title: Effect of smooth muscle specific PRDM6 depletion on Aorta and Ductus Arterious (DA) development

city: Chapel Hill

first: meng

last: zou

state: NC

address: 1521 E Franklin St, Apt C300

department: Pathology

institute: UNC-CH

summary: To investigate the function of PRDM6 in smooth muscle cells during outflow tract development, we have isolated the ascending aorta and the ductus arteriosus (DA) separatly from the E18.5 Wnt1Cre;PRDM6f/f mouse (PRDM6 KO) and PRDM6f/f mouse (Control) and compared the gene expression profile of the four groups of samples

overall_design: There are four groups of samples in our experiment (Control Aorta; PRDM6 KO Aorta; Control DA; PRDM6 KO DA), and we focused on comparing Control DA v.s PRDM6 KO DA

first: Meng

last: Zou

first: Chris

last: Mack

first: Terry

last: Furey


title: Determining the PRDM6 genomic binding sites in primary outflow tract smooth muscle cells

status: Public on Apr 12 2023

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for PRDM6 in primary outflow tract smooth muscle cells overexpressing FLAG taggged PRDM6

overall_design: Primary outfow tract smooth muscle cells overexpressing FLAG tagged PRDM6 was used as input, and then FLAG antibody was used for PRDM6 CHIP, with two replicates for the experiment


title: Deep RNA sequencing analysis after Malat1 silencing in mouse HL1 cells

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

type: Expression profiling by high throughput sequencing

summary: We have described role of Malat1 in cardiomyocyte proliferation and binucleation. Data shows regulated genes by LNA mediated silencing of Malat1

overall_design: Examination of 3 LNA control (ctrl2) and 3 LNA Malat1 treated mouse HL1 cells samples

first: Aslan

middle: G

last: Galip Servet


title: RNA-seq of rat Achilles tendon tissue from pefloxacin and/or dexamethasone treated animals

city: Kyoto

first: Kazuki

last: Nagayasu

address: 46-29 Yoshidashimoadachicho, Sakyo

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Kyoto University

summary: Tendinopathy is characterized by rupture, pain, or loss of tendon strength. Previous basic and clinical investigations have clarified multiple risk factors, including aging and fluoroquinolone use; however, the etiology remains unclear. We combined real-world data analysis with pharmacological experiments to overcome the gap between basic and clinical research. Analyses of self-reported adverse event databases and the US commercial claims database revealed that dexamethasone prevented fluoroquinolone-induced and age-related tendinopathy. Experimental validation suggested that co-treatment with dexamethasone attenuated pefloxacin-induced mechanical fragility in rat tendons. RNA-seq was conducted to further investigate the molecular mechanism of tendinopathy, focusing on fluoroquinolone.

overall_design: Achilles tendon mRNA profiles of vehicle-, pefloxacin-, dexamethasone-, or pefloxacin+dexamethasone-treated rats.

first: Haruka

last: Furuta

first: Shuji

last: Kaneko


title: Titration-based normalization of antibody amount improves consistency of ChIP-seq experiment

city: ROCHESTER

first: JEONG-HEON

last: LEE

state: Minnesota

address: 200 1ST STREET S.W.

department: Epigenomics program/CIM

institute: MAYO CLINIC

summary:
Chromatin immunoprecipitation (ChIP) is an antibody-based approach that is most frequently utilized in research areas of chromatin biology and epigenetics. The ENCODE Consortium provided guidelines about antibody but the fundamental aspect regarding antibody titer was not addressed. Here, we introduced a simple and quick DNA-based quantification of chromatin input, allowing to normalize the antibody amount in individual ChIP reaction to the optimal titer. We further demonstrated the titration-based normalization of antibody amount generates improved assay outcome with high consistency among samples in an experiment or recurrent experiments for a broad range of chromatin input amount.
Chromatin immunoprecipitation-sequencing (ChIP-seq) was performed for histone H3K27ac mark in the conditions of various titer of antibody in ChIP reactions..

overall_design: Chromatin were prepared from fixed K562 cells. Chromatin amount was aliquoted into 312, 625, 1,250, 2,500, 5,000, 10,000, and 20,000 ng in final 1 ml of ChIP buffer. 0.25 µg of anti-H3K27ac antibody was added to create the ChIP reactions with various antibody titers (the ratios between antibody amount per chromatin amount). Or normalized amounts of the antibody to the optimal titer was added into each reaction.

first: Jeong-Heon

last: Lee

first: JinSung

last: Jang

first: Geng-Xian

last: Shi


title: Gene expression profiling of FFPE normal and COVID19 lung tissues

city: La Jolla

first: Judith

last: Varner

state: CA

address: 3855 Health Sciences Dr.

department: Moores Cancer Center

institute: University of California, San Diego

summary:
SARS-CoV-2 infections induce aberrant pulmonary and systemic inflammation, vascular leak, coagulation and fatal organ damage. To identify therapeutic strategies to suppress COVID-19-associated inflammation, we characterized lung tissue of COVID-19 patients using tissue transcriptomics. FFPE lung tissue from anonymized normal and postmortem COVID19 patients and brochoalveolar lavage specimens from normal and COVID19 patients were sequenced using Tempo-Seq from Biospyder, Calrbad, CA. Bioinformatics analysis revealed that lungs of deceased patients exhibited substantial infiltration by neutrophils and wound-healing macrophages, fibrosis, vascular leak and alveolar type II cell depletion, with a pervasive wound-healing transcriptional profile.
Methods:Two five-micron FFPE sections from each of fourteen postmortem lung specimens from COVID patients, five normal lung specimens, nine BALF specimens from COVID patients and five BALF specimens from normal patients were used to perform TempoSeq FFPE human whole transcriptome RNA sequencing at BioSpyder Technologies, Inc, Carlsbad, CA, as described (Trejo et al., 2019; Turnbull et al., 2020). Prepared libraries were sequenced on NovaSeq6000; mapped reads were generated by TempO-SeqR alignment of demultiplexed FASTQ files using Bowtie, allowing for up to 2 mismatches in the 50-nucleotide target sequence.Unnormalized counts were obtained from BioSpyder TempO-seq. The R BioConductor packages edgeR (Robinson et al., 2010) and limma (Ritchie et al., 2015) were used to implement the limma-voom (Law et al., 2014) method for differential expression analysis. We analyzed normal lung, COVID-19 lung and COVID-19 BALF sample groups together and also lung samples alone due to low levels of alignment in the BALF samples. We also analyzed COVID-19 BALF and normal BALF together. One COVID-19 BALF sample was removed from downstream analysis because it had <300,000 quantified reads. Lowly expressed genes—those not having counts per million (cpm)  10 in at least 10 of the samples—were filtered out in the combined analysis and for lung samples only a less stringent filter of (cpm)  1 in at least 5 of the samples was applied. Trimmed mean of M-values (TMM) normalization (Robinson and Oshlack, 2010) was applied after filtering. The experimental design was modeled upon condition, called condition (~0 + condition). The voom method was employed to model the mean-variance relationship, after which lmFit was used to fit per-gene linear models and empirical Bayes moderation was applied with the eBayes function. Significance was defined by using an adjusted p-value cut-off of <0.05 after multiple testing correction (Benjamini and Hochberg, 1995) using a moderated t-statistic in limma. Functional enrichment of the differentially expressed genes was performed using SPIA (Tarca et al., 2009), gProfiler (Raudvere et al., 2019) and fGSEA (Korotkevich et al., 2021).

overall_design: We sequenced 5 normal and 8 COVID19 FFPE Bronchoalveolar lavage  samples as well as 5 normal Lung and 12 COVID 19 FFPE lung specimens using BioSpyder's TempoSeq sequencing protocol. Bioinformatics then compared normal lung to COVID-19 lung and Normal Balf to COVID Balf.

middle: A

first: Anghesom

last: Ghebremedhin

first: Roman

last: Sasik

first: Kathleen

last: Fisch


title: Nanostring GeoMx digital spatial profliing of myeloid cells from COVID-19 and normal lung

summary: To determine definitively whether lung myeloid cells exhibit a pro- or anti-inflammatory signature in COVID-19 disease, we performed digital spatial profiling using the nanoString GeoMx ImmuneOncology plus COVID-19 platform on CD68+ macrophages, myeloperoxidase+ granulocytes and cytokeratin+ epithelium in normal and COVID-19 lung tissue specimens, collecting RNA expression data for each type within 6-8 regions of 5mM tissue sections. One COVID-19 lung tissue yielded minimal sequence data and was excluded from analysis. A volcano plot and heat map of differentially expressed genes within macrophages demonstrate that COVID-19 lung macrophages when compared with normal lung macrophages exhibit a largely alternatively activated, wound-healing signature characterized by expression of the alternatively active macrophage marker CD163, complement/coagulation genes (C1QA, C1QB, THBS1, C1S, C1R), IL6 signaling (STAT2, STAT1) and wound healing (COL3A1, COL6A3), but also interferon response signatures (ISG15, OAS3, IFITM2, IFI6, HLA-A, HLA-B, HLA-C)  (Fig. 3H-J). As one of the tissues used for macrophage spatial profiling was from a patient was positive for the virus at the time of death, we compared the expression profiles of virus+ and virus- specimens and found that macrophages in virus+ tissues predominantly expressed an interferon-associated signature

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: 3 COVID-19 samples and 1 normal lung samples were analyzed by nanoString GeoMX digital Spatial profiling. Each of 6-8 regions of interest per tissue were profiled with 3 cell type specific markers : CD68 for macrophages, Myeloxperoxidase for neutrophils and cytokeratin for epithelial cells as well as DNA specific marker.


title: The characteristic of gene expression in htNSC senescence process due to ACP cystic fluid

city: Guangzhou

first: Yi

last: Liu

address: Guangzhou Dadao Bei Street 1838

country: China

institute: Nanfang Hospital of Southern Medical University

summary: To determine whether ISR signaling participates in inhibiting htNSC function due to cystic fluid or ox-LDL, we used an unbiased RNA sequencing (RNA-seq) transcriptome profiling approach to compare htNSCs from 3VF adjacent to ACP and NSCs from SVZ

overall_design: Comparative gene expression profiling analysis of RNA-seq data for htNSCs from 3VF adjacent to ACP and NSCs from SVZ

first: Chaohu

last: Wang

first: Huarong

last: Zhang

first: RongRong

last: Guo


title: The characteristic of cholesterol metabolism-related gene expression in ACP, PCP and PA

summary: To test whether high content of lipids was originated from ACP cells, we used an unbiased RNA sequencing (RNA-seq) transcriptome profiling approach to compare ACP, PCP and PA

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ACP, PCP and PA


title: Effect of C2S in RAW264.7 murine macrophages

city: guangzhou

first: Xingyang

last: Li

state: Guangdong

address: 195, dongfengxi road

department: Department of Temporomandibular Joint Surgery

institute: Affiliated Stomatology Hospital of Guangzhou Medical University

summary: This study aimed to investigate the mechanism of C2S-induced macrophagic inflammation and its’ effect on osteogenic differentiation of precursor cells. This study used the C2S (75-150 μg/ml) extract to induce macrophagic inflammation in RAW264.7 murine macrophages. RNA sequencing  was preformed for analyzing mechanism of mitochondrial function and autophagy.

overall_design:
The macrophages were treated with and without C2S (150 µg/ml) for 24h were used for RNA sequencing. Total RNA was extracted by using the Trizol kit (Invitrogen, Carlsbad, CA, United States), according to the manufacturer’s protocol. The RNA concentration was determined using Qubit, and the RNA amount and purity of each sample was assessed with a NanoDrop spectrophotometer. RNA was isolated in 40 µl of DEPC water and stored at -80. RNA-seq libraries were prepared by using the Illumina TruseqTM RNA sample prep Kit and were sequenced using an Illumina HiSeq.Low-quality base and adapters were removed by using “fastp”. Clean reads were aligned to the mouse genome (mm10) reference genome using STAR. Count the number of reads mapped to each gene by using RSEM. And the "edgeR" R software package was used to calculate the differential expression analysis between the two groups. KEGG analysis was performed using the “clusterProfiler” R package. KEGG terms with corrected p < 0.05 were considered significantly enriched.
contributor: National Collection of Authenticated Cell Cultures, TCM13, Shanghai, China


title: Cholesterol metabolism-related gene expression in ACP, PCP and PA; htNSC senescence process due to ACP cystic fluid

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

overall_design: Refer to individual Series


title: Single cell RNA-seq analysis of the transcriptomic profiles of endothelial cells and immune cells from the brain, spinal cord (SC), dorsal cranial dura, and spinal dura of naïve and EAE mice at the onset and peak of the disease

city: Helsinki

first: Zhilin

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: To understand transcriptomic changes in different CNS compartments following EAE, we sorted DAPI- viable CD31+ endothelial cells and CD45+ immune cells from the brain, SC, dorsal cranial dura, and spinal dura of naïve mice and MOG35-55-induced EAE mice at the onset (10 days post-immunization (dpi), EAE10) and peak (14 dpi, EAE14) of the disease by flow cytometry and performed scRNA-seq analysis.

overall_design: We analyzed in total 12 samples, aiming at sequencing 10,000 cells with an average depth of 50,000 reads per cell for every sample.

first: Kari

last: Alitalo


title: Translation regulation of specific mRNAs by RPS26 C-terminal RNA-binding tail integrates energy metabolism and AMPK-mTOR signaling

city: Rehovot

first: Tal

last: Havkin-Solomon

address: 234 Herzl

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

summary: Increasing evidence suggests that ribosome composition and modifications contribute to translation control. Much less is known about the regulatory roles of mRNA binding by ribosomal proteins to specific mRNA translation and ribosome specialization. Here we used CRISPR-Cas9, to mutate the RPS26 C-terminal tail (RPS26dC) predicted to bind AUG upstream nucleotides at the exit channel. RPS26 binding to positions -10 to -16 of short 5’UTR mRNAs exerts positive and negative effects on translation directed by Kozak and TISU, respectively. Consistent with that, shortening the 5′UTR from 16 to 10 nt diminished Kozak and enhanced TISU-driven translation. As TISU is resistant and Kozak is sensitive to energy stress, we examined stress responses and found that the RPS26dC mutation confers resistance to glucose starvation and mTOR inhibition. Furthermore, the basal mTOR activity is reduced while AMPK is activated in RPS26dC cells, mirroring energy-deprived WT cells. Likewise, the translatome of RPS26dC cells is correlated to glucose-starved WT cells. Our findings uncover the central roles of RPS26 C-terminal RNA binding in energy metabolism, in the translation of mRNAs bearing specific features and in the translation tolerance of TISU genes to energy stress.

overall_design: We used CRISPR-Cas9 mediated mutagenesis in mammalian cells to delete endogenous RPS26 C terminus (RPS26dC cells). For global translation analysis, the collected samples were merged to create the Light (2-5 ribosomes) and Heavy (6+ ribosomes) translated fractions. Equivalent RNA concentrations of Input, Light and Heavy translated ribosome were taken for the library preparation for MARS-Seq.

first: Nina

last: Reuven

first: Yosef

last: Shaul

first: Rivka

last: Dikstein


title: Effect of depletion of NUP62 on gene expression during Botrytis cinerea infection of Arabidopsis seedlings [Arabidopsis]

city: Beijing

first: Daoxin

last: Xie

address: School of Life Sciences, Room 407, Renhuan Building, Tsinghua University

institute: Tsinghua University

summary: To investigate NUP62 in the regulation of plant defense against Botrytis cinerea , we performed gene expression profiling analysis using data obtained from RNA-seq of nup62 mutant and WT arabidopsis with or without Botrytis cinerea infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Botrytis cinerea- infected and mock-treated nup62 mutant and WT Arabidopsis.

first: Jiaojiao

first: Dewei

last: Wu


title: Trypanosoma cruzi CLB vs Trypanosoma rangeli and Trypanosoma conorhini

status: Public on Apr 11 2023

city: São Paulo

first: José

middle: Franco

last: Da Silveira

state: São Paulo

address: Rua Botucatu, 862

department: Departamento de Microbiologia, Imunologia e Parasitologia

country: Brazil

institute: Universidade Federal de São Paulo

summary: Comparative genomic analysis of T. cruzi CLB vs Trypanosoma rangeli (strains SC, Choachí, C23, H14, R1625 and PIT10) and Trypanosoma conorhini

sample_organism:
Trypanosoma cruzi
Trypanosoma rangeli
Trypanosoma conorhini

overall_design: The 8x60K array was designed and produced by Agilent (Agilent Technologies, Santa Clara, CA,US) based on the T. cruzi clone CLB genome, release 9, available in TriTrypDB. Two groups of probes totaling 48,787 probes covering all the in silico chromosomes were

first: Rafaela

last: do Carmo

first: Jose

middle: F

last: da Silveira

first: Fernanda

middle: S

last: Marchiano


title: Abnormal thrombosis and neutrophil activation increase hospital-acquired sacral pressure injuries and morbidity in COVID-19 patients

city: Cleveland

first: Christine

last: McDonald

state: Ohio

address: 9500 Euclid Avenue

department: Inflammation & Immunity

institute: Cleveland Clinic

summary:
Characterization of the transcriptional signatures of 771 human genes and 19 coronavirus genes in skin samples collected from the borders of hospital-acquired sacral pressure injuries (HASPIs) that developed in individuals with and without COVID-19.
Samples included pressure ulcers from individuals without COVID-19 (10), pressure ulcers from individuals with COVID-19 (5), as well as pressure ulcers with thrombotic vasculopathy histopathology from individuals with COVID-19 (8).

overall_design: Patients with HASPIs were identified as having been hospitalized for greater than 5 days within Cleveland Clinic between March 1 and December 31, 2020, with an ICD-10 diagnosis of sacral ulcer or photographic documentation of sacral ulceration at some point during hospitalization. Histopathologic characteristics of biopsied patients were qualitatively and quantitatively assessed using hematoxylin & eosin (H&E) stained tissue specimens by a board-certified dermatopathologist. For COVID-19(+) patients, 4mm biopsies from (typically) areas of sacral purpura were obtained.  For control COVID-19(-) specimens, which were typically submitted to pathology during debridement, a search of Cleveland Clinic pathology archives was performed to find specimens from pressure ulcers. H&E sections of all available specimens were reviewed to identify those appropriate to use as control specimens. Any specimens with histologic features suggestive of secondary infection, extensive epidermal ulceration, or prominent fibrosis (supporting significant chronicity) were excluded. RNA was extracted from Formalin-Fixed and Paraffin Embedded (FFPE) tissue biopsies and analyzed using NanoString Human Autoimmune Profiling Panel and spike in Coronavirus Panel Plus probe sets. Raw data was initially processed using the nSolver Analysis Software (V.4.0).

first: Jatin

last: Narang

first: Samreen

last: Jatana

first: Andras

middle: K

last: Ponti

first: Anthony

middle: P

last: Fernandez


title: High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of  chemoresistance in leukemias. [methylation]

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

country: Italy

institute: Università degli Studi di Firenze

type: Methylation profiling by high throughput sequencing

summary: Aberrant DNA-methylation at CpG dinucleotides is a hallmark of cancer and is associated with the  emergence of resistance to anti-cancer treatment, though molecular mechanisms and biological signifi- cance remain elusive. Genome-scale methylation maps by currently used methods are based on chemical  modification of DNA and are best suited for analyses of methylation at CpG-rich regions (CpG islands).  We report the first high-coverage whole-genome map in cancer using the long-read nanopore technol- ogy, which allows simultaneous DNA-sequence and -methylation analyses on native DNA. We analyzed  clonal epigenomic/genomic evolution in Acute Myeloid Leukemias (AMLs) at diagnosis and relapse, af- ter chemotherapy. Long-read sequencing coupled to a novel computational method allowed definition  of differential methylation at unprecedented resolution (> 99% CpGs), extending analyses of CpG is- lands to sparse CpGs, which represent half of all differentially-methylated regions. We showed that the

overall_design: relapse methylome is characterized by hypermethylation at both CpG islands and sparse CpGs. Hyper- methylated genes, however, only accounted for < 5% of all differentially-expressed genes (DEGs) in the  relapsed AMLs and were not enriched for chemoresistance genes. A few under-expressed transcription- factors (1 to 6 in the different AMLs) hyper-methylated at sparse CpGs support ∼ 40% DEGs and are  highly-enriched in chemoresistance genes. Hypermethylated regions at sparse CpGs were poorly con- served in the relapsed AMLs, under-represented at their genomic positions and showed high methylation- entropy, as compared to CpG islands. Relapsed AMLs carried a few patient-specific structural-variants  and DNA-mutations, apparently not involved in drug-resistance. Thus, drug-resistance in AMLs is due to the selection of random epigenetic alterations at sparse CpGs of a few transcription factors, which then induce reprogramming of the relapsing phenotype, independently of clonal genomic-evolution.

first: Alberto

last: Magi

first: Alessandra

last: Mingrino

first: Chiara

last: Caprioli

last: Ronchini

first: GianMaria

last: Frig`e

first: Roberto

last: Semeraro

first: Davide

last: Bolognini

first: Alessandro

last: Rambaldi

first: Anna

last: Candoni

first: Emanuela

last: Colombo

first: Luca

last: Mazzarella

first: Pier

last: Pelicci


title: LaeA regulates mycelium growth by mediating H3K9 methylation in Myceliophthora thermophila [WGBS]

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

summary: The low efficiency of fungal growth and substrate utilization is a barrier to high yield and productivity of target products during fungal fermentation. However, elaborated and intricate regulatory mechanisms of fungal growth remains inconclusive. In this study, we found deletion of putative methyltransferase LaeA enhanced sugar consumption and fungal growth rate of M. thermophila. The exploration of the mechanism of LaeA regulation revealed that transcription factor (Cre-1, Grf-1, Grf-2 and Grf-3) acted as negative repressor of intracellular metabolism, of which expression was indirectly regulated by LaeA. Moreover, higher gluconeogenesis activity is crucial for elevated fugal growth rate and PCK might be the core notes of metabolism network relative to fungal vegetative growth. Further in vivo global histone methylation assay and in vitro biochemical analysis declared LaeA was a methyltransferase with histone H3 lysine 9 (H3K9) as the substrate and regulated growth properties by directly modulating H3K9 methylation levels. ChIP-seq analysis displayed significantly reduced H3K9me3 in region of pck locus in strain ΔlaeA, implying methylation modification of pck might be the way of LaeA regulating growth phenotypes. Additionally, whole-genome bisulfite sequencing (WGBS) analysis demonstrated methylation of cytosines (5mC) in genomic DNA was carried out and correlated to the methylation of H3K9 modified by LaeA. Taken together, our research declared LaeA possessed methyltransferase activity, targeting H3K9 and participated in regulation of fugal properties, including on sugar consumption, mycelium growth, cellulase production, secondary metabolism, and oxidative stress tolerance, providing new insights into the epigenetics of filamentous fungi.

sample_organism: Thermothelomyces thermophilus ATCC 42464

overall_design:
Whole Genome Bisulfite Sequencing (WGBS) for detecting DNA methylation in Myceliophthora thermophila strains.
Myceliophthora thermophila strains WT and ΔlaeA exposed to glucose for 24 h.

first: Jinge

first: Chaoguang

last: Tian


title: Expansion of the sagittal suture induces proliferation of skeletal stem cells and sustains endogenous calvarial bone regeneration

city: Pittsburgh

first: Giuseppe

last: Intini

state: Pennsylvania

address: 335 Sutherland Drive, 508 Salk Pavilion

department: Periodontics and Preventive Dentistry

institute: University of Pittsburgh

summary: In newborn humans, and up to approximately 2 y of age, calvarial bone defects can naturally regenerate. This remarkable regeneration potential is also found in newborn mice and is absent in adult mice. Since previous studies showed that the mouse calvarial sutures are reservoirs of calvarial skeletal stem cells (cSSCs), which are the cells responsible for calvarial bone regeneration, here we hypothesized that the regenerative potential of the newborn mouse calvaria is due to a significant amount of cSSCs present in the newborn expanding sutures. Thus, we tested whether such regenerative potential can be reverse engineered in adult mice by artificially inducing an increase of the cSSCs resident within the adult calvarial sutures.First, we analyzed the cellular composition of the calvarial sutures in newborn and in older mice, up to 14-mo-old mice, showing that the sutures of the younger mice are enriched in cSSCs. Then, we demonstrated that a controlled mechanical expansion of the functionally closed sagittal sutures of adult mice induces a significant increase of the cSSCs. Finally, we showed that if a calvarial critical size bone defect is created simultaneously to the mechanical expansion of the sagittal suture, it fully regenerates without the need for additional therapeutic aids. Using a genetic blockade system, we further demonstrate that this endogenous regeneration is mediated by the canonical Wnt signaling.This study shows that controlled mechanical forces can harness the cSSCs and induce calvarial bone regeneration. Similar harnessing strategies may be used to develop novel and more effective bone regeneration autotherapies.

overall_design: Freshly isolated cells obtained from the sutures of eight 4 day old, five 2 month old, five 2 month old NON-EXPANDED, six 2 month old EXPANDED, five 4 month old, and six 14 month old C57BL/6 wild type mice were utilized to perform scRNA-seq.

first: Zahra

last: Aldawood

first: Luigi

last: Mancinelli

first: Xuehui

last: Geng

first: Shu-Chi

last: Yeh

first: Roberta

last: DiCarlo

first: Taiana

middle: C

last: Leite

first: Jonas

last: Gustafson

first: Katarzyna

last: Wilk

first: Joseph

last: Yozgatian

first: Sasan

last: Garakani

first: Seyed

last: Hossein Bassir

first: Michael

middle: L

last: Cunningham

first: Charles

last: Lin


title: LaeA regulates mycelium growth by mediating H3K9 methylation in Myceliophthora thermophila [ChIP-seq]

first: Jingen

platform_organism: Thermothelomyces thermophilus ATCC 42464

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K79me3 in Myceliophthora thermophila strains.
Myceliophthora thermophila strains WT and ΔlaeA exposed to glucose for 24 h.


title: BLU667-adapted transcriptome in CCDC6-RET fusion papillary thyroid carcinoma (TPC) cells

city: Oklahoma City

first: Jie

last: Wu

state: OK

address: 975 NE 10th Street

department: Stephenson Cancer Center

institute: University of Oklahoma Health Sciences Center

summary: To investigate the short-termed and long-termed transcriptomic changes induced by the RET tyrosine kinase inhibitor BLU667 in TPC-1 human PTC cells

overall_design: RNA-seq was performed (2 biological replicates/each) on the parental TPC-1 cells treated with solvent (DMSO) or 5 µM BLU667 for 24 h, and three TPC-1-derived cell colonies (BR8, 10, 16) that were established from culturing TPC-1 cells with 5 µM BLU667 for more than 5 months.

first: Xueqing

last: Hu


title: ISWI ATP-ases, Smarca5 and Smarca1, are required for normal murine neocortical development

city: Ottawa

first: Dave

last: Picketts

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine

country: Canada

institute: OHRI

summary: Chromatin remodeling complexes modulate DNA accessibility permitting neuronal progenitor cells to proliferate and differentiate to form the mammalian neocortex. Smarca5 and Smarca1 are the ISWI ATP-ase proteins, within a variety of chromatin remodelling complexes. We created a mouse model with a truncated Smarca1, which inactivates the ATPase nucleosome rearranging activity of the protein. Secondly, using the cre/loxp system, we conditionally removed exon 5 of the Smarca5 gene, resulting in a null allele solely in the cortex of the mouse. Ultimately, we knockout (KO) both the Smarca5 and Smarca1 genes to analyze neocortical neurogenesis at E13.5  and identify their cooperative role during embryonic brain development. The DKO mice reveal significant forebrain hypoplasia.

overall_design: Smarca5 and Smarca1 DKO, Smarca1 KO and WT E13.5 cortical samples. All are forebrain whole tissue mRNA stranded libraries.

first: Gerardo

last: Zapata

first: David

middle: J

first: Keqin

last: Yan


title: Restored Hematopoietic Stem Cell Transcriptional Program in Fanconi Anemia Patients Following Gene Therapy

city: Pamplona

first: Miren

last: Lasaga

address: Av. de Pío XII, 55

country: Spain

institute: CIMA

summary: The effect of gene therapy in the Hematopoietic stem cells of patients with fanconi anemia has been analyzed. For this purpose 3 fanconi patients bone marrow and a healthy one has been aspirated and CD34+ cells sorted. The data was processed using the usual 10X protocol

overall_design:
Analysis of Hematopoietic Stem Cells after gene therapy in Fanconi Aneamia patients
Note from submitter: the raw sequencing files due to the privacy of patients.

last: Gomez-Cabrero

first: Juan

last: Bueren

first: Felipe

last: Prosper


title: The LARP1 homolog Slr1p controls the stability and expression of proto-5’TOP mRNAs in fission yeast

city: Aurora

first: Olivia

last: Rissland

state: CO

address: 12801 East 17th Ave

department: BMG

institute: University of Colorado Denver

summary: In vivo metabolic labelling of S. pombe RNA to measure transcriptome-wide mRNA half-lives

overall_design: 4SU labellig and RNA-Seq of WT and slr1- cells

first: Farnaz

last: Mansouri-Noori

first: Andreas

last: Pircher

first: Danielle

middle: Y

last: Bilodeau

first: Lidia

last: Siniavskaia

first: Jorg

last: Grigull

first: Mark

last: Bayfield


title: Myeloproliferative neoplasms show different signature in megakaryocyte-erythroid progenitors among different subtypes

first: Coral

last: Tong

address: 288 Nanjing Rd, Heping

institute: Institute of Hematology & Blood Disease Hospital

summary: In this study, we explored the transcriptome of megakaryocyte-erythroid progenitors (MEPs) in JAK2 V617F+ PV and ET and found distinctive gene expression patterns within MPN subtypes. The differentially expressed genes (DEGs) indicated that cellular processes and signaling pathways in MEPs from healthy donors (HDs, or NCs) are differentially modulated in PV and ET patients.

overall_design: Examination of gene expression in 2 different MPN subtypes as well as HDs (NCs) at MEP stage.

first: Jingyuan

first: Mankai

last: Ju

first: Lei

last: Zhang

first: Lihong

last: Shi


title: Normalization of Large Scale Transcriptome Data Using Heuristic Methods

city: Ramat Gan

first: Michael

last: Gurevich

address: Tel Hashomer

department: Multiple Sclerosis Center

institute: Sheba Medical Center

summary:
We introduce AI method for addressing batch effect of genetic data
The method does not rely on any assumptions regarding the distribution and the behavior of data elements. Hence, it does not introduce any new biases in the process of correcting for batch effect. It strictly maintains the integrity of measurements within the original batches.

overall_design: The human peripheral mononuclear blood cells (PBMC) samples from multiple sclerosis patients treated in Multiple Sclerosis Center, Sheba Medical Center, Israel were processed on Affymetrix HU-133A-2 microarrays (Santa Clara, CA) according to manufacturer protocol between 2006 and 2014 . A total 216 samples from 216 distinct individuals, combined from 24 batches associated with working sets consisting of more than seven samples of each were analyzed.

first: Arthur

last: Yosef

first: Eli

last: Shnaider

first: Moti

last: Schneider


title: Next Generation Sequencing to Study FLK-affected genes

city: Baltimore

first: HUA

last: LU

state: MD

address: 1000 Hilltop Circle

department: Biology

institute: University of Maryland Baltimore County

summary:
Purpose: The goals of this study are to compare RNA-seq profiles of Col-0, acd6-1, flk-1, flk-5, acd6-1flk-1, and acd6-1flk-5 to identify genes affected by FLK.
Methods: Total RNA was extracted from 25-d old plants. A total amount of 1 μg RNA per sample was used to generate cDNA libraries, using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Deep sequencing was performed using Illumina NovaSeq 6000 (Novogene Corporation Inc.). Triplicate biological samples were used for all genotypes except acd6-1flk-5, which had duplicate samples because one sample failed to pass quality control. The samples were multiplexed and sequenced with the standard paired-end sequencing that has a read length of 150bp per end and 20M reads per end per sample.
Results: We found that over 8000 genes are differentially affected by FLK based on the RNAseq analysis. GO analysis revealed that FLK-affected genes are enchriched for genes involved in primary metabolism and in response to abiotic and biotic stimuli.
Conclusions: The RNAseq analysis support a role of FLK in regulation of plant development and defense.

overall_design: 25-d old plants  were collected for RNA extraction followed by cDNA library preparation and high throughput.

first: Hua

last: Lu


title: ERCC6L2 mitigates replication stress and promotes centromere stability [Nascent_DNA_seq]

status: Public on Apr 10 2023

city: Oxford

first: Dragana

last: Ahel

state: Oxfordshire

address: South Parks Rd

department: Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

summary: Structurally complex genomic regions, such as centromeres, are inherently difficult to duplicate. The mechanism that underlies centromere inheritance is not well understood, and one of the key questions relates to the reassembly of centromeric chromatin following DNA replication. Here we define the SNF2 ATPase ERCC6L2 as a key regulator of this process. ERCC6L2 accumulates at centromeres and promotes efficient deposition of core centromeric factors. Our genomic analyses show that ERCC6L2 deficiency erodes centromeric chromatin, leading to unrestrained replication of centromeric DNA. We also establish that, beyond centromeres, ERCC6L2 facilitates replication at genomic repeats and non-canonical DNA structures. Notably, ERCC6L2 interacts with the major DNA replication factor PCNA through an atypical peptide, presented here as a co-crystal structure. Finally, we examine ERCC6L2 activities at DNA breaks, and show that it acts to restrict end resection independently of the 53BP1-REV7-Shieldin complex. Our observations allow us to propose a mechanistic model of ERCC6L2 activity, which reconciles its seemingly distinct functions in DNA repair and DNA replication. Together, these findings provide a new molecular context for studies linking ERCC6L2 to human disease.

overall_design: We used nascent DNA sequencing  to map relative positions of newly replicated DNA in ERCC6L2 proficient and ERCC6L2 deficient cells.


title: ERCC6L2 mitigates replication stress and promotes centromere stability

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

overall_design: Refer to individual Series


title: Zinc Transporter 8 Haploinsufficiency Protects Against Beta Cell Dysfunction in Type 1 Diabetes by Increasing Mitochondrial Respiration

first: Kristen

last: Wells

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

summary: Zinc transporter 8 (ZnT8) is a major humoral target in human type 1 diabetes (T1D). Polymorphic variants of Slc30A8, which encodes ZnT8, are also associated with protection from T2D, suggesting that ZnT8 might play a role beyond simply being a target of autoimmunity in the pathophysiology of T1D. To begin to investigate this possibility, we transferred a global Slc30a8 null allele to the well-established NOD mouse model of T1D. Unexpectedly, complete loss of ZnT8 accelerated spontaneous T1D, while heterozygosity was partially protective. In vivo and in vitro studies using ZnT8 mutants on a NOD.scid background suggested that the accelerated disease was due to more rampant autoimmunity. Conversely, beta cells in heterozygous animals uniquely displayed increased mitochondrial fitness under mild proinflammatory conditions. In pancreatic beta cells and immune cell populations, Zn2+ plays a key role as a regulator of redox signaling and as an independent secondary messenger. Importantly, Zn2+ also plays a major role in maintaining mitochondrial homeostasis. Our results suggest that regulating mitochondrial fitness by altering intra-islet zinc homeostasis may provide a novel mechanism to modulate T1D pathophysiology.

overall_design: RNA-seq of WT, ZnT8+/-, and ZnT8-/- islets with and without treatment of cytokines (6 total conditions).

first: Yong

last: Kim

first: Jay

last: Walters

first: Nicole

middle: D

last: Moss

first: Ryan

last: Sheridan

first: Jose

last: Miranda

first: Richard

last: Benninger

middle: M

last: O’Brien

first: Lori

last: Sussel

first: Howard

middle: W

last: Davidson


title: Astrocytic circadian clock control of energy expenditure by transcriptional stress responses in the ventromedial hypothalamus

city: Ciudad de México

first: Ricardo

last: Orozco-Solis

state: TLALPAN

address: Periférico Sur 4809, Arenal Tepepan

country: Mexico

institute: Instituto Nacional de Medicina Genomica

summary: Mice carrying a mutation which deletes Bmal1 in Gfap-expressing astrocytes, and control animals were fed either a standard diet or a high fat diet for 16 weeks. Conditional deletion of Bmal1 in Gfap cells decreased weight gain and increased energy expenditure under high fat diet, hence the transcriptome of Brown Adipose Tissue (BAT) and Ventromedial Hypothalamus (VMH) were obtained.

overall_design: Four experimental groups were studied: control mice fed standard diet, Gfap-Bmal1 cKO mice fed a standard diet, control mice fed a high fat diet and Gfap-Bmal1 cKO fed a high fat diet

first: Lucía

last: Mendoza-Viveros

first: Lorena

last: Aguilar-Arnal


title: Both Tamoxifen and Estradiol accelerate endothelial healing by targeting different sub-functions of ERa and distinct cell types in the arterial wall

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

country: France

institute: CNRS UMR 6290

summary:
Rationale: Tamoxifen prevents the recurrence of breast cancer and is also beneficial against bone demineralization and arterial diseases, as it acts as an Estrogen Receptor (ER) α antagonist in ER-positive breast cancers, whereas it mimics the protective action of 17β-estradiol (E2) in other tissues such as arteries. However, the mechanisms of these tissue-specific actions remain unclear.
Objective: Here we tested whether tamoxifen is able to accelerate endothelial healing and analyzed the underlying mechanisms.
Methods and Results: Using three complementary mouse models of carotid artery injury, we demonstrated that both tamoxifen and estradiol accelerated endothelial healing, but only tamoxifen required the presence of the underlying medial smooth muscle cells. Chronic treatment with E2 and tamoxifen elicited differential gene expression profiles in the carotid artery. The use of transgenic models mouse targeting either whole ERα in a cell-specific manner or ERα subfunctions (membrane/extra-nuclear versus genomic/transcriptional) demonstrated that E2-induced acceleration of endothelial healing is mediated by membrane ERα in endothelial cells, while the effect of tamoxifen is mediated by the nuclear actions of ERα in smooth muscle cells.
Conclusion: Whereas tamoxifen acts as an anti-estrogen and ERα antagonist in breast cancer, but also on the membrane ERα of endothelial cells, it accelerates endothelial healing through activation of nuclear ERα in smooth muscle cells, inviting to revisit the mechanisms of action of selective modulation of ERα.

overall_design: carotids arteries mRNA profiles of 3 weeks treated wild type mice with estradiol or tamoxifen, were generated by deep sequencing using  Illumina NovaSeq sequencer

first: Rana

last: Zahreddine

first: Morgane

last: Davezac

first: Natalia

last: Smirnova

first: Mélissa

last: Buscato

first: Emeline

last: Lhullier

first: Adrien

last: Lupieri

first: Romain

last: Solinhac

first: Alexia

last: Vinel

first: Daniel

last: Henrion

first: Marie-Ange

last: Renault

first: Alain-Pierre

last: Gadeau

first: Gilles

last: Flouriot

first: Françoise

last: Lenfant

first: Muriel

last: Laffargue

first: Jean-François

last: Arnal

first: Coralie

last: Fontaine


title: Multivalent vaccines demonstrate immunogenicity and protect against Coxiella burnetii aerosol challenge

city: Irvine

first: Sharon

last: Jan

address: 812 Medical Plaza Dr Rm 387 Med Surge II

department: Physiology & Biophysics

institute: UC Irvine

summary: C57BL/6 mice were immunized with Coxiella burnetii vaccine Q-VAX (Seqirus) and monitored for up to 83 days post immunization. Two different routes of immunization were observed - subcutaneous and intramuscular. Subcutaneously immunized animals were boosted on day 67.

overall_design: This study follows mice immunized with Q-VAX over the course of 83 days. Plasma from immunized animals were compared to naïve animals from day 0. There were 5 replicates for each route of immunization.

first: Alycia

last: Fratzke

first: Jiin

last: Felgner

first: Jenny

middle: E

last: Hernandez-Davies

first: Li

last: Liang

first: Rie

last: Nakajima

first: Algimantas

last: Jasinskas

first: Medalyn

last: Supnet

first: Aarti

last: Jain

first: Philip

first: D

middle: H

last: Davies

first: Anthony

last: Gregory


title: Blood transcriptome of Rasa Aragonesa rams with different sexual behavior phenotype reveals CRYL1 and SORCS2 as genes associated to this trait

city: Zaragoza

first: Kenza

last: Lakhssassi

state: Zaragoza

address: Av Montañana, 930,

institute: CITA

summary:
To understand the mechanisms of sexual behaviour in rams, transcriptomic sequencing technology was used to identify differentially expressed genes in peripheral blood
We then performed gene expression profiling analysis using data obtained from blood in rams with different sexual behaviours, intending to identify in vivo sexual behaviour biomarkers

overall_design:
Blood transcriptome of 12 Rasa Aragonesa rams (6 sexually active (A) and 6 not active (NA) for each tissue) were generated by Novaseq 6000 platform
EdgeR software was used to detect DEGs between active A and NA rams
Three genes identified to be differentially expressed in the blood by RNA-Seq were chosen for RT-qPCR validation

first: Jorge

last: Lacosta


title: Dual genetic lineage tracing reveals functional neuromesodermal progenitors

city: Shanghai

first: zixin

last: liu

address: 320 Yueyang road, Life Science Research Building A2112

institute: Center for Excellence in Molecular Cell Science

summary: In the past decades, the paradigm of three germ layers formed by gastrulation has been modified by data suggesting an existence of neuromesodermal progenitors (NMPs) that arise during gastrulation and contribute to both spinal cord and adjacent paraxial mesoderm1-5. However, there lacks direct genetic lineage tracing evidence and functional assessment of NMPs in vivo. Here, we develop a dual recombinases-mediated genetic system to specifically trace and genetically ablate Brachyury+Sox2+ NMPs. Genetic lineage tracing results and single-cell RNA sequencing analysis show that NMPs contain three distinct uni-potent and bi-potent progenitor populations for progressive differentiation into neural and mesodermal fates. Genetic ablation of NMPs by diphtheria toxin reveals a critical role of NMPs in tail formation. This study provides in vivo genetic evidence for heterogeneity of NMPs in their cell fate determination and their functional role in developing embryos.

overall_design: caudal tissue of C57BL/6J mice were isolated and analyzed using scRNAseq.

first: Hengwei

last: Jin

first: Zixin

last: Liu

first: Jialing

last: Mou

first: Muxue

last: Tang

first: Xiuzhen

last: Huang

first: Kuo

first: Qianyu

last: Zhang

first: Kathy

middle: O

last: Lui

first: Bin

last: Zhou


title: Plant recognition by Trichoderma harzianum elicits upregulation of a novel secondary metabolite cluster required for colonization

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

summary: The plant recognition specific PCA cluster mediates early chemical communication between plant and fungus, is required for colonization and it is likely responsible for the high potential of T. harzianum and closely related species for biocontrol applications.

overall_design: Strains of this study were grown on plates with Mandels Andreotti Minimal Medium containing 0.1 % w/v glucose as  carbon source

first: Guofen

last: Li

first: Miriam

last: Schalamun


title: Excessive R-loop-induced mitochondrial-dependent epithelial cell necroptosis drives spontaneous intestinal inflammation

city: Beijing

first: Yang

last: Xu

address: Beijing HaiDian District, Mingyuanxilu No.2

institute: China Agricultural University

summary: Inflammatory bowel disease (IBD), including ulcerative colitis and Crohn’s disease are chronic inflammatory disorders which mainly featured by damage of epithelial

overall_design: Intestinal epithelium mRNA profiles of 8-week-old wild type (WT) and Tdp-43 conditional knockout mice

first: Guilin

first: Xu

last: Yang

first: Zhengquan

last: Yu


title: NAMPT-dependent NAD+ biosynthesis controls circadian metabolism in a tissue-specific manner

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Molecular clocks in the periphery coordinate tissue-specific daily biorhythms by integrating input from the hypothalamic master clock and intracellular metabolic signals. One such key metabolic signal is the cellular concentration of NAD+, which oscillates along with its biosynthetic enzyme, nicotinamide phosphoribosyltransferase (NAMPT). NAD+ levels feed back into the clock to influence rhythmicity of biological functions, yet whether this metabolic fine-tuning occurs ubiquitously across cell types and is a core clock feature is unknown. Here we show that NAMPT-dependent control over the molecular clock varies substantially between tissues. Brown adipose tissue (BAT) requires NAMPT to sustain the amplitude of the core clock, whereas rhythmicity in white adipose tissue (WAT) is only moderately dependent on NAD+ biosynthesis and the skeletal muscle clock is completely refractory to loss of NAMPT. In BAT and WAT, NAMPT differentially orchestrates oscillation of clock-controlled gene networks and the diurnality of metabolite levels. NAMPT coordinates the rhythmicity of TCA cycle intermediates in BAT, but not WAT, and loss of NAD+ abolishes these oscillations similarly to high fat diet (HFD)-induced circadian disruption. Adipose NAMPT depletion also improved the ability of animals to defend body temperature during cold stress but this is independent of time-of-day. Thus, our findings reveal that peripheral molecular clocks and metabolic biorhythms are shaped in a highly tissue-specific manner by NAMPT-dependent NAD+ synthesis.

overall_design: Circadian comparative gene expression profiling analysis of RNA-seq data for wildtype and fat-specific Nampt knockout mice.

first: Astrid

last: Basse

first: Karen

middle: N

last: Nielsen

first: Iuliia

last: Karavaeva

middle: R

first: Tao

last: Ma

first: Jesper

last: Havelund

first: Thomas

first: Mikkel

last: Frost

first: Julia

last: Peics

first: Emilie

last: Dalbram

first: Morten

last: Dall

first: Juleen

last: Zierath

first: Romain

last: Barrès

first: Nils

last: Færgeman

first: Jonas

middle: T

last: Treebak

first: Zachary

last: Gerhart-Hines


title: Ixekizumab treatment of patients with moderate-to-severe plaque psoriasis.

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Objectives: To asses skin clearance and patient-reported outcomes for ixekizumab treatment. Methods: IXORA-R enrolled adults with moderate-to-severe plaque psoriasis, defined as static Physician’s Global Assessment ≥ 3, PASI ≥ 12 and involved body surface area ≥ 10%. The trial was registered with ClinicalTrials.gov (NCT03573323).

overall_design: Eligible patients were ≥ 18 years old with chronic plaque psoriasis with a static Physician’s Global Assessment of Disease (sPGA) score of ≥ 3 (moderate), a Psoriasis Area and Severity Index (PASI) ≥ 12, and ≥ 10% body surface area involvement at screening and baseline. Psoriatic plaque skin samples were collected at baseline, week 1, week2, and week 4 after ixekizumab treatment initiation.

middle: A

first: Neil

last: Mckenna


title: An integrative multiomics framework for identification of therapeutic targets in pulmonary fibrosis [CB1R KO]

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg

summary: Pulmonary fibrosis (PF) is a progressive disease with a poor prognosis and lack of effective treatments. Therefore, identifying effective therapeutic modalities is required to improve outcome. However, the lack of predictive progressive disease biomarkers in the clinic causes a significant gap in the preclinical to clinical translational process. Here, we assessed and identified progressive alterations in pulmonary function, transcriptomics, and metabolomics in mice lungs at 7, 14, 21, and 28 days after a single dose of oropharyngeal bleomycin. By integrating multi-omics data, we identified two central gene subnetworks associated with multiple critical pathological changes in transcriptomics and metabolomics as well as pulmonary function. We presented a multi-omics-based framework to establish a translational link between the bleomycin-induced PF model in mice and human idiopathic pulmonary fibrosis to identify druggable targets and test therapeutic candidates. Our study also indicated peripheral CB1R antagonism as a rational therapeutic target for clinical translation in PF.

overall_design: We measured Pulmonary Function Tests and performed genome-wide transcriptomics analysis on lung tissue obtained from control, fibrotic, and CB1R Knockout fibrotic lungs at 14 days post bleomycin.

first: Abhishek

last: Basu

first: Kaelin

last: Wolf

first: Park

last: Joshua K.

first: Lenny

last: Pommerolle

first: Madeline

last: Beehee

first: Bernadette

last: Gochuico

first: Resat

last: Cinar


title: Duf89 abets lncRNA control of fission yeast phosphate homeostasis via its antagonism of precocious lncRNA transcription termination

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: This RNA-Seq analysis compares gene expression of the Duf89 null mutant (duf89∆) contrasting to the WT in the fission yeast S. pombe

overall_design: 1 test sample (mutant) was analyzed; 1 WT control sample, sequenced at the same time, was previously deposited in GEO dataset GSE131237 (each sample has 3 replicate experiments)

first: Ana

last: Sanchez

first: Stewart

last: Shuman

first: Beate

last: Schwer


title: N6-Methyladenosine modification of mRNA regulates the transition from 2D to 3D growth in the moss Physcomitrium patens [MeRIP-seq]

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

institute: School of Chemistry, UNAM

summary: In this study, we identified the main genes of the m6A methyltransferase complex (MTC) in P. patens and we demonstrate that their inactivation by genome editing leads to loss of m6A presence in mRNA and results in defects in the moss life cycle. We detected a delay in the formation of gametophore buds, affecting the transition from 2D to 3D growth and subsequent gametophore formation in all MTC mutant plants. We also observed a defect in spore development, with mutant lines producing reduced-size spores that completely failed to germinate. We performed a genome-wide analysis that revealed several transcripts being affected in the Ppmta background. In addition, we demonstrate that the PpAPB1-4 transcripts, known to be central factors regulating the 2D to 3D transition, are m6A-modified, while in the Ppmta mutant the lack of the m6A mark is associated with a corresponding decrease in their transcript accumulation.

overall_design: A single replicate of poly-A+ RNA was generated from wild type P. patens plants and subjected to m6A immunoprecipitation followed by high throughput sequencing.

first: David

last: Garcias-Morales

first: V

first: Florence

last: Charlot

first: Fabien

last: Nogué

first: Alejandra

last: Covarrubias

first: Jose

last: Reyes


title: Bacteroides fragilis toxin induces epithelial-to-mesenchymal transition and stem-like phenotype in breast epithelial cells and concomitantly activates Notch and βcatenin axes

first: Dipali

last: Sharma

state: Maryland

address: 1550 Orleans Street

department: School of Medicine

institute: The Johns Hopkins University

summary: Aided by deep sequencing techniques, recent studies suggest the existence of distinct breast microbiota and a shift in microbial community composition in diseased breast compared to normal breast. However, their functional impact and underlying mechanisms are unknown. Present study examines the contribution of pro-carcinogenic bacteria in breast cancer initiation, growth and progression. Extensive data mining and metagenomic analyses of existing datasets revealed the presence of toxin producing Bacteriodes fragilis in malignant breast. B. fragilis is a pro-carcinogenic bacterium known for its potential to initiate and promote colon cancer; its pathogenicity has been attributed to its unique toxin ‘BFT’. About 35% of human population asymptomatically harbor ETBF colonization in the gut. Mice with enteric B fragilis infection exhibited a significant amount of circulating BFT and distinct morphological alterations in mammary gland similar to focal hyperplasia. Histological analysis revealed inflammation, fibrosis, breast duct thickening and hyperproliferation of breast epithelial cells. In vitro, upon treatment with BFT, prominent cytoskeletal reorganization, significant increase in migration and invasion potential and decreased adhesion of MCF10A and MCF7 cells were observed along with molecular markers of epithelial-to-mesenchymal transition. Decreased expression of epithelial marker, E-cadherin along with elevated levels of mesenchymal markers, N-cadherin and vimentin were observed. BFT also increased the expression of EMT-related transcription factors, Snail, Slug and Twist. BFT-treated cells attained stem cell-like phenotype exhibiting an increased ability to form secondary and tertiary mammospheres. Mechanistic studies showed that BFT induced expression and nuclear translocation of NICD and β-catenin resulting in activation of downstream targets. Inhibition of Notch1 and β-catenin using γ-secretase and β-catenin inhibitors successfully inhibited functional effects of BFT. Mammary gland implantation and in vivo limiting dilution assays were utilized to corroborate the in vitro findings. BFT-pretreated MCF7 cells exhibit increased tumor growth and form multifocal tumors in mice. In vivo limiting dilution assay using breast tumors from BFT-pretreated MCF7 cells exhibited a striking increase in tumor-initiating cells. Follow-up analyses of these tumors demonstrated increased migratory, invasive, and -mammospheres-forming behavior confirming that brief BFT exposure elicits long-term molecular changes. Altered expression of stemness markers was also confirmed by RNA sequencing.

overall_design: MCF7 cells were seeded in 10% serum supplemented DMEM media and allowed to grow for 24 hours. Cells were then treated with 100 ng/ml of BFT in 2% serum supplemented DMEM. Medium in the control group was changed to 2% serum supplemented DMEM. 3 days post tretment, cells were harvested in 0.25% trypsin/EDTA, neutralized with 10% FBS supplemented DMEM and centrifuged. Pellets were resuspended in serum free media and equal volume of matrigel was added to the cell suspension. 5 million cells were implanted on to the 4th mammary fat pad of SCID-NOD mice on either side with E2 supplementation. Tumors were allowed to grow for 8 weeks and monitored after which tumors were resected. The resecetd tumors were dissociated and tumor cells were isolated and subjected to in vivo limiting dilution; cells ranging from 5000 to 500000 were implanted in different mammary fat pads of SCID-NOD mice and tumors were allowed to grow. At the end of 8 weeks, resulting tumors were resected and RNA sequencing was performed. RNA sequencing was also performed on parental cells (MCF7 cells treated with 100ng/ml of BFT in vitro as described earlier).  There were 16 samples in total, comprising biological replicates for 4 sample classes, including untreated controls.

first: Sheetal

last: Parida

first: Conover

last: Talbot Jr

first: Haiping

last: Hao


title: Next Generation Sequencing Analysis of the single-cell Transcriptomes of the K562-Cas9 cell infected with lentiviral sgRNA library containing programmed scaffold RNA

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

summary: By performing RNA sequencing (RNA-seq) analysis on the K562-Cas9 cells which infected with genome-scale lentiviral sgRNA library, we want to investigate whether our strategy can be applied in CRISPR screen with single cell transcriptomic readout. RNA-seq analysis showed that we can capture the scaffold RNA together with the endogenous mRNA  precisely. The gene expression profile after genome perturbation can be easily identified together with the perturbation information in single experiment.We performed Single cell RNA-Seq by Smart-seq2/C1 platform for 73 cells. The gRNA scaffold was not detected in five cells, the numbers for these cells are NKC1.8, NKC1.11, NKC1.12, NKC1.27 and NKC1.37.

overall_design: Our framework offered strategies that can be conveniently applied to study the genotype and mRNA profiles after CRISPR-mediated genome perturbation with single-cell transcriptional  readout

first: Qingkai

last: Song

first: Ke

last: Ni

first: Min

last: Liu


title: Sex-Specific Effects of Early-Life Iron Deficiency and Prenatal Choline Treatment on Adult Rat Hippocampal Transcriptome

city: Minneapolis

first: Phu

middle: V

last: Tran

state: MN

address: 516 Delaware St., SE

department: Department of Pediatrics

institute: University of Minnesota

summary: Fetal-neonatal iron deficiency (ID) causes long-term and sex specific neurocognitive and affective dysfunctions. This study aims to illustrate sex- specific transcriptome alterations in adult rat hippocampus induced by fetal-neonatal ID and prenatal choline treatment.

overall_design: Hippocampi were collected from 16 female rats at postnatal day 65 (P65) and analyzed for changes in gene expression. Rats were fed one of the following diets: iron suficient (IS), iron suficient with choline supplementation (ISch), iron deficient (ID) or iron deficient with choline supplementation (IDch). There were 4 biological replicates per treatment. The same experimental design was applied separatedly to 16 male rats.

first: Shirelle

middle: X

first: Tenille

middle: K

last: Fredrickson

first: Natalia

last: Calixto Mancipe

first: Michael

last: Georgieff


title: ERCC6L2 mitigates replication stress and promotes centromere stability [ChIP-seq]

first: Dragana

last: Ahel

institute: University of Oxford

summary: Structurally complex genomic regions, such as centromeres, are inherently difficult to duplicate. The mechanism that underlies centromere inheritance is not well understood, and one of the key questions relates to the reassembly of centromeric chromatin following DNA replication. Here we define the SNF2 ATPase ERCC6L2 as a key regulator of this process. ERCC6L2 accumulates at centromeres and promotes efficient deposition of core centromeric factors. Our genomic analyses show that ERCC6L2 deficiency erodes centromeric chromatin, leading to unrestrained replication of centromeric DNA. We also establish that, beyond centromeres, ERCC6L2 facilitates replication at genomic repeats and non-canonical DNA structures. Notably, ERCC6L2 interacts with the major DNA replication factor PCNA through an atypical peptide, presented here as a co-crystal structure. Finally, we examine ERCC6L2 activities at DNA breaks, and show that it acts to restrict end resection independently of the 53BP1-REV7-Shieldin complex. Our observations allow us to propose a mechanistic model of ERCC6L2 activity, which reconciles its seemingly distinct functions in DNA repair and DNA replication. Together, these findings provide a new molecular context for studies linking ERCC6L2 to human disease.

overall_design: We used chromatin immunoprecipitation DNA sequencing (ChIP-seq)  to map relative positions of CENP-B in ERCC6L2 proficient and ERCC6L2 deficient cells


title: The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees

city: Chicago

first: Yoav

last: Gilad

state: IL

department: Genetic Medicine

institute: University of Chicago

summary: We used embryoid bodies to compare differences in gene expression between humans and chimpanzees in a large number of cell types

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design:
Single cell RNA-sequencing of human and chimpanzee embryoid bodies. We generated embryoid bodies from 3-6 human and 3 chimpanzee inividuals in three replicates. For each replicate, embryoid bodies from both species were dissociated and pooled prior to collecting ~40,000-60,000 cells with 10x scRNA-seq.

Single cell RNA-sequencing of human/chimpanzee tetraploid hybrid embryoid bodies. We generated embryoid bodies from one hybrid inividuals in three replicates. For each replicate, we collected ~20,000 cells and performed 10x 3' scRNA-seq v3.1.

first: Kenneth

last: Barr

first: Katie

last: Rhodes


title: Gene expression profiles of peripheral blood mononuclear cells before abatacept treatment in rheumatoid arthritis patients.

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

institute: Chiba University

summary: To explore markers which predict the efficacy of abatacept in rheumatoid arthritis, peripheral blood mononuclear cells were obtained before abatacept treatment.

overall_design: 30 rheumatoid arthritis patients receiving abatacept were participated in the study. Blood samples were obtained before the initiation of abatacept treatment. Density-gradient separeted peripheral blood mononuclear cells were subjected the DNA microarray analyses.

first: Hiroshi

last: Nakajima


title: Oncogenic RAD21 Amplification Suppresses Interferon Signalling to Promote Immune Evasion in Ovarian Cancer

city: Guangzhou

first: Peng

last: Deng

address: Panyu

institute: SYSUCC

summary: Ovarian cancer (OV) is the leading cause of mortality from gynaecological malignancies with poor prognosis and limited therapeutic options. Prevalent copy number alteration (CNA) is a genetic characteristic of OV, but its contribution to tumorigenesis remain unclear. Here, we identify RAD21, a component of the cohesin complex, as a frequently amplified and overexpressed oncogene in high grade serous ovarian cancer (HGSOC), the most common subtype of OV. RAD21 copy number amplification and overexpression are correlated with poor prognosis in HGSOC. In HGSOC cells and xenograft models, depletion of RAD21 inhibited cell proliferation by inducing mitotic phase arrest and thereby reducing tumour growth, whereas overexpression of RAD21 conferred resistance to carboplatin. Mechanistically, we found that RAD21 interacts with YAP/TEAD4 transcriptional co-repressors and recruits NuRD complex to suppress the downstream targets. Additionally, genetic and pharmacologic inhibition of YAP disrupts the co-repressor complex to suppress the oncogenic activity of RAD21 and recapitulates the phenotypes of RAD21 depletion in HGSOC. Therefore, our work sheds light on the oncogenic role of frequent CNAs and identifies a previously unrecognized role of RAD21/YAP complex which contributes to tumorigenesis and chemo-resistance in HGSOC.

overall_design: 1.RNA-seq for OVCAR8 cells upon knock-down of TEAD4. 2. ChIP-seq for TEAD4.

first: Shini

first: Jing

last: Tan


title: Podocyte injury in Fabry nephropathy

city: Hamburg

first: Nicola

last: Wanner

address: Martinistr

institute: UKE Hamburg-Eppendorf

summary: Current therapies for Fabry disease are based on reversing intra-cellular accumulation of globotriaosylceramide (Gb3) by enzyme replacement (ERT) or chaperone mediated stabilization, thereby alleviating lysosome dysfunction. However, the therapeutic effect in the regression of end-organ damage (ie. kidney damage) is limited. Ultrastructural analysis of serial human kidney biopsies showed that long-term use of ERT reduced Gb3 accumulation in podocytes but did not alter podocyte injury. A novel CRISPR-/CAS9-mediated -Galactosidase knockout podocyte cell line confirmed ERT-mediated reversal of Gb3 accumulation without resolution of lysosomal dysfunction. Transcriptomic-based connectivity mapping and SILAC-based quantitative proteomics identified alpha-synuclein (SNCA) accumulation as a key event mediating podocyte injury.

overall_design: Bulk RNA sequencing of CRISPR/CAS9 GLA KO

first: Ahmed

last: Abed

first: Fabian

last: Braun

first: Dominik

last: Sellung

first: Victor

middle: G

last: Puelles

first: Christoph

last: Schell

first: Tobias

middle: B

last: Huber


title: Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [ATAC-seq]

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

institute: Research Institute of Molecular Pathology (IMP)

summary:
The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. This means that, in the hand segment, the permissive chromatin state of the hand homeoprotein gene HoxA13 engages with regeneration regulatory elements, bypassing the upper limb program.
Profiling chromatin accessibility (ACRs) of Axoltol limb connective tissue cells, and compare among developmental limb buds, and mature limb at different segments and regeneration time points.

overall_design: We performed ACR profiling analysis using data obtained from ATAC-seq libraries of developmental limb buds (stage 40/41, stage 46 proximal and distal parts), and mature limb at different segments (mature UA vs LA vs hand). Therefore, we also performed libraries from the mature arm and 5, 9, 13 dpa (13 dpa blastema data have two different positions like proximal and distal parts) regenerating arm blastema.

first: Akane

last: Kawaguchi

first: Dunja

last: Knapp

first: Prayag

last: Murawala

first: Sergej

last: Nowoshilow

first: Wouter

last: Masselink

first: Yuka

last: Taniguchi-Sugiura

first: Jifeng

last: Fei

first: Elly


title: Epithelial dysfunction is prevented by IL-22 treatment in a Citrobacter rodentium-induced colitis model that shares similarities with Inflammatory Bowel Disease

city: Cambridge

first: Radhika

last: Goenka

state: MA

address: 200 Sidney St.

institute: Abbvie

summary: We unveiled the disease relevance of the C. rodentium induced colitis model to IBD and demonstrated the protective role of the mucosal healing therapy IL-22.Fc in ameliorating the epithelial dysfunction

overall_design:
10x scRNA-seq of Citrobacter rodentium infected FVB mice with or without treatment with IL22.Fc, as well as naïve non-infected FVB mice as controls
The HTO data has not been used for any analysis and is not included.

first: Jesus

last: Paez-Cortez

first: Yingtao

last: Bi


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and OsWRKY65-overexpression transgenic Transcriptomes

status: Public on Apr 09 2023

city: Jeonju-si

first: Sang ryeol

last: Park

state: Jeollabuk-do

address: 370, Nongsaengmyeong-ro, Deokjin-gu

country: South Korea

institute: Rural Development Administration

summary: The revolutionary next-generation sequencing (NGS) analysis has opened a new era of analyzing signaling pathways. This study aims to elucidate the correlation of genes involved with WRKY65. The transcriptome analysis was performed in 2-week-old OsWRKY65-overexpression plants and wild-type (WT) through transcriptome deep sequencing (RNAseq). Differentially expressed genes (DEGs) were analyzed by filtering through fold change (FC) greater than or equal to 2 and P-value less than 0.05. Applying these criteria, Over 1,000 DEGs were analyzed in the OsWRKY65-overexpression plant compared to WT. Interestingly, some DEGs were analyzed as phytohormone-related genes. This result indicated that the OsWRKY65 might have a role in the phytohormone signaling pathway. As the OsWRKY65 is one of the WRKY superfamily, we analyzed the FC of the WRKY family. Among the family, few genes showed DEGs, and these results indicated that OsWRKY65 might involve in the phytohormone pathway and related to WRKY transcription factor.

overall_design: mRNA expression profiles of the WT and OsWRKY65-2 by Illumina NovaSeq 6000.

first: Sangryeol

first: Seungmin

last: Son

first: Giha

last: Song


title: Effect of Omomyc on lymph node metastases from melanomas [SkMel147]

city: Barcelona

first: Mariano

middle: F

last: Zacarias-Fluck

address: Natzaret, 115-117

department: Preclinical and Translational Research Program

institute: Vall d'Hebron Institute of Oncology (VHIO)

summary:
Skin melanomas are highly aggressive and metastatic. Omomyc is the best MYC inhibitor currently available. We analysed the effect of Omomyc expression in a transgenic and inducible (upon Doxycycline addition) manner in spontaneous lymph node metastases from SkMel147 (mutated in NRAS) melanoma cells in vivo.
We used microarrays to detail the change in the gene expression programs induced by Omomyc on day 2.

overall_design: Melanomas from vehicle- or doxycycline-treated mice were excised, RNA extracted and hybridized on Affymetrix microarrays.

first: Laura

last: Soucek


title: Effect of Omomyc on the in vivo growth of melanomas [SkMel147]

summary:
Skin melanomas are highly aggressive and metastatic. Omomyc is the best MYC inhibitor currently available. We analysed the effect of Omomyc expression in a transgenic and inducible (upon Doxycycline addition) manner in melanoma cells in vivo in two different melanoma cell lines: A375 (mutated in BRAF), SkMel147 (mutated in NRAS).
We used microarrays to detail the change in the gene expression programs induced by Omomyc on day 7.


title: Oncogenic RAD21 Amplification Coordinates with YAP/TEAD Transcriptional Co-Repressor Complex to Drive Tumorigenesis in High Grade Serous Ovarian Cancer

first: Peng

last: Deng

overall_design: 1. Chromatin immunoprecipitation sequencing (ChIP-Seq) for H3K27ac and RAD21  or Input was performed in OVCAR8 cells. 2.RNA-seq for OVCAR8 cells upon knock-down of RAD21 or YAP.

first: Shini

last: Liu

first: Jing

last: Tan


title: Expression profile of knockout Mettl3 in CD4+ T cells with Imiquimod induced psoriasis mouse model

city: Xianmen

first: Yuchen

address: Xiangan South Road

institute: Xianmen University

summary: In the psoriasis mouse model, depletion of the RNA N6-methylase, Mettl3, from CD4+ T cells inhibits  psoriasis-like phenotype and inflammation.

overall_design: To isolate CD4+ T cells, mouse dorsal skin was excised and the fat layer was removed using a surgical scalpel. The skin tissue was treated with dispase II (2.5 mg/ml) in Hank’s Balanced Salt Solution for 60 min at 37 °C. The dermal fraction was collected by scraping and then cut into small pieces. Dermal single-cell suspensions were obtained after collagenase IV (1 mg/ml) treatment for 2 h at 37 °C, followed by filtering and centrifugation. Samples were stained for 30 min on ice. The following antibodies were used: anti-CD4-PE (100408, Biolegend) and anti-CD45-FITC (103108, Biolegend).

first: Tao

last: Huang

first: Shijun

last: Chen

first: Liyan

last: Yuan


title: Effect of Omomyc on the in vivo growth of melanomas


title: Effect of Omomyc on the in vitro growth of A375 human melanoma cell line

summary:
Skin melanomas are highly aggressive and metastatic. Omomyc is the best MYC inhibitor currently available. We analysed the effect of Omomyc expression in a transgenic and inducible (upon Doxycycline addition) manner in melanoma cells in vitro in A375 (mutated in BRAF) melanoma cell line.
We used microarrays to detail the change in the gene expression programs induced by Omomyc on day 4.

overall_design: Control or doxycycline-treated A375 cells were frozen on day 4, RNA extracted and hybridized on Affymetrix microarrays.


title: Deoxyshikonin-induced chromatin accesibility changes in porcine intestinal epithelial cells

last: Wang

address: Shuguanghuayuan middle road #9, Haidian district

department: Institute of Animal Husbandry and Veterinary Medicine

institute: Beijing Academy of Agriculture and Forestry Sciences

summary: The objectives of this study is to evaluate the chromatin accesibility changes after deoxyshikonin stimulation in porcine intestinal epithelial cells.

overall_design: Assay for Transpotase-Accessible Chromatin using sequencing (ATAC-seq)  for deoxyshikonin-stimulated porcine intestinal epithelial cells.


title: Transcriptomic profile of CD8+ circulating tumor-reactive lymphocytes (CTRL) isolated by MHC multimers

city: Evanston

first: Zongjie

state: Illinois

address: Silverman Hall - Room 4578, 2170 Campus Dr

department: Biomedical Engineering

country: USA

institute: Northwestern University

summary: Circulating tumor-reactive lymphocytes (CTRL) present in blood circulation at a very low frequency. We efficiently isolated them based on high-performance microfluidics and MHC multimer binding assay. Using an ultra-low input bulk RNAseq workflow, we systematically characterize the transcriptomic profile of tumor-reactive lymphocytes and identified novel biomarkers for multimer-free isolation. Two animal models were studied - B16 melanoma model and CT-26 colon cancer model.

overall_design: CD8+ lymphocytes in PBMC were isolated based on their binding against tumor-reactive multimers. Isolated subpopulations were sequenced. Differentially expressed genes were compared.

first: Shana

last: Kelley


title: RNA-seq results of the kidney of male kidney-specific G9a knockout mice after acute kidney injured

city: WuHan

first: Dong

last: Yang

address: No.5  HangKong Road

institute: Huazhong University of Science and Technology

summary: To understand key pathways and regulatory genes in male Kidney-specific G9a knockout mice after renal ischemia reperfusion

overall_design: Male kidney-specific G9a knockout mice and their age matched WT mice were treated with renal ischemia reperfusion. For each experimental group, two biological replicates of RNA samples were sent for RNA-seq. Each sample consists of a pool of RNAs extracted from kidney of 3 different mice.

first: Kun

first: Ling

last: Zheng


title: RNA-sequencing analysis of Nrf2 target genes in rat pulmonary arterial smooth muscle cells and endothelial cells

status: Public on Apr 08 2023

city: 咸阳

first: yangfan

last: jia

state: 陕西

address: 中国陕西省杨凌区

institute: 西北农林科技大学

summary: To investigate the genes regulated by Nrf2 in rat PASMC and PAEC, Nrf2 was knockdown by using siRNA. 48h after siRNA transfection， cells were collected for RNA-sequencing.

overall_design: Each treatment contains 3 biological replicates.

first: Ang

last: Luo

first: Haiyang

last: Tang

first: Yangfan

last: Jia


title: H4S47 O-GlcNAcylation regulates the activation of mammalian replication origins

city: Chaoyang

first: Liting

last: Lan

state: Beijing

address: Datun 15 Road

department: Institute of biophysics

institute: University of Chinese Academy of Sciences

summary: The transmission and maintenance of genetic information in eukaryotic cells rely on the faithful duplication of the entire genome. In each round of division, excessive replication origiNS are licensed, while only a fraction is activated to give rise to bi-directional replication forks travelling in the context of chromatin. However, it remaiNS elusive how eukaryotic replication origiNS are selectively activated. Here we demoNStrate that O-GlcNAc traNSferase (OGT) enhances replication initiation by catalysing H4S47 O-GlcNAcylation. Mutation of H4S47 impairs DBF4-dependent protein kinase (DDK) recruitment on chromatin, causing compromised phosphorylation of replicative helicase mini-chromosome maintenance (MCM) complex. Meanwhile, our short nascent-strand sequencing (SNS-seq) confirms the important role of H4S47 O-GlcNAcylation in origin activation. Together, H4S47 O-GlcNAcylation directs origin activation through facilitating MCM phosphorylation, and this may shed light on the spatial and temporal control of DNA replication by the dynamically changing chromatin environment.

overall_design: Analysis active replication origins in HEK293T cells expressing H4WT or H4S47A.

first: Yingying

last: zou

first: Jiayao

last: Pei

first: Haizhen

last: Long

first: Yunpeng

last: Feng


title: SENP3 and USP7 regulate Polycomb-rixosome interactions and silencing functions(ChIP-seq)

city: boston

first: Danesh

last: Moazed

address: 240 longwood avenue

department: cell biology

institute: Harvard medical school

summary: SENP3 deSUMOylates Rixosome and USP7 deubiquitylates PRC. This can protect Rixosome and PRC1 from displacement from chromatin

overall_design: ChIP-seq analysis of histone modifications and chromatin associated proteins

first: Haining

last: Zhou


title: SENP3 and USP7 regulate Polycomb-rixosome interactions and silencing functions

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

overall_design: Refer to individual Series


title: Deacetylation of Sirt2 regulates PKM2 ubiquitination and its effect on liver glucose metabolism

city: Beijing

first: Shuang

last: Li

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

summary: In order to explore the effects of SIRT2 on the liver metabolic function of mice under metabolic stress, we constructed SIRT2 knockout mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype and SIRT2 KO mice.

first: Junshu

last: Nie

first: Jingru

last: Guo

first: Bin

last: Xu


title: Hypothalamic and dorsal vagal glucose-dependent insulinotropic polypeptide receptor (GIPR) neurons employ distinct mechanisms to affect feeding

status: Public on Apr 07 2023

city: London

first: Alice

last: Adriaenssens

address: Room 420, Rockefeller Building, 21 University Street

institute: University College London

summary: Central glucose-dependent insulinotropic polypeptide (GIP) receptor (GIPR) signalling is critical for GIP-based therapeutics to lower body weight, but pathways leveraged by GIPR agonism pharmacology in the brain remain incompletely understood. We explored the role of Gipr neurons in the hypothalamus and dorsal vagal complex (DVC)—brain regions critical to the control of energy balance. Hypothalamic expression of Gipr expression was not necessary for the synergistic effect of GIPR/ agonism combined with GLP-1R co-agonism on body weight. While chemogenetic stimulation of both hypothalamic and DVC Gipr neurons suppressed food intake, activation of DVC Gipr neurons reduced ambulatory activity and induced conditioned taste avoidance, while there was no effect of a short-acting GIPR agonist (SAGIPRA). Within the DVC, Gipr neurons of the nucleus tractus solitarius (NTS), but not the area postrema (AP), projected to the parabrachial nucleus and paraventricular hypothalamic nucleusdistal brain regions. ScRNAseq and FISH analysis showed that Gipr neurons in the NTS and AP Gipr neurons were transcriptomically distinct. Peripherally-dosed fluorescent GIPR agonists (GIPRAs) revealed that GIPRA access was restricted to circumventricular organs in the CNS. Together tThese data demonstrate that while the hypothalamus, AP and NTS are key sites for Gipr expression, these subpopulations of Gipr neurons in the hypothalamus, AP and NTS differ in their connectivity, transcriptomic profile, peripheral accessibility to peripherally administered GIPRAs, and the appetite controlling pathways they employ. These results highlight the heterogeneity of the central GIPR signalling axis, and suggest that studies aimed at understandinginto the effects of GIP pharmacology on feeding behaviour should consider the interplay of multiple regulatory pathways.

overall_design: Gipr- or Glp1r-expressing cells were isolated from the hindbrain of either GiprEYFP or Glp1rEYFP mice, respectively, by Fluorescence-activated cell sorting (FACS) according to the presence or absence of EYFP signal and analyzed using scRNAseq.


title: Cell-generated forces contribute to bottleneck during somatic cell reprogramming

city: Irvine

first: Timothy

last: Downing

state: CA

address: University of California, Irvine

institute: University of California, Irvine

summary: Our study investigates the effects of cell adhesion and traction forces on reprogramming by utilizing a human fibroblast cell line (hiF-T) that can be reprogrammed by activating the expression of an OKSM (OCT4, KLF4, SOX2, C-MYC) gene cassette through the addition of doxycycline. We performed RNA interference experiments on 103 genes found in the ‘adhesome’ (encoding integrins, cadherins, and associated proteins) that are expressed and dynamically regulated (6-fold or more) across the reprogramming timeline. The impact of each shRNA on iPSC generation efficiency was assessed by immunostaining for TRA-1-60, a known pluripotency marker. From this RNAi screen, we identified the SHROOM3 knockdown as a potent reprogramming efficiency enhancer and generated RNA-seq timelines throughout reprogramming with or without shRNAs targeting SHROOM3 or a LacZ control. Gene co-expression network analysis highlights the existence of a critical state transition regulated through a SHROOM3-SRF signaling axis during late reprogramming, which coincides with cell-mediated force generation. Taken together, our data suggest that adhesome gene expression acts as a significant impediment to somatic cell reprogramming through the activation of mechano-signaling pathways associated with cell traction forces. These results provide important new insights into the role of cell adhesion and force generation during reprogramming to pluripotency and somatic cell fate transitions more broadly.

overall_design: Somatic reprogramming RNA-seq timelines with or without lentivirus expressing shRNA vectors targeting SHROOM3 or LacZ, a non-targeting control.

first: Tri

last: Phan

first: Zachary

last: Reitz

middle: L


title: Distinct Impacts of Alpha-Synuclein Overexpression on the Hippocampal Epigenome of Mice in Standard and Enriched Environments

city: Vancouver

first: Michael

last: Kobor

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

summary: Elevated alpha-synuclein (SNCA) gene expression is associated with transcriptional deregulation and increased risk of Parkinson’s disease, which may be partially ameliorated by environmental enrichment. At the molecular level, emerging evidence indicates that excess alpha-synuclein protein (aSyn) impacts the epigenome through direct and/or indirect mechanisms. However, the extents to which both aSyn and the environment converge at the epigenome and whether epigenetic alterations underpin the preventive effects of environmental factors on transcription remain to be elucidated. Here, we profiled five DNA and histone modifications in the hippocampus of wild-type and transgenic mice overexpressing human SNCA. Mice of each genotype were housed under either standard conditions or in an enriched environment (EE) for 12 months. SNCA overexpression induced similar hippocampal DNA hydroxymethylation and H3K27 acetylation changes in both environments, and was associated with environment-dependent changes to H3K4 methylation. These H3K4 methylation changes included loci where the EE ameliorated the impacts of the transgene as well as loci resistant to the effects of environmental enrichment in transgenic mice. In addition, select H3K4 monomethylation alterations were associated with changes in mRNA expression. Our results suggested an environment-dependent impact of excess aSyn on some functionally relevant parts of the epigenome, and will ultimately enhance our understanding of the molecular etiology of Parkinson’s disease and other synucleinopathies.

overall_design: Reduced representation bisulfite sequencing of paried oxidative bisulfite and bisulfite-converted libraries, for wild type and SNCA transgenic mice housed for 12 months in standard conditions or enriched environment

first: S

last: Schaffner

first: Z

last: Wassouf

first: T

last: Hentrich

first: M

last: Nuesch-Germano

middle: S

first: J

middle: M

last: Schulze-Hentrich


title: BCL7A is silenced by hypermethylation to promote acute myeloid leukemia

city: Granada

first: Pedro

middle: P

last: Medina

state: Andalucía

address: Av. de la Ilustración, 114

institute: Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica (GENYO)

summary: Differential expression analysis was performed to determine pathways and genes altered after BCL7A expression restoration.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of NB4 cells upon lentiviral transfection with wild-type BCL7A and its D27-mutant.

first: Juan

last: Patiño-Mercau


title: SENP3 and USP7 regulate Polycomb-rixosome interactions and silencing functions(RNA-seq ES)

first: Danesh

last: Moazed

overall_design: RNA-seq analysis of histone modifications and chromatin associated proteins

first: Haining

last: Zhou


title: SENP3 and USP7 regulate Polycomb-rixosome interactions and silencing functions(RNA-seq)


title: Mechanical stretch promotes invasion of lung cancer cells via activation of tumor necrosis factor-alpha

city: Taoyuan City

first: Yi-Chiung

last: Hsu

address: No. 300, Zhongda Rd., Zhongli District,

department: Department of Biomedical Sciences and Engineering

country: Taiwan

institute: National Central University

summary:
Most of the gas exchange in the human body is carried out by the lungs, and the physiological activities of the lungs are uninterrupted. Due to the deterioration of the external environment, pulmonary cell lesions are common clinical lung diseases. Mechanical cyclic stretching is one kind of bionic technology to observe lung cancer cells. The A549 cell line is the human lung adenocarcinoma cell line derived from a primary lung tumor. This study investigated the effects of mechanical cyclic stretching on A549 cell activity and gene expression profile. Whereas mechanical cyclic stretching had no significant difference in colony formation and cell migration of A549 cells, the cell invasion increased significantly in A549 cells after stretching.
In addition, the microarray data showed that mechanical cyclic stretching altered gene expression, induced inflammation of cells, and activation of Wnt/β-catenin and tumor necrosis factor pathways. More importantly, mechanical cyclic stretching activated the expression of tumor necrosis factor-alpha (TNF-α) protein. Therefore, the increase of cell invasion induced by mechanical cyclic stretching might be associated with the activation of TNF-α in human lung adenocarcinoma cells.

overall_design: Human Lung Adenocarcinoma cells from static and stretch culture ststems

first: Liang-Kun

last: Chen


title: Neutrophil extracellular trap induction by alcohol generates unique low-density neutrophils with defective functions and impaired clearance contributing to liver damage in alcoholic hepatitis

city: Boston

first: Ioannis

last: Vlachos

address: 330 Brookline Ave. 519A, Dana Building

department: Pathology

institute: Beth Israel Deaconess Medical Center

summary: Alcoholic hepatitis (AH) is characterized by severe liver and systemic inflammation and high mortality. Although numerous studies correlated neutrophil counts with poor clinical outcomes, the role of neutrophils in AH is poorly understood. Here, we report that neutrophils contribute to liver damage through increased neutrophils extracellular traps (NET) production in AH patients and mouse models with a concordant significant increase of low-density neutrophils (LDNs) in AH patients. Transcriptome analysis revealed that high-density neutrophils (HDNs) are activated and more prone to release NET, whereas LDNs exhibit exhausted phenotype. We show that alcohol-induced NET release in HDNs induces a unique LDN subset with decreased functionality and reduced clearance. Elimination of both defective HDNs and LDNs through in vivo neutrophil depletion or prevention of NET production with granulocyte colony stimulating factor (G-CSF) treatment ameliorate alcohol-induced liver damage. Our findings uncover alcohol-induced neutrophil phenotypic changes and provide mechanistic insights for therapeutic interventions in AH.

overall_design: Whole transcriptome sequencing of high-density neutrophils (HDNs) and low-density neutrophils (LDNs) isolated from collected blood of acute alcoholic hepatitis patients (n=4) and HDNs from healthy human subjects (n=3).

first: Yeonhee

last: Cho

first: Terence

last: Bukong

first: David

last: Tornai

first: Mrigya

last: Babuta

first: Eleni

last: Kanata

first: Donna

last: Catalano

first: Gyongyi

last: Szabo


title: RNA sequencing for AML patients with and without extramedullary infiltration

city: Dalian

first: Jinsong

last: Yan

state: Liaoning

address: 467 Zhongshan Road, Dalian 116027, Liaoning, P. R. China

department: Department of Hematology

institute: the Second Hospital of Dalian Medical University

summary: Extramedullary infiltration (EMI) is a concomitant manifestation indicating poor prognosis of acute myeloid leukemia (AML), yet the underlying mechanism remains poorly understood and therapeutic options are limited. Here, we employed single-cell RNA sequencing on bone marrow (BM) and EMI samples from an AML patient presenting pervasive leukemia cutis. A complement C1Q+ macrophage-like leukemia subset which is enriched within cutis and existed in BM prior to EMI manifestations was identified and further verified in multiple AML patients. RNA-sequencing and quantitative proteomics profiling revealed adverse prognosis of patients bearing C1Q+ population. C1Q expression endowed leukemia cells with tissue-infiltration ability which could establish prominent cutaneous or gastrointestinal EMI nodules in patient-derived xenograft (PDX) and CDX models. Fibroblasts attracted migration of the C1Q+ leukemia cells through surface C1Q-gC1QR recognition and subsequent stimulation of MAFB5 TGF-β signaling. Thus, C1Q orchestrates cancer infiltration pathways through communicating with fibroblasts and represents a compelling therapeutic target for EMI.

overall_design: Examination of gene expression in AML patients with and without extramedullary infiltration.


title: The little skate genome and the evolutionary emergence of wing-like fin appendages [RNA-seq, Adult]

city: Sevilla

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

institute: CABD/CSIC

summary: While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). We show that despite their derived morphology, the skate genome retains multiple features of the ancestral jawed vertebrate genome.

overall_design: RNAseq experiments in adult skate tissues

first: Ferdinand

last: Marlétaz

first: Elisa

last: de la Calle-Mustienes

first: Rafael

middle: D

last: Acemel

first: Tetsuya

last: Nakamura

first: Christina

last: Paliou

first: Silvia

last: Naranjo

last: Martínez-García

first: Ildefonso

last: Cases

first: Victoria

last: Sleight

first: Christine

last: Hirschberger

first: Ali

last: Andrescavage

first: Marina

last: Marcet-Houben

first: Ozren

last: Bogdanovic

first: Liyan

last: Yang

first: Lourdes

last: Gallardo-Fuentes

first: Ismael

last: Sospedra

first: Javier

last: Lopez-Rios

first: Fabrice

last: Darbellay

first: Axel

last: Visel

first: Job

last: Dekker

first: Neil

last: Shubin

last: Gillis

first: Toni

last: Gabaldón

middle: J

first: Dario

last: Lupianez

first: Daniel

last: Rokhsar

first: José

last: Gómez-Skarmeta


title: H3K27Ac CUT&Tag-Seq to characterize the epigenetic profiles in colonic macrophages from Tle4KO (Tle4fl/fl, Lyz2-Cre) and WT (Lyz2-Cre) mice

first: Xiaoyu

last: Li

address: Tsinghua University, Haidian District

institute: Tsinghua University

summary: We found that TLE4 maintained epigenetic landscape in colonic macrophages.

overall_design: Colonic macrophages were sorted from untreated WT and myeloid cell-specic Tle4 knockout mice. Epigenetic profiles were analyzed by H3K27Ac CUT&Tag-Seq.

first: Bin

last: Zhang


title: A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors

city: San Francisco

first: Alexis

middle: Leigh

last: Krup

address: 1650 Owens Street

department: Gladstone Institutes of Cardiovascular Disease

institute: Gladstone Institutes

summary:
Transcriptional networks governing cardiac precursor cell (CPC) specification are incompletely understood due in part to limitations in distinguishing CPCs from non-cardiac mesoderm in early gastrulation. We leveraged detection of early cardiac lineage transgenes within a granular single cell transcriptomic time course of mouse embryos to identify emerging CPCs and describe their transcriptional profiles. Mesp1, a transiently-expressed mesodermal transcription factor (TF), is canonically described as an early regulator of cardiac specification. However, we observed perdurance of CPC transgene-expressing cells in Mesp1 mutants, albeit mis-localized, prompting us to investigate the scope of Mesp1’s role in CPC emergence and differentiation. Mesp1 mutant CPCs failed to robustly activate markers of cardiomyocyte maturity and critical cardiac TFs, yet they exhibited transcriptional profiles resembling cardiac mesoderm progressing towards cardiomyocyte fates. Single cell chromatin accessibility analysis defined a Mesp1-dependent developmental breakpoint in cardiac lineage progression at a shift from mesendoderm transcriptional networks to those necessary for cardiac patterning and morphogenesis. These results reveal Mesp1-independent aspects of early CPC specification and underscore a Mesp1-dependent regulatory landscape required for progression through cardiogenesis.

This SuperSeries is composed of subseries.

overall_design: Study design referenced in individual series details.


title: TLE3 and TLE4-coordinated colonic macrophage-CD4+ T cell crosstalk maintains intestinal immune homeostasis