title: smallRNA sequencing of circulating miRNAs in blood from LGMD patients

city: Paterna

first: María José

last: Garzón Garzón

address: Carrer del Catedràtic Agustín Escardino Benlloch, 9

institute: EpiDisease SL

type: Non-coding RNA profiling by high throughput sequencing

summary: Limb-girdle muscular dystrophies (LGMDs) are a heterogeneous group of progressive and genetic neuromuscular disorders that involve weakness and wasting of predominantly pelvic and shoulder girdle muscles. More than 30 subtypes have been identified, with variable phenotype. In the early stages of the disease, these LGMD share common clinical and histopathological characteristics among different subtypes and with other neuromuscular disorders, complicating the disease-subtype identification and thus, lengthening the final diagnosis of the disease.  In the present study, we try to identify by a non-invasive method a molecular signature including biochemical and epigenetic parameters with a potential value for LGMD patient prognosis and stratification. Circulating miRNome was obtained by smallRNA-seq in plasma samples from LGMD patients (n=6) and matched controls (n=6). Over-representation analysis (ORA) using GO terms and KEGG database was used to study the functional enrichment of target genes. Biochemical parameters related to calcium metabolism, hormonal status, and muscle metabolism were also analyzed in these patients.   Thirteen differentially expressed miRs (FDR < 0.05) were able to separate each clinical group by hierarchical clustering. Indeed, most of differentially expressed miRs were up-regulated. Functional enrichment analysis of the target genes for the dysregulated miRs revealed that targets of up-regulated miRs modulated cell cycle and cancer related pathways, while targets of down-regulated miRs were involved in muscle tissue development, regeneration and senescence. Four of the circulating miRs (miR-19b-3p, miR-192-5p, miR-122-5p and miR 323-3p) were further validated by qPCR in LGMD and in the more frequent muscular dystrophies: Duchenne (DMD)(n=5) and facioscapulohumeral muscular dystrophy (FSHD)(n=4). Receiver operating characteristic curve analysis revealed high AUC values for selected miRs (1.0 for miR-19b-3p, miR-192-5p and miR-122-5p; 0.75 for miR-323-3p) suggesting that these miRs could be good biomarker candidates for LGMD. The covariates gender, age at disease onset, and ambulation did not correlate with the expression levels of these miRs. However, differential expression of miR-122-5p (≥10-60 fold, p< 0.0001), miR-192-5p (≥10-60 fold, p< 0.0001) and miR-323-3p (≤ 2-10 fold, p<0.05) levels compared to matched controls could discriminate LGMD from DMD or FSHD dystrophies. In addition, a strong correlation between some of these circulating miRs and biochemical variables such as CK, vitamin D3, ALP and PTH was found only in LGMD patients.

overall_design: A total of six patients diagnosed of LGMD at Hospital Universitari I Politècnic La Fe de Valencia (Spain) were used for the miRNome analysis. A cohort of patients of DMD (n=5) and patients affected by FSHD (n=4) were also included for further validation of results obtained by smallRNA-seq and to compare the miRs differentially expressed in LGMD with other neuromuscular diseases. Informed written consent was obtained from all participants. Blood samples were taken by venipuncture in the Hospital Universitari I Politècnic La Fe and immediately transported, processed, and stored according to the standard operating procedures in the CIBERER Biobank for further research (www.ciberer-biobank.es).Age and gender-matched controls (n=15) for all groups were provided by IBSP-CV Biobank and processed in the same way.   The selection process and all experimental methods were carried out in accordance with the relevant clinical guidelines, following standard operation procedures, and with the approval of the ethics and scientific committees (Ethics Committee from the Hospital Universitari I Politècnic La Fe, Registry number 2019/0094).

first: José

last: García Gimenez

first: Ana

last: Avilés-Alía

last: Ibañez Cabellos

first: Miquel

last: Bovea-Marco

first: Elena

middle: R

last: García-Trevijano

first: Teresa

last: Bas

first: Federico

middle: V

last: Pallardó

first: Juan

last: Viña

first: Rosa

last: Zaragozá


title: RNA-seq profiling of 22Rv1 prostate cancer cells exposed to repeated DNA damage for 6 weeks.

status: Public on Jul 18 2022

city: Hobart

first: Kate

last: Brettingham-Moore

state: Tasmania

address: 17 Liverpool Street

department: School of Medicine

country: Australia

institute: University of Tasmania

type: Expression profiling by high throughput sequencing

summary: RNA-seq profiling of 22Rv1 prostate cancer cell line either untreated, 6 weeks in culture (age matched) or treated daily for 6 weeks with 1 microgram per ml phleomycin to induce DNA damage (n=3 per sample).

overall_design: Illumina NovaSeq RNA-seq sequence production of a 100bp single end from RNA extracted from the 3 samples (with 2 biological replicates each) control (untreated 22Rv1 cells), 6 weeks phleomycin/DNA damage and age matched (6 weeks in culture without phleomycin induced DNA damage

first: Dayna

last: Challis


title: DNA methylation and RNA-seq profiling of 2Rv1 prostate cancer cells exposed to repeated DNA damage

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

overall_design: Refer to individual Series


title: DNA methylation profiling of prostate cancer cells exposed to daily DNA damage

summary: Illumina Infinium MethylationEPIC BeadChip profiling of 22Rv1 prostate cancer cell line either untreated, 6 weeks in culture (age matched) or treated daily for 6 weeks with 1 microgram per ml phleomycin to induce DNA damage (n=2 per sample).

overall_design: DNA extracted from the 3 samples (2 biological replicates each) hybridised to Illumina Infinium MethylationEPIC BeadChip (850K array). Samples are control (untreated 22Rv1 cells), 6 weeks phleomycin/DNA damage and age matched (6 weeks in culture without phleomycin induced DNA damage).


title: Single cell RNA sequencing analysis of bronchoalveolar lavage samples from SARS-CoV-2 challenged Rhesus macaques

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

country: USA

institute: SUNY Upstate Medical University

summary: Single cell RNA sequencing analysis was performed on bronchoalveolar lavage samples obtained from Rhesus macaques infected intranasally/intratracheally with SARS-CoV-2 after vaccination with mRNA-1273 vaccine

overall_design: Samples were obtained on days 2 and 7 post SARS-CoV-2 challenge from 4 animals previously vaccinated with 30ug of RNA-1273, 6 animals previously vaccinated with 1ug of mRNA-1273, and from control/unvaccinated animals (6 animals on day 2, 5 animals on day 7)

first: Jeffrey

last: Currier

first: Robert

last: Seder


title: C16orf72/HAPSTR1 is a molecular rheostat in an integrated network of stress response pathways

city: Chicago

first: Marc

last: Mendillo

state: IL

address: 303 E Superior St

institute: Northwestern University

summary: All cells contain specialized signaling pathways which enable adaptation to specific molecular stressors. Yet, whether these pathways are centrally regulated in complex physiological stress states remains unclear. Using genome-scale fitness screening data, we quantified the stress phenotype of 739 cancer cell lines, each representing a unique combination of intrinsic tumor stresses. Integrating dependency and stress perturbation transcriptomic data, we illuminate a network of genes with vital functions spanning diverse stress contexts. Analyses for central regulators of this network nominated C16orf72/HAPSTR1, an evolutionarily ancient gene critical for the fitness of cells reliant on multiple stress response pathways. We find that HAPSTR1 plays a pleiotropic role in cellular stress signaling, functioning to titrate various specialized cell-autonomous and paracrine stress response programs. This function, while dispensable to unstressed cells and nematodes, is essential for resilience in the presence of stressors ranging from DNA damage to starvation and proteotoxicity. Mechanistically, diverse stresses induce HAPSTR1, which encodes a protein expressed as two equally abundant isoforms. Perfectly conserved residues in a domain shared between HAPSTR1 isoforms mediate oligomerization and binding to the ubiquitin ligase HUWE1. We show that HUWE1 is a required cofactor for HAPSTR1 to control stress signaling, and that in turn, HUWE1 feeds back to ubiquitinate and destabilize HAPSTR1. Altogether, we propose that HAPSTR1 is a central rheostat in a network of pathways responsible for cellular adaptability, the modulation of which may have broad utility in human disease.

overall_design: Comparative RNA-seq profiling various cell lines after siRNA knockdown of HAPSTR1 and/or HUWE1 in the presence or absence of molecular stressors.

first: David

last: Amici


title: Single cell RNA sequencing analysis of bronchoalveolar lavage following SARS-CoV-2 B.1.351/beta variant challenge in mRNA-1273 vaccinated Rhesus macaques

summary: Single cell RNA sequencing analysis was performed on bronchoalveolar lavage samples obtained from Rhesus macaques on day 2 after intranasal/intratracheal infection with SARS-CoV-2 B.1.351/beta variant 4 weeks after the second dose of 30ug mRNA-1273 vaccine along with unvaccinated controls

overall_design: Bronchoalveolar lavage was obtained from a total of 8 animals 2 days after secondary SARS-CoV-2 challenge after a 6 month rest. Four animals were previously vaccinated twice with 30ug of mRNA-1273, each dose spaced 4 weeks apart. Four animals were injected with PBS in the same fashion as the vaccinated animals. All 8 animals were infected intranasally/intratracheally  with SARS-CoV-2 B.1.351/beta variant 4 weeks after the second injection of either PBS or mRNA-1273

first: Diane

last: Bolton

first: Heather

last: Friberg

first: Mario

last: Roederer


title: Analysis of the transcriptome of CD34+38- cord blood cells treated with 3-deazaadenosine (3DA)

status: Public on Jul 19 2022

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Cord blood cells were cultured in the presence of 10 mM 3-deazaadenosine (3DA) or DMSO. After 9 days, the CD34+38- population was sorted using FACS and subjected to RNAseq. Our previous experiments have shown that treating other cell types with 3DA partially prevents senescence. By performing RNAseq, we show how treating cord blood cells with 3DA affects senescence, stemness and differentiation

overall_design: 8 different samples. CD34+38- cells were obtained from cord blood cells (from 4 different donors: 338, 522, 535, 545) that have been treated for 9 days with DMSO (DMSO) or 10 mM 3-deazaadenosine (3DA).

first: Gerald

last: de Haan

first: Diana

last: Spierings

first: Ellen

last: Weersing

first: Sanjay

last: Khadayate


title: RNA-seq on HER2+ cell line upon treatments

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: We proceeded RNA-seq on HER2+ breast cancer line HCC1954 cells treated with DMSO, SNXB, Lapatinib and combination for 24 hours. By analyzing resulting data, we are trying to figure out the possilble mechanisms of Lapatinib resistance and how our regimen is able to potentiate and overcome resistance.

overall_design: HCC1954 cells were treated with DMSO, SNXB, Lapatinib and Combination for 24 hours. Samples were from three biological repeats.

first: Xiaokai

last: Ding

first: Hao

last: Ji

first: Eugenia

last: Broude


title: Trisomy 21 human iPSC derived interneuron progenitors

city: Madison

first: Anita

last: Bhattacharyya

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin - Madison

summary: Individuals with Down syndrome (DS, Ts21) have impaired neurogenesis during development. Using Ts21 human induced pluripotent stem cells (iPSCs) and isogenic controls, we carried out single cell RNA-sequencing of Ts21 interneuron progenitors .

overall_design: Ventralized progenitors at Day 17 from one pair of isogenic Ts21 and control lines (WC24).Differentiation to interneuron progenitors was carried out as described (PMID: 23928500).

first: Yathindar

last: Giffin-Rao

first: Jie

last: Sheng

first: André

middle: M

last: Sousa

first: Yunlong

last: Tao

first: Su-Chun

last: Zhang


title: Pneumococcal BgaA promotes host organ bleeding and coagulation in mouse sepsis model

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Streptococcus pneumoniae is a major cause of invasive diseases, such as pneumoniae, meningitis and sepsis resulting in high mortality. The molecular mechanisms and disease developing mechanism underlying pneumococcal infection remain unknown. Previously, we reported that S. pneumoniae β-galactosidase (BgaA) is evolutionarily conserved and contributes to pneumococcal pathogenesis in mouse sepsis model. BgaA is also known to play a role in pneumococcal growth, resistance to human neutrophil opsonophagocytic killing, bacterial adherence to human epithelial cells. In this study, since the detailed role that BgaA plays in sepsis remain unknown, we focused on the role of BgaA in pneumococcal sepsis. Our in vitro assays showed that BgaA promoted bacterial association with human lung epithelial and vascular endothelium cells. BgaA also contributes to pneumococcal survival with human blood by suppressing neutrophils killing, whereas BgaA did not affect pneumococcal survival in mouse blood. In a mouse sepsis model, mice infected with S. pneumoniae bgaA deletion mutant strain exhibited up-regulated host innate immunity pathways, and suppressed tissue damages and blood coagulation as compared to mice infected with the wild-type strain. These results suggest that BgaA works as a multifunctional virulence factor for inducing host tissue damages and blood coagulation. BgaA could be an attractive target for drug and vaccine development.

overall_design: To investigate the effect of BgaA on transcriptional response in sepsis mouse model, leukocyte RNA obtained from mice blood infected with WT, ΔbgaA strain and PBS at 12, 24 and 36 h after intravenous infection.

last: Motooka

first: Masaya

last: Yamaguchi


title: Trained immunity of alveolar macrophages depends on metabolic rewiring and type 1 interferon signaling

city: Vienna

first: Sylvia

last: Knapp

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

type: Genome binding/occupancy profiling by high throughput sequencing


title: Trained immunity of alveolar macrophages depends on metabolic rewiring and type 1 interferon signaling (RNA-Seq)

summary: Environmental microbial triggers shape the development and functionality of the immune system. Alveolar macrophages (AMs), tissue-resident macrophages of the lungs, are in constant and direct contact with inhaled particles and microbes. Such exposures likely impact AM reactivity to subsequent challenges by immunological imprinting mechanisms referred to as trained immunity. Here, we investigated whether a ubiquitous microbial compound has the potential to induce AM training in vivo. We showed that intranasal exposure to ambient amounts of lipopolysaccharide (LPS) protected mice from bacterial pneumonia six days later and discovered a pronounced AM memory response, characterized by enhanced reactivity upon pneumococcal challenge. Exploring the mechanistic basis of AM training, we identified a critical role of type 1 interferon signaling and found that trained AMs displayed a substantially modulated metabolite and lipid composition. Inhibition of fatty acid oxidation and glutaminolysis significantly attenuated the training effect, suggesting a key function of metabolic rewiring in LPS-induced AM memory. Collectively, our findings demonstrate the profound impact of ambient microbial exposure on pulmonary immune memory and highlight tissue-specific features of trained immunity.

overall_design: RNA-seq analysis of trained and control AMs following secondary (ex vivo) challenge: Wild type mice received LPS (Sigma; E.coli O55:B5) or endotoxin-free saline intranasally (i.n.). Six days later, LPS-exposed ("trained") and saline-exposed ("control") AMs were isolated by broncho-alveolar lavage from biological replicates (n=5 per group). Cells were counted, seeded (2 wells for each biological replicate) and left to adhere. After 2 h, non-adherent cells were removed and each biological replicate was incubated with heat-inactivated Streptococcus pneumoniae (HISP) in medium or with medium only for 3 h, generating a total of 20 samples.

first: Martin

middle: L

last: Watzenboeck

first: Sophie

last: Zahalka


title: smORF atlas

city: Singapore

first: Benjamin

last: Ng

address: 8 College Road

country: Singapore

institute: Duke-National University of Singapore Medical School


title: smORF atlas (part 2-RNASeq)

summary: Small open reading frames (smORFs) can have important regulatory roles and give rise to stable proteins, yet their discovery based on sequence-based predictions and proteomics has been challenging. Ribosome profiling (Ribo-seq) data can provide valuable experimental evidence of RNA translation. Stringent analysis of P-sites, representing 1.3 billion high-confidence ribosome locations, revealed 5308 uORFs, 1652 smORFs in lincRNAs and 807 dORFs that are translated in humans. We here provide a comprehensive database of Ribo-seq smORFs for a more complete understanding of the translated human genome.

overall_design: To validate smORF findings on a genome-wide level, we have collected, generated and processed RNAseq data from six primary human cell types and two human tissues.

first: Sonia

middle: P

last: Chothani

first: Eleonora

last: Adami

first: Anissa

middle: A

last: Widjaja

first: Sarah

last: Langley

first: Sivakumar

last: Viswanathan

first: Chee

middle: J

last: Pua

first: Nevin

middle: T

last: Zhihao

first: Nathan

last: Harmston

first: Giuseppe

last: D’Agostino

first: Nicola

last: Whiffin

first: Wang

last: Mao

first: John

middle: F

last: Ouyang

first: Wei

middle: W

last: Lim

first: Shiqi

first: Cheryl

middle: Q

last: Lee

first: Alexandra

last: Grubman

first: Joseph

last: Chen

first: J

last: Kovalik

first: Karl

last: Tryggvason

first: Lena

last: Ho

first: Jose

last: Polo

first: Stuart

last: Cook

first: Owen

last: Rackham

first: Sebastian

last: Schafer


title: Trained immunity of alveolar macrophages depends on metabolic rewiring and type 1 interferon signaling (ATAC-Seq)

first: Sylvia

last: Knapp

overall_design: ATAC-seq analysis of trained and control AMs: Wild type mice received LPS (Sigma; E.coli O55:B5) or endotoxin-free saline intranasally (i.n.). Six days later, LPS-exposed ("trained") and saline-exposed ("control") AMs were isolated by broncho-alveolar lavage from biological replicates (ctrl:n=4; LPS:n=5) and counted. For each biological replicate, 50.000 cells were pelleted and processed for ATAC-seq analysis.

first: Florian

last: Deckert

first: Sophie

last: Zahalka


title: smORF atlas (part 1-RiboSeq)

first: Benjamin

last: Ng

overall_design: To identify smORFs on a genome-wide level, we have collected, generated and processed Ribo-seq data from seven primary human cell types and two human tissues.

first: Sonia

last: Chothani

first: Eleonora

last: Adami

first: Anissa

last: Widjaja

first: Sarah

last: Langley

first: Sivakumar

last: Viswanathan

first: Chee

last: Pua

first: Nevin

last: Zhihao

first: Nathan

last: Harmston

first: Giuseppe

last: D’Agostino

first: Nicola

last: Whiffin

first: Wang

first: JP


title: WFA+ Mac-2 binding protein (M2BPGi) regulating signal in the HCC cells

city: Maebashi

first: Dolgormaa

last: Gantumur

state: Select a State or Province

address: 3-39-22 Showamachi

institute: Gunma University

summary: Wisteria floribunda agglutinin (WFA)+-Mac-2 binding protein glycan isomer (M2BPGi) is a novel serum marker for liver fibrosis. Although an elevated serum level of M2BPGi can predict aggressiveness in hepatocellular carcinoma (HCC), the effect of M2BPGi on HCC remains unclear. The present study aimed to clarify M2BPGi altered gene in HCC cells using CAGE analysis.

overall_design: Evaluation of M2BPGi-regulating signals in HCC cells using CAGE analysis.

first: Yamanaka

last: Takahiro

first: Yokobori

last: Takehiko

first: Ken

last: Shirabe


title: RNAseq of mouse colon epithelial cell fraction in Lingo2 and WT mice

city: Philadelphia

first: De'Broski

last: Herbert

state: PA

address: 3900 Spruce Street

department: Pathobiology

institute: University of Pennsylvania

summary: The purpose of this experiment is to deep sequence transcripts in WT mice and mice lacking Lingo2, and compare gene expression in the epithelial cells of the colon between wild type and mutant mice. Colon tissue was isolated from each mouse, and epithelial cells were isolated by EDTA wash

overall_design: wild type and Lingo2 mutant mice, 3 replicates for each condition

first: Kelly

last: Zullo

first: Annabel

last: Ferguson


title: RPA1 controls chromatin architecture and maintains lipid metabolic homeostasis

city: Beijing

first: Qi

last: Yin

address: 38 Xueyuan Rd

country: China

institute: Peking University

summary: Replication protein A1 (RPA1) is a single-stranded DNA binding protein that is known to participate in DNA replication, recombination and damage repair. However, little is known about RPA1’s role in controlling chromatin architecture and gene transcription. Further, physiological functions of RPA1 in mouse tissues still remain exclusive. Here we show that Rpa1 heterozygous mice developed age-depended fatty liver disease and are more susceptible to hepatic steatosis in response to high-fat diet. Liver specific deletion of Rpa1 impairs fatty acid oxidation, leading to hepatic steatosis and high incidence of hepatocellular carcinoma. Transcriptome analysis identified down-regulation of fatty acid oxidation related genes. Cleavage Under Targets and Tagmentation (CUT&Tag) and Assay for transposase-accessible chromatin using sequencing (ATAC-seq) revealed that RPA1 binds and regulates chromatin accessibility in regulatory regions of a group of genes involved in lipid metabolism in liver. Further, down-regulation of RPA1 was found in patients with fatty liver disease. Thus, our results not only established that RPA1 is critical controller of chromatin architecture and regulator of gene transcription, but also provided new insights into the epigenetic mechanism of fatty liver disease, which could inform future therapy.

overall_design: ATAC-seq on wild type (WT) and L-Rpa1-KO mice liver tissue. Liver mRNA profiles of wild type (WT) and L-Rpa1-KO mice. Examination of 3 different histone modifications, Pol II, HNF4A and RPA1 in mouse liver tissues.

first: Yuxin


title: Gene expression profile at single cell level of Treg cells (CD4+CD25+) from healthy Mycfl/flFoxp3Cre/WT female mice, in which Myc-sufficient (WT) and Myc-deficient (KO) Treg cells co-exist

status: Public on Jul 17 2022

city: Xiamen

first: Yudi

last: Hu

address: Xiangannan road

institute: Xiamen University

summary: We performed single cell transcriptome analysis of Treg cells (CD4+CD25+) from healthy Mycfl/flFoxp3Cre/WT female mice, in which Myc-sufficient (WT) and Myc-deficient (KO) Treg cells co-exist due to random inactivation of the X chromosome that harbors the Foxp3 gene.

overall_design: Cells (CD4+ CD25+ YFP+ and YFP- cells from Mycfl/flFoxp3Cre/WT mice) were sorted by flow cytometry into a well of a chilled 96-well plate (filled with 14 μl PBS with 0.06% BSA). Cells were encapsulated in one lane of a 10x Chromium single cell controller. Single- cell transcriptome library is prepared with a Single Cell 3′ Reagent Kit (V2 chemistry) following standard protocol

first: Chao

last: Yang

first: Yun

last: Liu


title: WGBS of Arabidopsis thaliana rll6 mutant

city: Nanjing

first: Xiangyu

last: Wang

address: No. 1 Weigang

institute: Nanjing agricultural university

type: Methylation profiling by high throughput sequencing

summary: To gain deeper insights into the mechanisms of DNA demethylation pathway, we conducted a genetic screen for proteins that are involved in preventing epigenetic silencing, and then the ones, which are also implicated in DNA demethylation pathway, are used for further studies. Eventually, a mutant with low luciferase luminescence (low LUC luminescence) was recovered, and named reduced LUC luminescence 6-1 (rll6-1). Map-based cloning revealed thatrll6-1 mutation is located in bacterial artificial chromosome (BAC) clone F5I10 on chromosome 4, and there are a total of 10 candidate genes were found within such a region. Analysis of genome-wide methylation patterns of rll6-1 mutant showed that rll6-1 mutation led to 3863 hyper-DMRs throughout the five Arabidopsis chromosomes, and elevated DNA methylation level of 2×35S promoter, which was similar to that found in ros1 mutant. Further analysis demonstrated that there are 1456 common hyper-DMRs shared by rll6-1 and ros1-7, which account for 2407 and 5642 hyper-DMRs, respectively, suggesting both proteins act together in a synergistic manner to remove DNA methylation. Further investigations demonstrated that rll6-1 mutation does not affect the expression of the four genes of the DNA glycosylase/lyase family. Thus, our results demonstrated that RLL6 not only participated in transcriptional anti-silencing, but is also involved in DNA demethylation pathway.

overall_design: BS-seq of rll6-1;Col-LUC;ros1-7.

first: Honggui

last: La

last: wang


title: Ecophysiological and molecular basis of drought responses in forest trees: the modulating role of canopy structure and light environment

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: Climate change forecasts increase the susceptibility of forest due to longer drier seasons. The adaptive management protocols have highlighted the reduction of the forest densification to improve their vulnerability to extreme climate events (i.g. drought). One of this sensitive woody species to climate change is the Abies pinsapo, a relic conifer tree endemic from the southern Spain. Previous works have shown changes in their trends because of the climate change action, being carried out experimental thinning management in their lowest distribution limit, in Sierra de las Nieves Natural Park (Malaga). Our objective is to evaluate the water improvements of thinned trees in terms of light availability by means of a shading treatment in those thinned trees. To do that we have evaluated the synergic effect of ecophysiology, metabolomics and transcriptomics in control, thinning and thinning+shading plots in wet and dry seasons for two years. The results showed strong differences between summer and spring seasons at the three studied levels. The water deficit shows a greater influence than light exposure in the ecophysiology and metabolomics tree response. And the transcriptomics suggested an improvement of thinned trees when light exposure was reduced. Our results support the necessity of adaptive forest management in order to improve the conservation status of A. pinsapo forest. The combination of different levels of tree response is paramount to understand and predict the tree physiology under water and light stress conditions.

overall_design: The study was carried out in natural stands of Abies pinsapo Boiss., a drought-sensitive fir, located near the lower elevation limit of the altitudinal species distribution range (Sierra de las Nieves Natural Park; 36°43′N, 4°57′W, 1200 m, aspect NW, slope ca. 40%). Abies pinsapo forests in the study area were subjected to intense grazing and logging by the inhabitants around the middle 20th century. During the second half of the 20th century until present times, these forests were protected whilst they underwent the abandonment of traditional uses. The suppression of the perturbation regime enhanced a regeneration process, which ended up in dense stands. An experimental thinning management was designed and performed in October 2004, attempting to enhance the stand structure diversity by reducing tree competition, increasing the equitability of size classes and randomizing tree spatial pattern.   As our objective was to analyse the availability of light and water resources to A. pinsapo in this managed stands, we designed three field-treatments where we could study the effect of both factors separately: (i) plots with reduced tree density and therefore decreased intra-specific competition for water and light: “Thinning” treatment; (ii) trees in adjacent forest stands where such adaptive management practices were not applied (high competition for both light and water; “Control” treatment), and (iii) trees in the thinned plot which were covered by a mesh to simulate a light environment similar to that in “Control” plots (high competition for light+low competition for water; “Thinning + Shading” treatment). In this way, it has been possible to experimentally evaluate the improvement in the light environment perceived by remaining trees in thinned plots. We selected three circular plots with 100 m2 surface per treatment where all trees were identified (tree species; tree status: alive, dead, stump), tagged and mapped, and their DBH (diameter at breast height) was measured.

first: Lucía

last: Álvarez-Garrido

first: Gianluca

last: de Moro

first: Francisco

last: Cánovas

first: Cymon

last: Cox

first: Víctor

last: Lechuga

first: Benjamín

last: Viñegla

first: José

last: Carreira


title: Colorectal cancer cells with Suppressed SMC4 display a diapause-like state showing slow proliferation and chemotherapy insensitivity

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

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

overall_design: Refer to individual Series


title: RNA-seq analysis of Eriocheir sinensis muscle

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

institute: College of Life Sciences, Tianjin Normal University

summary: the chromatin accessibility and gene expression of muscle in E. sinensis in pre-molt (D) and post-molt (A) stages were sequenced by Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) and RNA-seq, respectively.The differntial peaks in ATAC-seq and differntial genes in RNA-seq were analzed. The data was used to analysis the differentially expressed genes (DEGs) in muscle before and after molting by combining ATAC-seq and RNA-seq

overall_design: Muscle of healthy crabs in pre-molt (D stages) and post molt (A stages) were collected and used for ATAC-seq and RNA-seq analysis.in each stages, three muscle samples were collected as the experimental replications. RNA-seq was performed with Illumina novaseq platform with E. sinensis genome (accession number PRJNA555707) as the reference genome.

first: Jingjing

last: Li

first: Jinsheng

last: Sun


title: Impaired proteolysis of non-canonical RAS proteins drives clonal hematopoietic transformation [CRISPR]

city: South San Francisco

first: Simon

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

summary: Recently, screens for mediators of resistance to FLT3 and ABL kinase inhibitors in leukemia resulted in the discovery of LZTR1 as an adaptor of a Cullin-3 RING E3 ubiquitin ligase complex responsible for degradation of RAS GTPases. In parallel, dysregulated LZTR1 expression via aberrant splicing and mutations have been identified in clonal hematopoietic conditions. Here we identify that loss of LZTR1, or leukemia-associated mutants in the LZTR1 substrate and RAS GTPase RIT1 which escape degradation, drive hematopoietic stem cell expansion (HSC) and leukemia in vivo. LZTR1 null cells rely on multiple RAS GTPases for transformation. Consequently, RAS targeting bioPROTACs or reduction of GTP-loaded RAS overcomes LZTR1 loss-mediated resistance to FLT3 inhibitors. These data thereby reveal proteolysis of non-canonical RAS proteins as novel regulators of HSC function, define the function and spectrum of RIT1 and LZTR1 mutations in leukemia, and identify means to overcome drug resistance due to LZTR1 downregulation.

overall_design: Genome-scale CRISPR/Cas9 screem performed in 3x different variants of the TF-1 cell line genetically-modified to express mutant forms of RIT1 (M90I or F82C) or depleted in LZTR1 by CRISPR/Cas9, then infected with the Brunello sgRNA library (in technical duplicate) and cells collected following 7 days of selection ("day 0") or an additional 14 days in culture ("day 14") to assess drop-out of sgRNAs between days 0 and day 14 by next-generation sequencing.

first: Sisi

last: Chen

first: Abdel-Wahab

last: Omar


title: Loss of protein function of ZC4H2 gene causing severe phenotypes of female-restricted Wieacker Wolff Syndrome

city: Shanghai

first: Jiajun

last: Qiu

address: West BeiJing Road

institute: Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine

summary: Background: Pathogenic variants of zinc finger C4H2-type containing (ZC4H2) on the X chromosome caused a group of genetic diseases called ZC4H2-associated rare disorders (ZARD), including Wieacker-Wolff Syndrome (WRWF) and Female-restricted Wieacker-Wolff Syndrome (WRWFFR). Patients displayed arthrogryposis multiplex congenita (AMC), central and peripheral nervous system involvement, as well as multiple dysmorphic features. The underlying mechanisms of the complex syndrome remain to be elucidated.   Methods: Expression levels of ZC4H2 were knockdown in neural stem cells (NSCs) derived from induced pluripotent stem cells (iPSCs) by lentiviral-expressed shRNAs against ZC4H2. RNA sequencing (RNA seq) was subsequently applied to study the effects on gene expression profiles. The expression levels of differentially expressed genes were then verified by PCR array and RT-qPCR.   Results: neural stem cell-like cells were induced from human induced pluripotent stem cells (hiPSCs), which were confirmed to express biomarkers of Neural stem cells (NSCs) by immunofluorescence. The viability of NSCs were affected through inhibition of ZC4H2 expression after they were infected with lentivirus containing siRNA targeting to ZC4H2 gene. The RNA-seq results showed that the gene expression pattern in NSCs was changed after inhibition of ZC4H2. DEGs were significantly enriched in oxidative phosphorylation and neurodegenerative diseases signaling pathways. Down-regulation of ZC4H2 might affect neural development by affecting the expression of genes related to oxidative phosphorylation signaling pathway.  Conclusions: Down-regulation of genes related to the oxidative phosphorylation pathway might be involved in the pathogenity of the disease.  Keywords: Female-restricted Wieacker-Wolff Syndrome (WRWF), Wieacker-Wolff Syndrome (WRWFFR), ZC4H2, Arthrogryposis multiplex congenita (AMC), nonsense mutation

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ZC4H2 knockdown neural stem cells (NSCs).

first: Jing-Jing

first: Qin

last: Cai

first: Miao

last: Xu

first: Wan-Rui

first: Yi-Tao

last: Zeng

first: Zhao-Rui

last: Ren

first: Fanyi


title: Gene expression analysis from bulk RNA isolated from embryonic mouse hearts at time points E13.5 and E14.5 with and without disruption of endothelial Ino80

city: Stanford

first: Devin

middle: Aalpoel

last: King

state: CA

address: 371 Serra Mall

department: Biology

institute: Stanford University

summary: Non-compaction cardiomyopathy is a devastating genetic disease caused by insufficient consolidation of ventricular wall muscle that can result in inadequate cardiac performance. Despite being the third most common cardiomyopathy, the mechanisms underlying the disease, including the cell types involved, are poorly understood. We explore the endothelial cell-specific deletion of the chromatin remodeler gene Ino80, which results in defective coronary vessel development that leads to ventricular non-compaction in embryonic mouse hearts. We observed a pathological endocardial cell population in the non-compacted hearts, and identified multiple dysregulated angiocrine factors that dramatically affected cardiomyocyte behavior.

overall_design: Evaluation of 12 total samples, 3 each of WT and KO across 2 time points (E13.5 and E14.5)

first: Jae

last: Chung


title: Impaired proteolysis of non-canonical RAS proteins drives clonal hematopoietic transformation [scRNA-seq]

overall_design: Single cell RNA-sequencing (scRNA-seq) was used to assess changes in gene expression within murine bone marrow associated with Rit1-M90I mutation or Lztr1 knock-out, compared to a wild-type control, using a single replicate for each genotype on a 10X genomics platform.


title: microRNA expression in vaginal melanoma

status: Public on Jul 16 2022

city: Columbus

first: William

middle: E.

last: Carson III

state: OH

institute: The Ohio State University

summary: microRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from vaginal melanoma compared to adjacent healthy vaginal mucosa.

overall_design: In this study microRNA expression was assessed in formalin fixed, paraffin embedded vaginal melanoma and adjacent healthy vaginal mucosa (n=6, paired) using the Nanostring human miRNA assay.

first: Mallory

last: DiVincenzo

first: Colin

middle: D

last: Angell


title: Altered Cardiac Energetics and Mitochondrial Dysfunction  in Hypertrophic Cardiomyopathy

first: Daniel

last: Bernstein

address: 450 Serra Mall

institute: Stanford

summary: Hypertrophic cardiomyopathy (HCM) is a complex disease partly explained by the effects of individual gene variants on sarcomeric protein biomechanics. At the cellular level, HCM mutations most commonly enhance force production, leading to higher energy demands. Despite significant advances in elucidating sarcomeric structure-function relationships, there is still much to be learned about the mechanisms that link altered cardiac energetics to HCM phenotypes. In this work, we test the hypothesis that changes in cardiac energetics represent a common pathophysiologic pathway in HCM.    We performed a comprehensive multi-omics profile of the molecular (transcripts, metabolites, and complex lipids), ultrastructural, and functional components of HCM energetics using myocardial samples from 27 HCM patients and 13 normal controls (donor hearts). Integrated omics analysis revealed alterations in a wide array of biochemical pathways with major dysregulation in fatty acid metabolism, reduction of acylcarnitines, and accumulation of free fatty acids. HCM hearts showed evidence of global energetic decompensation manifested by a decrease in high energy phosphate metabolites (ATP, ADP, and phosphocreatine) and a reduction in mitochondrial genes involved in the creatine kinase and ATP synthesis. Accompanying these metabolic derangements, quantitative electron microscopy showed an increased fraction of severely damaged mitochondria with reduced cristae density, coinciding with reduced citrate synthase (CS) activity and mitochondrial oxidative respiration. These mitochondrial abnormalities were associated with elevated reactive oxygen species (ROS) and reduced antioxidant defenses. However, despite significant mitochondrial injury, HCM hearts failed to upregulate mitophagic clearance.     Overall, our findings suggest that perturbed metabolic signaling and mitochondrial dysfunction are common pathogenic mechanisms in patients with HCM. These results highlight potential new drug targets for attenuation of the clinical disease through improving metabolic function and reducing mitochondrial injury.

overall_design: mRNA profiles of human cardiac tissue from patients with HCM and donor controls

first: Sara

last: Ranjbarvaziri


title: PRL2 deficiency alters FLT3 mediated gene transcription in murine hematopoietic stem and progenitor cells

city: Chicago

first: Yan

last: Liu

state: Illinois

address: Northwestern University, 303 East Superior Street, Lurie 5-107

institute: Department of Medicine

summary: To gain insights into the molecular mechanisms underlying the role of PRL2 in hematopoietic stem and progenitor cells (HSPCs), we performed RNA-seq analysis to compare gene expression in Prl2+/+ and Prl2-/- fetal liver cells which are enrich with HSPCs.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of triplecate E14.5 fetal liver cells in each Prl2+/+ and Prl2-/- group .Comparative gene expression profiling analysis of RNA-seq data for E14.5 fetal liver cells Prl2-/-.

first: Hongxia

first: Shiyu

last: Xiao


title: mRNA expression in vulvar melanoma

summary: mRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from vulvar melanoma compared to primary cutaneous melanoma.

overall_design: In this study mRNA expression was assessed in formalin fixed, paraffin embedded vular melanoma (n=18) and primary cutaneous melanoma (n=9) Nanostring human tumor signaling 360 mRNA assay.


title: Expression of microRNAs and their target genes in melanomas originating from gynecologic sites

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


title: Exposure to a real traffic environment impairs brain cognition in aged mice

city: Hangzhou

first: Chenlu

address: Xihu street

institute: Zhejiang university

summary: Traffic-related air pollution has been a common public health problem, which is associated with central nervous system dysfunction according to large-scale epidemiological studies. Current studies are mostly limited to artificial laboratory exposure environments and specific genetic mechanisms remain unclear. In the spring, we transported the aged mice from the laboratory to the 1-meter-high dry platform in the campus and tunnel at the same time. Aged mice were exposed form 7 am to 7 pm each day for 2, 4 and 12 weeks, respectively. Compared with the control group (in campus), the memory function of mice in the exposure group (in tunnel) was significantly impaired in Morris water maze. Traffic-related air pollution exposure increased the number of activated microglia in the hippocampal DG and CA1, and up-regulated mRNA expression of inflammatory factors IL-18, IL-1β, IL-6 and TNF-α. By screening the risk genes of Alzheimer’s disease, we found the mRNA and protein levels of ABCA7 were down-regulated and those of PYK2 were up-regulated in the dorsolateral prefrontal cortex (dPFC) of aged mice. The DNA methylation ratio increased in four CpG sites of abca7 promoter region and decreased in one CpG site of pyk2 promoter region, which were consistent with the altered expression of ABCA7 and PYK2. In conclusion, exposure to the real traffic environment impaired memory function and enhanced neuroinflammation of aged mice, which could be relevant to the alteration of ABCA7 and PYK2 gene expression. Our work provided a new and promising understanding of the pathological mechanisms of cognitive impairment caused by traffic-related air pollution.

overall_design: The dorsolateral prefrontal cortex of aged mice exposed at campus and tunnel.

first: Yongtang

last: Jin

first: Jia

last: Zhang

first: Qinfeng

last: Zhou


title: Genome-wide analysis of gene expression regulated by APPL1/2 proteins in human PC-3U cells

city: Umea

first: Jie

last: Song

state: AC

address: Medical Biosciences Department, Pathology, M21

department: Medical Bioscience

country: Sweden

institute: Umea University

summary: Transforming growth factor β (TGFβ) is overexpressed in several advanced cancers and promotes tumor progression. How cancer cells evade TGFβ-induced growth inhibition and escape normal homeostasis is unclear. Here, we report that the TGFβ Type I receptor (TβRI), together with the endosomal adaptor proteins APPL1 and APPL2, promote expression of survivin and Aurora kinase B (AURKB). We show that the intracellular part of TβRI binds to AURKB during telophase in PC-3U prostate cancer and KELLY neuroblastoma cells. The TβRI/tumor necrosis factor receptor–associated factor 6 (TRAF6) complex activates AURKB by causing TRAF6-induced Lys63-linked polyubiquitination of AURKB at Lys85 and Lys87, promoting cancer cell division and survival. This mechanism may contribute to the pro-tumorigenic effects of TGFβ in advanced cancers.

overall_design: Total RNA obtained from PC-3U cells in which APPL1 and APPL2 were knocked down by siRNA, compared to the cells which were transfected with control siRNA. Three replicates per group were included.

first: Maréne

last: Landström


title: ATAC-seq analysis of Eriocheir sinensis muscle

first: Tong

last: Hao

overall_design: Muscle of healthy crabs in pre-molt (D stages) and post molt (A stages) were collected and used for ATAC-seq analysis.in each stages, three muscle samples were collected as the experimental replications. ATAC-seq was performed with Illumina Hiseq platform with E. sinensis genome (accession number PRJNA555707) as the reference genome.

first: Jingjing

last: Li

first: Jinsheng

last: Sun


title: Differential expression of miR-375, miR-7-5p, and miR-455-3p is associated with ASCL1-positive molecular subtype of small cell lung cancer

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

summary: Genome-wide profiling of chromatin modifications by Cleavage Under Targets and Tagmentation (CUT&Tag) assay in Lu134A, a SCLC-A cell line.

overall_design: CUT & Tag with H3K4me3, H3K27ac and H3K27me3.

first: Kazuko

last: Miyakawa

first: Akira

last: Saito


title: Restrained Wnt signaling pathway by enhanced EsGSK3β phosphorylation activity facilitates the infection of intracellular bacterium Spiroplasma and leads to neuropathic diseases in crustaceans

city: Xinxiang

first: Libo

last: Hou

state: Henan

address: 110 Room, College of Fisheries, 46 Jianshe East Road

institute: Henan normal university

summary:
To determine how Wnt-β-catenin regulates the innate immune response in crab hemocytes, Esβ-catenin and EsGSK3β RNA interference de novo transcriptomic analysis was performed to identify the innate immune-related genes regulated by this pathway.
Venn analysis of differentially transcribed genes from Esβ-catenin-dsRNA vs. GFP-dsRNA (significantly downregulated) and EsGSK3β-dsRNA vs. GFP-dsRNA (significantly upregulated) of the screening generated 434 candidates. KEGG enrichment analysis of those candidate genes showed that many innate immune-related genes belonged to the Toll and IMD signaling pathways.

overall_design: Transcriptomic analysis was performed to identify the down-regulated genes after Esβ-catenin RNAi and up-regualted genes after EsGSK3β RNAi. Each experiment was repeated three times. Venn analysis of differentially transcribed genes from Esβ-catenin-dsRNA vs. GFP-dsRNA (significantly downregulated) and EsGSK3β-dsRNA vs. GFP-dsRNA (significantly upregulated) to identify the target innate immune-related genes whose transcription was induced by Esβ-catenin and whose transcription was suppressed by EsGSK3β.

first: Qingguo

last: Meng


title: Single cell RNA sequencing of tumor sections from GEMM harboring KrasG12D/+ or  KrasG12D/+Lkb1fl/fl(KL) mutation.

city: Guangzhou

first: Xue

last: Bai

address: No. 1023-1063, Shatai South Road, Baiyun District

institute: Southern Medical University

summary: LKB1 deficiency is widely acknowledged to induce immune-desert tumors in the non small cell lung cancer. Dissecting the "cold" tumor microenvironment (TME) would promote a better understanding of mechnism of the immune evasion triggered by LKB1 loss, thereby facilitating to seek therapeutic targets. Here, we exploited single-cell RNA sequencing to show the immune landscape of genetically engineered mouse model  (GEMM) bearing a conditional activating mutation of endogenous Kras (KrasLSL-G12D/+)  with or without Lkb1 conditional knockout (Lkb1fl/fl). The heterogeneity of TME and celler communication were analyzed.

overall_design: The mice bearing KrasG12D/+ or KrasG12D/+Lkb1fl/fl(KL)  mutations were evaluated by Magnetic Resonance Imaging (MRI) to quantify the lung tumor burden, and their lung tumor nodules were harvested, followed by single cell RNA sequencing.

first: Zeqin

last: Guo

first: Yanpei

first: Lili

last: Long

first: Zhongyi

last: Dong


title: mRNA expression in vaginal melanoma

first: William

last: Carson III

summary: mRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from vaginal melanoma compared to adjacent healthy vaginal mucosa.

overall_design: In this study mRNA expression was assessed in formalin fixed, paraffin embedded vaginal melanoma and adjacent healthy vaginal mucosa (n=3, paired) Nanostring human tumor signaling 360 mRNA assay.

first: Mallory

last: DiVincenzo

first: Colin

last: Angell


title: AD-linked TREM2 mutation induces disease-enhancing proinflammatory microglial states in mice and humans [Now it is part of GSE183068]

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: The hemizygous R47H variant of TREM2, a microglia-specific gene in the brain, increases risk for late-onset Alzheimer’s disease (AD). To understand its pathogenicity, we performed single-nuclei RNA-sequencing of cortical tissue from AD patients with R47H or the common variant (CV)-TREM2 with matched sex, pathology and APOE status. we found that the R47H mutation is associated with cell type- and sex-specific transcriptional changes in human AD, with microglia exhibiting the most robust alterations. R47H-associated microglial subpopulations were characterized by hyperactivation of AKT, one of the signaling pathways downstream of TREM2, and enhanced inflammatory signatures. In tauopathy mouse models that carry one allele of human TREM2 (hTREM2) with either the R47H mutation or CV, the mutation induced spatial memory deficits and exacerbated tau-mediated deficits in female mice. Similar to the human data, the disease-enhancing effects of R47H microglia were associated with robust increases in proinflammatory cytokines, Syk-Akt-signaling, and elevation of a subset of disease-associated microglial signatures identified using single-cell sequencing from isolated microglia. Pharmacological Akt inhibition largely reversed the enhanced inflammatory signatures in R47H microglia treated with tau fibrils. By unraveling the disease-enhancing properties of the R47H mutation in mouse and human, our findings shed light on an immune-linked AD subtype and provide new directions for modulating brain immune responses to treat AD.

overall_design: Droplet-based single nuclear RNA sequencing of frontal cortical tissues from AD patient with and without the TREM2-R47H mutation and their age, pathology, and sex-matched, controls

first: Faten

last: Sayed

first: Lay

last: Kodama

first: Joe

middle: C

last: Udeochu

last: Fan

first: Gillian

middle: K

last: Carling

first: David

last: Le

first: Tara

middle: E

last: Tracy

first: Qingyun

first: Lu

last: Zhou

first: Hansruedi

last: Mathys

first: Minghui

last: Wang

first: Xiang

last: Niu

first: Linas

last: Mazutis

first: Xueqiao

last: Jiang

first: Xueting

first: Fuying

last: Gao

first: Maria

last: Telpoukhovskaia

first: Yueming

first: Georgia

last: Frost

first: Yungui

first: Yaqiao

first: Zuolin

last: Cheng

first: Guoqiang

last: Yu

first: John

last: Hardy

first: Giovanni

last: Coppola

first: Man

middle: Y

last: Wong

first: Matthew

last: Brendel

first: Shiaoching

last: Gong

first: Fei

first: Bin

last: Zhang

first: Lei

last: Xie

first: Li-Huei

last: Tsai

first: Wenjie

last: Luo

first: Dennis

last: Dickson


title: Characterization and Function of Neutrophils in Alcoholic Hepatitis in Humans and Mice: Roles for Neutrophilic p47phox in Disease Progression

city: Indianapolis

first: Zhihong

last: Yang

institute: Indiana University

summary: Intrahepatic neutrophil infiltration has been implicated in the pathogenesis of severe alcoholic hepatitis (SAH), a disease with high short-term morality; however, how neutrophils contribute to SAH progression remain obscure. This study aimed to characterize intrahepatic neutrophil infiltration and its involvement in AH pathogenesis.  We found that hepatic expression of neutrophil cytosolic factor 1 (NCF1), a key factor in controlling neutrophilic ROS production, was upregulated and correlated with neutrophil number, inflammation and ROS-associated genes in SAH patients. Ncf1 floxed mice were generated using CRISPR/Cas9 technology by inserting two LoxP sequences into intron 1 and intron 8 of the mouse Ncf1 gene, then crossed with Lyz Cre mice to generated myeloid cell-specific Ncf1 knockout (Ncf1Lyz-/-) mice. The LyzCre negative Ncf1 floxed mice were used as corresponding WT littermate control. The chronic-plus-binge ethanol feeding model was used in this study. The total RNAs were extracted from ETOH-fed 5 WT and 4 Ncf1Lyz-/- mouse livers and submitted for a Poly(A) RNA sequencing. Genetic deletion of the Ncf1 gene in neutrophils abolished hepatic ROS, inflammation, and fibrosis induced by ethanol feeding. RNA-sequencing analysis and the data from experimental models revealed that neutrophilic NCF1-dependent ROS promoted alcoholic liver injury by inhibiting AMP-activated protein kinase (a key regulator of lipid metabolism) and microRNA-223 (a key anti-inflammatory and anti-fibrotic microRNA). Our data suggest that divergent pathogeneses exist in SAH and neutrophilic NCF1-dependent ROS promotes alcoholic liver injury by inhibiting AMPK and microRNA-223.

overall_design: Mouse liver mRNA profiles of Etoh-fed wild type (WT) and myeloid cell-specific Ncf1 knockout (Ncf1-Lyz-/-; Ncf1-MKO) mice

first: Jing

last: Ma

first: Suthat

last: Liangpunsakul


title: ATAC-seq and RNA-seq analysis of Eriocheir sinensis muscle

first: Tong

last: Hao

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

overall_design: Refer to individual Series


title: Hepatoblastomas with carcinoma features represent a biological spectrum of aggressive neoplasms in children and young adults

status: Public on Jul 15 2022

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

institute: Baylor College of Medicine

summary: We molecularly characterized a class of histologically aggressive childhood liver cancers and showed that these tumors are clinically aggressive and that their observed histological features are associated with underlying recurrent molecular features. We proposed a diagnostic algorithm to identify these cancers using a combination of histological and molecular features, and our analysis suggested that these cancers may benefit from specialized treatment strategies that may differ from treatment guidelines for hepatoblastomas and hepatocellular carcinomas.

overall_design: 37 HB samples including 10 equivocal HCN NOS, 12 biphasic HCN NOS, 10 HB FPAs, and 5 HBs of older patients with classical HB, were transcriptomically profiled using the nCounter Human PanCancer Pathways Panel (catalog#: xt-cso-HIO360-12) NanoString platform.

first: Dolores

middle: H

last: Lopez-Terrada


title: LINGO Receptor Family Members Control Epithelial Wound Healing Pathways

city: Philadelphia

first: De'Broski

last: Herbert

address: 3900 Spruce Street

institute: University of Pennsylvania

summary: Wound healing requires orchestration of cellular migration, adhesion molecule synthesis, and cell cycle regulation. However, the cellular receptors necessary for the repair of damaged tissue remain poorly understood. This study investigated whether extracellular transmembrane receptors in the leucine rich repeat and nogo interacting protein family (LINGO) were required for the recovery of airway epithelial cells from from scratch wound injury.  CRISPR/Cas9-mediated deletion mutants for either LINGO1, LINGO2, or LINGO3 or their putative co-receptors, Tumor Necrosis Factor Receptor Superfamily, Member 19 (TROY) and Reticulon 4 Receptor (RTN4R) in the mouse airway epithelial cell line MLE-12 were used for mRNA sequencing.  Cells for all lines were grown to a monolayer and subjected to a scratch with a pipette tip.  Cells from each mutant line and the parental line were collected for sequencing after 24 hours post-scratch. In addition the parental line was sequenced under baseline un-scratch conditions.

overall_design: 6 samples total, no replicates, one parental line un-scratched, one parental line 24 hours post-scratch, Lingo1, Lingo2, Lingo3, and TROY mutant lines 24 hours post-scratch

first: Ray

last: Saunders

first: Annabel

last: Ferguson


title: microRNA expression in vulvar melanoma

first: William

last: Carson III

summary: microRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from vulvar melanoma compared to primary cutaneous melanoma

overall_design: In this study microRNA and mRNA expression was assessed in formalin fixed, paraffin embedded vulvar melanoma (n=22) compared to primary cutaneous melanoma (n=9) using the Nanostring human miRNA assay.

first: Mallory

last: DiVincenzo

first: Colin

last: Angell


title: Colonic TRPV4 overexpression is related to constipation severity

city: TOYAMA CITY

first: Hiroshi

last: Mihara

state: Toyama

address: 2630, Sugitani

institute: University Of Toyama

summary: Abstract  Background  Chronic constipation is prevalent and involves both colon sensitivity and various changes in intestinal bacteria, particularly mucosa-associated microflora. Here we examined regulatory mechanisms of TRPV4 expression by co-culturing colon epithelial cell lines with intestinal bacteria and their derivatives. We also investigated TRPV4 expression in colon epithelium from patients with constipation.   Methods  Colon epithelial cell lines were co-cultured with various enterobacteria (bacterial components and supernatant), folate, LPS, or short chain fatty acids (SCFAs). TRPV4 expression levels and promoter DNA methylation were assessed using pyrosequencing, and microarray network analysis. For human samples, correlation coefficients were calculated and multiple regression analyses were used to examine the association between clinical background, rectal TRPV4 expression level and mucosa-associated microbiota.  Results  Co-culture of CCD841 cells with P. acnes, C. perfringens, or S. aureus transiently decreased TRPV4 expression but did not induce methylation. Co-culture with clinical isolates and standard strains of K. oxytoca, E. faecalis, or E. coli increased TRPV4 expression in CCD841 cells, and TRPV4 and TNF-alpha expression were increased by E. coli culture supernatants but not bacterial components. Although folate, LPS, IL-6, TNF-alpha, or SCFAs alone did not alter TRPV4 expression, TRPV4 expression following exposure to E. coli culture supernatants was inhibited by butyric acid or TNF-alphaR1 inhibitor and increased by p38 inhibitor. Microarray network analysis showed activation of TNF-alpha, cytokines, and NOD signaling. TRPV4 expression was higher in constipated patients from the terminal ileum to the colorectum, and multiple regression analyses showed that low stool frequency, frequency of defecation aids, and duration were associated with TRPV4 expression. Meanwhile, incomplete defecation, time required to defecate, and number of defecation failures per 24 hours were associated with increased E. faecalis frequency.  Conclusions  Colon epithelium cells had increased TRPV4 expression upon co-culture with K. oxytoca, E. faecalis, or E. coli supernatants, as well as TNFα-stimulated TNFαR1 expression via a pathway other than p38. Butyrate treatment suppressed this increase. Epithelial TRPV4 expression was increased in constipated patients, suggesting that TRPV4 together with increased frequency of E. faecalis may be involved in the pathogenesis of various constipation symptoms.

overall_design: E coli culture supernatant induced gene expression in human colon cell  was measured.  n=1 experiments were performed at bouth for control and  E.coli supuernent treated cells.

first: Kunitoshi

last: Uchida

first: Yoshiyuki

last: Watanabe

first: Sohachi

last: Nanjo

first: Miho

last: Sakumura

first: Iori

last: Motoo

first: Takayuki

last: Ando

first: Masami

last: Minemura

first: Jibran

middle: S

last: Muhammad

first: Hiroyuki

last: Yamamoto

first: Fumio

last: Itoh

first: Ichiro

last: Yasuda


title: The nuclear general transcription factor TFIIFa interacts with the Topoisomerase VI complex and selectively controls the expression of genes encoding PPR proteins involved in organellar RNA editing.

city: Marseille

first: Christophe

last: Laloi

state: France

address: 163 avenue de Luminy

country: France

institute: Aix-Marseille Université

summary: The transcriptome analysis of the tfIIfα-1, and tfIIfα-2 comprises three biological replicates for mutant and WT genotypes.

overall_design: tfIIfα-1, and tfIIfα-2, and wild type

first: Laura

last: Dimnet

first: Cécile

last: Vriet

first: Dorine

last: Achard

last: Lecampion

first: Christian

last: Breuer

first: Ludivine

last: Soubigou-Taconnat

first: Keiko

last: Sugimoto

first: Etienne

last: Delannoy


title: Ameliorative effect of the oil components derived from sweet potato shochu on impaired short-term memory in mice after amyloid ß25-35 injection

city: 都城市

first: 超

last: 章

state: 宮崎県

address: 下川東4丁目28号1番

institute: 霧島酒造株式会社

summary:
In this study, we first analyzed the components of shochu oil and then investigated the effects of shochu oil on short-term memory, using a mouse model exhibiting spontaneous alternating behavior caused by the intracerebroventricular administration of Aß25-35. On the last day of the experiment, we examined gene expression in the mouse hippocampus using DNA microarrays. We confirmed the effect of the oil components derived from sweet potato shochu on impaired short-term memory in mice after amyloid ß25-35 injection.
Sweet potato shochu oil is a by-product of shochu production. We investigated the effects of shochu oil on short-term memory using a murine model of spontaneous alternating behavior induced by the intracerebroventricular administration of amyloid β25-35 (Aß25-35). Mice were orally administered shochu oil for 15 days. Experiments with a Y-maze model revealed that the Aß25-35 caused a significant decrease in spontaneous alternation behavior, and supplementation with shochu oil significantly improved this behavior. DNA microarray analysis revealed that the administration of shochu oil downregulated the expression of S100a9 and Ptgs2, which reportedly exacerbate amyloid β deposition in Alzheimer’s disease. The administration of shochu oil upregulated the expression of Dnaja1 and PP2A, which is typically downregulated in Alzheimer’s disease. These data suggest that shochu oil ameliorates symptoms of amyloid β lesions, as indicated by its effects on improving spontaneous alternation behavior and modulating the expressions of related genes.

overall_design: The experiment was divided into three groups: the normal control group (NCO), the Aβ25-35 injected-control group (ACO), and the Aβ25-35 injected-shochu oil group (ASO). The average weights of each group (10 mice) were equal, assessed using a random computerized sampling method. The experimental procedure is shown in Fig. 1.

first: Cho

last: Sho

first: Kuniaki

last: Kawano

first: De-Xing

last: Hou

first: Makoto

last: Yoshimato

first: Hironori

last: Okuno


title: Quercetin treatment lower Angiotensin-II-induced blood pressure

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of this study is to compare the differently expressed genes in renal tissue of C57BL/6 WT mice with or without Angiotensin II (AngII) treatment as well as differently expressed genes in the  renal tissue  of WT mice with AngII treatment with or without Quercetin (Que) treatment. The mice (n=18) were randomly divided into 3 groups: control, AngII,AngII+ Que (n=6 for each group). Mice in Control and AngII groups were infused with saline or 500 ng/kg/min of AngII respectively, and  intragastrically with double distilled water (dd H2O); while mice in AngII + Que groups were infused with AngII (500 ng/kg/min) and  intragastrically with 5mg/kg/D of Que for 4 weeks.  Then the renal tissue were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with renal tissue of  mice in 3 groups: control, AngII, Quercetin treated (n=6 for each group) to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Xiuli

last: Zhang

first: Ying

last: Wen


title: Integrated Analysis of T-cell Repertoire and Transcriptome Shed Light into the Mechanisms of Regulatory T cell (Treg) Suppression of Acute Graft-versus-Host-Disease

first: Juliane

last: Lohmeyer

address: 269 W. Campus Drive

institute: Stanford University

summary: CD4+ FOXP3+ regulatory T (Treg) cells are currently under clinical evaluation as an immunoregulatory cellular therapy for graft-versus-host disease (GvHD) prevention and treatment. Preclinical and clinical studies indicate that Treg are able to protect from GvHD without interfering with the graft-versus-tumor (GvT) effect of hematopoietic cell transplantation (HCT), although the underlying molecular mechanisms are largely unknown. To elucidate Treg suppressive function during in vivo suppression of acute GvHD, we performed paired T cell receptor (TCR) sequencing and RNA sequencing analysis on conventional T cells (Tcon) and Treg before and after transplantation in an MHC major-mismatch mouse model of HCT. We show that both Treg and Tcon underwent clonal expansion and that Treg did not interfere with the activation of alloreactive Tcon clones.  Transcriptomic analysis revealed that Treg predominantly affected CD4 Tcon and to a lesser extent CD8 Tcon transcriptome, modulating the transcription of genes encoding pro- and anti-inflammatory molecules as well as enzymes involved in metabolic processes, inducing a switch from glycolysis to oxidative phosphorylation. Finally, Treg did not interfere with the induction of gene sets involved in the GvT effect. Our results shed light into the mechanisms of acute GvHD suppression by Treg and will support the clinical translation of this immunoregulatory approach.

overall_design: Donor CD4 and CD8 conventional T cells and Treg from C57Bl6 mice before and 8 days post transplant in a major mismatch GVHD model (Bl6 --> Balb/c) treated with Treg on day 0 or not were sorted and analyzed by bulkRNA and TCR seq

first: Toshihito

last: Hirai

first: Mustafa

last: Turkoz

first: Stephane

last: Buhler

first: Teresa

last: Lopes Ramos

first: Natalie

last: Köhler

first: Jeanette

last: Baker

first: Xuhuai

last: Ji

first: Jean

last: Villard

first: Yves

last: Chalandon

first: Federico

last: Simonetta

first: Robert

last: Negrin


title: Genome-wide analysis of DSBs sites in HEK293T cells

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: For genome-wide identification and analysis of endogenous DSBs in HEK293T cells chromosomes the ligation-mediated PCR and deep sequencing of the DSBs library were used. The cells were included in low-melt agarose, and the plugs were used for isolation of DNA in a solid phase using incubation in the solution containing 0.5 M EDTA (pH 9.5), 1% sodium laurylsarcosine, and 1-2 mg of proteinase K per ml for 40-48 hr at 50°C. Then DNA was isolated by electro-elution and used for ligation with biotinylated ds-adapter. To shorten large DNA molecules the digestion with Sau3A endonuclease was performed. Then the short regions of DNA attached to DSBs sites were selected using the streptavidin magnespere paramagnetic particles. To prepare samples for amplification of DSBs library the Sau3A adapter was ligated at the opposite to DSBs sites. PCR amplification was performed using the primers corresponding to biotinylated and Sau3A adapters. The library was used for paired end sequencing. The corresponding reads were processed and used for analysis of their distribution in human genome.

overall_design: Analysis of human epigenome by the genome-wide analysis of DSBs

first: Yuri

middle: V

last: Kravatsky

first: Olga

last: Kretova


title: Inhibition of astrocytic DRD2 suppresses CNS inflammation in an animal model of multiple sclerosis

city: Shanghai

first: Yue

last: Wu

address: 320 Yueyang Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences


title: Inhibition of astrocytic DRD2 suppresses CNS inflammation in an animal model of multiple sclerosis [astrocyte]

summary: Astrocyte activation is associated with progressive inflammatory demyelination in multiple sclerosis (MS). The molecular mechanisms underlying astrocyte activation remain incompletely understood. Recent studies have suggested that classical neurotransmitter receptors are implicated in the modulation of brain innate immunity. We investigated the role of dopamine signaling in the process of astrocyte activation. Here, we show the upregulation of dopamine D2 receptor (DRD2) in reactive astrocytes in MS brain and non-canonical role of astrocytic DRD2 in MS pathogenesis. Mice deficient in astrocytic Drd2 exhibit a remarkable suppression of reactive astrocytes and inflammation which are highly correlated with the amelioration of experimental autoimmune encephalomyelitis (EAE). Mechanistically, DRD2 regulates the expression of 6-pyruvoyl-tetrahydropterin synthase which modulates NF-κB activity through protein kinase C-δ. Pharmacological blockade of astrocytic DRD2 with a DRD2 antagonist dehydrocorybulbine remarkably inhibits the inflammatory response in mice lacking Drd2 in neurons. Together, our findings reveal previously uncharted roles for a DRD2 in astrocyte activation during EAE-associated CNS inflammation. Its therapeutic inhibition may provide a potent lever to alleviate autoimmune diseases.

overall_design: Microarray analysis from sorted astrocyte from Drd2mGFAP cKO and control mice at basal and peak of EAE, 1 sample from 3 mice in each group, using Affymetrix GeneChip® Mouse Transcriptome Array 1.0.

first: Shenzhao

last: Lu

first: Shu

last: Yin

first: Yongshun

last: Guo


title: Inhibition of astrocytic DRD2 suppresses CNS inflammation in an animal model of multiple sclerosis [spinal cord]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for spinal cord from Drd2mGFAP cKO mice and control at basal and the peak of EAE


title: mRNA sequencing of breast cancer brain metastasis tumors FACS sorted for E-cadherin high and low levels

city: Amsterdam

first: Roebi

middle: de

last: Bruijn

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: In this study we want to compare the expression profiles of E-cadherin high and low tumor cells from 4 different mice with breast cancer brain metastasis. We used a breast cancer brain metastasis model derived from the PyMT E-cadherin-mCFP breast cancer model (Beerling et al. Cell Reports 2016) and FACS sorted samples based on endogenous E-cadherin-mCFP expression.

overall_design: Examination of expression profiles of E-cadherin high and Ecadherin low tumor cells from 4 mice. Per mouse we FACS sorted a population of E-cadherin high and e-cadherin low tumor cells.

first: Andreia

last: Margarido

first: Rebeca

last: Uceda-Castro

first: Kerstin

last: Hahn

last: de Bruijn

first: Lennart

last: Kester

first: Ingrid

last: Hofland

first: Jeroen

last: Lohuis

first: Danielle

last: Seinstra

first: Annegien

last: Broeks

first: Jos

last: Jonkers

first: Marike

middle: L

last: Broekman

first: Pieter

last: Wesseling

first: Claire

last: Vennin

first: Miguel

last: Vizoso

first: Jacco

last: van Rheenen


title: Genome-wide DNA accessibility in Gabra3a knockout and wildtype control mouse retinas.

city: Seattle

first: Timothy

middle: Joel

last: Cherry

state: WA

department: Pediatrics

institute: University of Washington/Seattle Children's Research Institute

summary: To assess DNA accessbility in adult Gabra3 knockout mouse retinas, especially at the Gabra1 promoter, we ultilized the Assay for Transposase Accessible Chromatin (ATAC-Seq; Buenrostro et al., 2013) on whole retinas from Gabra3 knockout mice and littermate controls. We observed no significant differences between WT and KO retinas with respect to DNA accessibility.

overall_design: Examination of DNA accessibility changes in adult littermate wildtype and Gabra3 knockout mouse retinas.

middle: J


title: Lens epithelial cells transcriptome analysis

city: Augusta

first: Xingjun

last: Fan

state: GA

address: 1460 Laney Walker Blvd, Room CB1119

department: Cellular Biology and Anatomy

institute: Augusta University

summary: We performed RNAseq of passage 15 and passage 42 lens epithelial cell (FHL124), a lens epithelial cellular aging model.

overall_design: three passage 15 FHL124 cells and three passage 42 FHL124 cells were used for deep sequencing


title: Combination therapy with nilotinib and PDL1 blockade reverses CD4 T cell dysfunction and prevents relapse in acute B cell leukemia

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Patients with acute lymphoblastic leukemia have experienced significantly improved outcomes due to the advent of chimeric antigen receptor T-cells and bispecific T-cell engagers, although a proportion of patients still relapse despite these advances. T cell exhaustion has been recently suggested to be an important driver of relapse in these patients. Indeed, phenotypic exhaustion of CD4+ T-cells are predictive of relapse and poor overall survival in B-ALL. Thus, therapies that counter T cell exhaustion, such as immune checkpoint blockade, may improve leukemia immunosurveillance and prevent relapse. Here, we used a murine model of Ph+ B-ALL as well as human bone marrow biopsy samples to assess the fundamental nature of CD4+ T-cell exhaustion and the preclinical therapeutic potential for combining anti-PDL1 based checkpoint blockade with tyrosine kinase inhibitors targeting the BCR-ABL oncoprotein. scRNA-seq analysis revealed that B-ALL induces a unique subset of CD4+ T-cells with both cytotoxic and helper functions. Combination treatment with the tyrosine kinase inhibitor nilotinib and anti-PDL1 dramatically improves long-term survival of leukemic mice. Depletion of CD4 T cells prior to therapy completely abrogates the survival benefit, implicating CD4 T cells as key drivers of the protective anti-leukemia immune response. Indeed, treatment with anti-PDL1 leads to clonal expansion of leukemia-specific CD4 T cells with the afore-mentioned cytotoxic/helper phenotype, as well as reduced expression of exhaustion markers. These findings support efforts to utilize PD1/PD-L1 checkpoint blockade in clinical trials and highlight the importance of CD4+ T-cell dysfunction in limiting the endogenous anti-leukemia response.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For the mouse study, C57BL/6 mice were injected with leukemia cell line (LM138) cells via tail vein, then treated with nilotinib 5 days/week for 2 weeks. Some mice were treated with anti-mouse PDL1 on days 14, 16 and 18 post-leukemia establishment. For the CD4 and CD8 T cell depletion studies, mice were treated with anti-CD4 or anti-CD8 depleting antibodies on days 7, 9 and 11 post-leukemia establishment. Sorted CD44+CD4+ T cells from the indicated experimental arms were labeled with arm-specific hashtag oligo (HTO) antibodies, as well as CITE-Seq antibody derived tags (ADT) antibodies to CD25, OX40, TIGIT, PD1, Tim3, LAG3. Cells were captured and single cell sequencing for gene expression (GEX), sample-specific and protein feature barcodes, and T-cell receptor (TCR) repertoires was performed using the 10X Genomics Chromium Next GEM Single Cell 5' (ver. 1.1) reagents, resulting in three (GEX, HTO/ADT, and TCR) libraries. For the human study, leukemia blasts, T cells (CD45+CD3+), and other immune cells (CD45+CD3-CD10-) were sorted from bone marrow biopsy samples from five leukemia patients. Cells from each patient were labeled with different HTO antibodies. Cells were captured and single cell sequencing for gene expression, sample-specific feature barcodes, and T-cell receptor repertoires was performed using the 10X Genomics Chromium Next GEM Single Cell 5' (ver. 1.1) reagents, resulting in three (GEX, HTO, and TCR) libraries.

first: Sean

middle: I

last: Tracy

first: Hrishi

last: Venkatesh

first: Can

last: Hekim

first: Lynn

last: Heltemes-Harris

first: Veronika

last: Bachanova

first: Michael

middle: A

last: Farrar


title: Transcriptomic m6A MeRIP-seq in human metastatic ovarian carcinoma and in situ ovarian carcinoma tissue

city: Xi'an City

first: Hongxi

last: Zhao

state: Shaanxi Province

address: Xinsi Road, Baqiao District

institute: The Fourth Military Medical University

summary: To investigate the mRNA m6A modification profiling in human metastatic ovarian carcinoma and in situ ovarian carcinoma tissue,  we performed m6A MeRIP-seq(GenSeq® m6A MeRIP Kit) with the total RNA extacted from these tissue samples.

overall_design: Comparative mRNA m6A modification profiling analysis of MeRIP-seq data for human metastatic ovarian carcinoma tissue and in situ ovarian carcinoma tissue were performed. Each tissue type has three replicates, i.e. Gql-cm, Lww-cm, Lyz-cm ("m" for metastasis), and Gql-c, Lww-c, Lyz-c(in situ ovarian carcinoma).

first: Lin

last: Guo

first: Nini

last: Xu

first: Daner

last: Qiu

first: Xiaozhe

last: Yang

first: Shasha


title: Genome-wide profiling of transcription factor-DNA binding interactions in Candida albicans: a comprehensive CUT&RUN method and data analysis workflow

city: Merced

first: Clarissa

middle: Jane

last: Nobile

address: 5200 North Lake Rd

department: Molecular and Cell Biology

institute: University of California, Merced

summary: Regulatory transcription factors control many important biological processes including cellular differentiation, responses to environmental perturbations and stresses, and host-pathogen interactions. Determining the genome-wide binding of regulatory transcription factors to DNA is essential to understanding the function of transcription factors in these often complex biological processes. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a modern method for genome-wide mapping of in vivo protein-DNA binding interactions that is an attractive alternative to the traditional and widely used chromatin immunoprecipitation followed by sequencing (ChIP-seq) method. CUT&RUN is amenable to a higher throughput experimental setup and has a substantially higher dynamic range with lower per-sample sequencing costs compared to ChIP-seq. Here, we describe a comprehensive CUT&RUN protocol and accompanying data analysis workflow that is tailored for genome-wide analysis of transcription factor-DNA binding interactions in the human fungal pathogen Candida albicans. This detailed protocol describes all necessary experimental procedures, from epitope tagging of transcription factor coding genes, to library preparation for sequencing; additionally, it includes our customized computational workflow for CUT&RUN data analysis.

overall_design: Nuclei isolation using zymolyase. TF-DNA complex were isolated with antibody.

first: Mohammad

last: Qasim

first: Ashley

last: VArevalo


title: HK2 gene expression in response to osmolytes

city: Bonn

first: Sibylle

last: von Vietinghoff

address: Venusbergcampus 1

country: Germany

institute: University Clinic Bonn

summary: Renal tubular epithelial cells are exposed to a range of osmolytes.

overall_design: We here studied gene expression of the HK2 human tubular cell lines after 24h exposure to isoosmolar NaCl, urea and mannitol.

last: vonVietinghoff


title: mRNA-seq of Pea3 triple mutants in 10ss Danio rerio larvae

city: Davis

first: Bruce

middle: W.

last: Draper

address: University of California Davis One Shields Ave.

department: MCB

institute: University of California, Davis

summary: We performed differential DGE analysis on RNA-seq data to determine the genes misregulated in triple mutant embryos (3etv)  for etv4, etv5a, and etv5b transcription factors. 3etv mutants had defects in posterior mesoderm formation, somitogenesis, and body axis straightening, as well as other Fgf related phenotypes.

overall_design: 10ss whole embryo mRNA profiling of WT and 3etv mutants

first: Matt

last: McFaul

middle: W


title: single-cell RNA-seq of murine spleen by TAS-Seq

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

summary: Single-cell RNA-sequencing (scRNA-seq) is valuable for analyzing cellular heterogeneity. Cell composition accuracy is critical for analyzing cell-cell interaction networks from scRNA-seq data because cell abundancy might affect to the network. We developed terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq), a scRNA-seq method that relied on terminator, terminal transferase, and nanowell/beads-based scRNA-seq platform, that could acquire scRNA-seq data with higher correlation with flow-cytometric data, gene-detection sensitivity, and robustness than widely-used methods.

overall_design: To clarify performance of TAS-Seq, we analyzed mouse spleen cells collected from subcutaneous lewis lung carcinoma (LLC) model. 5x105 LLC cells were subcutaneously injected to 10 week old C57BL/6J female mice, treated with 200 μg/shot anti-CD4 antibody at on day 5 and day 9 post injection, and spleen were recovered at day 12. Resulted spleen cells were subjected by BD Rhapsody workflow, and half of BD Rhapsody beads were processed by TAS-Seq. and the other half of the beads were processed by BD official WTA protocol.

first: Chang-Yu

last: Chen

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima


title: single-cell RNA-seq of murine and human lungs by TAS-Seq

overall_design: To clarify performance of TAS-Seq, we analyzed 8-week-old C57BL/6J female mouse lung and lungs from lung cancer patients with pulmonary fibrosis who underwent curative surgical resection from August 2015 to December 2019 at Nara Medical University Hospital, who was diagnosed as rheumatoid arthritic-associated interstitial lung disease by TAS-Seq.

first: Shinichi

last: Hashimoto

first: Masahiro

last: Kitabatake

first: Takuya

last: Nakajima

first: Noriko

last: Ouji-Sageshima

first: Shigeto

last: Hontsu

first: Noriyoshi

last: Sawabata

first: Takeshi

last: Kawaguchi


title: mRNA-seq of Pea3 triple mutants in 30hpf Danio rerio larvae

overall_design: 30hpf whole embryo mRNA profiling of WT and 3etv mutants


title: single-cell RNA-seq by TAS-Seq

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

overall_design: Refer to individual Series


title: Expression data of mesenchymal stem cells (MSCs) obtained from spinal entheseal tissues in groups of control and patient with ankylosing spondylitis (AS)

city: New Taipei City

first: Chin-Hsiu

last: Liu

address: Zhonghe road

department: Rheumatology and clinical immunology

country: Taiwan

institute: Taipei Tzu Chi General Hospital

summary: The osteogenic mechanisms of transcriptional regulation underlying human MSCs in syndesmophytes formation in AS are largely unknown.  We show that RARB/TNAP promotes the abnormal osteogenesis of MSCs originated from spinal entheseal tissue involved in spinal ankylosis of AS

overall_design: To study the regulatory mechemism of abnormal osteogenesis in AS, we compared the transcription profiles of MSCs during osteogenic induction at day 0, day3 and day7 between group of normal control and pateint with AS.

first: Kuo-I

last: Lin

first: Shih-Chieh

last: Hung


title: Transcriptomics of AML12 transfected with PAV-TBG-P2A-GFP-Chrna4 over-expression plasmid

city: Nanjing

first: Jun

address: Longmiandadao

institute: CPU

summary: We reported the transcriptomics responses from RNA-seq of AML12 transfected with Chrna4 over-expression plasmid. We used cultured AML12  from 3 to 5 generations and transfected it with pCMV6-AC-GFP or PAV-TBG-P2A-GFP-Chrna4 plasmid. After 24 h, total RNA of cultured AML12 was extracted with RNAiso Plus (TaKaRa). Then we delegated it to Novogene company for RNAseq aiming to identify key factors promoting this transition.

overall_design: Examination of AML12 transcriptomics after being transfected with pCMV6-AC-GFP or PAV-TBG-P2A-GFP-Chrna4 plasmid

first: Lirui

last: Wang

first: Haiyang

last: Hu

first: Yingsheng

last: Gao


title: Functional analysis across model systems implicates ribosomal proteins in growth and proliferation defects associated with hypoplastic left heart syndrome

status: Public on Jul 14 2022

city: La Jolla

first: Georg

last: Vogler

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Hypoplastic left heart syndrome (HLHS) is the most lethal congenital heart disease (CHD). The pathogenesis of HLHS is poorly understood and due to the likely oligogenic complexity of the disease, definitive HLHS-causing genes have not yet been identified. Postulating that impaired cardiomyocyte proliferation as a likely important contributing mechanism to HLHS pathogenesis, and we conducted a genome-wide siRNA screen to identify genes affecting proliferation of human iPSC-derived cardiomyocytes (hPSC-CMs). This yielded ribosomal protein (RP) genes as the most prominent class of effectors of CM proliferation. In parallel, whole genome sequencing and rare variant filtering of a cohort of 25 HLHS proband-parent trios with poor clinical outcome revealed enrichment of rare variants of RP genes. In addition, in another familial CHD case of HLHS proband we identified a rare, predicted-damaging promoter variant affecting RPS15A that was shared between the proband and a distant relative with CHD. Functional testing with an integrated multi-model system approach reinforced the idea that RP genes are major regulators of cardiac growth and proliferation, thus potentially contributing to hypoplastic phenotype observed in HLHS patients. Cardiac knockdown (KD) of RP genes with promoter or coding variants (RPS15A, RPS17, RPL26L1, RPL39, RPS15) reduced proliferation in generic hPSC-CMs and caused malformed hearts, heart-loss or even lethality in Drosophila. In zebrafish, diminished rps15a function caused reduced CM numbers, heart looping defects, or weakened contractility, while reduced rps17 or rpl39 function caused reduced ventricular size or systolic atrial dysfunction, respectively. Importantly, genetic interactions between RPS15A and core cardiac transcription factors TBX5 in CMs, Drosocross, pannier and tinman in flies, and tbx5 and nkx2-7 (nkx2-5 paralog) in fish, support a specific role for RP genes in heart development. Furthermore, RPS15A KD-induced heart/CM proliferation defects were significantly attenuated by p53 KD in both hPSC-CMs and zebrafish, and by Hippo activation (YAP/yorkie overexpression) in developing fly hearts. Based on these findings, we conclude that RP genes play critical roles in cardiogenesis and constitute an emerging novel class of gene candidates likely involved in HLHS and other CHDs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from human induced pluripotent stem cells (hPSCs) and hPSC-derived cardiomyocytes (hPSC-CMs) and its KD derivatives (siRPL39, siRPS15A).

first: Alexandre

middle: R

last: Colas


title: HECTD1-mediated ubiquitination and degradation of Rubicon regulates autophagy and osteoarthritis pathogenesis

city: Hangzhou

first: Yuzi

last: Xu

state: Zhejiang

address: Yuhangtang Road

institute: Zhejiang University

summary: Osteoarthritis (OA) is one of the most common degenerative joint diseases and is associated with autophagy suppression. However, the molecular mechanism of autophagy regulation in the context of OA is not fully understood.

overall_design: We resorted to RNA-sequencing analysis to explore the differential expression of E3-ubiquitin ligase genes in healthy and osteoarthritic human cartilage.

first: Shiyao

last: Liao

first: Qiangqiang

last: Zheng

first: Haotian

last: Shen

first: Yang

last: Guang

first: Xiaolei

last: Zhang

first: Hongwei

last: Ouyang

first: Zongyou

last: Pan


title: Transcriptional changes thymic lymphomas with overexpression of mutant MYC

city: Portland

first: Rosalie

last: Sears

state: OR

address: 2730 SW Moody Ave, CL4RS

department: Molecular and Medical Genetics

institute: Oregon Health & Science University

summary: The goal of this study was to determine gene expression changes in thymic lymphomas with overexpression of mutant MYC

overall_design: 12 samples were analyzed. Three reps were from control tissue. Three reps each for thymic lymphoma from MYCT58A and MYCS62A, and three reps for thymic mass from MYCS62A splenomegaly.

first: Colin

last: Daniel

first: Carl

last: Pelz


title: Transcriptomic response of Nostoc sp. MG11 under desiccation stress

city: Tehran

first: Fatemeh

last: Khani-Juyabad

address: North Sheikh Bahaee St., Deh-e Vanak

department: Microbiology

country: Iran

institute: Alzahra University

summary: To identify the mechanisms of the adaptation to terrestrial ecosystems, an RNA-seq based transcriptome analysis was conducted on a desiccation resistant cyanobacterium, Nostoc sp. MG11.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control cells (0 hour desiccation) and desiccated cells (3 hours desiccation).

first: Parisa

last: Mohammadi

first: Mahbubeh

last: Zarrabi


title: FSH-deficiency in gonadotrope-specific GATA2 knockout mice is associated with a loss of gremlin expression [snATAC-Seq]

city: Los Angeles

first: Michel

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: Mammalian reproduction is dependent on the gonadotropins, follicle-stimulating hormone (FSH) and luteinizing hormone, which are secreted by pituitary gonadotrope cells. The zinc-finger transcription factor, GATA2, was previously implicated in FSH production in male mice, although its mechanisms of action and role in females were not determined. To address these gaps in knowledge, we generated and analyzed gonadotrope-specific Gata2 knockout mice using the Cre-lox system. While conditional knockout (cKO) males exhibited ~50% reductions in serum FSH levels and pituitary FSHβ subunit (Fshb) expression relative to controls, FSH production was apparently normal in cKO females. RNA-seq analysis of purified gonadotropes from control and cKO males revealed a profound decrease in expression of gremlin (Grem1), a bone morphogenetic protein (BMP) antagonist. Grem1 was expressed in gonadotropes, but not other cell lineages, in the adult male mouse pituitary. Gata2, Grem1, and Fshb mRNA levels were significantly higher in pituitaries of wild-type males relative to females but decreased in males treated with estradiol and increased following ovariectomy in control but not cKO females. Recombinant gremlin stimulated Fshb expression in pituitary cultures from wild-type mice. Collectively, the data suggest that GATA2 promotes Grem1 expression in gonadotropes and that the gremlin protein potentiates FSH production. The mechanisms of gremlin action have not yet been established but may involve attenuation of BMP binding to activin type II receptors in gonadotropes, potentiating induction of Fshb transcription by activins or related ligands.

overall_design: Single nucleus chromatin accessibility profiling of adult mouse GATA2 control and cKO pituitaries by single nuclei ATAC-seq, using Illumina

first: Gauthier

last: Schang

first: Luisina

last: Ongaro

first: Emilie

last: Brûlé

first: Xiang

last: Zhou

first: Ying

last: Wang

first: Yeu-Farn

last: Lin

first: Ulrich

last: Boehm

first: Frederique

last: Ruf-Zamojski

first: Yongchao

last: Ge

first: Natalia

last: Mendelev

first: Nitish

last: Seenarine

first: Mary

last: Amper

first: Venugopalan

last: Nair

first: Stuart

middle: C

last: Sealfon

first: Daniel

last: Bernard


title: Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids

city: Santa Cruz

first: Spencer

last: Seiler

state: CA

address: 1156 High Street

department: Biomolecular Engineering

institute: UC Santa Cruz

summary: Organ-on-a-chip systems combine microfluidics, cell biology, and tissue engineering to culture 3D organ-specific in vitro models that recapitulate the biology and physiology of their in vivo counterparts. Here, we have developed a multiplex platform that automates the culture of individual organoids in isolated microenvironments at user-defined media flow rates. Programmable workflows allow the use of multiple reagent reservoirs that may be applied to direct differentiation, study temporal variables, and grow cultures long term. Novel techniques in polydimethylsiloxane (PDMS) chip fabrication are described here that enable features on the upper and lower planes of a single PDMS substrate. RNA sequencing (RNA-seq) analysis of automated cerebral cortex organoid cultures shows benefits in reducing glycolytic and endoplasmic reticulum stress compared to conventional in vitro cell cultures.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H9 cerebral cortex organoids cultured in suspension and in automated microfluidics

middle: T

first: Gary

last: Mantalas

first: John

last: Selberg

first: Sergio

last: Cordero

first: Sebastian

last: Torres-Montoya

first: Pierre

last: Baudin

first: Victoria

last: Ly

first: Finn

last: Amend

first: Liam

last: Tran

first: Ryan

middle: N

last: Hoffman

first: Marco

last: Rolandi

first: Richard

middle: E

last: Green

first: David

last: Haussler

first: Sofie

last: Salama

first: Mircea

last: Teodorescu


title: FSH-deficiency in gonadotrope-specific GATA2 knockout mice is associated with a loss of gremlin expression

first: Michel

last: Zamojski


title: FSH-deficiency in gonadotrope-specific GATA2 knockout mice is associated with a loss of gremlin expression [snRNA-Seq]

overall_design: Single nucleus gene expression profiling of adult mouse GATA2 control and cKO pituitaries by single nuclei RNA-seq, using Illumina

first: Gauthier

last: Schang

first: Luisina

last: Ongaro

first: Emilie

last: Brûlé

first: Xiang

last: Zhou

first: Ying

last: Wang

first: Yeu-Farn

last: Lin

first: Ulrich

last: Boehm

first: Frederique

last: Ruf-Zamojski

first: Yongchao

last: Ge

first: Natalia

last: Mendelev

first: Nitish

last: Seenarine

first: Mary

last: Amper

first: Venugopalan

last: Nair

first: Stuart

last: Sealfon

first: Daniel

last: Bernard


title: FSH-deficiency in gonadotrope-specific GATA2 knockout mice is associated with a loss of gremline expression

city: New York

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

overall_design: Bulk RNAseq profiling of adult mouse GATA2 control and cKO pituitaries


title: Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome [genome]

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

summary: Here we analysed the widespread disruption of gene expression that accompanies yeast ageing, and surprisingly observed that this is completely independent of ERCs. Furthermore, we could not find subsets of genes that are differentially regulated in the presence of ERCs. High throughput imaging showed that the accumulation of Tom70-GFP which accompanies the onset of cell division defects at the Senescence Entry Point (SEP) also correlated poorly to ERC abundance, but allowed determination of a gene expression signature for the SEP. This signature included overexpression of mRNA from the chromosome XII region between the rDNA and the telomere (ChrXIIr), which has been previously noted to amplify during ageing.

overall_design: Mother Enrichment Project (MEP) yeast were harvested at log phase or aged for 24 or 48 hours in YPD. Cells were embedded in agarose, DNA extracted, sonicated and processed into libraries using a NEBNext Ultra II DNA kit.

first: Hanane

last: Hadj-Moussa

first: Andre

last: Zylstra

first: Jon

last: Houseley


title: Analysing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome [RNA]

overall_design: Mother Enrichment Project (MEP) yeast were harvested at log phase or aged for 24 or 48 hours in YPD. Mother cells were purified, total RNA extracted and libraries processed using a NEBNext Ultra II directional RNAseq kit with poly(A)+ selection module.


title: Next Generation Sequencing Facilitates Quantitative Analysis of SETD6 Knock-out and stable expression of TWIST1 in Glioblastoma cells

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

summary: The goal of this study was to identifiy shared target genes for SETD6 and TWIST1 in Glioblastoma.

overall_design: mRNA of U251 control and SETD6 KO cells and mRNA of U251 stably expressing empty vector or FLAG-TWIST1

first: Lee

last: Admoni-Elisha

first: Dan

last: Levy

first: Noam

last: Shomron