title: Gene expression profiling of CTCL cell line Hut78 via IKZF2 knockdown by RNA-seq

status: Public on Feb 28 2022

city: Beijing

first: Bufang

last: Xu

address: No.8 Xishiku Street, Xicheng District

country: China

institute: Peking University

type: Expression profiling by high throughput sequencing

summary: IKZF2 is an important nuclear matrix protein and plays a pivotal role in T cell development and differentiation, while its expression and function in Cutaneous T cell lymphoma (CTCL) remain ambiguous. Our study aimed to investigate the expression pattern, biological function of IKZF2 in a large clinical cohort. IKZF2 is specifically over-expressed in malignant T cells with MF tumor-stage. In order to explore the function of IKZF2 in the pathogenesis of CTCL, transcriptome sequencing  was performed  among  Hut78 cells transfected with shRNAs targeting IKZF2 (shIKZF2) and scrambled shRNA(sh0) to investigate genes regulated by IKZF2 in CTCL cells .

overall_design: CTCL cell line Hut78 : sh0 vs shIKZF2 .  Biological replicates: 2 sh0 replicates, 2 shIKZF2 replicates

first: Yang

last: Wang


title: Circulating extracellular vesicles with liver-specific RNA species are potential biomarkers for early cholestasis-induced liver fibrosis [mRNA-seq]

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

type: Non-coding RNA profiling by high throughput sequencing

summary: Aims Biliary diseases represent around 10% of all chronic liver diseases and affect both adults and children. Currently available biochemical tests detect cholestasis but not early liver fibrosis. Circulating extracellular vesicles (EVs) provide a real-time molecular snapshot of the injured organ in a non-invasive way. We thus aimed at searching for a panel of EV-based biomarkers for cholestasis-induced early liver fibrosis using mice models. Results: Progressive and detectable histological evidence of collagen deposition and liver fibrosis was observed as from Day 8 after bile duct ligation (BDL) in mice. Whole transcriptome and small RNA-seq analyses of circulating EVs revealed differentially enriched RNA species after BDL versus sham controls. Unsupervised hierarchical clustering identified a signature that allowed for discrimination between BDL and controls. In particular, 151 microRNAs enriched in BDL-derived EVs were identified, of which 66 were conserved in humans. The liver was an important source of circulating EVs in BDL animals as evidenced by the enrichment of several hepatic mRNAs, such as Albumin, Haptoglobin, Transferrin receptor 1 and Alas2. Interestingly, among experimentally validated miRNAs, miR194-5p and miR29-3p showed similar enrichment patterns also in EVs derived from DDC-treated (drug-induced cholestasis) and MDR2-/- (genetic cholestasis) mice. Innovation A panel of mRNAs and miRNAs contained in circulating EVs, when combined, provides sensitive biomarkers for the early detection of hepatic damage and fibrosis. Conclusion Analysis of EVs for enrichment in miR29-3p and miR194-5p, in combination with hepatic injury RNA markers, could represent a sensitive biomarker panel for the early detection of cholestasis-induced liver fibrosis.

overall_design: BDL treated C57BL/6J (6 animals at each time point) were sacrified at 8 days after surgery. Control animals (sham, 6 animals at each time point), were sacrified at 8 days after surgery

first: Sharmila

last: Fagoonee

first: Maddalena

last: Arigoni

first: Marta

last: Manco

first: Martina

last: Olivero

first: Francesca

last: Bizzaro

first: Cinzia

last: Magagnotti

first: Annapaola

last: Andolfo

first: Barbara

last: Miniscalco

first: Marco

last: Forni

first: Stefano

last: Todeschi

first: Emanuela

last: Tolosano

first: Elena

last: Bocchietto

first: Fiorella

last: Altruda


title: Thyrotropin Receptor Signaling Deficiency Impairs Spatial Learning and Memory

city: Jinan

first: Sisi

last: Luan

state: Shandong

address: 544 Jingsi Road

department: Endocrinology

institute: Shandong Provincial Hospital Affiliated to Shandong University

summary: Subclinical hyperthyroidism, a disease characterized by decreased thyroid-stimulating hormone (TSH) and normal concentration of thyroid hormone, is associated with an elevated risk for cognitive impairment. TSH is the major endogenous ligand of TSH receptor (TSHR) and its role dependent on the process of signal transduction of TSHR. It has not, however, been established whether TSHR signaling are involved in the regulation of cognition. In the current study, Tshr deletion leads to significantly compromised performance in hippocampus-dependent tasks, along with reduced dendritic spine density and excitatory synaptic density as well as altered synaptic structure in CA1 subfield of the hippocampus. Furthermore, the synapse-related gene expression was altered in the hippocampus of Tshr-/- mice. These findings suggest the ablation of TSHR signaling impairs spatial learning and memory, which reveals a fresh role of TSHR signaling in brain.

overall_design: Hippocampal mRNA profiles of 3-month old wild type (WT) and Tshr-/- mice were generated by deep sequencing from five biological replicates, using Illumina Novaseq6000

first: Jiajun

last: Zhao


title: Evolutionary transcriptomics of Eutherian gene expression gains and the origins of decidualization [Set 7]

city: Buffalo

first: Vincent

middle: J.

last: Lynch

state: NY

address: 551 Cooke Hall

department: Department of Biological Sciences

country: USA

institute: University at Buffalo, SUNY

summary: We used human endometrial stromal fibroblast cell line to perform an siRNA knockdown coupled with RNA-seq screen of a series of transcription factors that gained expression in the endometrial tissue of Eutherian mammals.

overall_design: mRNA-Seq in ESF cells treatd with negative control siRNAs or siRNA targeting a series of human transcription factors

first: Mirna

last: Marinic

middle: J


title: Genome wide expression change by 786-O cells treated with MST1/2 inhibitor XMU-MP-1

city: Xinxiang

first: Ting

last: Zhuang

state: Henan

address: Jinsui Road 601

institute: Xinxiang Medical University

summary: We aim to the investigate the role of MST1/2 inhibitor XMU-MP-1 in kindy renal clear cell carcinoma (ccRCC) progression. 786-O cells were used as the model.

overall_design: The 786-O cells were treated with vehicle or 4 μM XMU-MP-1 . After 6 hours, cells were harvested and the total RNA was extacted by Qiagen kit. The RNA sample was sent to BGI for RNA expression anaylsis.

first: Shu

last: Zhuo

first: Jian

last: Zhu

first: Jin

last: Jiang


title: Evolutionary transcriptomics of Eutherian gene expression gains and the origins of decidualization [Set 5]


title: Zfp335 establishes neonatal immune tolerance through safeguarding effector Treg lineage commitment and maintenance [RNA-seq]

city: xi'an

first: xin

last: wang

address: yanta west road 76

institute: xi'an jiaotong university

summary: Regulatory T (Treg) cells are crucial for maintaining peripheral immune tolerance and preventing destructive autoreactive responses, but how heterogeneous Treg populations establish tolerant status remains unclear. Here, we found that Zinc finger protein 335 (Zfp335) is indispensable for the differentiation and maintenance of effector Treg (eTreg) population and immunological self-tolerance in neonates.Mice with Zfp335 deletion in Treg cells exhibit early-onset autoimmune disease with severe inflammation in multiple organs and unrestricted activation and expansion of conventional T cells.

overall_design: Examination of CD4+YFP+CD25+ Tregs from the lymph nodes of WT and Zfp335 deficient mice

first: Baojun

last: Zhang

first: Xin

last: Wang

first: Lina

last: Sun

first: Cangang


title: Dysregulated myokines and signaling pathways in skeletal muscle dysfunction in a Cigarette Smoke-induced Model of Chronic Obstructive Pulmonary Disease

first: Chunxiao

last: Li

address: Huayuan road

summary:
Purpose: To explore myokines and signaling pathways in skeletal muscle dysfunction in a Cigarette Smoke-induced Model of Chronic Obstructive Pulmonary Disease
Methods: Total RNA was extracted from the muscle tissues using Trizol (Invitrogen, Carlsbad, California, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, and then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, and then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Results: The sequencing data were filtered with SOAPnuke (v1.5.2) (Li et al., 2008)by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) was more than 20%; (3) Removing reads whose unknown base ('N' base) ratio was more than 5%, and afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)(Kim et al., 2015). Bowtie2 (v2.2.5)(Langmead and Salzberg, 2012) was applied to align the clean reads to the reference coding gene set，and then expression level of gene was calculated by RSEM (v1.2.12)(Li and Dewey, 2011). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA profiles of the gastrocnemius muscle of COPD mice

first: Yongchang

first: Lijiao


title: Evolutionary transcriptomics of Eutherian gene expression gains and the origins of decidualization [Set 1]


title: Zfp335 establishes neonatal immune tolerance through safeguarding effector Treg lineage commitment and maintenance.

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: SR0726 deletion leads to altered transcriptome of cultured Borrelia burgdorferi

status: Public on Feb 27 2022

city: PULLMAN

first: Michael

last: Crowley

state: WA

address: 100 Dairy Rd

department: VMP

institute: Washington State University

summary: Differential gene expression analysis was performed to assess the affects of the deletion of sRNA SR0726 on the in vitro transcriptome of Borrelia burgdorferi in order to investigate a potential regulatory role for the sRNA

overall_design: Triplicate cultures of wild type and D7 (SR0726 deletion mutant) were grown in BSK-II under standard conditions until mid-log phase, sub-cultured (1:100) to room temperature BSK-II, grown back to mid-log phase, subcultured (1:100) to 35°C, and grown to late-phase. Triplicate cultures for each strain were then pooled and pelleted. RNA was extracted, DNase treated, and was sent to the Novogene Corporation for library preparation, sequencing, and bioinformatic analysis.

first: Troy

last: Bankhead


city: Shenyang

first: Funan

last: Liu

state: Liaoning

address: Nanjing Street 155

institute: first affiliated hospital of china medical university

summary: As a key protein in the tumor microenvironment, FN1 has been proven to promote cancer in a variety of cancer species. However, in our previous study on gastric cancer, it was found that FN1 protein expression in patient tissues was not significantly correlated with prognosis, and clinical data analysis was only correlated with T stage of gastric cancer. Analysis of the relationship between FN1 mRNA expression level and prognosis by TCGA-STAD database revealed that high FN1 mRNA expression was significantly correlated with poor prognosis. Moreover, many miRNA binding sites were found on FN1 3' UTR by database prediction, so we speculated that FN1 played different functions at mRNA and protein levels, and FN1 3' UTR might function as ceRNA. At present, FN1 3' UTR overexpression has been proved to significantly promote the invasion and metastasis of gastric cancer in vivo and in vitro, and its effect is stronger than FN1 protein. Therefore, in this study, miRNA sequencing, which was used to find those miRNAs bound to FN1 3’UTR, was carried out to further explore its cancer-promoting mechanism.

overall_design: miRNA-sequencing of HGC27 and AGS cells with FN1 3' UTR overexpression.

first: Siwei

last: Pan


title: Paternal preconception plasticizer alters sperm methylome and embryonic programming.

city: Amherst

last: Pilsner

state: Massachusetts

address: 686 N PLEASANT

department: Environmental Health Sciences

institute: University of Massachusetts Amherst

type: Methylation profiling by high throughput sequencing

summary: Preconception environmental conditions have been demonstrated to shape sperm epigenetics and subsequently offspring health and development. Our previous findings in humans showed that urinary anti-androgenic phthalate metabolites in males were associated with altered sperm methylation and blastocyst-stage embryo development. To corroborate this, we examined the effect of preconception exposure to di(2-ethylhexyl) phthalate (DEHP) on genome-wide DNA methylation and gene expression profiles in mice. We found that male preconception DEHP exposure resulted in 704 differentially methylated regions (DMRs; q-value < 0.05; ³ 10% methylation change) in sperm, 1,716 DMRs in embryonic, and 3,181 DMRs in extra-embryonic tissue. Of these, 29 DMRs overlapped between sperm and F1 tissues, half of which showed concordant methylation changes between F0 and F1 generations. F1 transcriptomes at E7.5 were also altered by male preconception DEHP exposure including developmental gene families such as Hox, Gata, and Sox. Additionally, gene ontology analyses of DMRs and differentially expressed genes showed enrichment of multiple developmental processes including embryonic development, pattern specification and morphogenesis.

overall_design: Eight-week old C57BL/6J male mice were exposed to either a vehicle control, low, or high dose of DEHP (2.5 and 25 mg/kg/weight, respectively) for 67 days (~ 2 spermatogenic cycles) and were subsequently mated with unexposed females. Reduced representation bisulfite sequencing (RRBS) of epididymal sperm was performed and gastrulation stage embryos were collected for RRBS and transcriptome analyses in both embryonic and extra-embryonic lineages.

first: J

middle: R

first: Oladele

last: Oluwayiose


title: Gene expression in retinal tissue and off-target tissue derived from human iPSCs

status: Public on Feb 26 2022

city: Kobe

first: Kenji

last: Watari

address: 5th floor, 1-5-2 Minatojima Minamimachi, Chuo-ku

country: Japan

institute: Sumitomo Pharma Co., Ltd.

summary: Three-dimensional retinal organoids (3D-retinas) are a promising graft source for transplantation therapy. We previously developed self-organizing culture for 3D-retina generation from human induced pluripotent stem cells (hiPSCs). Toward clinical applications on hPSC-derived retinal sheets, the establishment of a quality control (QC) strategy for 3D-retinas and dissected retinal sheets has remained a major challenge. We performed a microarray analysis for retinal tissue and off-target tissue to identify the major off-target tissue in hiPSC-culture.

overall_design: hiPSC-derived retinal tissue and off-target tissue were analyzed for microarray analysis.

first: K

first: S

last: Yamasaki

first: A

last: Kuwahara


title: Circulating extracellular vesicles with liver-specific RNA species are potential biomarkers for early cholestasis-induced liver fibrosis.

first: Raffaele

last: Calogero


title: Evolutionary transcriptomics of Eutherian gene expression gains and the origins of decidualization [Set 6]

first: Vincent

last: Lynch

first: Mirna

last: Marinic


title: Total transcriptome sequencing of papillary thyroid carcinoma samples

first: Yujing

state: Shandong Province

address: No. 107, Wenhua West Road, Lixia District

department: Department of Endocrinology

institute: Qilu Hospital, Cheeloo college of medicine, Shandong University

summary:
To evaluate the expression profiles of circular RNAs (circRNAs) in papillary thyroid cancer (PTC) and to find new PTC biomarkers.
Objective: The goal of this study was to characterize the expression profiles of circular RNAs (circRNAs) in papillary thyroid carcinoma (PTC), analyze their biological function, and discover new biomarkers for PTC.
Methods: From June 2019 to July 2020, 68 patients admitted to Qilu Hospital and confirmed with PTC were included in this study. PTC and paired healthy tissue samples were collected and analyzed. The circRNA expression profiles of 4 pairs of samples were determined using high-throughput sequencing. Differentially expressed circRNAs were discovered to be associated with multiple related microRNAs (miRNAs) and messenger RNAs using bioinformatics analysis (mRNAs).
Results: 89 upregulated and 14 downregulated circRNAs were identified in PTC tissues using high-throughput sequencing (fold change ≥ 2; p < 0.05). Among the upregulated circRNAs, we identified 14 significantly regulated circRNAs that play an important role in the pathogenesis of thyroid cancer using the network map of circRNA–miRNA–mRNA interactions. Following that, we validated the expression levels of seven candidate circRNAs (hsa_circ_0031584, hsa_circ_0082002, hsa_circ_0000660, hsa_circ_0067938, hsa_circ_0002483, hsa_circ_0003692, and hsa_circ_0006509) and discovered that among the circRNAs that we verified to be significantly differentially expressed
Conclusions: The findings imply that dysregulated circRNAs may play an important role in the pathogenesis of PTC. We also discovered 14 circRNAs that were significantly upregulated and could be used to diagnose and treat PTC.

overall_design: Four papillary thyroid cancer and their adjacent normal tissues.

first: Li

last: Chen

first: Xinguo

last: Hou

first: Yan

last: liu


title: Zfp335 establishes neonatal immune tolerance through safeguarding effector Treg lineage commitment and maintenance [ChIP-seq]

first: xin

last: wang

summary: Regulatory T (Treg) cells are crucial for maintaining peripheral immune tolerance and preventing destructive autoreactive responses, but how heterogeneous Treg populations establish tolerant status remains unclear. Here, we found that Zinc finger protein 335 (Zfp335) is indispensable for the differentiation and maintenance of effector Treg (eTreg) population and immunological self-tolerance in neonates. Mice with Zfp335 deletion in Treg cells exhibit early-onset autoimmune disease with severe inflammation in multiple organs and unrestricted activation and expansion of conventional T cells. Zfp335-deficient Treg cells display dysfunctional and pathogenic features together with multiple defects in proliferation, survival and suppressive function. Importantly, our single-cell RNA sequencing (scRNA-seq) analyses reveal distinct Treg populations and that Zfp335 deficiency causes an almost complete loss of eTreg population along with significant accumulation of dysfunctional Treg populations. Mechanistically, Zfp335 controls both fate decision and homeostasis of eTreg cells by directly targeting genes associated with homeostasis and oxidation-fueled oxidative phosphorylation (OXPHOS) and PI3K-Akt-mTOR metabolic pathways. Our data establish the concept that Zfp335 serves as a checkpoint and safeguard for eTreg lineage commitment and maintenance.

overall_design: Examination of Treg cells from the lymph nodes of WT mice

first: Baojun

last: Zhang

first: Xin

last: Wang


title: Transcellular chaperone signaling is an intercellular stress-response that is distinct from the HSF-1 mediated HSR [RNA-seq]

city: Leeds

first: Patricija

last: van Oosten-Hawle

state: --Select State--

address: Woodhouse Lane

department: Molecular and Cell Biology

country: United Kingdom

institute: UNIVERSITY OF LEEDS

summary: The goal of this RNA-Seq analysis was to identify genes differentially expressed in a C. elegans strain expressing a neuron-specific or gut-specific hsp-90 hairpin RNAi construct compared to control animals of the same genetic background (strain AM994). Tissue-specific expression of an hsp-90 hairpin RNAi construct knocks down hsp-90 in a tissue-specific manner and induces transcellular chaperone signalling that enhances organismal proteostasis. This study aimed to identify components of the signalling pathway responsible for this effect.

overall_design: Gene expression profile of Day 1 adults C. elegans expression a gut-specific (hsp-90int) or neuron-specific (hsp-90neuro) hsp-90 hairpin RNAi construct compared to control animals harboring the same genetic background (strain AM994) and wild type (N2 Bristol), grown at 20C. 3 replicates of each sample.

last: Miles

first: P


title: To detect full-length genome of intron 19 of ARFGEF1 [intron19arfgef1]

city: Taipei

first: Trees-Juen

last: Chuang

address: 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan

department: Genomics Research Center

country: Taiwan

institute: Academic Sinica

summary: Analysis of high-throughput transcriptome sequencing (RNA-seq) data often observed numerous 'non-co-linear' (NCL) transcripts, which may originate from genetic rearrangements (gene fusion) indicated the importance of fusion events and circRNAs in carcinogenesis; however, the role of ts-RNAs remains largely uninvestigated. Here we developed a hybrid sequencing pipeline ("NCLscan-hybrid"), which integrated different types of short (Illumina-based) and extra-long (PacBio-based) RNA-seq data to eliminate potential false positives from experimental artifacts, fusion events, and circRNAs. We applied NCLscan-hybrid to investigate of ts-RNAs in human breast cancer, the most malignant tumors diagnosed in women worldwide. Through multiple experimental validation steps, we confirmed that the intragenic ts-RNA, ts-ARFGEF1, was highly expressed in breast cancer cells but absent in normal breast cells. Furthermore, we experimentally validated that ts-ARGEF1 can contribute to cell proliferation and apoptosis. Analysis of xenograft in nude mice showed that disruption of ts-ARFGEF1 expression can significantly attenuate tumor growth. Microarray analysis revealed that ts-ARFGEF1 knockdown could trigger PERK/ATF4/CHOP signaling pathway, implying the function of ts-ARFGEF1 in ER homeostasis. Taken together, our findings provide an in-depth view of the true complexity of intragenic NCL events and, for the first time, show further insight into the potential roles of intragenic ts-RNAs in tumor cell development.

overall_design: We designed primer to amplify the region of intron 19 of ARFGEF1 and then the purified PCR products were subjected to nanopore sequencing


title: MicroRNA global profiling in cystic fibrosis cell lines reveals dysregulated pathways related with oncogenesis, inflammation, growth and glucose metabolism

city: Parma

first: Mariolina

last: Gulli

address: Parco Area delle Scienze 11a

department: Life Sciences

institute: University of Parma

summary: Global profiles of 754 human miRNAs from CFBE41o- (F508del/F508del), and IB3 (F508del/W1282X) cell lines, carrying the most common mutations for Cystic Fibrosis, were analysed. 16HBE14o- cells, derived from normal bronchus, were used as calibrator. The relative abundance of each miRNA was calculated and fold-changes≥+2 or ≤-2 (p-value≤0.05) were considered significant. MiRNA target genes and KEGG pathways were identified using miRWalk v.3 and DIANA-mirPath v3.0, respectively and a protein-protein interaction network was performed by STRING 11.0.  In CF cell lines 41 miRNAs showed significant changes. Eight miRNAs were regulated in CFBE41o- only and 23 in IB3 only, suggesting genotype-specific effects. Five miRNAs were up-regulated and 1 down-regulated in both CFBE41o- and IB3. The 41 miRNAs regulated genes within pathways involved with cancer, inflammation, body growth, glucose metabolism and lipid metabolism. Interestingly, key genes involved with Ras, TGF-beta, Jak-Stat and insulin signaling were highlighted.

overall_design: miRNA expression profiling was performed on total RNA, including small RNAs, purified from each cell line in two replicates. Cell lines  16HBE14o- constitutes the healthy control, CFBE41o- are the model for the homozygous mutation of the CFTR gene responsible of cystic fibrosis, IB3 are the model for the hetorozygote mutation

first: Maria

middle: E

last: Street

first: Francesca

last: Cirillo

first: Cecilia

last: Catellani

first: Luisa

last: Montanini

first: Sara

last: Graziano

first: Nelson

last: Marmiroli

last: Gullì


title: Evolutionary transcriptomics of Eutherian gene expression gains and the origins of decidualization [Set 4]

first: Vincent

last: Lynch

first: Mirna

last: Marinic


title: CHD7 Regulates Bone-fat Balance via Suppressing PPAR-γ Signaling Pathway

city: ChengDu,SiChuan

first: Caojie

last: Liu

address: No.14,3Rd Section Of Ren Min Nan Rd.

institute: West China Hospital of Stomatology, Sichuan University

summary: Chromodomain helicase DNA-binding protein 7 (CHD7) is an ATP-dependent eukaryotic chromatin remodeling enzyme that plays a critical role in epigenetics. Previous studies showed CHD7 is essential in development of organs and mutation of CHD7 is the main cause of CHARGE syndrome, but the function of CHD7 in skeletal system remained elusive. Here we show that conditional knockout of Chd7 in bone marrow mesenchymal stem cells (MSCs) and pre-osteoblasts leads to a pathological phenotype in mice, manifested as skeletal system development disorder, low bone mass and severely high marrow adiposity. Mechanistically, we identify up-regulated peroxisome proliferators-activated receptors (PPAR) signaling pathway in Chd7-deficient MSCs. Knockout of Chd7 reduces the restriction of PPAR-γ, then PPAR-γ associates with tri-methylated histone H3 at lysine 4 (H3K4me3), activates the transcription of the downstream adipogenic genes, and disrupts the balance between osteogenic and adipogenic differentiation. Our work illustrates the pathological manifestations of Chd7 mutation in MSCs and reveals novel epigenetic mechanism in skeletal health and diseases.

overall_design: 12 samples were analyzed.

first: Qiuchan

last: Xiong

first: Qiwen

last: Li

first: Weimin

last: Lin

first: Shuang

last: Jiang

first: Yaqian

last: Chen

first: Danting

first: Yuan

first: Xiaobo

last: Duan

first: Quan

last: Yuan

first: Ning

last: Kang

first: Ping

last: Gong


title: Evolutionary transcriptomics of Eutherian gene expression gains and the origins of decidualization [Set 2]

overall_design: mRNA-Seq in ESF cells treated with negative control siRNAs or siRNA targeting a series of human transcription factors


title: Circulating extracellular vesicles with liver-specific RNA species are potential biomarkers for early cholestasis-induced liver fibrosis [RNA-seq]

first: Raffaele

last: Calogero

summary: Aims Biliary diseases represent around 10% of all chronic liver diseases and affect both adults and children. Currently available biochemical tests detect cholestasis but not early liver fibrosis. Circulating extracellular vesicles (EVs) provide a real-time molecular snapshot of the injured organ in a non-invasive way. We thus aimed at searching for a panel of EV-based biomarkers for cholestasis-induced early liver fibrosis using mice models. Results: Progressive and detectable histological evidence of collagen deposition and liver fibrosis was observed as from Day 8 after bile duct ligation (BDL) in mice. Whole transcriptome and small RNA-seq analyses of circulating EVs revealed differentially enriched RNA species after BDL versus sham controls. Unsupervised hierarchical clustering identified a signature that allowed for discrimination between BDL and controls. In particular, 151 microRNAs enriched in BDL-derived EVs were identified, of which 66 were conserved in humans. The liver was an important source of circulating EVs in BDL animals as evidenced by the enrichment of several hepatic mRNAs, such as Albumin, Haptoglobin, Transferrin receptor 1 and Alas2. Interestingly, among experimentally validated miRNAs, miR194-5p and miR29-3p showed similar enrichment patterns also in EVs derived from DDC-treated (drug-induced cholestasis) and MDR2-/- (genetic cholestasis) mice. Innovation A panel of mRNAs and miRNAs contained in circulating EVs, when combined, provides sensitive biomarkers for the early detection of hepatic damage and fibrosis. Conclusion Analysis of EVs for enrichment in miR29-3p and miR194-5p, in combination with hepatic injury RNA markers, could represent a sensitive biomarker panel for the early detection of cholestasis-induced liver fibrosis.

overall_design: BDL treated C57BL/6J (6 animals at each time point) were sacrified at 8 and 15 days after surgery. Control animals (sham, 6 animals at each time point), were sacrified at 8 and 15 days after surgery

first: Sharmila

last: Fagoonee

first: Maddalena

last: Arigoni

first: Marta

last: Manco

first: Martina

last: Olivero

first: Francesca

last: Bizzaro

first: Cinzia

last: Magagnotti

first: Annapaola

last: Andolfo

first: Barbara

last: Miniscalco

first: Marco

last: Forni

first: Stefano

last: Todeschi

first: Emanuela

last: Tolosano

first: Elena

last: Bocchietto

first: Fiorella

last: Altruda


title: RNA-seq profiling of ductal macrophages, stromal macrophages and dendritic cells from the mammary glands of virgin, pregnant, lactating and post-weaning mice

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary:
Macrophages are diverse immune cells that reside in all tissues. Although macrophages have been implicated in mammary gland function, their diversity has not been fully addressed. By exploiting high-resolution 3D imaging and flow cytometry, we have identified a unique population of tissue-resident ductal macrophages (DMs) that form a contiguous network between the luminal and basal layers of the entire mammary gland throughout post-natal development. DMs are long-lived and constantly survey the epithelium though dendrite movement based on advanced 3D intravital imaging. While they initially originate from embryonic precursors, DMs derive from monocytes as they expand during puberty. Moreover, they undergo proliferation in pregnancy to maintain complete coverage of the epithelium in lactation, where they are poised to phagocytose milk-producing cells post-lactation and facilitate remodelling. Interestingly, DMs strongly resemble mammary tumour macrophages and form a network that pervades the tumour epithelium. Thus, the mammary epithelium programs specialised resident macrophages in both physiological and tumorigenic contexts. RNA-seq profiling demonstrates that DMs have a distinct gene expression signature from stromal macrophages or mammary-resident antigen-presenting cells and that substantial expression changes occur as DMs proliferate during pregnancy and lactation.

This SuperSeries is composed of the SubSeries listed below.


title: Disrupting the Myc-Tfeb circuit confers vulnerabilities targeting amino acid homeostasis and provokes metabolic anergy

city: Tampa

first: Mario

last: Fernandez

address: 12902 Magnolia Dr.

department: Tumor Biology

institute: Moffitt Cancer Center

summary: Metabolic reprogramming sustains cancer cell anabolism, and MYC oncoproteins control many aspects of this response. Normal cells adapt to nutrient-limiting conditions by activating autophagy, which is required for amino acid (AA) homeostasis. Surprisingly, here we report the autophagy-lysosomal pathway is suppressed by Myc in normal B cells, in premalignant and neoplastic B cells of Eµ-Myc transgenic mice, and in MYC-driven human Burkitt lymphoma. Myc suppresses autophagy by antagonizing expression and function of TFEB, a master regulator of autophagy/lysosome genes. Notably, compensatory mechanisms that sustain AA pools in MYC-expressing B cells include marked increases in AA transport and coordinate induction of the proteasome. Finally, reactivation of the autophagy-lysosomal pathway by constitutively active TFEB disables the malignant state, by perturbing mitochondrial functions and disrupting proteasome activity, amino acid transport, and disrupts amino acid and nucleotide metabolism, leading to growth arrest and apoptosis. This scenario provides therapeutic opportunities that disable MYC-driven tumorigenesis, including AA restriction and treatment with proteasome inhibitors.

overall_design: A B-cell lymphoma isolated from Eµ-Myc;Eµ-rtTA transgenic moused was transduced with either a bicistronic retrovirus expressing the selection marker puromycin or a mutated form of the TFEB gene at Ser-211 to Ala fused to a mutated ligand domain of the human estrogen Receptor domain (ER-T2) and puromycin. The lymphoma was selected with 1 µg/mL and puromycin-resistant cells were plated in vehicle or  250 ng/mL 4-hydroxytamoxifen (4-OHT) to induced TFEB activity for 4 days. Lymphomas were collected, in triplicate, and processed for subsequent RNA purification, labeling and samples processed in a Nugen_Ovation_Mouse RNASeq Kit. .

first: John

middle: L

last: Cleveland


title: Evolutionary transcriptomics of Eutherian gene expression gains and the origins of decidualization [Set 3]

first: Vincent

last: Lynch

summary: We used human endometrial stromal fibroblast cell line to perform an siRNA knockdown coupled with RNA-seq screen of a series of transcription factors that gained expression in the endometrial tissue of Eutherian mammals.

overall_design: mRNA-Seq in ESF cells treatd with negative control siRNAs or siRNA targeting a series of human transcription factors

first: Mirna

last: Marinic


title: Transcriptome analysis of FMF-04-159-2 treated  MDA-MB-231 cells

city: wuhan

first: Mengna

last: Zhang

state: State...

address: Donghu Road, No. 115, Wuchang District

institute: wuhan university

summary: Wnt/β-catenin signaling pathway has become a key signaling pathway regulating mammary organogenesis and oncogenesis. However, the therapeutic methods by targeting Wnt pathway against breast cancer has been limited. To address this challenge, we investigated the function of cyclin-dependent kinase 14 (CDK14), a member of Wnt signaling pathway, in mammary development and breast cancer progression. We showed that CDK14 was expressed in the mammary basal layer and elevated in triple negative breast cancer (TNBC). CDK14 knockdown reduces colony formation ability and regeneration capacity of mammary basal cells, and significantly inhibits murine MMTV-Wnt-1 basal-like mammary tumor progression. Excitingly, knockdown of CDK14 or pharmacological inhibition of CDK14 by FMF-04-159-2 significantly inhibited the progression and metastasis of human TNBC. Mechanistically, CDK14 inhibition inhibits mammary regeneration and TNBC progression by attenuating Wnt/β-catenin signaling. Together, we demonstrated that CDK14 regulates mammary regeneration and breast tumorigenesis, and is a promising therapeutic target for TNBC.

overall_design: Examination the different mRNA level in FMF-04-159-2 treated and control MDA-MB-231 cells

first: Cheguo

last: Cai

first: Lingxian


title: Evolutionary transcriptomics of Eutherian gene expression gains and the origins of decidualization


title: To detect full-length transcript of  ts-ARFGEF1 in MCF-7 cell [captureRNA]

first: Trees-Juen

last: Chuang

overall_design: We designed oligo probes against NCL junction region of ts-ARFGEF1 and then use it to pull down ts-ARFGEF1. The pull-down products are subjected to nanopore sequencing.


title: Transcriptomic profiles of Candida albicans grown in the presence or absence of mucins

city: Cambridge

first: Julie

last: Takagi

state: CA

address: 70 Massachusetts Ave, 56-230

institute: MIT

summary: We use high-throughput sequencing to profile the response of the opportunistic fungal pathogen Candida albicans to mucins from the mucosal niche. We find that C. albicans undergoes a genome-wide phenotypic shift in response to mucins suppressing virulence-associated pathways.

overall_design: Examination of differential gene expression in C. albicans in response to mucins

middle: S

first: Katharina

last: Ribbeck

first: Clarissa

last: Nobile


title: Global and p53-dependent transcriptional response of fibroblasts to Klebsiella pneumoniae

city: Solna

first: Sylvain

last: Peuget

state: Stockholm

address: Solnavägen 9

department: MTC

country: Sweden

institute: Karolinska Institute

summary: Increasing evidence highlights the role of bacteria in the physiopathology of cancer. However, the underlying molecular mechanisms remains poorly understood. Several cancer-associated bacteria have been shown to produce toxins which modulate the tumor suppressor p53 and thereby interfere with the host defense against tumorigenesis. Here, we show that lipopolysaccharides from Klebsiella pneumoniae (Kp) strongly inhibit the host p53 pathway and impairs p53 transcriptional activity upon DNA damage and oncogenic stress, preventing its tumor suppressive function.

overall_design: mRNA profiles (in triplicates) of BJ hTert immortalized fibroblasts treated with supernatant from Klebiella pneumoniae culture, doxorubicin and p53 shRNA

first: Marie-Stéphanie

last: Aschtgen

first: Gema

last: Sanz


title: Epicardial Hdac3 promotes myocardial growth through a novel microRNA pathway [mRNA-seq]

city: Baltimore

first: Deqiang

last: Li

state: Maryland

address: 800W Baltimore street

department: Surgery

institute: University of Maryland

summary: The purpose of the study was to compare epicardial transcript abundance between control and Hdac3 knockout (KO) epicardial cells (MEC).

overall_design: Total RNA extracted from CTL (EV) and Hdac3 CRISPR/CAS9 knockout (KO) in mouse epicardial cells. RNA libraries were prepared and Illumina HiSeq NGS preformed (Novogene Corporation Inc, Sacramento, CA) per standard protocols. For experiments with a biological replicate, as the DESeq2 has already eliminated the biological variation, our threshold is normally set to the following, padj < 0.05.

first: Jihyun

last: Jang


title: Epicardial Hdac3 promotes myocardial growth through a novel microRNA pathway [miRNA-seq]

summary: We report the application of small-RNA sequencing for high-throughput profiling in mouse epicardial cell (MCEC).


title: Human striatal organoids derived from pluripotent stem cells recapitulate striatal development and compartments

city: Shanghai

first: Lixiang

last: Ma

address: Dong'an road No.130

department: School of Basic Medical Sciences

institute: Fudan University

summary: Single cell RNA-seq and bulk RNA-seq characterization of stem cell derived organoids resembling the human striatum

overall_design: Bulk RNA sequencing of day 60 and 80 human striatal organoids(hStrOs) drived from human embryonic stem cells (hESCs) H9 and human induced pluripotent stem cell (hiPSCs) 8-12; Single-cell RNA sequencing of day 110 human striatal organoids(hStrOs) drived from human embryonic stem cells (hESCs) H9 and human induced pluripotent stem cell (hiPSCs) 8-12.

first: Xinyu

last: Chen

first: Hexige

last: Saiyin

first: Yang

last: Liu


title: Specific loss of remote fear memory by knockdown of a neuron-specific nucleosome remodeling factor BAF53b in the amygdala

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

summary: Despite recent advances, molecular events and mechanisms involved in long-lasting memory formation are unclear. Here, we report a critical role for nucleosome remodeling factor BAF53b in mice. We observed an increase of BAF53b expression beyond 24 h after fear conditioning in the lateral amygdala, which was crucial for memory retention at remote time. RNA-seq analyses and behavioral rescue experiments identified fibroblast growth factor-1 (FGF1) as a candidate downstream effector.

overall_design: RNA sequencing performed with the lateral amygdala of the mice which were conducted 1 day post-training injection of BAF53b siRNA.

first: M

last: Yoo

first: S

last: Park

first: I

first: J

middle: H

last: Han


title: Effect of Heat stress on m6A modification in CaSki cell

status: Public on Feb 25 2022

city: Hangzhou

first: Lingfang

last: Wang

state: Zhejiang Province

address: 866 Yuhangtang Road

department: Department of Obstetrics and  Gynecology

institute: Zhejiang University

summary: N6-methyladenosine (m6A) occurs extensively on multiple RNA species and is the most abundant internal modification of eukaryotic messenger RNA (mRNA). RNA m6A methylation is a dynamic and reversible process subjected to regulation by three categories of m6A modifier proteins, including m6A methyltransferases/writers (e.g., METTL3/14 methyltransferase complex and METTL16), m6A demethylases/erasers (e.g., FTO and ALKBH5) and m6A binding proteins/readers (e.g., YTH family proteins and IGF2BPs). The dynamic and adjustable nature makes m6A a key regulator in RNA metabolism, and the fate of m6A-modified RNA is modulated by m6A readers.   Previous studies have demonstrated that fever can benefit survival of cancer patients, and currently hyperthermia (elevating body temperature beyond normal) is either administered alone or in combination with radiotherapy or chemotherapy to treat various neoplasms with unclear mechanisms. Accruing evidence has revealed favorable effects of fever/hyperthermia in cancer treatment through affecting the properties of oncogenic proteins (e.g., stability, posttranslational modification, ability to interact with other molecules). Accordingly, we sought to investigate whether and how heat stress affects cancer development by m6A modification.

overall_design: CaSki cells were subjected to heat treatment (42°C, 60 min) before the assay. RNA was extracted for m6A MeRIP sequencing.

first: Guankai

last: Zhan

first: Xiaodong

last: Cheng

first: Chih-Hung

last: Hsu


title: Epicardial Hdac3 promotes myocardial growth through a novel microRNA pathway

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

overall_design: Refer to individual Series


title: m6A modification of circSPECC1 attenuates age-related macular degeneration by resisting oxidative stress injuries and maintaining lipid metabolism in retinal pigment epithelium

city: Nanjing

first: Ying

address: Guangzhou Road

institute: NanJing Medical University

summary:
Background: Retinal pigment epithelium (RPE) is the major site of pathological alterations in AMD, yet the mechanism governing its degeneration is poorly understood.
Results: We found that expression of circSPECC1, a circular RNA derived from the SPECC1 gene, was down-regulated in RPE treated with oxidative stress and inflammation. CircSPECC1 insufficiency elevated mitochondrial superoxide in RPE, leading to oxidative stress induced RPE ferroptosis and depolarization. CircSPECC1 silencing also interfered RPE metabolism, causing irregular lipid metabolism and lipid accumulation. In mice, circSPECC1 deficiency leads to decreased visual ability, atrophic fundus presentations, as well as structural anomalies and reduced epithelial integrity in RPE. Moreover, retinal homeostasis was messed up upon circSPECC1 loss, as shown by photoreceptor dysfunction and microglia activation. Mechanically, decreased circSPECC1 expression in dysfunctional RPE was due to reduced N6-methyladenosine (m6A) levels of circSPECC1 transcript, which interrupted its back-splicing and circularization depending on m6A reader YTHDC1. CircSPECC1 regulated RPE features via directly sponging miR-145-5p to block its interaction with CDKN1A. Overexpressing miR-145-5p aggravated RPE dysfunctions in vivo and in vitro, mimicking effects of circSPECC1 silencing. Additionally, miR-145-5p inhibition alleviated RPE anomalies induced by circSPECC1 insufficiency, while miR-145-5p overexpression aggravated the retinal phenotypes.
Conclusions: Collectively, circSPECC1, mediated by m6A modification and sponges miR-145-5p, resists oxidative stress injuries and maintains lipid metabolism in RPE. Pharmacological supplementation of circSPECC1, miR-145-5p inhibitor or m6A regulator is promising therapeutic option for atrophic retinopathies.

overall_design: Examination of 3 different treatments in ARPE-19 cells.

first: Chen

last: Xue


title: 5 tissues from cattle RNA-seq analysis

city: Beijing

first: caixia

last: yu

address: No.1 Beichen West Road

institute: Beijing Institute of Bioinformatics Chinese Academy of Science

summary: We performed RNA sequencing analyses from cattle, investigating their cell types.

overall_design: Five samples from cattle

first: Li

last: Yang

first: Tan

last: Xu


title: Study of HBV and HDV transcriptomic modulation in HepaRG and PHHs

city: Foster City

first: Ricardo

last: Ramirez

address: 333 Lakeside Drive

institute: Gilead Sciences

summary: Chronic co-infection with HBV and HDV leads to the most aggressive form of chronic viral hepatitis. In this study, we aimed at elucidating the molecular mechanisms leading to the interference on HBV observed in most of patients co-infected with HDV. We performed transcriptomic analyses of in vitro samples in order to  compare the HBV and HDV-induced modulations in viral transcription, immune response, and pathway regulation.This is of importance because beside providing basic knowledge on the interplay between a satellite virus and its helper virus, the data will help the identification of new antiviral target that may affect both viruses.

overall_design: We used two in vitro models: HepaRG cancer cells and primary human hepatocytes. Cells were infected with HBV and/or HDV or mock infected with or without IFN treatment.

first: Julie

last: Lucifora

first: David

last: Durantel

first: Stephane

last: Daffis


title: Diminished trophoblast differentiation in early onset preeclampsia

city: Maplewood

first: Nick

last: Illsley

state: NJ

address: Richmond Ave

institute: Placental Research Group LLC

summary: Comparison of genes associated with the EMT between undifferentiated cytotrophoblast cells (CTB) and differentiated extravillous trophoblast cells (EVT) from third trimester human placenta. Cells isolated from control (placenta previa) and cases (preeclampsia). Cells isolated by immunomagnetic separation using anti-integrin beta4 antibody to purify CTB  and anti-HLA-G antibody to purify EVT.

overall_design: RNA extracted from CTB and EVT from cases and controls, reverse transcribed and analysed on a PCR Array containing probes for 84 genes associated with the EMT (Qiagen RT2 Profiler PCR Array Cat# PAHS-090Z). Relative gene expression compared between CTB and EVT.

first: Nicholas


title: Modeling endogenous HTT/mHTT pathogenesis in fibroblasts and striatal GABAergic neurons from a Mongolian family with Huntington’s disease

first: Lixiang

last: Ma

summary: Single cell RNA-seq and bulk RNA-seq characterization of  human induced pluripotent stem cell (hiPSCs) derived Huntington's disease organoids resembling the human striatum

overall_design: Bulk RNA sequencing of day 60 and 80 human striatal organoids(hStrOs) drived from  human induced pluripotent stem cell (hiPSCs) 7-2 (CAGs 59)  and 12-4 (CAGs 55); Single-cell RNA sequencing of day 110 human striatal organoids(hStrOs) drived from human induced pluripotent stem cell (hiPSCs) 7-2. Both hiPSC-7-2  (CAGs 59) and hiPSC-12-4 (CAGs 55) are from Huntington’s disease patients.

last: Xinyu

first: Saiyin

last: Hexige

first: Liu

first: Ma

last: Lixiang


title: HBV and HDV transcriptomic modulation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Regulation of Liver Regeneration by Hepatocyte O-GlcNAcylation in Mice

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

summary: We studied the role of the post-translational modification called O-GlcNAcylation during liver regeneration. Here we generated O-GlcNAc transferase (OGT-KO) and O-GlcNAcase (OGA-KO) hepatocyte-specific knock-out mice. 70% partial hepatectomy (PHX) was performed to induce liver regeneration. We showed that OGA-KO mice had normal liver regeneration whereas OGT-KO mice had a defect in the termination of liver regeneration.

overall_design: We performed RNA-sequencing on 14 and 28 days after PHX on hepatocyte-specific OGT-KO and OGA-KO male, 8 week old mice as well as their respective controls. Equal amounts of RNA was pooled for each sample (n of 3) in each group. Each sample was ran in two different lanes for a targeted 25 million reads.

first: Udayan

last: Apte


title: Study of HBV and HDV transcriptomic modulation

summary: We performed transcriptomic analyses of in vitro and in vitro samples in order to compare the HBV and HDV-induced modulations in different models (in comparison with an IFN-a treatment for in vitro samples)

overall_design: Study was conducted using humanized mouse liver model FRG KO. 3 mouse livers were collected from each cohort: uninfected (control mice), HBV mono-infected, and HBV & HDV co-infected


title: A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems

city: shanghai

first: zheng

last: Yuan

state: Shanghai

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

summary: We have used high-throughput single-cell RNA sequencing to profile rice inflorescence cells, and construct a genome-scale gene expression resource covering the inflorescence-to-floret transition during early reproductive development.

overall_design: Two replicate inflorescence samples were staged by length — stage 1 (S1) was <2 mm, while stage 2 (S2) was 2–3 mm — to coincide with commencement of branching, spikelet, and floret meristem development . A single young flag leaf (L) covering the inflorescence was used as the control, as bracts could not be removed from the inflorescence . Each replication contains around 100 young inflorescences or leaves.

first: Zheng

first: Jie

last: Zong


title: Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single-cell sequencing

first: Wu

last: Bing

address: No.163 Xianlin Avenue

department: School of the Environment

institute: Nanjing university

summary: Plastic particles in water environment can adsorb heavy metals, leading to combined toxicity to aquatic organisms. However, current conclusions are mostly obtained based on cell population-average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 μg/L 100 nm polystyrene nanoplastics (PS-NPs), 50 μg/L lead (Pb), and their combined exposures on zebrafish intestine cells by single-cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations, including enterocytes, macrophages, neutrophils, B cells, T cells, enteroendocrine cells, and goblet cells.Co-exposure of PS-NPs and Pb caused similar transcriptome profiles with PS-NPs exposure in macrophages, which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However, the Pb alone and combined exposures induced similar modes of action in the enterocytes, including the generation of oxidative stress and abnormal lipid metabolism.

first: Bing

last: Wu

first: Jing

last: Yu


title: Expression data from lung cancer cells subjected to chronic cyclic strain

city: Taoyuan City

first: TSAI

middle: CHI

last: LIU

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

department: Department of Biomedical Sciences and Engineering

institute: National Central University

summary: Human lung cancer cell line A549 and H322m were subjected to cyclic strain (the frequency set in 15%, 0.5HZ) on 0h, 4h and 24h. We compared invasion assay, migration assay, colony formation and microarray assay in stretching and non-stretching groups.

overall_design: human lung epithelial cells from 3 different cell lines

first: Yuan-Jung

last: Huang

first: Yi-Chiung

last: Hsu


title: Pharmacologic inhibition of EphB3 receptor kinase ameliorates EAE

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: To evaluate the potential of EphB3 as a therapeutic target during CNS inflammation, we induced EAE in B6 WT mice and starting at the peak of the disease we initiated treatment with A38 administered. A38 administration ameliorated EAE, and the transcriptional analysis of the astrocytes and microglia revealed the decreased expression of genes associated to inflammation and neurodegeneration.

overall_design: Astrocytes and microglia were isolated from CNS of mice undergoing EAE and which have been treated with A38 or the vehicle as control. Healthy mice were also included in the comparison.

first: Cristina

last: Gutierrez-Vazquez

first: Francisco

last: Quintana


title: Astrocytes and microglia establish physical interactions during CNS inflammation

summary: To investigate astrocyte-microglia interactions in vivo, we took advantage of the recombinant rabies virus (RV). We used glycoprotein G-deficient RV expressing the fluorescent protein mCherry and pseudotyped with glycoprotein EnvA, in combination with GFAP-Cre RABVgp4/TVA transgenic mice that express TVA protein and glycoprotein G in astrocytes under the control of the Gfap promoter. Following injection into GfapRABVgp4/TVA mice, RV initially infects TVA expressing astrocytes, and following its replication RV infect cells in direct contact with astrocytes. We then sorted mCherry+ or mCherry- microglia on EAE mice and prove that microglia that had interacted with astrocytes had a more proinflammatory transcriptional profile.

overall_design: Microglia were isolated from CNS of Gfap-RABVgp4/TVA mice undergoing EAE that had been transduced with Rab-deltaG-mCherry EnvA pseudotyped a week in advanced.


title: Comprehensive gene expression profile of mouse explant retinas expressing shNmnat1, shNmnat2, Nmnat1 and Nmnat2

city: Bunkyo-ku

first: Hiroshi

last: Kuribayashi

state: Tokyo

address: 7-3-1 Hongo

department: Hospital

institute: The University of Tokyo

summary: Nmnat1 and Nmnat2 are NAD synthases that localize to the nucleus and cytoplasm, respectively. They contribute to not only metabolic pathway but also the gene expression through the regulation of NAD-dependent enzymes. Both genes have been shown to be essential for normal retinal development, but the differences between these downstream factors are not well understood. In this study, we performed RNA-sequencing using mouse retinal explants transfected with control, Nmnat1-, Nmnat2-, shNmnat1-, shNmnat2-expressing plasmids. Mouse retinas at postnatal day 0.5 were electroporated with the plasmids and cultured for 3 days. EGFP-expressing cells were purified by a cell sorter, and RNA-seq was carried out.

overall_design: mRNA profiles of control, Nmnat1-knockdown, Nmnat1-overexpressed, Nmnat2-knockdown and Nmnat2-overexpressed retinal explants

first: Masaya

last: Fukushima

first: Sumiko

last: Watanabe


title: RNA-seq Analysis of Fat Tissue Before and After Grafting in Mice

city: Guangzhou

first: Niu

last: Xingtang

state: Guangdong

address: 1838 Guangzhou North Road, Guangzhou, Guangdong, China.

institute: Nanfang Hospital, Southern Medical University

summary: Purpose: To investigate the influence of grafting on adipose tissues, samples were collected from the inguinal fat tissues of mice before grafting and 1 week after grafting.   Methods: The RNA-seq analysis was performed by Novogene (Beijing, China). Total RNA was drawn from the tissues with TRIzol reagent (Absin, Shanghai, China). Transcriptome sequencing were performed by using the Illumina HiSeq X Ten (Novogene Bioinformatics Technology Co., Ltd., Beijing, China). Mapping of 150-bp paired-end reads to the genes was undertaken.   Result: In fat tissues one week after grafting, 28145 genes were detected. And 3271 genes were found to be upregulated, while 3745 genes were downregulated (padj < 0.05 and log2(FC) > 1), when compared with that in the natural fat tissues.   Conclusions: Our study firstly reported the differentially expressed genes in adipose tissues after grafting, providind a valuable reference for fat grafting studies.

overall_design: RNA was extracted from the fat tissues before grafting and 1 week after fat grafting in mice for RNA-seq analysis (3 biological replicates per group).

first: Xingtang

last: Niu

first: Zhuhao

last: Lai

first: Xihang

last: Chen

first: Jianhua

last: Gao

first: Yi


title: miRNA overexpression modulates neutrophil migration

city: West Lafayette

first: Qing

last: Deng

state: Indiana

address: 915 W. State Street

department: Department of Biological Sciences

institute: Purdue University

summary: We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils, and RNAseq for identification of mRNA targets of  miRNA-31, miRNA-190 and miRNA-375  in neutrophils

overall_design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR-31, 190, 375 or vector control

first: Alan

middle: Y

first: Sheng

last: Liu

first: Jun

last: Wan


title: Eph Receptor B3/EphrinB3 signaling impact CNS pathology during EAE

summary: We aimed to investigate the role of EphB3 and EfnB3 on the regulation of astrocyte and microglial responses in the context of CNS inflammation, we KD Efnb3 in microglia or EphB3 in astrocytes both resulting in a comparable amelioration of EAE. The transcriptional analysis of the two cell types revealed the decreased expression of genes associated to inflammation and neurodegeneration in both KD conditions.

overall_design: astrocytes and microglia were isolated from CNS of mice undergoing EAE and which have been intrathecally injected with lentviral vectors either ctrl, shEphB3 astrocyte specfic or shEfnB3 microglia specific.


title: CITE-seq of in vitro control and memory-like human NK cells

city: St Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 S Euclid Ave, Campus Box 8007

department: Department of Medicine

institute: Washington University

summary: Peripheral blood NK cells were cultured into either control or cytokine-induced memory-like NK cells as described in PMID: 32614951. After differentiation, cells were labeled with hashtag antibodies and cite-seq antibodies and control and memory-like NK cells were combined and loaded onto the 10x Genomics Chromium Instrument a the McDonnell Genome Institute at Washington University School of Medicine. The following samples were analyzed to develop a classification tool for unbiased identification of memory-like NK cells in a bulk single-cell RNA-seq population.

overall_design: 1 sample: control and memory-like NK cell generated from the same normal donor are hashtagged into the same files


title: RNA-seq profiling of mammary duct macrophages from virgin, pregnant, lactating and post-weaning mice

city: Parkville

first: Gordon

last: Smyth

address: 1G Royal Pde

institute: Walter and Eliza Hall Institute of Medical Research

summary:
Macrophages are diverse immune cells that reside in all tissues. Although macrophages have been implicated in mammary gland function, their diversity has not been fully addressed. By exploiting high-resolution 3D imaging and flow cytometry, we have identified a unique population of tissue-resident ductal macrophages (DMs) that form a contiguous network between the luminal and basal layers of the entire mammary gland throughout post-natal development. DMs are long-lived and constantly survey the epithelium though dendrite movement based on advanced 3D intravital imaging. While they initially originate from embryonic precursors, DMs derive from monocytes as they expand during puberty. Moreover, they undergo proliferation in pregnancy to maintain complete coverage of the epithelium in lactation, where they are poised to phagocytose milk-producing cells post-lactation and facilitate remodelling. Interestingly, DMs strongly resemble mammary tumour macrophages and form a network that pervades the tumour epithelium. Thus, the mammary epithelium programs specialised resident macrophages in both physiological and tumorigenic contexts.

To explore expression changes as DMs profilerate in pregnancy and lactation, we sorted DMs from the mouse mammary glands of virgin, pregnant, lactating and post-weaning mice and undertook RNA-seq profiling. Results from this data series are shown in Figure 5 of Dawson et al (2020).

overall_design: Three biological replicates were prepared of ductal macrophages from the breast tissue of female mice at four developmental time points: virgin, 16.5 days pregnant, lactating and 1 month post weaning.


title: High-resolution spatial RNA profiling of tissues with immuno-labeling based LCM

first: Xiaodan

last: Zhang

address: 800 Dongchuan Rd

department: Biomedical Engineering

summary:
We report a robust protocol to effectively maintain high RNA quality for immuno-fluorescence-based laser capture microdissection (LCM), enabling finely resolved spatial transcriptome acquisition with only tens of cells from snap-frozen or RNAlater-treated tissues. With the repertoire of readily-available antibodies, this method fulfils the potential of LCM to determine native transcriptomic landscapes, as exemplified here with the characterization of mouse lacteal tip and tube cells.
Methods: mRNA profiles of mouse small intestine epithelial cells (labeled by panCK) and lateal tip and tube cells (labele by Lyve1), as well as human jejunum lymphatic vessel cells were generated by deep sequencing, lacteal tip and tube samples in triplicate, using Illumina hiseq2000. The sequence reads that passed quality filters were analyzed at both the gene expression level and transcript isoform level with Stringtie.
Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per epithelial sample and about 50 million reads per lymphatic vessel cells (in cluding lacteal) to the mouse genome (GRCm38,mm10) and identified average more than 12,000 genes for each sample. RNA-seq data had a average pearson correlation higher than 0.88 for same type samples. Approximately 1.3% of the expressed genes showed differential expression between the lacteal tip and tube samples, with a log2(fold change) ≥2 or ≤-2 and padj value <0.01. This also indicate the overall sameness of lacteal tip and tube cells (the small difference is that tip cells exist filopodia structrue). Differentially expressed genes uncovered several intersting genes that reflected the potential mechanism responsible for the filopodia stucture difference.
Conclusions: We have developed an easily adaptable approach that enables high-quality RNA analysis from a few 10s of cells using IF/LCM from tissues either snap-frozen or preserved with RNAlater. Such methods are uniquely required for the comprehensive delineation of spatial transcriptomic landscapes of complex tissues under near-native conditions. Only with this information can we start to unravel the basic principles that underlie the physiological and pathophysiological processes within these tissues as well as the identity and fundamental characteristics of the resident cells contained therein.

overall_design: mRNA profiles of mouse (6-8 weeks old ) small intestine epithelial and lacteal cells

first: Chuansheng

last: Hu


title: Pharmacologic or genetic inhibition of EphB3 receptor kinase impacts CNS pathology during progressive EAE

first: Zhaorong

last: Li

summary: We evaluated the role of EphB3 on the regulation of astrocyte and microglial responses and its potential as a therapeutic target during progressive EAE. We induced EAE in NOD mice that will develop a progressive form of the disease. Starting at the beginning of the progressive phase, A38 was administered and alternatively EphB3 was KD in astrocytes. Both treatments ameliorated the EAE. The transcriptional analysis of astrocytes and microglia revealed the decreased expression of genes associated to inflammation and neurodegeneration in both conditions.

overall_design: Astrocytes and microglia were isolated from CNS of mice undergoing progressive model of EAE and which have been intrathecally injected with lentviral vectors either ctrl, or shEphB3 astrocyte specific. shCtrl were additionally treated with A38 or the vehicle as control.

first: Cristina

last: Gutierrez-Vazquez

first: Francisco


title: Next Generation Sequencing Facilitates Quantitative Analysis of retinal of db/db mice with KeLuoXin Capsule-treatment

city: Chengdu

first: litao

last: liu

address: Shuxi Road  36

institute: Chengdu Kanghong Pharmaceutical Co., Ltd.

summary:
Purpose:The aim of this study was to investigate the potential effect of KeLuoXin on expression of miRNAs in DR with db/db mouse models
Meathod: Six db/db mice of Group II were treated with 1560mg/kg KeLuoXin for 20 weeks, intragastrically, once a day, six model control mice were treated with equal volume normal saline.After 12 mice were sacrificed,retinal tissues were removed and stored in cryopreservation tubes. Total RNA was isolated from retina samples and used to prepare the miRNA sequencing library, The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 51 cycles on Illumina NextSeq 500 according to the manufacturer's instruction. Raw sequencing data generated from Illumina NextSeq 500 that pass the Illumina chastity filter are used for following analysis. Differentially expressed miRNAs analyses were performed with R package edgeR. Fold change (cutoff 1.5), p-value (≤ 0.05) and CPM (≥ 1 mean in one group) were used for filtering differentially expressed miRNAs.  Cluster analysis arranges samples into groups based on their expression level (CPM values), which allows us to hypothesize the relationships among samples. The heatmap were performed using significant differentially expressed miRNAs. The Scatter-Plot is a visualization method used for assessing the miRNA expression variation between the two compared groups.The Volcano plot is a visualization method for quick visual identification of miRNAs displaying large magnitude changes which are also statistically significant. MiRNA target prediction analysis for top 10 differentially expressed miRNAs were filtered based on miRNA target databases.
Results: We obtained a total of 61,925,224 and 68,473,799 clean reads, 58,159,780 and 61,600,656 adapter-trimmed reads from the T2DM model group and KLX-treatment group.  In detail, a total of 52 miRNAs up-regulated and 12 miRNAs were down-regulated in KLX-treatment group. The absolute fold changes ranged from 1.53 to 7.35 for up-regulated miRNAs, and from 0.020 to 0.008 for the down-regulated ones. The differential expression analysis identified 64 miRNAs that were differentially expressed from T2DM model group to KLX-treatment group and potently regulated by Keluoxin capsule.  Up-regulated miRNAs targets were assigned to 45 categories (FDR<0.05, up-regulated miRNAs) as follows: 29 were associated with biological processes, 15 were associated with cellular components, 1 were involved in molecular functions. The KEGG pathways analysis indicated that the predicted targets of the miRNAs are involved in several important pathwayssuch as insulin secretion signaling pathway and TGF-beta signaling pathway.
Conclusions: Keluoxin capsule may exert the retinal protection in T2DM by targeting miRNAs and regulating miRNAs-mediated signaling pathways downstream.

overall_design:
Retinal miRNA profiles of db/db mice with Keluoxin-treatment and model mice were generated by deep sequencing, in sextuplicate, using Illumina NextSeq 500.
Contributor: Chengdu Kanghong Pharmaceutical Group Co., Ltd.


title: Ferroptosis in oligodendrocyte progenitor cells mediates white matter injury after hemorrhagic stroke

status: Public on Feb 24 2022

first: Danmin

last: Shen

address: No. 10, xitoutiao, youanmenwai

institute: Capital Medical University

summary: Oligodendrocyte progenitor cells (OPCs) differentiate to myelin-producing mature oligodendrocytes and enwrap growing or demyelinated axons during development and post central nervous diseases. Failure of remyelination due to cell death or undifferentiation of OPC contributes to severe neurologic deficits and motor dysfunction. However, how to prevent the cell death of OPCs is still poorly understood, especially in hemorrhagic diseases. In this current study, we injected autologous blood into the mouse lateral ventricular to study the hemorrhage induced OPC cell death in vivo. The integrity of the myelin sheath of the corpus callosum was disrupted post intraventricular hemorrhage (IVH) assessed by using magnetic resonance imaging, immunostaining, and transmission electron microscopy. Consistent with the severe demethylation, we observed massive cell death of oligodendrocyte lineages in the periventricular area. In addition, we found that ferroptosis is the major cell death form in Hemin-induced OPC death by using RNA-seq analysis, and the mechanism was glutathione peroxidase 4 (GPx4) expression and activity reduction-resulted lipid peroxide accumulation. Furthermore, inhibition of ferroptosis rescued OPC cell death in vitro, and in vivo attenuated IVH-induced white matter injury and promoted recovery of neurological function. These data demonstrate that ferroptosis is an essential form of OPC cell death in hemorrhagic stroke, and rescuing ferroptotic OPCs could serve as a therapeutic target for stroke and related diseases.

overall_design: RNA-seq of OPCs treated with vehicle or hemin.

first: Qian


title: Next Generation Sequencing from Tumor Tissues And Tumor-adjacent Tissues of Renal Cell Carcinoma

city: Shanghai

first: Yuchen

address: No.301, Yanchang Middle Road, Jing'an District, Shanghai

department: Department of Urology

institute: Shanghai Tenth People's Hospital, Tongji University School of Medicine

summary: Tumor-adjacent tissues are very important for tumor research. This study aimed to identify hub genes in tumor-adjacent tissues of mice transplanted with 786-o renal cell carcinoma cells. 786-o cells were implanted in nude mice raised to 1 month of age, and normal tissues, tumor tissues, and adjacent tissues were obtained for RNA sequencing. All tissues were sequenced for transcriptome genes. This was the first systematic exploration of the hub genes in the tumor-adjacent tissues of mice transplanted with 786-o renal cell carcinoma cells, which provides a genetic basis for further in-depth study on the underlying regulatory mechanism of renal cell carcinoma.

overall_design: Ten 4-week-old male BALB/c nude mice were obtained from the Animal Center of Shanghai Tenth People’s Hospital (Shanghai, China), every five mice were kept in a cage, kept under specific pathogen-free conditions at 21±2°C and 55±10% humidity under a 12 h light/dark cycle, and fed normal chow with ad libitum access to water. All mice were treated humanely. The 786-o cells were cultured in a 10 cm dish (DMEM medium, 10% fetal bovine serum, PS double antibody). When the cell density was 70-80%, the cells were collected, mixed into a cell suspension with 100 µl sterile phosphate-buffered saline solution, and injected into the right back of a nude mouse at approximately the midpoint of the spinal column and right lower limb. Before injection, 0.5 cm of tissue was taken from the tail of each nude mouse. The mice were fed normally, and the growth of transplanted tumors was observed every day. Seven of the ten mice transplanted tumors successfully. One month later, three mice with tumor diameter of 1-1.5 cm were selected for the next study. Mice were euthanized in a carbon dioxide box, and the tumor and tumor-adjacent tissues (more than 1 cm from tumor tissue capsule) were removed. All tissues were stored in liquid nitrogen and sent to Shanghai Majorbio company for RNA-seq analysis. Different tissues of each mouse were self-compared, three mice were repeated three times.

first: Yunfei

last: Xu

first: Tiancheng

last: Xie

first: Hongmin

last: Zhou


title: CHIP-seq in THP1 cells

first: Jia

last: Yuan

address: Yueyang road 320, Xuhui, Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: In our model, p53 is acting through recruitment of SIRT1 to reduce histone acetylation. A common myeloid cell line THP-1 are p53 mutant cells that have a significant deletion in p53 coding sequence leading to loss of p53 expression.We immunoprecipitated chromatin in THP1 cells using antibodies against H3K27ac and SIRT1 to identify the bingding peak in NEAT1 gene promoter to confirm P53' function

overall_design: We immunoprecipitated chromatin in THP1 cells using antibodies against H3K27ac and SIRT1 to identify the potential binding genes.

first: Yichuan

last: Xiao

first: Qingchen

last: Zhu


title: Genome-wide maps of gene transcription levels in RAW264.7 infected with CdhM-related Mycobacterium tuberculosis H37Ra strain.

city: Wuhan

first: Peng

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary: We report the application of RNA-seq technology for high-throughput profiling of gene transcription in RAW264.7 infected with Mycobacterium tuberculosis H37Ra. By obtaining over six billion bases of sequence from mRNA, we generated genome-wide gene transcription maps of RAW264.7 infected with CdhM-related Mycobacterium tuberculosis H37Ra. We find that numerous genes involved in ER stress are significantly affected by CdhM. This finding indicates that CdhM may induce ER stress during Mtb infection of host cells.

overall_design: Examination of gene expression levels in RAW264.7 infected with CdhM-related Mycobacterium tuberculosis H37Ra strain.

first: Zhengguo

last: He


title: Analyzing ceRNA networks involved in KSHV lytic replication mediated by vIRF1 or vFLIP.

first: Liuxue

last: Sheng

state: Jiangsu

address: Tian Yuan East Road

institute: Nanjing Medical University

summary: Whole-transcriptome sequencing (RNA sequencing [RNA-seq]) was performed in the viral producer cell lines iSLK-RGB BAC16,iSLK-RGB-K9 mutant and iSLK-RGB-K13 mutant cells to uncover the global landscape of long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), mRNAs and microRNAs (miRNAs) in KSHV replication mediated by vIRF1 or vFLIP.

overall_design: iSLK-RGB BAC16, iSLK-RGB-K9 mutant and iSLK-RGB-K13 mutant cells were induced with doxycycline for 72 h and then collected for the whole-transcriptome sequencing.

first: Yuheng

last: Chen

first: Chen

first: Wan

first: Chun

last: Lu


title: Single-nucleus transcriptomic profiles of glial cells in human dorsal root ganglion and spinal cord

first: Donghang

state: Sichuan

address: No.37, guoxue lane, wuhou district, chengdu city, sichuan province

institute: West China Hospital of Sichuan University

summary: Glial cells are present throughout the entire nervous system and paly a crucial role in regulating physiological and pathological functions, such as infections, acute injuries and chronic neurodegenerative disorders. The glial cells mainly include astrocytes, microglia, and oligodendrocytes in the central nervous system (CNS), and satellite glial cells (SGCs) in the peripheral nervous system (PNS). Although the glial subtypes and functional heterogeneity is relatively well understood in mice by recent studies using single-cell or single-nucleus RNA-sequencing, no evidence yet has elucidate the transcriptomic profiles of glia cells in PNS and CNS. Here, we used high-throughput single-nucleus RNA-sequencing to map the cellular and functional heterogeneity of SGCs in human dorsal root ganglion (DRG), and astrocytes, microglia, and oligodendrocytes in human  spinal cord. In addition, we compared the human findings with previous single-nucleus transcriptomic profiles of glial cells from mouse DRG and spinal cord. This work will comprehensively profile glial cells heterogeneity and will provide a powerful resource for probing the cellular basis of human physiological and pathological conditions related to glial cells.

overall_design: Single-nucleus transcriptomic profiles of glial cells in DRG and spinal cord from 3 human donors

first: Yiyong

last: Wei

first: Jin

last: Liu

first: Tao

first: Cheng


title: Affymetrix SNP array data for kidney transplant samples

first: Liang

address: Shatai Road 1023

department: Department of Medical Genetics

institute: Southern Medical University

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Tacrolimus (TAC) is an immunosuppressant widely used in kidney transplantation. TAC displays considerable inter-individual variability in pharmacokinetics (PK). Genetic and clinical factors play important roles in TAC PK.  To define genetic factors associated with tacrolimus blood trough concentration, we performed a genome-wide association study of renal transplant samples from 251 Chinese renal transplant recipients. We identified 23 single nucleotide polymorphisms (SNPs) related to TAC PK variability. All 23 genome-wide significant SNPs (p<5E-8) were located on chromosome 7, including rs776746. These findings suggest that these SNPs may be associated with the unexlained TAC PK variability in renal transplant recipients and require further investigation.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.
Single nucleotide polymorphism analysis of Affymetrix 800K SNP arrays was performed for 251 renal transplant cases.

first: Siyao

last: Yang


title: Global genomic profiling of HIF-1a-regulated genes in bone marrow B cells under hypoxia or normoxia

city: Erlangen

first: Zhen

last: Lin

address: Schloßplatz 4

country: Germany

summary: HIF-1a works as a stress-induced transcription factor to induce target genes mediating cell proliferation, meabolism and inflammation. To gain new insights into HIF-1a biology, we used high-throughput sequencing to analyze global HIF-1a transcriptional networks in WT or HIF-1a deficient bone marrow B cells under hypoxia or normoxia.

overall_design: RNA-seq was used to define HIF-1a regulated genes in bone marrow B cells from WT and HIF-1a deficient mice.

first: Xianyi

last: Meng

first: Aline

last: Bozec


title: Global genomic profiling of estrogen-regulated genes in bone marrow B cells under hypoxia

summary: In women, estrogen deficiency after menopause frequently accelerates osteoclastic bone resorption, leading to osteoporosis, the most common skeletal disorder. However, mechanisms underlying osteoporosis resulting from estrogen deficiency remain largely unknown. To gain new insights into the impact of estrogen on bone marrow B cells, we used high-throughput sequencing to analyze global estrogen transcriptional networks in WT bone marrow B cells under hypoxic culture.

overall_design: RNA-seq was used to define estrogen regulated genes in bone marrow B cells from WT mice.


title: Robust Expansion of Human Pancreatic Progenitors by Small Molecules [RNA-seq]

city: Hangzhou

first: Yunkun

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

summary: An unlimited source of functional human pancreatic β cells are in highly demand. Even with recent advances in pancreatic β-like cell differentiation from human pluripotent stem cells (hPSCs), several hurdles obviously remain and the differentiation protocols need to be further improved. Chemical strategies are particularly useful to address these challenges. Here, through chemical screening, we unexpectedly identified that BET bromodomain inhibitor I-BET151 could robustly promote the expansion of PDX1 and NKX6.1 double-positive human pancreatic progenitors (PPs). These hPSC-derived expandable pancreatic progenitors (ePPs) can proliferate extensively in a chemically defined condition with I-BET151. Even after long-term expansion, these ePPs maintain pancreatic progenitor cell status. In addition, ePPs can efficiently differentiate into pancreatic β-like cells (ePP-β cells). These ePP-β cells are functional and demonstrate glucose-stimulation insulin-secretion (GSIS) capacity. Mechanistically, I-BET151 can activate Notch signaling and promote the expression of key pancreatic progenitor-associated genes and transcriptional network. Conclusively, our studies achieve the long-term goal of robust expansion of human pancreatic progenitors and represent a significant step towards unlimited supplies of functional human pancreatic β cells that are of great interest for biomedical research and regenerative medicine.

first: Xiaojie

last: Ma

first: Ziyu

first: Saiyong


title: Diverging metabolic effects of two energy restricted diets differing in nutrient quality: a 12-week randomized controlled trial in subjects with abdominal obesity

status: Public on Feb 23 2022

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Background: Despite the established relation between energy restriction and metabolic health, the most beneficial nutrient composition of a weight-loss diet is still subject of debate. Objectives: The aim of the study was to examine the additional effects of nutrient quality on top of energy restriction(ER). Methods: A parallel-designed 12-week 25%ER dietary intervention study was conducted. Participants aged 40-70 years with abdominal obesity were randomized over three groups: a 25%ER high nutrient quality diet (n = 40); a 25%ER low nutrient quality diet (n = 40); or a habitual diet (n = 30). Both ER diets were nutritionally adequate, the high nutrient quality ER diet was enriched in monounsaturated and n-3 polyunsaturated fatty acids, fiber, and plant protein and reduced in fructose. Before and after the intervention intra-hepatic lipids, body fat distribution, fasting and postprandial responses to a mixed meal shake challenge test of cardio-metabolic risk factors, lipoproteins, vascular measurements, and adipose tissue transcriptome were assessed. Results: The high quality ER diet (-8.4 ± 3.2) induced 2.1 kg more weight loss (P = 0.007) than the low quality ER diet (-6.3 ± 3.9), reduced fasting serum total cholesterol (P = 0.014) and plasma triglycerides (P < 0.001), promoted an anti-atherogenic lipoprotein profile and induced a more pronounced decrease in adipose tissue gene expression of energy metabolism pathways than the low quality ER diet. Explorative analyses showed that the difference in weight loss between both ER diets were specifically present in insulin sensitive subjects (HOMA-IR ≤ 2.5), in whom the high nutrient quality diet induced 3.9 kg more weight loss than the low nutrient quality diet. Conclusion: A high nutrient quality 25%ER diet is more beneficial for cardiometabolic health than a low nutrient quality 25%ER diet. Overweight insulin sensitive subjects may benefit more from a high than a low nutrient quality ER diet with respect to weight loss, due to potential attenuation of glucose-induced lipid synthesis in adipose tissue. Trial registration: ClinicalTrials.gov NCT02194504.

overall_design: The effects of a 12 week intervention with a 1) 25% energy restriction (ER) high nutrient quality diet, 2) a 25% ER low nutrient quality diet, and 3) a habitual diet was evaluated on adipose tissue gene expression in human subjects at the fasted state, or 4hrs postprandial a mixed-meal challenge.

first: Sophie

last: Schutte

first: Diederik

last: Esser

first: Els

last: Siebelink

first: Charlotte

last: Michielsen

first: Monique

last: Daanje

first: Juri

middle: C

last: Matualatupau

first: Lydia

last: Afman


title: STUB1 dampens IFNγ response in tumors by destabilizing the IFNγ receptor complex

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

institute: Netherlands Cancer Institute

summary: Despite its success, immune checkpoint blockade (ICB) cannot induce durable responses in most patients. This is partially attributed to reduced sensitivity to interferon gamma (IFNγ). Thus, elevating tumor IFNγ-receptor 1 (IFNγ-R1) expression to enhance IFNγ-mediated cytotoxicity is of clinical interest. Here, we demonstrate higher IFNγ-R1 expression to sensitize tumors to IFNγ-mediated killing. To unveil the largely undefined mechanisms of IFNγ-R1 expression, we performed a genome-wide CRISPR/Cas9 knockout screen for suppressors of IFNγ-R1 tumor cell surface abundance. We uncovered STUB1 as key mediator for proteasomally degrading IFNγ-R1/JAK1 complex. Conversely, STUB1 inactivation in tumor cells amplified IFNγ signaling and sensitized to cytotoxic T cells, but permitted IFNγ-induced PD-L1 expression. Rationally combining STUB1 inactivation with anti-PD-1 treatment effectively eliminated tumors in vivo. Clinically corroborating this is a STUB1 transcriptomic signature that associates with response to anti-PD-1 treatment in two patient cohorts. Thus, uncovering STUB1 as a pivotal regulator of IFNγ signaling and a synergistic target for anti-PD-1 treatment.

overall_design: Human melanoma cell lines (Control or with STUB1 knock-out) were grown in the presence of Tcell, IFNgamma or control. Three timepoints were taken, 0 hours, 4 hours and 8 hours.

first: Georgi

last: Apriamashvili

first: David

middle: W

last: Vredevoogd

first: Daniel

last: Peeper


title: Global circulating miRNA screen after morphine delivery

city: Scarborough

first: Adriana

last: Lelis Carvalho

address: 81 Research Drive

institute: MMCRI

summary:
Opioid use is detrimental to bone health, causing both indirect and direct effects on bone turnover.
The aim of the study was to develop a mouse model to evaluate the impact of sustained morphine exposure on bone turnover of both male and female mice and to identify candidate miRNA-mediated regulatory mechanisms that could affect bone.

overall_design: We evaluated the effects of sustained morphine treatment on the skeleton, metabolism, and body composition of male and female C57BL/6J mice by treating with vehicle (0.9% saline) or morphine (18 mg/kg) using subcutaneous osmotic minipumps for 25 days.

last: Carvalho

last: Brooks

first: Deborah

last: Barlow

first: Audrie

last: Langlais

first: Breanna

last: Morrill

first: Karen

last: Houseknecht

first: Mary

last: Bouxsein

first: Jane

middle: B

last: Lian

first: Tamara

last: King

first: Nicholas

last: Farina

first: Katherine

last: Motyl


title: Expression alteration of plasma exosomal circular RNAs in OSA patients with acute myocardial infarction

city: Fuzhou

first: Jie-feng

last: Huang

address: No 20, Chazhong road, Taijiang district

institute: First affiliated hospital of Fujian Medical University

summary: This study demonstrated that there were a number of dysregulated circRNAs in exosomes from OSA with AMI patients, which might be effectively served as a promising diagnostic biomarker and therapeutic targets. Objectives: Circular RNAs (circRNAs) are recently identified as a class of non-coding RNAs that participate in the incidence of acute myocardial infarction(AMI)

overall_design: The plasma exosomal circRNAs profile of three healthy subjects, three OSA without AMI and three OSA with AMI were analyzed using high-throughput sequencing. Bioinformatic analyses were carried out to assess potential core circRNAs and functional analyses were conducted to study biological functions.

first: Ning-Fang

first: Guo-Fu

last: Lin

first: Han-Sheng

last: Xie

first: Bi-Ying

last: Wang

first: Goog-Ping

last: Chen

first: Qi-Chang


title: Genome-wide DNA methylation analysis one year post-COVID-19 infection

city: Madison

first: Andy

last: Madrid

state: Wisconsin

address: 600 Highland Ave

department: Neurological Surgery

institute: University of Wiconsin - Madison

summary: Genome-wide DNA methylation analysis of COVID-19 severity using the Illumina HumanMethylationEPIC microarray platform to analyze over 850,000 methylation sites, comparing COVID-19 patients during and one year after infection, using whole blood tissue.

overall_design:
Bisulfite converted DNA from whole blood tissue from 15 COVID-19 patients during infection and one year post-infection were run on the Illumina HumanMethylationEPIC platform.
This dataset:  blood from COVID-19 patients one year after infection
GSE174818:  blood from COVID-19 patients during infection


title: Estrogen-mediated downregulation of HIF-1 signaling in B lymphocytes influences postmenopausal bone loss

first: Zhen

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

overall_design: Refer to individual Series


title: Pharmacological modulation of the Wnt/β-catenin pathway inhibits the proliferation of long-lived latently-infected memory CD4+ T-cells in ART-suppressed SIV-infected macaques

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: The major obstacle to human immunodeficiency type 1 (HIV-1) eradication is a reservoir of latently-infected cells that persists despite long-term antiretroviral therapy (ART) and is maintained through cellular proliferation. Long-lived memory CD4+ T-cells with high self-renewal capacity such as central memory T-cells (CM) and T memory stem cells (SCM) are major contributors to the viral reservoir in HIV-infected individuals on ART. The Wnt/β-catenin signaling pathway regulates the balance between self-renewal and differentiation of SCM and CM T-cells and pharmacological manipulation of this pathway offers an opportunity to interfere with the proliferation of latently-infected cells. Here, we evaluated in vivo a novel approach to inhibit self-renewal of SCM and CM CD4+ T-cells in the rhesus macaque (RM) model of SIV infection. We used an inhibitor of the Wnt/β-catenin pathway, PRI-724, that blocks the interaction between the co-activator CREB binding protein (CBP) and β-catenin, resulting in the cell fate decision to differentiate rather than proliferate. Our study shows that PRI-724 treatment of ART-suppressed SIVmac251-infected RMs: (i) was well tolerated, with blood counts, liver enzymes, and renal function within normal limits and no alteration of tri-lineage hematopoiesis observed in bone marrow, (ii) resulted in decreased proliferation of SCM and CM T-cells, (iii) modified the SCM and CM CD4+ T-cell transcriptome towards a profile of more differentiated memory T-cells, and (iv) reduced SIV-DNA levels in CM and TFH CD4+ T-cells in the lymph nodes, but did not decrease the overall viral reservoir size. This work is the first demonstration in vivo that  pharmacological modulation can effectively target T cell stemness in long-lived memory CD4+ T-cells, and represents a potential strategy to reduce HIV persistence.

overall_design: Examination of CD4+ T-cell subsets under treatment with PRI-724, 8 macaques were treated and 4 were untreated as controls.

first: M

last: Mavingner

last: Zanoni

first: G

first: J

last: Habib

first: C

last: Mattingly

first: H

last: Kouji

first: B

middle: O

last: Lawson

first: T

last: Vanderford

last: Silvestri

first: S

last: Bosinger

first: A

last: Chahroudi


title: Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro

city: New York

first: Bingjie

last: Zhang

state: New York

address: New York Genome Center, 101 Avenue of the Americas, 7th

institute: New York Genome Center

summary: New technologies that profile chromatin modifications at single-cell resolution offer enormous promise for functional genomic characterization. However, the sparsity of these measurements and the challenge of integrating multiple binding maps represent significant challenges. Here we introduce scCUT&Tag-pro, a multimodal assay for profiling protein-DNA interactions coupled with the abundance of surface proteins in single cells. In addition, we introduce scChromHMM, which integrates data from multiple experiments to infer and annotate chromatin states based on combinatorial histone modification patterns. We apply these tools to perform an integrated analysis across nine different molecular modalities in circulating human immune cells. We demonstrate how these two approaches can characterize dynamic changes in the function of individual genomic elements across both discrete cell states and continuous developmental trajectories, nominate associated motifs and regulators that establish chromatin states, and identify extensive and cell type-specific regulatory priming. Finally, we demonstrate how our integrated reference can serve as a scaffold to map and improve the interpretation of additional scCUT&Tag datasets.

overall_design: We focused on acquiring scCUT&Tag-pro data from healthy human PBMC, and aimed to study the genome-wide localization patterns for six histone modifications (H3K4me1, H3K4me2, H3K4me3, H3K27ac, H3K27me3, and H3K9me3).

first: Avi

last: Srivastava

first: Rahul

last: Satija


title: The histone demethylase PHF8 regulates TGFβ signaling and promotes melanoma metastasis [ChIP-seq]

first: Igor

last: Dolgalev

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: The contribution of epigenetic dysregulation to metastasis remains understudied. Through a meta-analysis of gene expression datasets followed by a mini-screen, we identified PHF8, a histone demethylase of the Jumonji C protein family, as a novel pro-metastatic gene in melanoma. Loss- and gain-of-function approaches demonstrate that PHF8 promotes cell invasion without affecting proliferation in vitro, and increases dissemination but not sub-cutaneous tumor growth in vivo, thus supporting its specific contribution to the acquisition of metastatic potential. PHF8 requires its histone demethylase activity to enhance melanoma cell invasion. Transcriptomic and epigenomic analyses revealed that PHF8 orchestrates a molecular program that directly controls the TGFβ signaling pathway and as a consequence, melanoma invasion and metastasis. Our findings bring a mechanistic understanding of epigenetic regulation of metastatic fitness in cancer, which may pave the way for improved therapeutic interventions.

overall_design: PHF8 loss-of-function (sgRNA) cellular model was generated in SKMEL-147 melanoma cell line.

first: Rana

last: Moubarak

first: Eva

last: Hernando


title: TCF-1 mediates 3D genome reconfiguration during T cell development (HiC)

city: Philadelphia

first: Wenliang

last: Wang

state: PENNSYLVANIA

address: 421 Curie Boulevard

institute: University of Pennsylvania

summary: Lineage-determine transcription factors (LDTFs) can determine gene expression programs of a specific cell type, by rewiring the linear regulatory network. However, it’s not clear whether and how LDTFs can alter the 3D genome organization during development. Here, we investigated the effect of T cell factor 1 (TCF-1) on the reconfiguration of 3D genome during T cell development. Topologically associated domains (TADs) that have higher density of TCF-1 gain more intra-TAD interactions during T cell development. TCF-1 colocalized with CCCTC-binding factor (CTCF) substantially reduced the insulation and increased the local interactions, which additionally have stronger interactions with T cell development genes. We further found that a considerable number of boundaries are lost during T cell development, and that TCF-1 is enriched at the lost boundaries, including the ones near key T cell development genes. Overexpression of TCF-1 in fibroblast demonstrates that both high density of TCF-1 and TCF-1 colocalized with CTCF can optimally increase the local interactions. Correspondingly, knocking out of TCF-1 in DN3 cell line leads to decreased intra-TAD interactions and gain of insulation at some of its binding sites. Finally, we found that TCF-1 can recruit and maintain cohesin at its binding sites, which probably cause reconfiguration of the 3D genome. Taken together, our study shows that TCF-1 can change the 3D genome at both TAD level and finer scale potentially through the recruitment of cohesin.

overall_design: Study the 3D genome reorganization mediated by TCF-1

first: Aditi

last: Chandra

first: Golnaz

last: Vahedi


title: Robust Expansion of Human Pancreatic Progenitors by Small Molecules [ATAC-seq]

first: Yunkun

last: Lu

first: Xiaojie

last: Ma

first: Ziyu

last: Zhou

first: Saiyong

last: Zhu