions were identified in the FMs, with microglia as the major cell population. Additionally, our analysis revealed a spectrum of microglia activation states with distinct molecular signatures and intercellular interactions in disease-specific microenvironment.  This description of microglia phenotypes in the FM of PVR and PDR may offer insight into the activation of microglia in the FM pathogenesis, as well as potential signaling pathways amenable to disease-specific intervention.

overall_design: Fibrous membrane samples from one paitient with proliferative vitreoretinopathy and three patients with proliferative diabetic retinopathy were surgically incised and and sequenced using the scFTD-seq protocol.

first: Qinghuai

last: Liu

first: Zizhong

last: Hu

first: Xiying

last: Mao


title: A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis [scATAC-Seq]

first: Eneritz

last: Agirre

summary: Multiple sclerosis (MS) is a disease characterized by a targeted immune attack on myelin in the central nervous system (CNS). We have previously shown that oligodendrocytes (OLs), myelin producing cells in the CNS, and their precursors (OPCs), acquire disease-specific transcriptional states in MS. To understand how these alternative transcriptional programs are activated in disease, we performed single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) on the OL lineage in the experimental autoimmune encephalomyelitis (EAE) mouse model of MS. We identified regulatory regions with increased accessibility in oligodendroglia (OLG) in EAE, some of which in the proximity of immune genes. A similar remodeling of chromatin accessibility was observed upon treatment of postnatal OPCs with interferon-gamma (IFNg), but not with dexamethasone. These changes in accessibility were not exclusive to distal enhancers, but also occurred at promoter regions, suggesting a role for promoters in mediating cell-state transitions. Notably, we found that a subset of immune genes already exhibited chromatin accessibility in OPCs ex vivo and in vivo, suggesting a primed chromatin state in OLG compatible with rapid transitions to an immune-competent state. Several primed genes presented bivalency of H3K4me3 and H3K27me3 at promoters in OPCs, with loss of H3K27me3 upon IFNg treatment. Inhibition of JMJD3/KDM6B, mediating removal of H3K27me3, led to the inability to activate these genes upon IFNg treatment. Importantly, OLGs from the adult human brain showed chromatin accessibility at immune gene loci, particularly at MHC-I pathway genes. A subset of single-nucleotide polymorphisms (SNPs) associated with MS susceptibility overlapped with these primed regulatory regions in OLG from both mouse and human CNS. Our data suggest that susceptibility for MS may involve activation of immune gene programs in OLG. These programs are under tight control at the chromatin level in OLG and may therefore constitute novel targets for immunological-based therapies for MS.

overall_design: We have performed plate based scATAC-seq (PI-scATAC) from FACS sorted Sox10GFP+ and nonGFP cells from the multiple sclerosis mouse model (EAE) at the peak of the disease and non EAE Ctrl Sox10GFP+ and nonGFP  cells, both from brain and spinal cord.

first: Mandy

last: Meijer

first: Mukund

last: Kabbe

first: Cassandra

last: van Tuijn

first: Abeer

last: Heskol

first: Ana

last: Falcao

first: M

last: Corces

first: Thomas

last: Montine

first: Xingqi

last: Chen

first: Howard

last: Chang

first: Gonçalo

last: Castelo-Branco


title: Satellite cell – specific deletion of CIPC alleviates myopathy in mdx mice.

city: suzhou

first: zheng

middle: ji

last: qing

address: renairoad

institute: szdx

summary: The regeneration of skeletal muscle relies on satellite cells which can proliferate, differentiate and form new myofibers upon injury. Emerging evidence suggests that misregulations of satellite cell fate and function influence the severity of Duchenne Muscular Dystrophy (DMD). The myogenic identity and maintenance of the pool of satellite cells is determined by the transcription factor PAX7. Satellite cell proliferation and self-renewal is regulated by the circadian clock. Here, we show that the CLOCK-interacting protein, Circadian (CIPC), a negative-feedback regulator of the circadian clock, is up-regulated during myoblast differentiation. Specific deletion of CIPC in satellite cells alleviated myopathy, improved muscle function and reduced fibrosis in mdx mice. CIPC deficiency led to activation of the ERK1/2 and JNK1/2 signaling pathways, which in turn activated the transcription factor SP1 to trigger the transcription of PAX7. Therefore, CIPC is a negative regulator of satellite cell function and loss of CIPC in satellite cells promotes muscle regeneration.

overall_design: Total RNA from Cipc+/+ and Cipc-/- satellite cells.

first: Yao-Hua

last: Song

first: Jiqing

last: Zheng


title: An in vivo CRISPR screen identifies stepwise genetic dependencies of metastatic progression

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

institute: ETH Zurich

summary: In vivo genome-wide loss-of-function CRISPR screen identifies critical genes required for individual steps of the metastatic cascade in human CTC-derived xenografts, suggesting novel drivers and vulnerabilities of breast cancer metastasis.

overall_design: We isolated cells from Bone, Brain, Liver and Lymphnode metastases from a breast cancer xenograft (BR16), after bioluminescence imaging of organs with metastasis conducted with IVIS Lumina II (Perkin Elmer). mRNA was isolated and amplified according to the Smart-Seq2. Subsequently, libraries were prepared with Nextera XT (Illumina) and sequenced on NextSeq75, single read for RNA

first: Manuel

last: Scheidmann

first: Aino

last: Paasinen-Sohns

first: Karin

last: Strittmatter

first: Ilona

last: Krol

first: Ramona

last: Scherrer

first: Cinzia

last: Donato

first: Barbara

last: Szczerba

first: Sofia

last: Gkountela

first: Leo

last: Kunz

first: Timm

last: Schroeder

first: Marcus

last: Vetter

first: Christoph

last: Rochlitz

first: Randall

last: Platt

first: Nicola

last: Aceto


title: Endotype reversal as a novel strategy for screening drugs targeting familial Alzheimer's disease

city: La Jolla

first: Shankar

last: Subramaniam

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California, San Diego

summary: While amyloid-β (Aβ) plaques are considered a hallmark of Alzheimer's disease, clinical trials focused on targeting gamma secretase, an enzyme involved in aberrant Aβ peptide production, have not led to amelioration of AD symptoms or synaptic dysregulation. Screening strategies based on mechanistic, multi-omics approaches that go beyond pathological readouts can aid in the evaluation of therapeutics. Using early-onset Alzheimer's (EOFAD) disease patient lineage PSEN1A246E iPSC-derived neurons, we performed RNA-seq to characterize AD-associated endotypes, which are in turn used as a screening evaluation metric for two gamma secretase drugs, the inhibitor Semagacestat and the modulator BPN-15606.

overall_design: hiPSC-derived neurons were generated from donor non-demented control (NDC) or EOFAD-causing psen1 A246E patients. Total RNA was extracted from: NDC hiPSC-derived neurons treated with DMSO (vehicle), n=2; PSEN1A246E hiPSC-derived neurons treated with DMSO (vehicle), n=3;  PSEN1A246E hiPSC-derived neurons treated with BPN-15606 (G), n=3; and PSEN1A246E hiPSC-derived neurons treated with Semagacestat (S), n=3. Samples were sequenced on a illumina HiSeq 4000 generating Paired End, 75bp reads.

first: Andrew

middle: B

last: Caldwell

first: Qing

last: Liu

first: Can

last: Zhang

first: Gary

last: Schroth

first: Douglas

last: Galasko

first: Rudolph

last: Tanzi

first: Shauna

middle: H

last: Yuan

first: Steven

middle: L

last: Wagner


title: Ectopic expression data of bacterial effects on NNE and NPC cells

status: Public on Jan 26 2022

city: Nanning

first: Bo

last: Li

state: Guangxi

address: No. 22 Shuangyong road

department: Radiation oncology

institute: Guangxi Medical University

summary:
Compared with nasopharyngeal carcinoma cell line C666-1, we found that pro-inflammatory cytokines in NP69 cells were significantly upregulated after PGN treatment
We used microarray technology to identify genes that were significantly different after PGN treatment of NP69 cell lines

overall_design: A NPC cell line and a NNE cell line were included in the microarray analysis. Nasopharyngeal carcinoma cell line C666-1 and nasopharyngeal epithelial cell NP69 were treated with LPS and PGN.

first: Yifang

last: Wang

first: Xiaoying

last: Zhou


title: ChIP-seq of the binding DNA by NS5

city: Shenzhen

first: Ping

address: Gongchang Road

institute: Sun Yat-sen University

summary: The ChIP-seq and RNA-seq data provide evidence that ZIKV-NS5 binds to the gene body of the key neuro-factors and then inhibits their transcription, thus disrupting the neurogenesis of human NPCs.

overall_design: Overexpressed ZIKV-NS5 in hNPCs and collected cells 48 hours post infection by lentivirus. And the input was set as the control.

first: Liping

last: Guo


title: Expression profiling of 1-day old C. elegans adult circ-crh-1(syb385), crh-1(n3315) versus wild-type

city: Reno

first: Pedro

last: Miura

state: Nevada

address: 1664 N VIRGINIA ST MS 0314

department: Biology

institute: University of Nevada, Reno

summary: poly(A)-selected mRNA-seq of circ-crh1(syb385), crh-1(n3315) versus wild-type (N2)

overall_design: mRNA profiles of four independent replicates of wild type (N2) and circ-crh-1 knockout [circ-crh-1(syb385)] and CREB null [crh-1(n3315)] 1-day adult worms.

first: David

last: Knupp

first: Alexander

last: van der Linden


title: Single-cell RNA-seq of Wild Type and Cd226-/- Thymus Transcriptomes

city: Xi'an

first: Yitian

state: Shannxi

institute: Fourth Military University

summary: Thymi from WT and Cd226 strain knockout mice were digested to obtain single-cell suspensions and then loaded onto microfluidic devices for scRNA-seq. The scRNA-seq libraries were constructed and  sequencing outputs were demultiplexed using the bcl2fastq to convert Binary Base Call files into FASTQ format.

overall_design: Single-cell RNA-seq of 5-week old wild type (WT) and Cd226-/- mice

first: Ran

last: Zhuang

first: Jingchang

last: Ma

first: Wei

last: Hu


title: Expression data from RVLM of Wistar-Kyoko (WKY) rats and spontaneously hypertensive rats (SHR)

city: Shanghai

first: Xing

last: Tan

address: 880 Xiangyin Road

department: Department of Marine Biomedicine and Polar Medicine, Naval Medical Center

institute: Naval Medical University (Second Military Medical University)

summary:
The six samples of RVLM tissues from three WKY rats and three SHRs
We used microarrays to identified distinct classes of genes involved in the central regulation of blood pressure.

overall_design: The six samples of RVLM tissues from three WKY rats and three SHRs were tested by gene chip (Affymetrix Rat 230 2.0 Array).

first: Peng

last: Ye

first: Yuan

last: Gao

first: Wei-Zhong


title: Pembrolizumab and decitabine for refractory or relapsed acute myeloid leukemia

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

summary: Background: The powerful ‘graft versus leukemia’ effect thought partly responsible for the therapeutic effect of allogeneic hematopoietic cell transplantation in acute myeloid leukemia (AML) provides rationale for investigation of immune-based therapies in this high-risk blood cancer. There is considerable preclinical evidence for potential synergy between PD-1 immune checkpoint blockade and the hypomethylating agents already commonly used for this disease. Methods: We report here the results of 17 H-0026 (PD- AML, NCT02996474), an investigator sponsored, single- institution, single-arm open-label 10-subject pilot study to test the feasibility of the first-in-human combination of pembrolizumab and decitabine in adult patients with refractory or relapsed AML (R-AML). Results: In this cohort of previously treated patients, this novel combination of anti-PD-1 and hypomethylating therapy was feasible and associated with a best response of stable disease or better in 6 of 10 patients. Considerable immunological changes were identified using T cell receptor β sequencing as well as single-cell immunophenotypic and RNA expression analyses on sorted CD3+ T cells in patients who developed immune- related adverse events (irAEs) during treatment. Clonal T cell expansions occurred at irAE onset; single-cell sequencing demonstrated that these expanded clones were predominately CD8+ effector memory T cells with high cell surface PD-1 expression and transcriptional profiles indicative of activation and cytotoxicity. In contrast, no such distinctive immune changes were detectable in those experiencing a measurable antileukemic response during treatment. Conclusion: Addition of pembrolizumab to 10-day decitabine therapy was clinically feasible in patients with R-AML, with immunological changes from PD-1 blockade observed in patients experiencing irAEs.

overall_design: 48 samples are analyzed. 8 samples are for 2 patients at day 0 and relapse time point using 10x Genomics 3' with both gene expression and protein libraries. The same two patients have samples for MissionBio at relapse time point with DNA and protein . 10x Genomics 5' experiments are performed for 4 patients at 3 different time points with gene expression, protein and VDJ libraries.

first: Meghali

last: Goswami

first: Gege

last: Gui

middle: W

first: Christopher

middle: S

last: Hourigan


title: Single-molecule mapping of replisome progression

city: new york

first: clemence

last: claussin

state: New York

address: 1275 York Avenue

department: molecular biology

institute: Memorial sloan kettering cancer center

summary: Replicon-seq is a method to study the progression of sister replisomes during DNA replication. This method relies excision of the full-length of replicons by the fusion of MNase to MCM4 and sequencing via Nanopore technology.

overall_design: MCM4 was fused to Miccrococcal nuclease ( MNase) to generate DNA double strand break at the site of replisomes. DNA ends are repaired and MinION compatible DNA adaptors are ligated. Full length molecules are sequenced. Because cells have been released from a G1 arrest in presence of BrdU, we can select for replicon reads (reads that contain BrdU) informatically using DNAscent.

first: Clemence

last: Claussin

first: Jacob

last: Vazquez

first: Iestyn

last: Whitehouse


title: Early anti-tumor activity of oral Langerhans cells is compromised by a carcinogen

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Early diagnosis of oral squamous cell carcinoma (OSCC) remains an unmet clinical need. Therefore, elucidating the initial events of OSCC preceding tumor development could benefit OSCC prognosis. Here we define the Langerhans cells (LC) of the tongue and demonstrate that LC protect the epithelium from carcinogen-induced OSCC by rapidly priming αβT cells capable of eliminating γH2AX+ epithelial cells, whereas γδT and NK cells are dispensable. The carcinogen, however, dysregulates the epithelial resident mononuclear phagocytes, reducing LC frequencies while dendritic cells (DC), macrophages, and plasmacytoid DC (pDC) populate the epithelium. Single-cell RNAseq analysis indicates that these newly differentiated cells display an immunosuppressive phenotype accompanied by an expansion of T regulatory (Treg) cells. Accumulation of the Treg cells was regulated, in part, by pDC and precedes the formation of visible tumors. This suggests LC play an early protective role during OSCC, yet the capacity of the carcinogen to dysregulate the differentiation of mononuclear phagocytes facilitates oral carcinogenesis.

overall_design: The mice were treated with the carcinogen 4NQO in the drinking water to induce carcinogenesis in the tongue epithelium, the scRNAseq analysis was performed on cells purified from the tongue epithelium after enrichment to CD45+ cells.

first: Avi-Hai

last: Hovav

first: Simon

last: Yona

first: Yasmn

last: Saba

first: Eya

last: David


title: single-nucleotide resolution sequencing of N6-methyladenine in E. coli genomes and mammalian mitochondrial DNA

city: 北京

first: li

middle: gao

last: jie

state: beijing

address: Building 104, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenine (6mA) is a natural DNA modification and functions primarily in restriction-modification (R-M) systems in prokaryotes. Recent studies uncovered the existence and revealed the genome-wide distribution of 6mA in eukaryotes. Specifically, it was reported that 6mA was mainly enriched in mammalian mitochondrial DNA (mtDNA) and could regulate mitochondrial activity. we achieved the genome-wide mapping of 6mA in E. coli genome and mammalian mtDNA at single-nucleotide resolution.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: Mapping of N6-methyladenine DNA modification in E. coli genomes and mammalian mitochondrial DNA

first: Cheng-Jie

last: Ma

first: Gao-Jie

last: Li

first: Wen-Xuan

last: Shao

first: Bi-Feng

last: Yuan


title: Paraxial mesoderm organoids model development of human somites

city: Boston

first: Christoph

last: Budjan

state: MA

address: 450 Brookline Ave

department: Data Sciences

institute: Dana-Farber Cancer Institute

summary: During the development of the vertebrate embryo, segmented structures called somites are periodically formed from the presomitic mesoderm (PSM), and give rise to the vertebral column. While somite formation has been studied in several animal models, it is less clear how well this process is conserved in humans. Recent progress has made it possible to study aspects of human paraxial mesoderm development such as the human segmentation clock in vitro using human pluripotent stem cells (hPSCs), however, somite formation has not been observed in these monolayer cultures. Here, we describe the generation of human paraxial mesoderm (PM) organoids from hPSCs (termed Somitoids), which recapitulate the molecular, morphological and functional features of paraxial mesoderm development, including formation of somite-like structures in vitro. Using a quantitative image-based screen, we identify critical parameters such as initial cell number and signaling modulations that reproducibly yielded somite formation in our organoid system. In addition, using single-cell RNA sequencing and 3D imaging, we show that PM organoids both transcriptionally and morphologically resemble their in vivo counterparts and can be differentiated into somite derivatives. Our organoid system is reproducible and scalable, allowing for the systematic and quantitative analysis of human spinal cord development and disease in vitro.

overall_design: Single-cell mRNA sequencing of human iPSC-derived paraxial mesoderm organoids (Somitoids).

first: Shichen

last: Liu

first: Sahand

last: Hormoz


title: Transcriptomic profiling of NASH in guinea pigs fed a high or low fat diet with either high or low vitamin C content

city: Frederiksberg C.

first: Josephine

last: Skat-Rørdam

address: Ridebanevej 9

department: Department of Veterinary and Animal Sciences

institute: Københavns Universitet

summary: This study investigated the effect of vitamin C deficiency combined with/without a change to a low fat diet on the NAFLD/NASH hepatic transcriptome in the guinea pig NASH model. Vitamin C deficiency per se did not accelerate disease induction. However, the results showed a clear effect of the diet change on resolution of hepatic hallmarks (p<0.05), and indicated a positive effect of a high vitamin C intake compared to both high fat groups. The data suggest that a poor vitamin C status delays the reversion towards a healthy hepatic transcriptome and phenotype. In conclusion, the findings support a beneficial role of adequate vitamin C intake in the regression of NASH and may indicate that vitamin C supplementation in addition to lifestyle modifications could accelerate recovery in NASH patients with poor vitamin C status.

overall_design: Animals were subjected to a preintervention period and fed either a low fat diet/high vitamin C, a high fat diet/high vitamin C, or a high fat/low vitamin C diet. After 16 weeks the animals fed the high fat/low vitamin C diet were divided into 4 groups: one group continuing on high fat/low vitamin C diet, one group receiving high fat/highvitamin C content, and two groups switching to a low fat diet with either high or low vitamin C. After another 16 weeks on the new diets, transcriptomic analysis was performed on animals from each group.

first: David

last: Højland-Ipsen

first: Gry

middle: F

last: Skovsted

first: Markus

last: Latta

first: Jens

last: Lykkesfeldt

first: Pernille

last: Tveden-Nyborg


title: RNA sequencing of 6 HGSOC and 5 FTE

city: Jinan

first: Zhiyuan

last: Dou

address: No.44, Wenhua Xi Road

department: Obstetrics and Gynecology Department

institute: Qilu Hospital of Shandong University

summary: Ovarian cancer is the most lethal gynecological malignancy. Recurrence and chemoresistance are tough challenges leading to poor prognosis. To further identify key genes in tumor progression, we performed RNAseq for 6 high-grade serous ovarian cancer and 5 fallopian tube and analysis of differentially expressed genes for hub genes selection.

overall_design: The assay was performed on 6 HGSOC and 5 FTE for RNA seq.

first: Beihua

last: Kong

first: Kun

last: Song

first: Chunping

last: Qiu