title: KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure

status: Public on Jun 01 2022

city: Tianjin

first: Niannian

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

summary: Neural differentiation of embryonic stem cells (ESCs) requires precisely orchestrated gene regulation, a process governed in part by changes in 3D chromatin structure. How these changes regulate gene expression in this context remains unclear. In this study, we observed enrichment of the transcription factor KLF4 at some poised or closed enhancers at TSS-linked regions of genes associated with neural differentiation, such as Pax6. Combination analysis employing ChIP, HiChIP and RNA-seq data indicated that KLF4 loss in ESCs induced changes in 3D chromatin structure, including increased chromatin interaction loops between neural differentiation-associated genes and active enhancers. And changes of chromatin structure upregulated expression of neural differentiation-associated genes and promoted early neural differentiation. This study reveals that KLF4 has a differentiation inhibitory effect in regulating 3D chromatin structure and suggests KLF4 inhibits early neural differentiation by regulation of 3D chromatin structure, which is a new mechanism of early neural differentiation.

overall_design: 2 biological replicates were analyzed for WT  and KLF4-KO by RNA-seq and HiChIP analysis.

first: Jinfang

last: Bi

first: Wenbin

last: Wang

first: Lei

last: Zhang

first: W

last: Lu


title: Mechanistic study of Lcr35 probiotic properties using C. elegans model

status: Public on May 19 2022

city: Tours

first: Cyril

last: Poupet

address: 31 avenue Monge

department: Faculty of pharmacy

country: France

institute: University of Tours

type: Expression profiling by high throughput sequencing

summary: To investigate the anti-candidiasis mechanisms of action of Lcr35 strain, a prophylactic and a curative treatments have been implemented in the C. elegans experimental model

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C. elegans wild type (N2 strain) whole organism.

first: Etienne

last: Rifa

first: Sébastien

last: Theil

first: Muriel

last: Bonnet

first: Philippe

last: Veisseire

first: Guillaume

last: Cardin

first: Elise

last: Guéret

first: Stéphanie

last: Rialle

first: Christophe

last: Chassard

first: Adrien

last: Nivoliez

last: Bornes


title: Next generation sequencing facilitates quantitative analysis of transcriptional profiling of Candida albicans wild type and cys4 mutant strains

city: Jinan

first: Wenqiang

last: Chang

state: Shandong

address: No. 44 West Wenhua Road

country: China

institute: Shandong University

summary: mRNA profiles of Candida albicans wild-type (CAF2-1),cys4 mutant and CYS4 integrated strains were generated by deep sequencing, in triplicate, using Illumina HiSeq X Ten. The sequence reads that passed quality filters were analyzed at the transcript isoform level. qRT–PCR validation was performed using SYBR Green assay. We find that filament or biofilm-specific regulators such as UME6, TEC1 and BRG1  and adhesins such as hypha-specific genes ECE1 and  ALS3 were downregulated and negative hyphae regulator NRG1 was upregulated in cys4 mutant. Genes invovled in cell wall synthesis and oxidative stress response were also accordingly regulated in cys4 mutant.

first: Hongxiang

last: Lou


title: polyA+ RNA seq of zebrafish gonad at 25 dpf and 30dpf

status: Public on May 18 2022

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary: In this study, we explored the biological process of zebrafish gonad differentiation through Poly(A)-enriched RNA sequencing，and found that the differences in the gonads differentiating towards testis or ovary were represented through types and expression levels of different genes. Using the GO enrichment classification, it is found that, in the differentiating ovary, the differentially expressed genes are enriched in processes of material synthesis and metabolic pathway, indicating that oocyte requires the accumulation of maternal RNA, protein, sugar, lipids, vitamins and other substances, which is consistent with its basic function of providing primary materials for early development of fertilized embryo. In addition, during ovarian differentiation, the biological processes associated with the nucleus, mitochondria, and cytoplasmic particles are more active, and the genes associated with sperm egg recognition are also expressed during this period. Unlike the differentiating ovary, when the gonad differentiates into testis, the differentially expressed genes are more enriched in biological regulation and development processes, including morphogenesis, cell proliferation, etc.The cytometers adapted to these biological processes are associated with cell membrane, such as membrane receptors, extra-cellular regions, extra-cellular matrix, and cell connections, and also associated with nuclear chromatin. In addition, we enriched 14 signaling pathways involved in testis differentiation, and showed the expression heat map of every differentially expressed gene of each pathway. Overall, the study reveals the different biological processes existing in the differentiation of the zebrafish gonads into ovary or testis, helping us to get a comprehensive understanding of the basis on biological events and molecules during this process.

overall_design: Zebrafish larvae were anesthetized in 0.2 mg/mL MS-222 and disected to isolate gonads. Each gonad is placed under a microscope to identify either the testis or the ovary. Six 25 dpf and six 30 dpf undamaged gonads with sound integrity were choosen for PolyA+ RNA-sequencing.

first: Ding

last: Ye

first: Yixuan

last: Tu

first: Yonghua

last: Sun

first: Zhenxia


title: RNA-seq from the kidney  of 50-weeks-old db/db mice that underwent 40 weeks atorvastatin treatment

status: Public on May 15 2022

city: Guangzhou

first: SHENG

middle: TONG

last: HUANG

state: Guangdong

address: No. 74, Zhongshan 2nd Road, Guangzhou

institute: Sun Yat-Sen University

summary: Statin play an important role in the treatment of diabetic nephropathy (DN). In recent years, increasing attention has been given to the relationship between statin and insulin resistance, but many randomized controlled trial (RCT) studies confirm that the therapeutic effect of statin on DN is more beneficial than harmful. However, further confirmation of whether the beneficial effects of long-term statin administration on DN still outweigh the detrimental effects is needed. In the current study, we found that long-term statin administration may exacerbate insulin resistance, interfere with glucose and lipid metabolism, lead to renal cell apoptosis, inflammation and severe renal fibrosis, and ultimately decrease renal function. Mechanistically,Through RNA seq analysis, we found that long-term statin administration affects lipid metabolism and exacerbates inflammation and fibrosis.

overall_design: 50-weeks-old db/db mice that underwent 40 weeks atorvastatin treatment(10mg/kg.day)

first: Weibin

last: Cai

first: Tongsheng

last: Huang

first: Teng

last: Wu


title: Tumor-intrinsic IRE1α signaling controls protective immunity in lung cancer.

status: Public on May 13 2022

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Ave

department: Biochemistry

country: USA

institute: Weill Cornell Medicine

summary: The IRE1α-XBP1 arm of the unfolded protein response (UPR) has emerged as a central orchestrator of malignant progression and immunosuppression in various cancer types. Yet the role of this pathway in non-small cell lung cancer (NSCLC) has remained largely unexplored. Using an RNA-seq based computational XBP1s detection method applied to TCGA datasets, we uncovered that expression of the IRE1a-generated XBP1s mRNA isoform predicts poor survival in NSCLC patients. Ablation of IRE1a in malignant cells delayed tumor progression and extended survival in an XBP1-dependent fashion in mouse models of NSCLC. This protective effect was accompanied by marked alterations in both lymphoid and myeloid intratumoral cell subsets that elicited durable adaptive anti-cancer immunity. Mechanistically, cancer cell-intrinsic IRE1α activation sustained mPGES-1 expression, enabling production of the immunosuppressive lipid mediator PGE2 in the tumor microenvironment (TME). Accordingly, restoring mPGES-1 expression in IRE1αKO cancer cells rescued normal tumor progression. By identifying the dominant transcriptional networks controlled by IRE1α in mouse lung tumors, we further developed a new gene signature that predicted immune cell infiltration and overall survival in human NSCLC. Hence, our study unveils a key immunoregulatory role for cancer cell-intrinsic IRE1α activation and suggests that targeting this pathway may help enhance anti-tumor immunity in NSCLC.

overall_design: Examination of IRE1α WT and KO murine NSCLC cell line (KRAS;p53), sorted from lung lesions at two time points (day 10 and day 14).

first: Mittal

last: Vivek


title: Gonadectomy-induced transcriptome changes in the ventral cervical spinal cord of male and female rats

city: MINNEAPOLIS

first: Brendan

middle: J.

last: Dougherty

state: MN

address: 420 Delaware Street SE, MMC 388

department: Rehabilitation Medicine

institute: University of Minnesota - Twin Cities

summary: Circulating sex steroids are critical for the development of neuroplasticity in the respiratory motor system.  A primary locus of inducible respiratory neuroplasticity is the phrenic motor nucleus, a column of motor neurons in the ventral cervical spinal cord (C3-C5). In specific, exposure to acute intermittent hypoxia (AIH) induces strengthened synaptic connections to phrenic motor neurons and increased motor output; a form of neuroplasticity called phrenic long-term facilitation (pLTF). Gonadectomy (surgical removal of the testes in males and ovaries in females) reduces circulating sex steroids and eliminates AIH-induced phrenic pLTF in both females and males, implicating sex steroids as critical mediators for the development of neuroplasticity. To begin interrogating mechanisms of sex steroid influence on phrenic motor neurons and to determine the effect of gonadectomy on local gene expression, we performed RNA sequencing on ventral cervical spinal cord samples containing the phrenic motor nucleus. Our findings identified sex-specific gene expression in gonadally-intact rats and suggested that gonadectomy caused greater changes to the transcriptomes of male rats compared to females.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ventral cervical spinal cord tissue (C3-C6) of female and male rats with and without gonadectomy.

first: Shawn

last: Miller

first: Juan

middle: E

last: Abrahante

first: Avtar

last: Roopra

middle: J


title: The M3 Muscarinic Acetylcholine Receptor Promotes Epidermal Differentiation

status: Public on May 06 2022

city: Irvine

first: Bogi

last: Andersen

address: Sprague Hall Rm 206

institute: University of California, Irvine

summary: The M3 muscarinic acetylcholine receptor (CHRM3) is predominantly expressed in the basal epidermal layer where it mediates the effects of the auto/paracrine cytotransmitter acetylcholine. Patients with the autoimmune blistering disease pemphigus develop autoantibodies to CHRM3 and show alterations in keratinocyte adhesion, proliferation and differentiation, suggesting that CHRM3 controls these cellular functions. Chrm3 mice display altered epidermal morphology resembling that seen in patients with pemphigus vulgaris. Here, we characterized the cellular and molecular mechanisms whereby CHRM3 controls epidermal structure and function. We used single cell (sc)RNA-seq to evaluate keratinocyte heterogeneity and identify differentially expressed genes in specific subpopulations of epidermal cells in Chrm3 KO neonatal mice.

overall_design: skin samples were collected from postnatal day 0 Chrm3 KO C57BL/6J mice

first: Junyan

last: Duan

first: Charles

last: Grando

first: Shuman

last: Liu

first: Alex

last: Chernyavsky

first: Jefferson

first: Sergei

middle: A


title: miR-486 is an epigenetic modulator of Duchenne muscular dystrophy pathologies

status: Public on May 05 2022

city: Birmingham

first: Matthew

middle: S

last: Alexander

state: AL

address: 1900 University Blvd. THT 929 Box# 96

department: Pediatrics

institute: University of Alabama at Birmingham

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

overall_design: Refer to individual Series


title: Expression data of tigecycline-treated liver cancer cells

status: Public on Apr 26 2022

city: Shanghai

first: Wenxin

last: Qin

address: No.25, Lane 2200 Xie-Tu Road.

institute: Shanghai Jiao Tong University School of Medicine

summary: Treatment of advanced liver cancer still faces great challenges. Identification of tumor dependencies is  important for developing novel therapeutic strategies for liver cancer. Here, we identified mitochondrial  translation as a major vulnerability of liver cancer by genome-wide CRISPR screen. Targeting  mitochondrial translation by tigecycline showed therapeutic potential in liver cancer. While some liver cancer cells were extremely insensitive to tigecycline.Thus,RNA sequencing was performed to explore mechanisms.

overall_design: mRNA profiles of MHCC97H and PLC/PRF/5 cells treated with tigecycline.

first: Yangyang

last: Zhou


title: Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription

status: Public on Apr 30 2022

city: Bethesda

first: Kathleen

middle: Shaindel Metz

last: Reed

state: MD

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

type: Genome binding/occupancy profiling by high throughput sequencing

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

3D chromatin structure, enhancers, and gene transcription function together to regulate cellular differentiation, establish cellular identity, and respond to external stimuli; however, the functional interplay between these regulatory elements remains incompletely understood.

To infer potential causal relationships, we mapped 3D chromatin architecture, histone H3 K27 acetylation, chromatin accessibility, and gene expression across eight narrowly-spaced time points of macrophage activation.

Enhancers and genes that were connected by a loop exhibited stronger correlation between histone H3K27 acetylation and expression than can be explained by distance or proximity alone, suggesting that the presence of a chromatin loop may facilitate functional regulatory connections via methods beyond simply increasing their frequency of physical proximity. Changes in enhancer acetylation preceded changes in gene expression by 30-60 minutes further supporting a causal relationship. Changes in gene expression exhibit a directional bias at differential loop anchors. The anchors of gained enhancer-promoter loops are associated with increased gene expression of genes oriented away from the center of the loop. Surprisingly, lost enhancer-promoter loops were also associated with increased gene expression, particularly within the bounds of the loop. Analysis of absolute levels of transcription revealed that lost loops were characterized by particularly high levels of internal transcription.

Taken together, these results are consistent with a reciprocal relationship between looping and transcription. In this model, loops can enhance transcription by facilitating enhancer-promoter contacts, but also high levels of transcription can negatively impact loop strength by antagonizing loop extrusion mechanisms.

overall_design:
Refer to individual Series.

Genome-wide time course of chromatin accessibility (ATAC-Seq), enhancer activity (H3K27ac ChIP-Seq), chromatin structure (in situ Hi-C), and gene expression (RNA-Seq) in human THP-1-derived macrophages treated with LPS/IFNg for 0, 0.5, 1, 1.5, 2, 4, 6, and 24 hours.


title: Genome-wide identification of genes critical for in vivo fitness of porcine extraintestinal pathogenic Escherichia coli by using transposon-directed insertion site sequencing

city: WuHan

first: Yin

last: Fan

state: HuBei

address: Shizishan street

summary: This study was aimed to do genome-wide identification of  fitness factors of ExPEC using an mouse infection model. A transposon (Tn) mutagenesis library (input) containing insertions of 72% of the total chromomose encoded genes was used to infect mouse. Bacteria were then recovered from the brain, lung, and spleen (output libraries) at 12 hours post infection. The genomic DNA was extracted from the input and the output libraries. The genomic fragment flanking the transposon was enriched by PCR which was then sequenced by Illumina sequencing. The insertion sites were then mapped to the genome of ExPEC PCN033 strain to identify differentially depleted genes which are genes potentially involved in fitness during infection.

overall_design: Examination of transposon insertion sites before and after mouse infection with a transposon mutagenesis library

first: Qi

last: Huang

first: Fan

last: Yin


title: Transcriptional responses of V. parahaemolyticus to Zn limitation.

status: Public on Apr 24 2022

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

institute: Yangzhou University

summary: RNA sequencing analysis of the transcriptome of V. parahaemolyticus RIMD2210633 strain grown under Zn-deficient (LB pretreated with 35 μM TPEN) and Zn-replete conditions (LB pretreated with 35 μM TPEN along with 500 μM Zn).

overall_design: The RIMD2210633 strain was grown in LB broth to the early-exponential phase (OD600 of ~0.7). Subsequently, two aliquots (1 mL) of the culture were removed and bacterial cells were collected by centrifugation at 6 000 rpm for 5 min. The two bacterial pellets were resuspended with 1 mL LB pretreated with eiher 35 μM TPEN alone or 35 μM TPEN along with 500 μM Zn. After incubation for 15 min at 37°C, total RNA was isolated and subjected to RNA sequencing analysis. Biological triplicate samples obtained from three independent experiments were used.

first: Jun

last: Qiu

first: Yimeng

last: Zhai


title: Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription [Hi-C]

summary: 3D chromatin structure, enhancers, and gene transcription function together to regulate cellular differentiation, establish cellular identity, and respond to external stimuli; however, the functional interplay between these regulatory elements remains incompletely understood. To infer potential causal relationships, we mapped 3D chromatin architecture, histone H3 K27 acetylation, chromatin accessibility, and gene expression across eight narrowly-spaced time points of macrophage activation. Enhancers and genes that were connected by a loop exhibited stronger correlation between histone H3K27 acetylation and expression than can be explained by distance or proximity alone, suggesting that the presence of a chromatin loop may facilitate functional regulatory connections via methods beyond simply increasing their frequency of physical proximity. Changes in enhancer acetylation preceded changes in gene expression by 30-60 minutes further supporting a causal relationship. Changes in gene expression exhibit a directional bias at differential loop anchors. The anchors of gained enhancer-promoter loops are associated with increased gene expression of genes oriented away from the center of the loop. Surprisingly, lost enhancer-promoter loops were also associated with increased gene expression, particularly within the bounds of the loop. Analysis of absolute levels of transcription revealed that lost loops were characterized by particularly high levels of internal transcription. Taken together, these results are consistent with a reciprocal relationship between looping and transcription. In this model, loops can enhance transcription by facilitating enhancer-promoter contacts, but also high levels of transcription can negatively impact loop strength by antagonizing loop extrusion mechanisms.

overall_design: Genome-wide time course of chromatin structure (in situ Hi-C) in human THP-1-derived macrophages treated with LPS/IFNg for 0, 0.5, 1, 1.5, 2, 4, 6, and 24 hours. Coupled with datasets for gene expression (RNA-Seq), and enhancer activity (ATAC-Seq, H3K27ac ChIP-Seq).

middle: M

first: Eric

last: Davis

first: Marielle

middle: L

last: Bond

first: Alan

last: Cabrera

first: Eliza

last: Thulson

first: I

middle: Y

last: Quiroga

first: Shannon

last: Cassel

first: Kamisha

middle: T

last: Woolery

first: Hyejung

last: Won

first: Issac

last: Hilton

first: Michael

middle: I

last: Love

first: Douglas

middle: H

last: Phanstiel


title: Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription [RNA-Seq]

first: Kathleen

last: Reed

overall_design: Genome-wide time course of gene expression (RNA-Seq) in human THP-1-derived macrophages treated with LPS/IFNg for 0, 0.5, 1, 1.5, 2, 4, 6, and 24 hours. Coupled with datasets for chromatin structure (in situ Hi-C) and enhancer activity (ATAC-Seq, H3K27ac ChIP-Seq).


title: Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription [ChIP-Seq]

overall_design: Genome-wide time course of enhancer activity (H3K27ac ChIP-Seq) in human THP-1-derived macrophages treated with LPS/IFNg for 0, 0.5, 1, 1.5, 2, 4, 6, and 24 hours. Coupled with datasets of chromatin accessibility (ATAC-Seq), chromatin structure (in situ Hi-C), and gene expression (RNA-Seq).


title: Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription [ATAC-Seq]

overall_design: Genome-wide time course of chromatin accessibility (ATAC-Seq) in human THP-1-derived macrophages treated with LPS/IFNg for 0, 0.5, 1, 1.5, 2, 4, 6, and 24 hours. Coupled with datasets of enhancer activity (H3K27ac ChIP-Seq), chromatin structure (in situ Hi-C), and gene expression (RNA-Seq).


title: Multi-organ profiles of respiratory syncytial virus (RSV)-infected BALB/c mice

city: Chongqing Provence

first: Yu

last: He

address: No.136, Zhongshan 2nd Road, Yuzhong District

institute: Children's Hospital of Chongqing Medical University

summary: Respiratory syncytial virus (RSV) a leading cause of pediatric and adult morbidity and mortality worldwide. It can cause complications in multiple organs, thus increasing hospital stays and costs. However, RSV-based studies have primarily focused on effects in the lungs and blood, thereby potentially neglecting critical genes and pathways. Hence, studying RSV infection via a novel multi-organ approach is important. In this study, lung, intestine, brain, and spleen tissues from six BALB/c mice (6–8 weeks old; three in control group and three in RSV-infected group) were subjected to RNA sequencing. Differentially expressed genes (DEGs) in each organ were obtained and functional enrichment analysis was performed. We first used CIBERSORT to evaluate the immune-infiltration landscape. Subsequently, common DEGs (co-DEGs) among the four organs were analyzed to identify key genes and pathways. After quantitative reverse transcription-polymerase chain reaction, western blotting, and external validation analysis of key hub genes, their correlation with immune cells and potential functions were explored. We found that the host response to RSV infection varied among the four organs regarding gene expression profiles and immune cell infiltration. Analysis of the 16 co-DEGs indicated enrichment in the platelet and neutrophil degranulation pathways. Importantly, the key gene hemopexin (Hpx) was strongly correlated with the immune cell fraction in the lungs and may participate in the regulation of platelet activation and immune response.

overall_design: Lung, intestine, brain, and spleen tissues from six BALB/c mice (6–8 weeks old; three in control group and three in RSV-infected group) were subjected to RNA sequencing

first: Zhili

last: Wang

last: Zang

first: Enmei

last: Liu


title: Renalase Alleviates Left Ventricular Hypertrophy and Fibrosis in a Chronic Kidney Disease Mouse Model

status: Public on May 01 2022

city: shanghai

first: YI

last: WANG

address: Yishan Road No.600

institute: Shanghai Sixth People’s Hospital

summary: RNLS global knockout (KO) and wild-type (WT) mice were used in the present study to establish a long-term CKD model (up to 18 weeks post-surgery) via 2-step 5/6 Nx, and we observed the role of RNLS by over-expressing it using a cardiac-specific adeno-associated virus (AAV). 2-weeks post-surgery, we injected AAV9-cTnT-RNLS or vector to WTor KO CKD mice by tail vein and the hearts were harvested at week 18. Then RNA-sequencing (RNA-seq) analysis was performed to explore the underlying molecular mechanism.

overall_design: Cardiac mRNA profiles of wild type (WT) and Rnls -/- CKD mice, wild type (WT) and Rnls -/- CKD mice +AAV9-cTnT-RNLS, and WT sham.

first: Yi

first: Jianyong

last: Yin

first: Niansong


title: Evidence for toxic CAG trinucleotide repeats contributing to Huntington’s disease though RNA interference

status: Public on Apr 27 2022

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary: Mutant huntingtin CAG trinucleotide repeat mimetic hairpins are loaded into the RISC and kill cells through RNAi

overall_design: Striatum of mouse brains of wt, 250CAG and 450CAg mice was lized. Subsequently, Ago protein associated short RNAs were pulled down using a GW182 peptide and subjected to smRNA Seq

first: Andrea

last: Murmann

first: Elizabeth

last: Bartom


title: The conserved histone chaperone Spt6 facilitates DNA replication and mediates genome instability

status: Public on Apr 28 2022

city: Boston

first: Catherine

middle: LW

last: Miller

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard


title: S1PR1 Overexpression cells activates endogenous complement signaling and inflammasome to induce tumor metastasis in mice

status: Public on Apr 15 2022

city: Charleston

first: Alhaji

middle: Harune

last: Janneh

state: SC

address: 86 Jonathan Lucas Street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary: Cancer metastasis remains one of the major causes of cancer deaths. The molecular mechanisms of pro-survival lipid signaling activation in inducing cancer cell migration and metastasis are largely unknown. Here, our RNA seq data showed that S1PR1 overexpression B16 melanoma cells injected in C57BL/6 mice via tail vein, activates endogenous complement signaling and inflammasome to induce tumor lung metastasis.

overall_design: C57BL/6 mice (Wildtype) and C3 knockout mice, were injected with S1PR1 overexpression B16 melanoma cell lines, via tail vein. Empty vector was injected in wildtype mice as control. After 21-30 days, mice were euthanized and lung extracted and stored in RNA stabilizer solution (ThermoFisher Scientific, cat# AM7022), until ready to use. Total RNA from mice lungs were isolated and sent for RNA sequencing.


title: Transcriptome analysis provides insights into the mechanism of salt tolerance in rice colonized by arbuscular mycorrhizal fungi

status: Public on Apr 18 2022

city: Taipei

first: Shu-Yi

last: Yang

address: Life Science Building, NTU. No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: Institute of Plant Biology

summary: Although previous studies have addressed the possible benefits of arbuscular mycorrhizal (AM) symbiosis for rice plants under salinity, the underlying molecular mechanisms are still unclear. Here, we showed that rice colonized with AM fungi had better growth performance and higher K+/Na+ ratio under salt stress. Differentially expressed genes (DEGs) responding to AM symbiosis especially under salt stress were obtained from RNA sequencing. AM-regulated DEGs in cell wall modification and peroxidases categories were mainly upregulated in shoots, suggesting AM symbiosis might assist in relaxing the cell wall and scavenging reactive oxygen species (ROS). AM symbiosis indeed improved ROS scavenging capacity in rice shoots under salt stress. In addition, genes involved in Calvin cycle and terpenoid synthesis were enhanced by AM symbiosis in shoots and roots under salt stress, respectively. AM-upregulated cation transporters and aquaporin in both shoots and roots were highlighted. Strikingly, “protein tyrosine kinase activity” subcategory was the most significantly over-represented GO term among all AM-upregulated and downregulated DEGs in both shoots and roots, highlighting the importance of kinase on AM-enhanced salinity tolerance. Overall, our results from the transcriptomic analyses indicate that AM symbiosis uses a multipronged approach to help plants achieve salt stress tolerance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for rice (Oriza. sativa japonica) plants colonized without (mock) or with AM fungi Rhizophagus irregularis and grown without or with salt stress

first: Yun-Hsin

last: Chen


title: Chromatin and transcription dynamics regulate  flower development during  chilling accumulation in peach buds

status: Public on Apr 06 2022

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

summary: In deciduous fruit trees, entrance into dormancy occurs in later summer/fall, concomitantly with the shortening of day length and decrease in temperature. Generally speaking, dormancy can be divided into endodormancy, ecodormancy and paradormancy. In Prunus species flower buds, entrance into the dormant stage occurs when the apical meristem is partially differentiated; during dormancy, flower verticils continue their growth and differentiation. In this work we focused our attention on flower bud development during winter in peach. In order to understand how bud development progress is regulated during winter we integrated cytological epigenetic and chromatin genome wide data with transcriptional outputs to obtained a complete picture of the main regulatory pathways involved in endodormancy.

overall_design: Illumina RNA-Seq analysis of peach flower bud development during winter dormancy process. Flower buds were collected at four time points, corresponding to 0, 200, 475 and 770 chilling units (CU),  during the autumn/winter vegetative arrest season.

first: Monica

last: Canton

first: Gianpiero

last: Marconi

first: Esther

last: Carrera

first: Claudio

last: Bonghi

first: Serena

last: Varotto


title: Genomic Analyses of early-stage diffuse-type gastric cancer lacking  Helicobacter pylori infection

status: Public on Mar 25 2022

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

summary:
We performed the expression RNA-seq experiments for mRNA of gastric cancer tissue.
Most of gastric cancers (GCs) are accompanied by Helicobacter pylori (HP) infection. However, a very limited fraction lacks any signs of HP infection and exhibits early-stage diffuse (ED) phenotype. Although previous genomic cohorts have identified multiple driver mutations for gastric cancers including diffuse-type histology, any driver event of GC without HP has not been elucidated. The present study aims to explore the molecular mechanism with comprehensive genomic and transcriptomic analyses by comparing EDGC with and without HP. EDGCs were classified as HP-negative based on the following criteria: 1) no antibiotic eradication history, 2) no atrophic appearance by endoscopy, 3) no atrophic appearance by histology, 4) negativity in two or more tests such as rapid urease, urease breath, serum antibody, stool antigen and serum pepsinogen tests. DNAs and RNAs were extracted from EDGCs with over 10 mm in diameter to secure sufficient amount of cancer tissues. Laser-capture microdissection was then used to reduce contamination of normal cells for further molecular assays. For transcriptome analyses, we conducted RNA-seq of 2 HP-positive and 4 HP-negative fresh frozen EDGCs obtained endoscopically

overall_design:
Messenger RNAs were extracted from 6 primary gastric cancer samples with or without H. pylori infection. Libraries were then prepared with True  Seq RNA Access Sample Preparation Kit (Illumina) and sequenced on the  HiSeq 2000(Illumina).

***Raw data are not available for this series due to patient privacy concerns. Furthermore, the raw data will not be available through controlled-access resources such as dbGaP or EGA. The IRB prohibits public access to the raw data.

first: Fujisaki

last: Junko


title: Pro-survival lipid metabolism activates intracellular complement signaling to induce inflammasome-mediated tumor metastasis

status: Public on Mar 23 2022

summary: Tumor metastasis remains one of the major causes of cancer-related deaths in patients with solid tumors. Mechanisms by which metabolic alterations regarding pro-survival lipid signaling   activation in inducing cancer cell migration and metastasis are largely unknown. Here, we demonstrate that S1P metabolism activates endogenous complement signaling for inducing tumor metastasis via inducing inflammasome-mediated pro-inflammation. Our studies using molecular, pharmacologic and genetic tools showed that activation of sphingosine 1-phosphate (S1P) and S1P receptor 1 (S1P/S1PR1) induces tumor metastasis via enhanced intracellular complement signaling by the regulation of the C3-PPIL1 complex and subsequent inflammasome activation in cancer cells and in vivo xenograft-derived tumors.

overall_design: PPIL1 gene was stably knocked out in B16 cell line using CRISPR-Cas9, and treated with JTE-013+ S1P lyase inhibitor (DPO). Total RNA was extracted from the PPIL1 KO treated vs untreated samples,  as well as  scrambled treated vs untreated as controls.


overall_design: NB7 cells were transfected with different HP mimicking two different mHTT variants or CAG contorl siRNAs. Subsequently, Ago protein associated short RNAs were pulled down using a GW182 peptide and subjected to smRNA Seq


title: RNA-seq in H1299 cell lines

status: Public on Mar 30 2022

city: Zhengzhou

first: zhuoyu

last: gu

state: China

address: No. 50, Jianshe East Road, Erqi District

institute: First Affiliated Hospital of Zhengzhou University

summary:
Purpose: The goals of this study are to investigate the primary biological process of HNRNPC.
Methods: Briefly, samples (H1299 cells transfected with control or HNRNPC shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.).
Results: RNA-seq in H1299 cell lines revealed that HNRNPC mainly regulated cell growth, cell migration, extracellular matrix organization, angiogenesis, collagen fibril organization, and T cell mediated cytotoxicity.
Conclusions: HNRNPC mainly regulated cell growth, cell migration, extracellular matrix organization, angiogenesis, collagen fibril organization, and T cell mediated cytotoxicity.

overall_design: mRNA profiles of H1299 HNRNPC shNC cells and H1299 HNRNPC knockdown cells

first: Zhuoyu

last: Gu


title: In vivo reprogramming drives dedifferentiation and enhances liver regeneration

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Mammalian tissues have a limited regenerative capacity. Previous studies showed that dedifferentiation contributes to tissue regeneration in non-mammalian vertebrate species such as zebrafish and newt. However, dedifferentiation is rarely observed in mammalian tissues even in the neonatal stage and therefore artificial induction of dedifferentiation might enhance regeneration in mammalian tissues. Here we demonstrate that short-term expression of Yamanaka 4 factors (4F) induces dedifferentiation and proliferation in the liver by using lineage-traceable, hepatocyte-specific 4F inducible mouse model. Global transcriptome analysis shows that 4F expression transiently reduces the expression of hepatic-lineage markers and induces the expression of a large set of proliferative markers and epigenetic modifiers along with global epigenetic changes as assessed by DNA-accessibility analysis. More importantly, lineage-tracing experiments showed that 4F-expressing hepatocytes acquire liver stem/progenitor cell markers, suggesting that 4F induces partial reprogramming. Moreover, 4F enhances MyoD-mediated transdifferentiation in the liver, suggesting that 4F endows hepatocytes with plasticity. Lastly, 4F expression attenuated liver injury associated with more proliferative capacity and better survival rate, indicating that 4F enhances liver regeneration. Taken together, these results demonstrate that liver-specific 4F expression induces dedifferentiation and promotes liver regeneration.

overall_design: The Hep-4F mouse model carries Alb-Cre, tetO-4F and LoxP-STOP-LoxP-rtTA-IRES-GFP (Fig. 1a). In this mouse model, LoxP-STOP-LoxP cassette is excised by Alb-Cre, resulting in expression of rtTA together with GFP as a lineage-tracing marker, allowing for specific 4F induction in the liver when doxycycline (Dox) is administrated. We performed bulk RNA-Seq, bulk ATAC-Seq to determine the effect of 4F on liver tissue dedifferentiation and regeneration. We also performed single-cell RNA-Seq to identify the 4F responses within each cell population of liver tissues using +Dox and -Dox tissue samples. Regarding the bulk sequencing analysis, hte mice were treated with and without Dox in a time-series setup and then the liver tissues were collected for sequencing. Another set of controls with mice treated with carbon tetrachloride (CCl4) to induce liver injury and liver regeneration were also included in the bulk sequencing.

first: Tomoaki

last: Hishida

first: Ling

last: Huang


title: Reduced Representation Bisulfite Sequencing (RRBS) of fluorescence-activated cell sorted (FACS) human spermatozoa stained with Chromomycin A3 (CMA3) and YO-PRO-1 (YOPRO) in fertile donors and infertile patients with short anogenital distances.

status: Public on Apr 04 2022

city: Geneva

first: Ludwig

last: Stenz

address: Rue Michel-Servet 1

department: Department of Genetic Medecine and Development

country: Switzerland

institute: University of Geneva

type: Methylation profiling by high throughput sequencing

summary: Infertile patients with short AGD are considered as having poorly been exposed to androgen during their past fetal lives.  Sub-populations of spermatozoa were selected for their protamine content (CMA3+ versus CMA3-) and for apoptosis (YOPRO+ versus YOPRO-).

overall_design:
Pairwise comparisons of the epigenomic data between donors and patients, ranked according to the staining and sorting results:
C3_[YOPRO-_patients]_VS_[YOPRO-_donors]
C8_[YOPRO+patients]_VS_[YOPRO+_donors]
C2_[CMA3-_patients]_VS_[CMA3-_donors]
C9_[CMA3+_patients]_VS_[CMA3+_donors]
Pairwise comparisons of the epigenomic data according to the staining and sorting results:
C6_[YOPRO-_donors]_VS_[YOPRO+_donors]
C7_[YOPRO-_patients]_VS_[YOPRO+_patients]
C5_[CMA3-_donors]_VS_[CMA3+_donors]
C4_[CMA3-_patients]_VS_[CMA3+_patients]

first: Matthias

last: Beyens

first: Mark

last: Gill

first: Ariane

last: Paoloni-Giacobino

first: Christian

last: De Geyter


title: The purinergic P2Y14 receptor links hepatocyte death to hepatic stellate cell activation and fibrogenesis in the liver

status: Public on Apr 07 2022

city: NEW YORK

first: Robert

middle: F

last: Schwabe

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

summary: Characterization of genes specifically expressed in mouse primary quiescent hepatic stellate cells (HSC) compared to the whole liver by RNA-sequencing and single cell RNA sequencing as well as effect of UDP-glucose treatment on mouse primary HSC.

overall_design: Bulk RNA sequencing of 13 samples: 4 quiescent HSC, 3 whole liver, 3 cultured-HSC untreated, 3 cultured HSC treated with UDP-glucose for 24h. Single cell RNA sequencing of normal untreated liver.

first: Aveline

last: Filliol

first: Ingmar

last: Mederacke

first: Silvia

last: Affo

first: Francesco

last: Brundu


title: RNA-Seq analysis of estrogen-deprived MM134 HER2WT and HER2L755S cells

status: Public on Mar 07 2022

city: Houston

first: Rashi

last: Kalra

state: TX

address: ABBR R531A, One Baylor Plaza, One Baylor Plaza

department: BREAST CENTER

institute: Baylor College of Medicine

summary: We conducted RNA sequencing of MM134 lobular cell line expressing HER2 WT and L755S cells grown in low estrogen conditions followed by Gene Set Enrichment Analysis (GSEA) to identify altered gene expression pathways in L755S cells. mTOR (also called MTORC1) signaling was the top significantly up-regulated pathway in HER2 L755S cells as compared to HER2 WT cells

overall_design: mRNA profiles of two different cell lines to identify altered gene expression upon estrogen deprivation.

first: Meghashyam

last: Kavuri


title: Chromatin and transcription dynamics regulate flower development during chilling accumulation in peach buds

first: Cristian

last: Forestan

overall_design: ChIP-Seq analysis of H3K4me3 and H3K27me3 histone modification dynamics winter dormancy process in peach flower bud development. Flower buds were collected at three time points, corresponding to 0, 475 and 770 chilling units (CU), during the autumn/winter vegetative arrest season.

first: Monica

last: Canton

first: Gianpiero

last: Marconi

first: Esther

last: Carrera

first: Claudio

last: Bonghi

first: Serena

last: Varotto


title: RNA sequencing of blastocyst-stage mouse embryos in the presence or absence of RNA decay activator UPF2

status: Public on Mar 16 2022

city: La Jolla

first: Heidi

last: Cook-Andersen

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

summary:
Purpose: The goal of this study is to compare transcriptome profiles of whole blastocysts in the presence or absence of UPF2, via an approach optimized for low-input samples.
Methods: Blastocyst mRNA profiles of wild-type (WT) and Upf2 knockout (Upf2−/−) mice were generated by deep sequencing, using Illumina 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with DESeq2 and with IsoformSwitchAnalyzeR.
Results: We identified transcripts targeted for decay by UPF2 and the NMD pathway in the blastocyst via multiple methods. We found that NMD regulates a cohort of RNAs involved in cell survival.

overall_design: Blastocyst-stage embryo RNA profiling in  Upf2−/− and WT mice.

first: Jennifer

last: Chousal


title: Investigation of the AR cistrome in response to RB depletion in castration-resistant prostate cancer

status: Public on Apr 01 2022

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

summary: These studies examine the consequence of RB loss on AR function in late stage disease

overall_design: AR cistrome alterations in response to RB depletion after DHT treatment in castration-resistant prostate cancer

first: Karen

last: Knudsen

first: Amy

middle: C

last: Mandigo


title: Total RNA-sequencing in TC28a2 cell line with or without hypertrophic medium

status: Public on Apr 03 2022

city: Seoul

first: Dong Suk

last: Yoon

address: Yonsei-ro 50-1

department: Orthopaedic Surery

country: South Korea

institute: Yonsei University College of Medicine

summary: We report the results of performing RNA sequencing using RNA extracted from TC28a2 cells grown in the presence of hypertrophic differentiation medium compared to RNA extracted from TC28a2 cells grown in growth medium. For preparation of samples for RNA sequencing, total RNAs were extracted from TC28a2 cells treated with growth medium (n=2) or hypertrophic medium (n=3) at day 5 of differentiation. RNA was extracted using Trizol (Invitrogen) following the protocols provided by the manufacturer. Isolated RNAs were submitted to the Macrogen Inc. (Macrogen Inc., Seoul, South Korea) for total RNA-sequencing. The overall quality of the extracted total RNAs were validated using spectrophotometry. To remove low quality and adapter sequence, the raw was read by the sequencer before analysis and align the processed reads to the Homo sapiens using HISAT2 v2.1.059. The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from the NCBI, and transcript assembly of known transcripts was then processed by StringTie v2.1. Base on the result of that, expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample. The expression profiles are used to do additional analysis such as DEG (Differentially Expressed Genes). The relative abundances of gene were measured in read count using StringTie. Genes with one more than zeroed read count values in the samples were excluded. Filtered data were log2-transformed and subjected to RLE Normalization. Statistical significance of the differential expression data was determined using DESeq2 nbinomWaldTest and fold change in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm. For DEG set, hierarchical clustering analysis was performed using complete linkage and Euclidean distance as a measure of similarity. Enrichment of gene ontology analysis was performed for DEGs using g:Profiler and KEGG pathway analysis was tested based on KEGG pathway (https://www.genome.jp/kegg/) database. We used multidimensional scaling (MDS) method to visualize the similarities among samples. We applied to the Euclidean distance as the measure of the dissimilarity. Hierarchical clustering analysis also was performed using complete linkage and Euclidean distance as a measure of similarity to display the expression patterns of differentially expressed transcripts which are satisfied with fold change ≥2 and raw p <0.05. All data analysis and visualization of differentially expressed genes was conducted using R 3.6.1(www.r-project.org).

overall_design: Total RNA sequencing in TC28a2 cells grown with 2 different medium (growth or differentiation) for 5 days

first: Dong

first: Sung-Hwan

last: Kim


title: Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19 [RNA-Seq]

status: Public on Mar 09 2022

city: Bethesda

first: William

middle: W

last: Lau

address: 4 Memorial Drive

department: Laboratory of Immune System Biology

institute: National Institute of Allergy and Infectious Diseases

summary: Acute viral infections can have durable functional impacts on the immune system long after recovery, but how they affect homeostatic immune states and responses to future perturbations remain poorly understood. Here we use systems immunology approaches, including longitudinal multimodal single cell analysis (surface proteins, transcriptome, and V(D)J sequences), to comparatively assess baseline immune statuses and responses to influenza vaccination in 33 healthy individuals after recovery from mild, non-hospitalized COVID-19 (mean: 151 days after diagnosis) and 40 age- and sex-matched controls who never had COVID-19. At baseline and independent of time since COVID-19, recoverees had elevated T-cell activation signatures and lower expression of innate immune genes in monocytes. COVID-19-recovered males had coordinately higher innate, influenza-specific plasmablast, and antibody responses after vaccination compared to healthy male and COVID-19-recovered females, partly because male recoverees had monocytes with higher IL-15 responses early after vaccination coupled with elevated pre-vaccination frequencies of "virtual memory" like CD8+ T-cells poised to produce more IFNg upon IL-15 stimulation. In addition, the expression of the repressed innate immune genes in monocytes increased by day 1 through day 28 post-vaccination in recoverees, thus moving towards the pre-vaccination baseline of healthy controls. In contrast, these genes decreased on day 1 and returned to the baseline by day 28 in controls. Our study reveals sex-dimorphic impacts of prior mild COVID-19 and suggests that viral infections in humans can establish new immunological set-points impacting future immune responses in an antigen-agnostic manner.

overall_design: Blood samples were collected on 33 subjects with prior symptomatic SARS-CoV-2 infection (diagnosed by nasal PCR test) or asymptomatic infection (by antibody test), and 40 age- and sex-matched healthy controls with no history of COVID-19, at each of the following timepoints relative to seasonal influenza vaccination (day 0): days -7, 0, 1, 7, 14, 28, 70, 100. Subjects between ages 18 – 64 years were administered the Flucelvax Quadrivalent seasonal influenza vaccine (2020-2021; Seqirus Inc, Summit, NJ), whereas those aged 65 years old and above were administered the high-dose Fluzone Quadrivalent seasonal influenza vaccine (2020-2021; Sanofi Pasteur Inc, Swiftwater, PA).    Samples from days -7, 0, 1, 7, and 28 were selected and drawn directly into the Tempus™ Blood RNA Tube (Thermo Fisher Scientific, Waltham, MA) according to manufacturer’s protocol. The RNA samples were isolated in groups of 12-22 samples per batch based on age, gender, and patient group. Each RNA isolation batch had a technical control, which was tempus blood collected from one healthy donor, who was also a part of this study. RNA from this sample was isolated with almost every batch except for a few due to technical issues. For each sample, 500ng of total RNA was used to isolate mRNA via poly(A) selection. All libraries were sequenced on the NovaSeq 6000 instrument across five plates. A total 11 samples were re-sequenced on a NextSeq 500 instrument to replace some of the initial samples with low output. Technical replicates were placed on each plate to control for plate variability.

first: Rachel

last: Sparks

first: Can

last: Liu

first: Kyu-Lee

last: Han

first: Kiera

last: Vrindten

first: Guangping

last: Sun

first: Milann

last: Cox

first: Sarah

last: Andrews

first: Neha

last: Bansal

first: Laura

last: Failla

first: Jody

last: Manischewitz

first: Gabrielle

last: Grubbs

first: Lisa

middle: R

last: King

first: Galina

last: Koroleva

first: Stephanie

last: Leimenstoll

first: LaQuita

last: Snow

first: Princess

last: Barber

first: Valerie

last: Mohammed

first: Cindy

last: Palmer

first: Deitra

last: Shipman

first: Anne

last: Carmona

first: Jean

last: Hammer

first: Ericka

last: Garrett

first: Jinguo

last: Chen

first: Juanjie

last: Tang

first: Amrita

last: Mukherjee

first: Brian

last: Sellers

first: Richard

last: Apps

first: Adrian

last: McDermott

first: Andrew

last: Martins

first: Evan

last: Bloch

first: Hana

last: Golding

first: Surender

last: Khurana

first: John

last: Tsang


title: Next-generation sequencing Facilitates Quantitative Analysis of Wild Type and Arid1a haploinsufficiency mice excitatory neuron Transcriptomes and Genome-wide maps of chromatin state  in Wild Type and Ar id1a Haploinsufficiency mice in excitatory neuron

status: Public on Mar 21 2022

city: beijing

first: Peipei

last: liu

address: No. 25-1 West Beisihuan Rd, Haidian District, Beijing

department: State Key Laboratory of Stem cells and Reproductive Biology

institute: institute of zoology,Chinese academy of sciences

summary:
Purpose: The goals of this study are to compare WT and Arid1a in excitatory neuron transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) differentially expressed genes and find target genes. We performed chromatin-immunoprecipitation coupled to sequencing (ChIP-seq) to dissect the relationship between the differentially expressed genes and the occupancy of  H3K27ac and Arid1a.
Methods: Excitatory neurons mRNA profiles of adult wild-type (WT) and Arid1a Het mice were generated by deep sequencing,  in  duplicate,using  Illumina HiSeq 2500 system.All RNA-Seq data were aligned to mouse genome version mm10 using  Salmon (v.1.1.0) .We use cluster software and Euclidean distance matrix for the hierarchical clustering analysis of the expressed gene and sample program at the same time, the clustering results can be viewed with javaTreeview. qRT–PCR validation was performed using SYBR Green assays. we performed ChIP-seq using freshly isolated P14 from  Wild Type and EED-/-  cerebellar tissues  . DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 50bp.
Results:Only transcripts that showed more than 1.5-fold differential expression compared to control were subjected to relevance network analysis. 3815 candidate genes that were differentially expressed with biological functional groups as compared between WT and Arid1a Het mice .We found that the enrichment of H3K27acwas decreased  in Arid1a Het mice.
Conclusions: Our study represents the first detailed analysis of Wild Type and Arid1a haploinsufficiency mice excitatory neuron transcriptomes, with two biologic replicates, generated by RNA-seq technology. We report the application of ChIP-sequencing technology for high-throughput profiling of histone modifications in excitatory neurons.

overall_design: mRNA profiles  and  histone modifications of adult wild-type (WT) and ARID1A haploinsufficiency mice

first: Pei-Pei

last: Liu

first: Chang-Mei


title: Schwann cells contribute to keloid formation

city: Vienna

first: Martin

last: Direder

state: Vienna

address: Lazarettgasse 14

department: Orthopedic and Trauma Surgery

country: Austria

institute: Medical University Vienna

summary: Due to limited availability of proper models to study keloid development, the underlying pathomechanisms of this severe skin disease is still poorly understood. Here we performed single-cell sequencing of keloids and identified the occurrence of a so far unrecognized keloidal Schwann cell population, remaining in the scar tissue after wound healing. In contrast to normal skin, keloidal Schwann cells possess a repair-like phenotype and high cellular plasticity. Our data reveal that keloidal Schwann cells directly contribute to the formation of the extracellular matrix and affect M2 polarization of macrophages. Indeed, we show that macrophages in keloids predominantly display a M2 polarization and produce factors inhibiting Schwann cell differentiation. Our data suggest that this cross-talk contribute to the infinite growth of keloids and that targeting Schwann cells might represent a novel treatment option for keloids.

overall_design: Single cell RNA-sequencing gene expression comparison of keloid tissue with normal scars and healthy skin. Single-cell suspension from four keloids, one normal skin and three normal scars were prepared using MACS Miltenyi Whole Skin Dissociation Kit (Miltenyi). Libraries were generated using Chromium Next GEM Single Cell 3´GEM, Library & Gel Bead Kit v3.1, Chromium Nexxt GEM Chip G Single Cell Kit and Single Index Kit T Set A (all 19x Genomics, Pleasanton, CA, USA). Data were analysed in combination with healthy skin data from Tabib et al. 2018 (PMID:29080679) as well as neurofibroma data from Brosseau et al. 2021 (PMID: 33413690)

first: Tamara

last: Weiss

first: Dragan

last: Copic

first: Vera

last: Vorstandlechner

first: Maria

last: Laggner

first: Caterina

last: Mildner

first: Katharina

last: Klas

first: Werner

last: Haslik

first: Christine

last: Radtke

first: Matthias

last: Farlik

first: Lisa

last: Shaw

first: Bahar

last: Golabi

first: Erwin

last: Tschachler

first: Konrad

last: Hötzenecker

first: Hendrik

middle: J

last: Ankersmit

first: Michael


title: Genome-Wide DNA Methylation Profiling of the Failing Human Heart with Mechanical Unloading Identifies LINC00881 as an Essential Regulator of Calcium Handling in the Cardiomyocyte [RNAseq]

status: Public on Mar 04 2022

city: New York

first: Veli

middle: K

last: Topkara

department: Cardiology

summary:
Background: Human heart failure is characterized by global alterations in the myocardial DNA methylation profile, yet little is known about epigenetic regulation of non- coding transcripts and potential reversibility of DNA methylation with left ventricular assist device (LVAD) support.
Method: High-density genome-wide mapping of myocardial DNA methylation was performed in 36 patients with end-stage heart failure at the time of LVAD implant and 8 patients at the time of LVAD explant using bead-based array platform. Transcriptomic and functional studies were performed in human induced pluripotent stem cell derived cardiomyocytes (iPSCs).
Results: Etiology-specific analysis revealed 2079 differentially methylated positions (DMPs) in ischemic cardiomyopathy (ICM) and 261 DMPs in non-ischemic cardiomyopathy (NICM).  192 DMPs were common to ICM and NICM. Analysis of paired samples before and after LVAD support demonstrated reverse methylation of only 3.2% of HF-specific DMPs. Methylation-expression correlation analysis yielded several protein-coding genes that are hypomethylated and upregulated (HTRA1, FAM65A, FBXO16, EFCAB13, AKAP13, RPTOR) or hypermethylated and downregulated (TBX3) in ICM and NICM patients. A novel cardiac-specific super-enhancer lncRNA (LINC00881) is hypermethylated and downregulated in the failing human heart. LINC00881 is an upstream regulator of sarcomere and calcium channel gene expression including MYH6, CACNA1C, and RYR2. LINC00881 knockdown significantly reduced peak calcium amplitude in the beating human iPSCs.
Conclusions:  Failing human heart exhibits etiology-specific changes in DNA methylation including coding and non-coding regions, which are minimally reversible with mechanical unloading. Epigenetic reprogramming may be necessary to achieve transcriptional normalization and sustained clinical recovery from heart failure.

overall_design: We report the effect of LINC00881 overexpression and knockkown on the transcriptomes of human induced pluripotent stem cell derived cardiomyocytes (iPSCs). RNA Sequencing analysis of human iPSCs LINC00881 overexpression (4 biological replicates per LINC00881 versus control plasmid overexpression) and LINC00881 knockdown (4 biological replicates per LINC08881 versus scrambed oligo control GapmeR knockdown).

first: Xianghai

last: Liao


title: RNAseq transcriptome analysis of THP-1 macrophages activated by VHL-deficient kidney tubule cells

status: Public on Mar 12 2022

city: Taichung

first: Tien

last: Hsu

address: No.91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Sciences

institute: China Medical University

summary: Clear-cell renal cell carcinoma (ccRCC) is the most prevalent subtype of renal cell carcinoma (up-to 70% of all RCC types). There is a very close causal correlation between ccRCC and inactivation of the tumor suppressor gene von Hippel-Lindau (VHL) located on chromosome 3p25‐26. Up to 80% of sporadic ccRCC carry genomic mutations or epigenetic inactivation of VHL and nearly 100% familial ccRCC (in VHL disease) contain VHL deficiency. Accumulating evidence has indicated that ccRCC arises at the site of chronic inflammation and this solid tumor contains a substantial number of infiltrated immune cells. This indicates that ccRCC may be induced by the interaction between kidney tubule cells carrying inactivated VHL gene and the inflammatory microenvironment. In this study we characterized the interaction between VHL-deficient kidney tubule cells and macrophages with relevance to ccRCC formation, and found that human macrophages induced by VHL-deficient kidney tubule cells exhibit distinct gene expression program containing the signatures of tumor-associated macrophages that can promote ccRCC progression.

overall_design: The partially differentiated macrophages derived from human monocyte precursor THP-1 cells [with 50 ng/ml phorbol 12-myristate-13-acetate (PMA)] were cocultured  in the Boyden chamber with human kidney tubule cell line HK-2 with (shVHL61) or without (shLuc) VHL knockdown. After 48 hr, total RNA was purified from macrophages and prepared sequencing.

first: Thi-Ngoc

last: Nguyen

first: Hieu-Huy

last: Nguyen-Tran

first: Yi-Xiu

last: Lan


title: Baf250A, Brd9 and Baf180 knockdown impact on myoblast transcriptome

city: Farmington

first: Sabriya

last: Syed

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

summary: We performed RNA-seq to investigate global changes in gene expression in proliferating myoblasts transduced with either the scramble, Baf250A, Brd9 or Baf180 shRNAs. This study revelaed that the Baf250-containing BAF complex and the Brd9-containing ncBAF complex contribute to myoblast proliferation but the Baf180-containing PBAF subfamily does not.

overall_design: Gene expression profiles of proliferating C2C12 myoblasts cells transduced with either the scramble, Baf250A, Brd9 or Baf180 shRNAs.

middle: A

first: Teresita

last: Padilla-Benavides

first: Anthony

middle: N

last: Imbalzano


title: RNA-seq of wild-type and mfn1-/-,mfn2-/- tibialis anterior muscle (mouse).

status: Public on Mar 14 2022

city: Dallas

first: Prashant

last: Mishra

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: We report the transcriptome changes in tibialis anterior muscle in response to deletion of the Mfn1 and Mfn2 genes.

overall_design: Floxed alleles for Mfn1 and Mfn2 were combined with Myl1-Cre driver to knockout these genes in fast-twitch muscle fibers. Tibialis anterior muscles were colleceted from wild-type (control) and knockout littermates at various ages (4 weeks, 6 weeks, 8 weeks, and 10 weeks).

first: Zhenkang

last: Chen


title: Genome-Wide DNA Methylation Profiling of the Failing Human Heart with Mechanical Unloading Identifies LINC00881 as an Essential Regulator of Calcium Handling in the Cardiomyocyte [DNA Methylation]

type: Methylation profiling by genome tiling array

overall_design: We used bead-array based platform (Illumina 450K and Illumina EPIC) for genome-wide profiling of myocardial DNA methylation. 51 cardiac samples are analyzed from 43 patients including 36 patients with end-stage heart failure (12 Ischemic and 24 Non-ischemic) before-LVAD (n=36 samples) and after LVAD at the time of cardiac transplantation (n=8 samples) , and non-failing controls (n=7).


title: RNA-seq analysis of wildtype and GPD2 knockout cancer cells

first: Sean

last: Oh

address: Gwanakro

institute: Seoul National University

summary: Our purpose of the RNA-seq analysis in WT and GPD2 KO was to observe the overall changes in cancer cell's metabolism. In perspective of metabolomics, the RNA-seq result showed that there is not much change in carbohydrate and energy metabolism, such as glycolysis, galactose metabolism, and oxidative phosphorylation, and there was more change in lipid metabolism, especially in steroid boisynthesis and ether lipid metabolism. In the meaning of Gene Set Enrichment Analysis by KEGG pathway, almost half of Top 20 significantly enriched pathways in 4T1-GPD2 KO cell line was signaling pathways. This RNA-seq analysis between 4T1 WT and GPD2 KO has proven some significant changes in cell metabolism and pathways.

overall_design: Examination of changes in metabolism by GPD2 KO in cancer cells

first: Sunghyouk

last: Park

first: Oh

last: Sehyun


title: Transcriptomic analysis of GC7- and Mock-treated mouse CD8 cytotoxic T cells

status: Public on Mar 11 2022

city: Edinburgh

first: Thomas

last: Tan

address: Charlotte Auerbach Road

department: Institute of Immunology and Infection Research

country: United Kingdom

institute: The University of Edinburgh

summary: Ex vivo OT-1 T cells were stimulated with recombinant SIINFEKL peptide for 2 days, and then expanded in IL-2-containing culture in the presence or absence of 20 µM GC7 for another 2 days. 2 million cells were harvetsed at the end of the culture and total RNA was extracted. Library construction and sequencing was perfomed by Novogene using an Illumina-based platform.

overall_design: Mouse activated CD8 T cells, expanded with or without GC7 (GC7/Mock).

first: Rose

last: Zamoyska


title: Functional crosstalk between the cohesin loader and a chromatin remodeler

status: Public on Mar 01 2022

city: Salamanca

first: Sofía

last: Muñoz Félix

address: Campus Miguel de Unamuno

department: Cancer Research Institute (CIC)

country: Spain

institute: Universidad de Salamanca

summary: The Scc2-Scc4 complex interacts with a conserved RSC ATPase motor module. The cohesin loader enhances RSC remodeling activity in vitro and promoter nucleosome eviction in vivo.

overall_design: MNase-seq analysis of the nucleosome positioning comparing wild type to Scc2Degron cells and Scc2Degron cells expressing either Scc2 full lengh, Scc2C or Scc2N following endogenous Scc2 depletion.

last: Muñoz

first: Andrew

last: Jones

first: Céline

last: Bouchoux

first: Tegan

last: Gilmore

first: Harshil

last: Patel

first: Frank

last: Uhlmann


title: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human tonsil]

city: Seattle

first: Stephanie

last: Zimmerman

state: WA

address: 530 Fairview Ave N

institute: NanoString Technologies

summary: Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). We validated the human and mouse WTA assays using cell lines to demonstrate concordance with orthogonal gene expression profiling methods in profiled region sizes ranging from ∼10-500 cells. By benchmarking against bulk RNAseq and single-molecule fluorescence in situ hybridization, we demonstrate robust transcript detection possible down to ∼100 transcripts per region. To assess the performance of WTA across tissue and sample types, we applied WTA to biological questions in cancer, molecular pathology, and developmental biology. We show that spatial profiling with WTA can detect expected spatial gene expression differences between tumor and tumor microenvironment, identify spatial disease-specific heterogeneity in gene expression in histological structures of the human kidney, and comprehensively map transcriptional programs in anatomical substructures of nine organs in the developing mouse embryo. Digital Spatial Profiling technology with the WTA assays provides a flexible method for spatial whole transcriptome profiling applicable to diverse tissue types and biological contexts.

overall_design: This dataset contains RNA expression from regions of FFPE and fresh frozen human tonsil  using the mouse Whole Transcriptome Atlas for Digital Spatial Profiling


title: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Density dependent regulation of inflammatory responses in macrophages

city: Oxford

first: Alun

last: Vaughan-Jackson

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: Macrophage distribution density is tightly regulated within the body, yet the importance of macrophage crowding during in vitro culture is largely unstudied. Using a human induced pluripotent stem cell (iPSC)-derived macrophage model of tissue resident macrophages, we demonstrate how increasing macrophage culture density changes their morphology and phenotype before and after inflammatory stimulation.  In particular, density drives changes in macrophage inflammatory cytokine and chemokine secretion in both resting and activated states. This density regulated inflammatory state is also evident in blood monocyte derived-macrophages, the human monocytic THP-1 immortalized cell line, and iPSC-derived microglia. A potential cause we identify are anti-inflammatory products in the culture supernatant accumulating as density increases. However, the precise mechanism remains unknown. Our findings highlight cell plating density as an important but frequently overlooked consideration of in vitro macrophage research relevant to a variety of fields ranging from basic macrophage cell biology to disease studies.

overall_design: We generated human iPSC-macrophages from the SFC840-03-03 cell line at 3 different densities. Macrophage precursor cells were harvested from differentiation cultures on 3 separate occasions and cultured for a further 7 days in terminal differentiation medium to make authentic macrophages. At this point cells were lysed for collection of RNA for RNA-Seq.

first: Szymon

last: Stodolak

first: Kourosh

last: Ebrahimi

first: Errin

last: Johnson

first: Paul

last: Reardon

first: Maeva

last: Dupont

first: Shengpan

last: Zhang

first: James

last: McCullagh

first: William

middle: S

last: James


title: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [mouse cell pellet array]

overall_design: This dataset contains RNA expression from 11 mouse cell lines from a fixed frozen and an FFPE cell pellet array using the mouse Whole Transcriptome Atlas for Digital Spatial Profiling


title: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human kidney]

overall_design: This dataset contains RNA expression from regions of 7 FFPE human kidneys using the human Whole Transcriptome Atlas for Digital Spatial Profiling


title: NanoString analysis of mouse brain endothelial cells in response to peripheral LPS treatment.

status: Public on Feb 01 2022

city: NYC

first: Z

last: Chen

address: 1425 Madison Ave

institute: Ichan School

summary: Four daily intraperitoneal injections of the Gram-negative bacterial endotoxin lipopolysaccharide (LPS) transiently protects the cerebral cortex against traumatic brain injury. Underlying mechanisms associated with this neuroprotection include increased neuronal production of anti-apoptotic and neurotrophic molecules, microglial-mediated displacement of inhibitory presynaptic terminals innervating the soma of cortical projection neurons, and synchronized firing of cortical projection neurons. The molecular mechanisms responsible for inducing this neuroprotection and microglial activation are unknown. A fundamental question is whether LPS enters the central nervous system (CNS) or mediates it actions on the luminal surface of brain endothelial cells. In this study, we demonstrate that LPS injected into the peritoneum does not enter the CNS or alter tight junctions of brain endothelial cells. However, LPS activation of vascular endothelial cells was substantiated by increased expression of activation markers (CD54 and CD105) and the LPS receptor, TLR4, on CD31-positive brain endothelial cells isolated by flow cytometry. Transcript analyses further revealed significant upregulation of Cxcl10, C3, Ccl2, Il1b, Cxcl2, and Cxcl1 in these activated endothelial cells, consistent with identification of MyD88 as a regulator of these transcripts by pathway analysis. Using conditional brain endothelial gene ablation strategies, we establish that MyD88-dependent endothelial TLR4 signaling and endothelial Cxcl10 expression are essential for LPS-induced neuroprotection and microglial activation. CXCL10 production by brain endothelial cells in response to circulating TLR ligands thus provides a pathway to directly or indirectly signal to CXCR3 on neurons and/or microglia. Targeting activation of brain endothelial receptors provides an attractive and practical approach for inducing transient neuroprotection.

overall_design: Four groups of three WT C57Bl/6 mice were treated with PBS or LPS (1 mg/kg, IP). Group one treated with PBS and euthanized the next day (24h); group 2 was treated with LPS, eurhanized the next day; group 3 was terated with PBS daily for four days, and euthanized on day 5; the last group was treated with LPS daily for four days, and euthanzied on day 5. following euthanization, their brains were collected and brain endothelial cells were isolated by FACS. RNA from each endothelial sample was ectracted and sent over to NanoString for quantitative analysis.

first: Zhihong

first: Weiwei

last: Hu

first: Bruce

middle: B

last: Trapp


title: Deciphering COVID-19 host transcriptomic complexity and variations for therapeutic discovery against new variants

status: Public on Feb 28 2022

city: Grand Rapids

first: Bin

state: Michigan

address: 400 Monroe Ave NW

department: Department of Pediatrics and Human Development

institute: MICHIGAN STATE UNIVERSITY

summary: COVID-19 has infected 244 million people globally and evolved several variants with higher infectivity. Drug repurposing could be an efficient and timely means of drug discovery for the pandemic. To date, more than two hundred repurposed SARS-CoV-2 inhibitors have been reported but with moderate efficacy or acute toxicity. Thus, there is a great need to find new effective candidates against SARS-CoV-2, especially the new variants, with good safety profiles. We analyzed 17 hundred published host RNA-seq samples of SARS/MERS/SARS-CoV-2 infection derived from pre-clinical models or patients, together with the reported coronavirus inhibitors to summarize a robust coronavirus-induced host gene expression change signature, which captured biological processes involved in host cell machinery hijacking and immune evasion. Then we searched for drugs potently reversing the infection signature and discovered IMD-0354 as a promising candidate with nanomolar IC50 against SARS-CoV-2 and 6 variants, showing a wide therapeutic window of more than 100-fold. The RNA-seq of IMD-0354 treated cells infected with SARS-CoV-2 reaved that this drug could stimulate type I interferon antiviral response, inhibit viral entry and down-regulate hijacked proteins. This work demonstrated the power of biological big data and the efficiency of a system-based drug discovery approach, which can be used in future pandemic.

overall_design: we setup three sets of experiments including control, SARS-CoV-2 infection and IMD-0354 treatment followed by SARS-CoV-2 infection in Calu-3 cells. RNA was isolated from each replicate using KAPA RNA HyperPrep Kit as per manufacturer instructions. Total RNA was processed further using the Ribominus kit to remove the ribosomal RNAs.  RNA-Seq library was generated for individual samples from the ribo-depleted RNA. Sequencing of library was done on illumina Nextera 500 sequencing platform.

first: J

last: Xing

first: R

last: Shankar

first: M

last: Ko

first: K

first: S

first: A

last: Drelich

last: Paithankar

first: E

last: Chekalin

first: T

last: Dexheimer

last: Chua

last: Rajasekaran

first: C

last: Tseng

last: Zheng

last: Kim

first: B


title: Genome-Wide DNA Methylation Profiling of the Failing Human Heart with Mechanical Unloading Identifies LINC00881 as an Essential Regulator of Calcium Handling in the Cardiomyocyte

first: Veli

last: Topkara

state: NY

institute: Columbia University


title: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [E13.5 mouse embryo]

first: Stephanie

last: Zimmerman

overall_design: This dataset contains RNA expression from regions of interest in 9 organs in 6 sections of a single fixed-frozen E13.5 mouse embryo


title: Bead-Jet printing of high-density mesenchymal stem cell-laden Matrigel beads augments skeletal muscle and hair follicle regeneration [MSC]

city: Shen Zhen

first: Shaohua

last: Ma

state: Guangdong Sheng

address: nanshan street

institute: Tsinghua University

summary: We reported high-density encapsulation of MSCs in Matrigel beads, augmenting MSCs function, including increasing MSCs proliferation, migration, and extracellular vesicles (EVs) production via elevated PI3K-AKT pathway activity.

overall_design: Three groups were designed accordingly: high-density encapsulation of MSCs in Matrigel beads, low-density bead and high-density bulk encapsulation of the equivalent number of MSCs.

first: Yuanxiong

last: Cao

first: Yifan

last: Cheng


title: Bead-Jet printing of high-density mesenchymal stem cell-laden Matrigel beads augments skeletal muscle and hair follicle regeneration [skeletal muscle]

summary: We reported high-density encapsulation of MSCs in Matrigel beads, distributed in sparse pattern, augmenting mouse volumetric skeletal muscle tissue with reduced fibrosis.

overall_design: Five groups were designed accordingly: (1) Normal group (without defect, normal regeneration); (2) non-treated group (defect only, without any treatment);  (3) Matrigel HDG-MSCs group; (4) Matrigel LDB-MSCs group; (5) Matrigel HDB-MSCs group. The mice  received the same amount of MSCs loaded in these three types of hydrogel in the traumatic injury.


title: Bead-Jet printing of high-density mesenchymal stem cell-laden Matrigel beads augments skeletal muscle and hair follicle regeneration


title: HiCAR analysis of human embryonic stem cell differentiation reveals principles of cis-regulatory chromatin reorganization controlling developmental gene expression

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

summary: we report a novel method, Hi-C on Accessible Regulatory DNA (HiCAR), which leverages principles of ATAC-seq and high-throughput 3C-assay for genome-wide profiling of chromatin accessibility and open chromatin anchored cRE interactions.

overall_design: cross-linked cells were treated with Tn5 transposase that were assembled with an engineered DNA adaptor . The Tn5 adaptor contains a Mosaic End (ME) sequence for Tn5 recognition as well as a single-stranded flanking sequence that can be ligated to the CviQI-digested DNA fragment with a splint oligo. Next, restriction enzyme digestion was performed using the 4-base cutter CviQI, followed by in situ proximity ligation to ligate the Tn5 adaptor to the spatially proximal genomic DNA. After in situ ligation, cross-links were reversed, and the purified DNA was digested by another 4-base cutter NlaIII, followed by circularization and PCR amplification to generate HiCAR DNA libraries for Next-Generation-Sequencing (NGS)

first: Yarui

last: Diao

first: Xiaolin

last: Wei

first: Yu

last: Xiang


title: Identify key factors regulated by transcription factor Cebpd in the kidney during heart regeneration in zebrafish

status: Public on Feb 25 2022

summary: In previous studies, we  identified and demonstrated that a 1.2kb cebpd downstream element (CEN) is capable and neccessary for the induction of cebpd in the kidney after cardiac injury. The goal of this study is to unveal the Cebpd regulated responses of kidney to cardiac regeneration in zebrafish. we profiled responses by kidney in cebpd mutant and enhancer (CEN) mutant fish zebrafish to massive injuries of the heart.

overall_design: cebpd+/+ and  cebpd-/-  kidney RNA-seq profiling after cardiac injury; CEN+/+ and  CEN-/-   kidney RNA-seq profiling after cardiac injury；

first: Fei

last: Sun

first: Jianhong

last: Ou

first: Kenneth

middle: D

last: Poss


title: Cell type diversity in the octopus brain

status: Public on Jan 31 2022

city: Leuven

first: Ruth

last: Styfhals

address: Naamsestraat 61

department: Biology

country: Belgium

institute: KU Leuven

summary: Octopuses are mollusks that evolved intricate neural systems which are comparable with vertebrates in terms of cell number, complexity and size. Exactly how an octopus increases its neural cell number so dramatically and whether an increase in cell type diversity enables higher cognitive function and complex behavior is still unknown. To profile the cell diversity of the developing octopus brain we applied 10x Genomics’ single-cell/nuclei RNA sequencing technology. At hatching, the Octopus vulgaris brain possesses the main lobes and connections of an adult brain, but which cell types are present remains elusive. We were able to identify 42 robust cell types comprising mostly neural cells, as well as multiple glial subtypes and other non-neuronal populations such as endothelial cells and fibroblasts. In situ expression analysis of marker genes allowed spatial mapping of clusters, including vertical lobe cells and several optic lobe cell types. Investigation of cell type conservation indicated similar gene expression signatures between glial cells of mice, fly and octopus. Genes related to memory and learning were found enriched in vertical lobe cells, that showed molecular similarities with Kenyon cells in Drosophila but not to any mouse cell type. Lastly, we also analyzed the expression of newly expanded gene families (protocadherins, C2H2 zinc-finger transcription factors and G-protein coupled receptors) and found that these are enriched in specific cell types. Taken together, our data gives insight into cell type evolution and the composition of the complex octopus brain.

overall_design: We performed single cell and single nuclei RNA sequencing on a pool of 30 paralarval brains of Octopus vulgaris. Library preparations for the sc/snRNA-seq experiments were performed using 10X Genomics Chromium Single Cell 3’ Kit, v3 chemistry (10X Genomics, Pleasanton, CA, USA). We aimed for a targeted cell recovery of 6000-10 000 cells/nuclei. Post cell count and QC, the samples were immediately loaded onto the Chromium Controller. Single cell or single nuclei RNAseq libraries were prepared using manufacturers recommendations (Single cell 3’ reagent kits v3.1 user guide; CG000204 Rev D), and at the different check points the library quality was assessed using Qubit (ThermoFisher) and Bioanalyzer (Agilent). With a targeted sequencing coverage of 25-50 K reads per cell, single cell libraries were sequenced on Illumina’s NovaSeq 6000 platform  using paired-end sequencing workflow and with recommended 10X; v3.1 read parameters (28-8-0-91 cycles). A total of 202 402 758 reads were obtained for the nuclei and 247 457 191 reads for the cells.

first: Stein

last: Aerts

first: Eve

last: Seuntjens


title: Transcriptional mapping of the macaque retina and RPE-choroid reveals conserved inter-tissue transcription drivers and signaling pathways

status: Public on Jan 24 2022

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

institute: NIH

summary: The macula and fovea comprise a highly sensitive visual detection tissue that is susceptible to common disease processes such as age-related macular degeneration (AMD).  Unfortunately our understanding of the molecular determinants of high acuity vision remains unclear, as few model organisms possess a human-like fovea.  We explore transcription factor networks and receptor-ligand interactions to elucidate tissue interactions in the macula and peripheral retina and concomitant changes in the underlying retinal pigment epithelium (RPE)/choroid.

overall_design: Poly-A selected, 100 bp paired-end RNA-s equencing (RNA-seq) was performed across the macular/foveal, perimacular, and temporal peripheral regions of the neural retina and RPE / choroid tissues of four adult  Rhesus macaque eyes to characterize region- and tissue-specific gene expression.  RNA-seq reads were mapped to both the macaque and human genomes for maximum alignment and analyzed for differential expression and G ene O ntology (GO) enrichment.

first: Ameera

last: Mungale

first: Temesgen

last: Fufa

first: Robert

last: Hufnagel


title: CHD8 Suppression Impacts on Histone H3 Lysine 36 Trimethylation and Alters RNA Alternative Splicing

city: Basel

first: Emanuela

last: Kerschbamer

state: Basel Stadt

address: Mattenstrasse 28

department: Department of Biomedicine

institute: University of Basel

summary:
Disruptive mutations in the chromodomain helicase DNA binding protein 8 (CHD8) have been recurrently associated with Autism Spectrum Disorders (ASD). Here we investigated how chromatin reacts to CHD8 suppression by analyzing a panel of histone modifications in induced pluripotent stem cell-derived neural progenitors. CHD8 suppression led to significant reduction (47.82%) in histone H3K36me3 peaks at gene bodies, particularly impacting on transcriptional elongation chromatin states. H3K36me3 reduction specifically affects highly expressed, CHD8-bound genes and correlates with altered alternative splicing patterns of 462 genes implicated in “regulation of RNA splicing”, “mRNA catabolic process”. Interestingly, mass-spectrometry analysis uncovered a novel interaction between CHD8 and the splicing regulator Heterogeneous Nuclear Ribonucleoprotein L (hnRNPL), providing the first mechanistic insights to explain CHD8-suppression splicing phenotype, partially implicating SETD2, H3K36me3 methyltransferase.
In summary, our results point toward broad molecular consequences of CHD8 suppression, entailing altered histone deposition/maintenance and RNA processing regulation as important regulatory processes in ASD.

overall_design:
ChIP sequencing was conducted to examine 6 different histone modifications in 2 experimental conditions, CHD8 knock-down (obtained by short-hairpin (sh) administration, 3 different Sh were used and tested) and control (2 replicates from cells treated with control Sh, Sh-GFP) human neural progenitor cells.

Poly-A RNA sequencing was conducted to examine alternative splicing comparing 2 experimental conditions: siRNA-mediated hnRNPL knock-down (si-C) versus si-Scrambled controls (si-SCR). iPS-derived human neuronal progenitors were used. siRNA treatment was conducted for 72h.

first: Michele

last: Arnoldi

first: Takshashila

last: Tripathi

first: Miguel

last: Pellegrini

first: Serkan

last: Erdin

first: Elisa

last: Salviato

first: Francesca

last: Di Leva

first: Endre

last: Sebestyén

first: Erik

last: Dassi

first: Giulia

last: Zarantonello

first: Matteo

last: Benelli

first: Eric

last: Campos

first: M Albert

last: Basson

first: James

last: Gusella

first: Stefano

last: Gustincich

first: Silvano

last: Piazza

last: Demichelis

first: Michael

middle: E

last: Talkowski

first: Francesco

last: Ferrari

first: Marta

last: Biagioli


title: Activation of STAT3 through SRC and EGFR Drives Resistance to a Mitotic Kinesin Inhibitor in Glioblastoma [bulk RNA-seq]

status: Public on Jan 09 2022

middle: G

last: Argenziano

state: New York

address: 1130 St. Nicholas Ave

institute: Columbia University Vagelos College of Physicians and Surgeons

summary: Inhibitors of the mitotic kinesin Kif11 are anti-mitotics that, unlike vinca alkaloids or taxanes, do not disrupt microtubules and are not neurotoxic. However, development of resistance has limited their clinical utility. While resistance to Kif11 inhibitors in other cell types is due to mechanisms that prevent these drugs from disrupting mitosis, we find that in glioblastoma (GBM), resistance to the Kif11 inhibitor ispinesib works instead through suppression of apoptosis driven by activation of STAT3. This form of resistance requires dual phosphorylation of STAT3 residues Y705 and S727, mediated by SRC and EGFR, respectively. Simultaneously inhibiting SRC and EGFR reverses this resistance, and combined targeting of these two kinases in vivo with clinically available inhibitors is synergistic and significantly prolongs survival in ispinesib-treated GBM-bearing mice. We thus identify a translationally actionable approach to overcoming Kif11 inhibitor resistance that may work to block STAT3-driven resistance against other anti-cancer therapies as well.

overall_design: RNAseq on 6 samples: three naïve murine glioma cell line, three ispinesib resistant murine glioma cell line.

first: Steven

last: Rosenfeld

first: Peter

last: Sims

last: Canoll

first: Athanassios

last: Dovas


title: Colocalization of GWAS and molecular QTL signals in human vascular smooth muscle cells predict candidate causal genes for coronary artery disease and vascular disorders

status: Public on Jan 20 2022

city: Charlottesville

first: Mete

last: Civelek

state: Virginia

address: 21 Hospital Drive, Old Medical School Room 3836

department: Biomedical Engineering

institute: University of Virginia

summary: Coronary artery disease (CAD) is the leading cause of death worldwide. A recent meta-analysis of genome-wide association studies (GWAS) identified 175 loci associated with CAD. The majority of these loci are in non-coding regions and are predicted to regulate gene expression. We hypothesized that a subset of the CAD GWAS loci was associated with the regulation of transcription in vascular smooth muscle cells (SMCs), which play critical roles in the development of CAD. We measured gene expression in SMCs isolated from the ascending aortas of 151 ethnically diverse heart transplant donors in quiescent or proliferative conditions and calculated the association of their expression and splicing with ~6.3 million imputed single nucleotide polymorphism (SNP) markers across the genome. We identified 4,910 expression and 4,412 splice quantitative trait loci (sQTL) that represent regions of the genome associated with transcript abundance and splicing. 3,660 of the expression quantitative trait loci (eQTL) had not been observed in the publicly available Genotype-Tissue Expression dataset. Further, 29 and 880 of the eQTLs were SMC- and sex-specific, respectively. To identify the effector transcripts regulated by the CAD GWAS loci, we used four distinct colocalization approaches and identified 84 eQTL and 164 sQTLs that colocalized with CAD loci, suggesting a more significant role for the genetic regulation of mRNA splicing as a molecular mechanism for CAD genetic risk. 20% and 35% of the eQTLs were unique to quiescent or proliferative SMCs, respectively. Two of the CAD loci colocolized with SMC eQTL showed sex-specific (AL160313.1 and TERF2IP) and one of the loci colocalized with SMC-specific eQTLs (ALKBH8). 27% and 37% of the sQTLs were unique to quiescent or proliferative SMCs, respectively. The most significantly associated CAD locus, 9p21, was an sQTL for the long non-coding RNA CDKN2B-AS1, also known as ANRIL, in proliferative SMCs. Collectively, these results provide evidence for the molecular mechanisms of genetic susceptibility to CAD in vascular smooth muscle cells.'

overall_design: RNA sequencing data across proliferative and quiescent smooth muscle cells (SMCs) in ~150 multiethnic donors.

first: Civelek

last: Mete

first: Aherrahrou

last: Redouane


title: Rationally designed, self-assembly, multifunctional hydrogel depot repairs severe spinal cord injury

status: Public on Jan 01 2022

city: Yiwu

first: jingjia

last: ye

state: zhejiang

address: chouzhoubeilu 1575

institute: zhejiang university

summary: Following severe spinal cord injury (SCI), dysregulated neuroinflammation causes neuronal and glial apoptosis, resulting in scar and cystic cavity formation during wound healing process and ultimately atrophic nerve regrowth inhibitory microenvironment. Because of this complex and dynamic nature of SCI pathophysiology, a systemic solution for scar and cavity free wound healing while remodeling microenvironment for nerve regrowth has been rarely explored. To address this challenge, we provided a one-step solution through a self-assembly, multifunctional hydrogel depot punctually releasing the anti-inflammatory drug methylprednisolone sodium succinate (MPSS) and growth factors locally according to its pathophysiology to repair severe SCI. We found release of growth factors alone could only provide some tissues/axons protection, but failed to eliminate all cystic cavity formation. Sustained release of MPSS is sufficient to modulate dysregulated neuroinflammation and eliminate almost all cystic cavity but unable to alleviate impenetrable scar boundaries, which are largely responsive for nerve regrowth failure. Strikingly, synergically releasing anti-inflammatory drugs MPSS and growth factors in the hydrogel depot along SCI pathophysiology protected spared tissues/axons from secondary injury, promoted scar boundary and cavity free wound healing and made permissive bridges for remarkable axonal regrowth. Behavior and electrophysiology studies indicated that the remnant of spared axons but not regenerating axons mediated functional recovery, strongly suggesting that additional interventions are still required to make the rebuilt neuronal circuits perform functions. Taken together, these findings pave the way to develop a systemic solution to treat acute SCI.

overall_design: 5 animals for each hydrogel injection (PBS, G-HD, MPG-HD) samples

first: Jingjia

last: Ye

first: Xuhua

last: Wang


title: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [mouse organ array]

first: Stephanie

last: Zimmerman

overall_design: This dataset contains RNA expression from 3 FFPE mouse organ arrays from 3 mouse strains each with 7 different tissues using the mouse Whole Transcriptome Atlas for Digital Spatial Profiling


title: Botrytis cinerea infection accelerates ripening and cell wall disassembly in tomato fruit to promote disease

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

summary: Postharvest fungal pathogens benefit from the increased host susceptibility that occurs during fruit ripening. In unripe fruit, pathogens often remain quiescent and unable to cause disease until ripening begins, emerging at this point into destructive necrotrophic lifestyles that quickly result in fruit decay. Here, we demonstrate that one such pathogen, Botrytis cinerea, actively induces ripening processes in order to facilitate infections and promote disease. Assessments of ripening progression revealed that B. cinerea accelerated external coloration, ethylene production, and softening in unripe fruit, while mRNA sequencing of inoculated unripe fruit confirmed the corresponding upregulation of host genes involved in ripening processes, such as ethylene biosynthesis and cell wall degradation. Furthermore, ELISA-based glycomics profiling of fruit cell wall polysaccharides revealed remarkable similarities in the cell wall polysaccharide changes caused by both infections of unripe fruit and ripening of healthy fruit, particularly in the increased accessibility of pectin polysaccharides. Virulence and additional ripening assessment experiments with B. cinerea knockout mutants showed that induction of ripening is dependent on the ability to infect the host and break down pectin. The B. cinerea double knockout Δbcpg1Δbcpg2 lacking two critical pectin degrading enzymes was found to be incapable of emerging from quiescence even long after the fruit had ripened at its own pace, suggesting that the failure to accelerate ripening severely inhibits fungal survival on unripe fruit. These findings demonstrate that active induction of ripening in unripe tomato fruit is an important infection strategy for B. cinerea.

sample_organism:
Solanum lycopersicum
Botrytis cinerea

platform_organism:
Solanum lycopersicum
Botrytis cinerea

overall_design: 18  RNA-Seq samples

first: Christian

last: Silva

first: Jaclyn

last: Adaskaveg

first: Saskia

last: Mesquida-Pesci

first: Isabel

last: Ortega-Salazar

first: Sivakumar

last: Pattathil

first: Lisha

last: Zhang

last: Hahn

first: Jan

last: van Kan

first: Dario

last: Cantu

first: Ann

middle: L

last: Powell


title: Identification of enhancer elements that direct long-range responses to tissue injury

first: jianhong

last: ou

summary: The goal of this study is to unveal the responses of uninjured tissue to distant tissue injury and the structures required for long-range responses to tissue injuries. we profiled responses by the brain and kidney in zebrafish to massive injuries of the heart and identified cebpd transcript induction in both tissue. We also identified and demonstrated that a 1.2kb cebpd downstream element is capable and neccessary for the induction of cebpd in the brain after cardiac injury.

overall_design: Brain and kidney RNA-seq and ATAC-seq profiling after cardiac injury; cebpd+/+ and  cebpd-/-brain RNA-seq profiling after cardiac injury

first: Fei

last: Sun

first: Jianhong

last: Ou

first: Adam

last: Shoffner

first: Lingyun

last: Song

first: Alexis

last: Safi

first: Gregory

last: Crowford

first: Kenneth

last: Poss