title: Combined application of whole transcriptome sequencing and ceRNA theory: lncRNA LOC110519952 participates in glucose transport under hypoxia stress in rainbow trout (Oncorhynchus mykiss) by regulating novel-m0023-5p/glut1a axis

city: Lanzhou

first: Jinqiang

last: Huang

address: Yintanlu stress

institute: Gansu Agricultural University

summary: Hypoxia is a tricky and unavoidable environmental stressor for aquaculture with ongoing ecological deterioration and increasing stocking density, resulting in serious economic losses. Rainbow trout (Oncorhynchus mykiss), a commercially important fish species worldwide, exhibits extraordinarily poor tolerance to hypoxia; however, the regulatory mechanisms under hypoxia stress have not been elucidated. In this study, rainbow trout were separately subjected to moderate (Tm12L) and acute hypoxia for 12 h (Ts12L) and 12 h reoxygenation to investigate the changes of histology, biochemical parameters and transcriptomes (mRNA, miRNA and lncRNA) in liver, and interactions between LOC110519952-novel-m0023-5p-glut1a were further verified. The results showed that acute hypoxia resulted in more severe liver oxidative injury than moderate hypoxia, and anaerobic metabolism and lipid and protein metabolism were enhanced to some extent, especially in Ts12L. We also found that innate immune response was strengthened in Tm12L, while it was inhibited in Ts12L. In addition, dozens of hypoxia-related ceRNA networks derived from 1824 differentially expressed (DE) mRNAs, 427 DEmiRNAs and 545 DElncRNAs were identified, including LOC110519952-novel-m0023-5p-glut1a, LOC110520012-miR-206-y-vegfaa, LOC118965299-novel-m0179-3p-epoa and MSTRG.7382.2-miR-184-y-hmox. Further studies validated that LOC110519952 acted as a ceRNA that can positively regulate glut1a expression by adsorbing novel-m0023-5p. Overexpression of novel-m0023-5p could promote liver cell viability and proliferation, and introduction of LOC110519952 attenuated the effects.  The findings contribute to deepen our understanding of the adaptive mechanisms used by rainbow trout in response to hypoxia stress, and provide valuable information for hypoxia-tolerant varieties breeding.

first: Shenji

last: Wu


title: High-Fat Diet Alters the Retinal Transcriptome in the Absence of Gut Microbiota

status: Public on Aug 05 2023

city: Chicago

first: Rohan

middle: Nishant

last: Shah

state: IL

address: CLSC 856, 920 E. 58th Street

country: USA

institute: University of Chicago

type: Expression profiling by high throughput sequencing

summary: The relationship between retinal disease, diet, and the gut microbiome has shown increasing importance over recent years. In particular, high-fat diets (HFDs) are associated with development and progression of several retinal diseases, including age-related macular degeneration (AMD) and diabetic retinopathy. However, the complex, overlapping interactions between diet, gut microbiome, and retinal homeostasis are poorly understood. Using high-throughput RNA-sequencing (RNA-seq) of whole retinas, we compare the retinal transcriptome from germ-free (GF) mice on a regular diet (ND) and HFD to investigate transcriptomic changes without influence of gut microbiome. After correction of raw data, 53 differentially expressed genes (DEGs) were identified, of which 19 were upregulated and 34 were downregulated in GF-HFD mice. Key genes involved in retinal inflammation, angiogenesis, and RPE function were identified. Enrichment analysis revealed that the top 3 biological processes affected were regulation of blood vessel diameter, inflammatory response, and negative regulation of endopeptidase. Molecular functions altered include endopeptidase inhibitor activity, protease binding, and cysteine-type endopeptidase inhibitor activity. Human and mouse pathway analysis revealed that the complement and coagulation cascades are significantly affected by HFD. This study demonstrates novel data that diet can directly modulate the retinal transcriptome independently of the gut microbiome.

overall_design: To explore how diet impacts retinal transcription in the absence of gut microbiota, we fed GF mice a HFD or ND for 8 consecutives weeks, starting at 7 weeks of age. The mice were then sacrificied, and their retinas were dissected and processed for high-throughput RNA-sequencing. In addition to filtering for differentially expressed genes, we performed enrichment analysis to identify over-represented gene ontology functional classification.

first: David

last: Dao

first: Bingqing

last: Xie

first: Urooba

last: Nadeem

first: Jason

last: Xiao

first: Dimitra

last: Skondra


title: Sex differences and effect of testosterone on the transcriptome in brain regions underlying quail sexual behavior

status: Public on Aug 06 2023

city: Liege

first: Brett

middle: C

last: Mommer

state: Wallonia

address: Tour Pharmacie (Bat. B36) Quartier Hôpital, Avenue Hippocrate 15

department: GIGA-Neurosciences

country: Belgium

institute: University of Liege

summary: To understand the sex differences in brain function that underlie sex differences in behavior we measured the transcriptome of POM, VMN and TnA of adult quail of both sexes either left gonadally intact or gonadectomized and treated with testosterone. Gonadectomy and testosterone-treated groups allowed us to distinguish a suite of genes whose expression is sensitive to testosterone and a suite of genes that are not, the magnitude and pattern of which differs by sex and nucleus.

overall_design: differential expression analysis in POM, TnA and VMN between adult T-treated and intact male and female quail

first: Rodrigo

last: Gularte-Merida

first: Wouter

last: Coppieters

first: Jacques

last: Balthazart

first: Charlotte

middle: A

last: Cornil


title: Single-cell RNA sequencing reveals profibrotic roles of three kinds of cells in pulmonary fibrosis

city: Jinan

first: Weibin

last: Qian

state: Shandong

address: 16369 Jingshi Road

country: China

institute: Affiliated Hospital of Shandong University of Traditional Chinese Medicine

summary: Pulmonary fibrosis (PF) is a serious chronic pulmonary disease, and lung transplantation is currently the only treatment option that can prolong patient survival. A greater understanding of the transcriptomes of cells related to the pathogenesis of PF can elucidate the impact of different cell types on its occurrence and development. To this end, we performed single cell RNA sequencing (scRNA-seq) to identify key cells and their biological processes in PF. We analyzed the transcriptomes of a total of 36400 cells isolated from the lungs of control and bleomycin-stimulated mice, and observed significant changes in the macrophages, fibroblasts and epithelial cells in the PF model. The macrophages were divided into alveolar macrophages (AMs) and interstitial macrophages (IMs). Based on the anatomical location, the fibroblasts were classified as alveolar fibroblasts, adventitial fibroblasts and peribronchial fibroblasts. Finally, the epithelial cells were divided into the type I alveolar epithelial cells, transitional type II alveolar epithelial cells, and Scgb3a2+ epithelial cells. The subgroups were further classified into key cell clusters to identify the signaling pathways involved in fibrotic progression. Finally, we identified several ligand-receptor complexes that mediate the communication between microphages, fibroblasts and epithelial cells during PF development. Our findings provide new insights into the mechanisms underlying PF, along with potential therapeutic targets.

overall_design: we induced PF in a mouse model using bleomycin (BLM), and performed single-cell RNA sequencing (scRNA-seq) on the single-cell suspensions obtained from the control and fibrotic lungs.In the single-cell sequencing in this paper, the overall model was constructed according to the modeling time gradient (control group, M-14, M-28). After the completion of modeling, three mice were selected from each group, and after each mouse lung tissue was enzymatically digested into individual cells, equal amounts of cells were selected from all three mice in the same group with the same modeling time for mixing, and one sample was prepared. A total of 3 samples were obtained from the control group, M-14, and M-28, and were tested separately.

first: Shan

last: Zhao

first: Xinrui

last: Cai


title: Keratinocyte Wnt5β promotes dermal adipogenesis by simultaneously regulating adipocyte precursor cell conversion and adipogenic signaling

city: Kangwon

first: Geon Seong

last: Lee

address: 1447 Pyeongchang-Ro, Daewha, Pyeongchang

country: South Korea

institute: Seoul National University

summary: Skin is the largest organ in the body and comprises several types of cells. The intercellular plasticity of keratinocytes, fibroblasts, and skin adipocytes contributes to wound healing and dermal adipogenesis. Although keratinocyte activates dermal adipose tissue (dWAT) differentiation upon hair follicular cycle, regulating dWAT hyperplasia through keratinocyte reprogramming is still unknown. We used the CRISPR/Cas9 base editor to induce single nucleotide polymorphisms in Forkhead-box N1 (Foxn1) and identified the p.L19M variant that induced the formation of a thicker dWAT regardless of hair follicular cycle or wound healing. Foxn1 p.L19M activates Wnt5β through transcriptional activity. Wnt5β signaling induces the conversion of dWAT dermal fibroblasts into adipose precursor cells (APCs) and promotes APC adipocyte differentiation through keratinocyte epithelial-mesenchymal transition (EMT) and adipogenic signaling. Wnt5β is involved in the entire process of dWAT hyperplasia through APC supply and adipogenic signaling as a single factor. Foxn1 p.L19M and Wnt5β are expressed in keratinocytes, and a keratinocyte-derived adipogenic signal is critical for dermal adipogenesis. In addition, transient expression of Foxn1 p.L19M or Wnt5β using adeno-associated virus reproduced dermal adipocyte hyperplasia in mice. Considering the increasing importance of dWAT in functions such as the immune response, wound healing, hair follicle growth, and temperature control, this finding has potential applications in skin regeneration

overall_design: To investigate the keratinocyte function between Foxn1 and Foxn1 L19M in murine epidermis.

first: Geon

middle: S

first: Su

last: Yeom


title: Decoding the spermatogonial stem cell niche under physiological and recovery conditions in adult mice and humans

city: Beijing

first: Cheng

last: Jin

state: State...

address: dongdansantiao num5

institute: Chinese Academy of Medical Sciences

summary: The intricate interaction between spermatogonial stem cell (SSC) and testicular niche is essential for maintaining SSC homeostasis; however, this interaction remains largely uncharacterized. In this study, to characterize the underlying signaling pathways and related paracrine factors, we delineated the intercellular interactions between SSC and niche cell in both adult mice and humans under physiological conditions and dissected the niche-derived regulation of SSC maintenance under recovery conditions.

overall_design: We performed scRNA-seq on the whole testicular cells of adult wild type C57BL/6 mice (WT), KitW/Wv mice (W), and busulfan-treated KitW/Wv mice for 3 or 5 days (W3 and W5) using the 10x Genomics Chromium platform.

first: Zhipeng

last: Wang


title: C-X-C chemokine receptor 4 ablation-driven transcriptional changes in monocyte-derived macrophage in response to lipopolysaccharide

city: Hangzhou

first: Ning

last: Zhang

state: Zhejiang

address: 88 Jiefang Rd, Hangzhou, Zhejiang Province

institute: Second Affiliated Hospital, Zhejiang University College of Medicine

summary:
Purpose: Next-Generation Sequencing (NGS) RNA was subjected to analysis genome-wide expression. The goals of this study are to identify differentially expressed genes in CXCR4 knockout macrophages compared to CXCR4-expressed macrophages.
Methods: Total RNA of macrophage transfected with CXCR4 siRNA (MΦsiCXCR4) or siRNA negative control (MΦsiNC), then, stimulated with 100ng/ml lipopolysaccharide (LPS) for 12 hours. Preparation of library and sequencing of transcriptome was performed by Illumina NovaSeq 6000.
Results: A large number of differentially expressed genes were screened by high-throughput sequencing at the genome-wide level using RNA-Seq technology. Loss of CXCR4 in bone-marrow-derived macrophages results in attenuated pro-inflammatory cytokine and decorin production under LPS stimulation compared to control macrophages.
Conclusions: Our study reveals that CXCR4 orchestrated the pro-inflammatory cytokine and decorin production in macrophages.

overall_design: Gene expression profiling from macrophage transfected with CXCR4 siRNA (MΦsiCXCR4) or siRNA negative control (MΦsiNC) after LPS (100ng/ml, 12hours) treatment.

first: Qunchao

last: Ma

first: Zhuo

first: Xiaojie


title: NRF1 promotes primordial germ cell development, proliferation and survival [ChIP-seq]

city: shanghai

first: wang

last: pengxiang

address: No.500, Dongchuan Road

institute: ECNU

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
To investigate the role of NRF1 in regulating primordial germ cell development, We established conditional knockout mice of Nrf1 in primordial germ cell to observe the effect of Nrf1 knockout on the development of primordial germ cell.
At the same time, we utilized a pluripotent stem cell differentiation system in vitro to obtain PGCL cells for chip_ Seq, analyze which genes Nrf1 directly binds to.
Meanwhile, we established a pluripotent stem cell line induced by Nrf1 overexpression and performed RNA_seq analysis on PGCL cells overexpressing Nrf1 obtained in vitro

first: Pengxiang

last: wang

last: jun

first: Junpeng

first: Yilin

last: Xie

first: Wei

last: Chen

first: Yuan


title: NRF1 promotes primordial germ cell development, proliferation, and survival [RNA-seq]

overall_design: performed RNA-seq analyses on somatic cells (BV-) and PGCLCs (BV+) isolated from differentiated control PSCs and PSCs with enforced NRF1 expression


title: NRF1 promotes primordial germ cell development, proliferation, and survival

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

overall_design: Refer to individual Series


title: N57.Dataset

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary: Cytosine methylation data generated on mammalian methylation platform

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The data includes 1 Cortex, 1 Heart, 2 Kidney, 3 Liver, 2 Muscle, 96 Skin of Balaena mysticetus

last: Ferguson


title: N14.Dataset

overall_design: The data includes 140 Skin of Orcinus orca

first: Kim

last: Parsons


title: N87.Dataset

overall_design: The data includes 48 Blood, 48 Cortex, 48 Liver, 48 Muscle, 48 Skin of Mus musculus


title: N27.Pinniped Dataset

sample_organism:
Zalophus californianus
Odobenus rosmarus divergens
Phoca vitulina
Eumetopias jubatus
Phoca groenlandica
Neophoca cinerea

overall_design: The data includes 1 Skin of Eumetopias jubatus, 1 Skin of Neophoca cinerea, 11 Blood of Odobenus rosmarus divergens, 2 Skin of Odobenus rosmarus divergens, 1 Blood of Pagophilus groenlandicus, 1 Skin of Pagophilus groenlandicus, 57 Blood of Phoca vitulina, 11 Skin of Phoca vitulina, 69 Blood of Zalophus californianus, 17 Skin of Zalophus californianus

first: Todd

middle: R

last: Robeck


title: Effect of endocannabinoid AEA on HIV1 TAT activated Normal Human Primary Astrocytes

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To analyse the effect of endocannabinoid AEA on the expression of inflammation related miRNAs in HIV1 TAT activated Normal Human Astrocytes.

overall_design: Agilent Human 'miRNA Microarray Profiling 8X60K -AMADID: 70156

first: Nivedita

last: Chatterjee

first: Durairaj

last: Duraikkannu

first: Kamini

last: Khatak


title: RNA sequencing analysis of prostate cancer cells with ectopic expression of circ0003553 or circ0004592

city: Wuhan

first: Gang

last: Luo

state: Hubei

address: 26 Shengli Street

institute: Huazhong University of Science and Technology

summary: Transcriptome analysis was performed to determine the effect of overexpression of circ0003553 or circ0004592 in prostate cancer cells

overall_design: Prostate cancer cells PC3 and DU145 transfected with expression vector containing circ0003553 or circ0004592 were used for RNA-seq analysis.


title: To explore the downstream genes of PKP2

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

summary: To explore the downstream genes of PKP2,we performed RNA-seq to screen after overexpression of PKP2 in A549 cells.

overall_design: We used  SFB-tag delivering PKP2 to overexpression of PKP2  in A549 cells.

first: Chun

last: Cheng


title: Identification of genes differentially expressed between the prostates of PtenPC+/- mice and the prostate tumors of PtenPC+/-;Ncoa6PC-/- mice at the age of 9 months

city: Houston

first: Yonghong

last: Liu

state: Texas

address: One Baylor Plaza

department: Molecular & Cellular Biology

institute: Baylor College of Medicne

summary: In this study, we aimed to characterize the suppressive role of NCOA6 in prostate cancer development, uncover the underlying molecular mechanism, and identify potential therapeutic targets for treating NCOA6 loss-induced prostate cancer. Gene expression microarray analysis and RNA-Seq analysis were performed to identify differentially expressed genes influenced by NCOA6 in 22Rv1 human prostate cancer cells and mouse prostate tumors, respectively. Pathway enrichment analysis and gene set enrichment analysis were performed to identify NCOA6-regulated signaling pathways, particually the cancer-associated pathways. ChIP-Seq analysis was further performed to identify NCOA6-associated genomic regions in 22Rv1 cells. The potential direct target genes of NCOA6 were identified by combined analysis of the gene expression profiling data and ChIP-Seq data. Finally, we identified EGFR as one of the 264 NCOA6 direct target genes and deomonstrated that NCOA6 suppressed prostate cancer progression by preventing EGFR overexpression.

overall_design: Gene expression profiles in the prostates of PtenPC+/- mice and the prostate tumors of PtenPC+/-;Ncoa6PC-/- mice at the age of 9 months were examined.

first: Jianming

last: Xu


title: Identification of differentially expressed genes influenced by NCOA6 in 22Rv1 human prostate cancer cells

overall_design: Gene expression profiles in the 22Rv1Par., 22Rv1Ctrl, 22Rv1NCOA6KO #2-74, 22Rv1NCOA6KO #2-96, 22Rv1NCOA6KO #4-91 and 22Rv1NCOA6KO #4-105 cells cultured in RPMI-1640 complete medium were measured at 24 hours after cell passage. Eight samples were analyzed, including two 22Rv1Par. sample replicates and two 22Rv1Ctrl sample replicates that were used as controls as well as four different 22Rv1NCOA6KO cell clones.


title: Identification of NCOA6-associated genomic regions in 22Rv1 human prostate cancer cells

overall_design: NCOA6-associated genomic regions in 22Rv1 cells cultured in RPMI-1640 complete medium were measured at 24 hours after cell passage. Three samples were analyzed by using FLAG antibody, including one 22Rv1Par. sample that was used as a control and two NCOA6-3xFLAG knock-in samples


title: NCOA6 is a potent prostate cancer suppressor essential for NFY-mediated restriction of EGFR overexpression

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

summary: RNA-seq for SARS-CoV-2 infection of human embryonic stem cell-derived lung organoids

overall_design: We analyzed the RNA-seq for SARS-CoV-2 [strain EPI_ISL_402124] infection of human embryonic stem cell-derived lung organoids.


title: DCX knockout ferret disentangles cellular landscape of lissencephaly syndrome and novel functions of DCX in neural progenitors

status: Public on Aug 04 2023

first: Shaonan

last: Wen

address: Beijing 100875, China

institute: Beijing Normal University

summary: Lissencephaly (LIS) represents a range of gene-associated brain abnormalities characterized by a smooth cortical surface (due to the absence or reduction of gyri and sulci) in humans. This condition manifests through various symptoms such as seizures, muscle spasms, developmental delays, cognitive impairments, and learning discrepancies, etc.1-3 To date, nearly twenty gene mutations related to lissencephaly have been identified, with DCX and LIS1 being the most commonly reported risk genes in humans1-5. Our understanding of this disease remains limited due to the absence of suitable models that accurately represent human phenotypes. In this study, we conducted a comprehensive examination of the phenotypes, cytoarchitecture, and cellular profiles of the neocortex in DCX knockout ferrets we generated previously 6. Our findings indicate that the DCX knockout ferrets effectively replicate the morphological and pathological phenotypes observed in human patients. Furthermore, we discovered a novel function of DCX in neural progenitor cells (NPCs), that DCX inhibits the proliferation of NPCs and regulates the extension of radial glial fibers, which serve as a migration scaffold for neurons. We also present evidence suggesting that inhibitory neurons pair with their excitatory counterparts in a subtype-specific manner during their migration and distribution in the neocortex, which was also dysregulated in DCX knockout ferrets.

overall_design: To investigate the DCX gene function in brain, we established ferret model in which target gene has been knocked down.

first: Xiaoqun

last: Wang

first: Qian

last: Wu


title: Secreted-frizzled-related protein 5 modulates calcium handling in human iPSC-cardiomyocytes

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: End-stage heart failure caused by myocardial injury is a leading cause of death in the developed world, with high prevalence and poor prognosis. Current therapies focus on attenuating cardiac remodeling after a cardiovascular event such as myocardial infarction or pressure overload, but no therapy is currently available to halt or reverse disease progression. Recent studies have suggested a cardioprotective function of the Wnt5a inhibitor secreted frizzled-related protein 5 (SFRP5) in preventing adverse cardiac remodeling. However, until now, the underlying molecular mechanisms of SFRP5 treatment in the human heart are not well understood. In this study, we investigated the mechanistic and functional consequences of SFRP5 by establishing knockout and overexpression models in human iPSC-derived cardiomyocytes. Transcriptome profiling and deep pathway analysis revealed an involvement of SFRP5 in the regulation of calcium handling, cardiac contraction, and apoptosis. Functional analysis of iPSC-cardiomyocytes by live-cell calcium imaging confirmed the regulatory role of SFRP5 on calcium homeostasis. Our study uncovered a novel role of SFRP5 as a modulator of calcium handling, providing a deeper molecular understanding of the cardioprotective role of SFRP5 in the human heart.

overall_design: RNA-Seq

first: Lukas

last: Cyganek


title: Functional Adaptations of Endogenous Retroviruses to the Drosophila host Reveal Principles of their Evolutionary Diversification [RNA-seq]

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

summary: Transposable elements profoundly affect the biology and evolution of their hosts, yet their own evolutionary dynamics remain poorly understood. Here, we investigate insect endogenous retroviruses (iERVs), a monophyletic group of LTR retrotransposons that have acquired the trait of infectivity, likely through capture of a Baculovirus envelope gene. In Drosophila ovaries, iERVs with functional envelope have adapted their cis-regulatory sequences to be expressed in any somatic cell type, from where they infect the germline. Strikingly, related retroviruses show distinct expression patterns, indicating niche partitioning. In contrast, all non-infectious iERVs that emerged through secondary envelope-loss are specifically expressed in the germline. Co-evolving with iERVs, the genome-protecting piRNA pathway has assimilated iERV promoter and sequence information into piRNA clusters, underscoring the functional significance of iERV expression in somatic niches. We propose that the evolutionary innovation of cell-to-cell infectivity has triggered the adaptive radiation of iERVs through trait diversification and antagonistic virus-host interactions, processes that likely underpin niche-specific expression of endogenous retroviruses in vertebrates as well.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data from ovaries with tissue specific knock-downs of control and piRNA pathway essential genes
Comparative gene expression profiling analysis of RNA-seq data from early embryos layed by females with tissue specific knock-downs of control and piRNA pathway essential genes

first: Kirsten-Andre

last: Senti

first: Baptiste

last: Rafanel

first: Carolin

last: Kosiol

first: Christian

last: Schlötterer

first: Julius

last: Brennecke


title: Functional Adaptations of Endogenous Retroviruses to the Drosophila host Reveal Principles of their Evolutionary Diversification [PRO-seq]

overall_design: Promoter profiling analysis of Pro-seq data from OSCs.


title: Functional Adaptations of Endogenous Retroviruses to the Drosophila host Reveal Principles of their Evolutionary Diversification [sRNA-seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design:
Comparative smallRNA profiling analysis of sRNA-seq data from ovaries with control and piRNA cluster 77B mutant genotype.
Comparative smallRNA profiling analysis of sRNA-seq data from Ovarian Sheet Cells (OSCs) siRNA knock-downs of GFP (control) and Armitage.


title: The efficient induction of human retinal ganglion-like cells provides a platform for studying optic neuropathies

city: Taipei

first: Yu-Hui

last: Wong

state: Taiwan

address: (NYCU) No. 155, Sec. 2, Linong St., Beitou Dist.

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Retinal ganglion cells (RGCs) are essential for vision perception. In glaucoma and other optic neuropathies, RGCs and their optic axons undergo degenerative change and cell death; this can result in irreversible vision loss. Here we developed a rapid protocol for directly inducing RGC differentiation from human induced pluripotent stem cells (iPSCs) by the overexpression of ATOH7, BRN3B and SOX4. The hiPSC-derived RGC-like cells (iRGCs) show robust expression of various RGC-specific markers, such as BRN3A, EBF1, ISL1 and RBPMS. A functional assessment was also carried out and this demonstrated that these iRGCs display stimulus-induced neuronal activity, as well as spontaneous neuronal activity. Ethambutol (EMB), an effective first-line anti-tuberculosis agent, is known to cause serious visual impairment and irreversible vision loss due to the RGC degeneration in a significant number of treated patients. Using our iRGCs, EMB was found to induce significant dose-dependent and time-dependent increases in cell death and neurite degeneration. Western blot analysis revealed that the expression levels of p62 and LC3-II were upregulated, and further investigations revealed that EMB caused a blockade of lysosome-autophagosome fusion; this indicates that impairment of autophagic flux is one of the adverse effects of that EMB has on iRGCs. In addition, EMB was found to elevate intracellular reactive oxygen species (ROS) levels increasing apoptotic cell death. This could be partially rescued by the co-treatment with the ROS scavenger NAC. Taken together, our findings suggest that this iRGC model, which achieves both high yield and high purity, is suitable for investigating optic neuropathies, as well as being useful when searching for potential drugs for therapeutic treatment and/or disease prevention.

overall_design: To characterize iRGC identity transitions during ATOH7/BRN3B/SOX4-based differentiation, we designed time-course RNA-seq experiments of week 1, 2 and 4 from three independent hiPSC cell lines.

first: Roxanne Hsiang-Chi

last: Liou

first: Shih-Wei

last: Chen

first: Hui-Chen

first: Pei-Chun

first: Yu-Fen

last: Chang

first: An-Guor

first: Ming-Ji

last: Fann


title: The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

summary: While global transcription factors (TFs) have been studied extensively in Escherichia coli model strains, conservation and diversity in TF regulation between strains is still unknown. Here we use a combination of ChIP-exo--to define ferric uptake regulator (Fur) binding sites--and differential gene expression--to define the Fur regulon in nine E. coli strains. We then define a pan-regulon consisting of 469 target genes that includes all Fur target genes in all nine strains. The pan-regulon is then divided into the core regulon (target genes found in all the strains, n=36), the accessory regulon (target found in two to eight strains, n=158) and the unique regulon (target genes found in one strain, n=275). Thus, there is a small set of Fur regulated genes common to all nine strains, but a large number of regulatory targets unique to a particular strain. Many of the unique regulatory targets are genes unique to that strain. This first-established pan-regulon reveals a common core of conserved regulatory targets and significant diversity in transcriptional regulation amongst E. coli strains, reflecting diverse niche specification and strain history.

overall_design: Identification of genome-wide Fur bindings for transcription factors in multi-strains using ChIP-exo technology

first: Bernhard

last: Palsson


title: The effect of Bcl-xL overexpression on H3K3me3

city: New York

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: To detect H3K4me3 histone modifications globally in HA-Bcl-xL overexpressing BON1 cells, we performed CUT&RUN assays.

overall_design: We used cells overexpressing HA-Bcl-xL (BON1/TGL/HA-Bcl-xL) and the control cells (BON1/TGL/pQ). CUT&RUN was performed from 500,000 cells per condition in triplicates.

first: Tiantian

last: Zhang

first: Adrian

middle: Y

last: Tan

first: Jenny

middle: Z

last: Xiang

first: Yi-Chieh

middle: N

last: Du


title: TP63 fusions drive multicomplex enhancer rewiring, lymphomagenesis, and PRC2 dependence

city: Salt Lake City

first: Xiaoyang

address: 1950 CIrcle of Hope

institute: University of Utah

summary: Identification of enhancer-promoter contacts in the T-lymphoma cell line SMZ1

overall_design: Applying H3K27ac HiChIP to identify enhancer-promoter interactions in the T-lymphoma cell line SMZ1

first: Gongwei

last: Wu


title: Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells

first: James

middle: J

last: Bieker

state: NY

address: One Gustave Levy Place

department: Cell, Developmental, and Regenerative Biology

institute: Mount Sinai School of Medicine

summary: The onset of erythropoiesis is under strict developmental control, with direct and indirect inputs influencing its derivation from the hematopoietic stem cell. A major regulator of this transition is KLF1/EKLF, a zinc finger transcription factor that plays a global role in all aspects of erythropoiesis. Here, we have identified a short, conserved enhancer element in KLF1 intron 1 that is important for establishing optimal levels of KLF1 in mouse and human cells. Chromatin accessibility of this site exhibits cell-type specificity and is under developmental control during the differentiation of human CD34+ cells towards the erythroid lineage. This site binds GATA1, SMAD1, TAL1, and ETV6. In vivo editing of this region in cell lines and primary cells reduces KLF1 expression quantitatively. However, we find that, similar to observations seen in pedigrees of families with KLF1 mutations, downstream effects are variable, suggesting that the global architecture of the site is buffered towards keeping the KLF1 genetic region in an active state. We propose that modification of intron 1 in both alleles is not equivalent to complete loss of function of one allele.

overall_design: We performed RNA seq on triplicate samples derived from the larger dual guide-edited or control CD34+ cells isolated at the end of the differentiation protocol.

first: Antanas

last: Planutis


title: Transcriptomic analysis to identify  genes associated with chloroquine-mediated radiosensitization of glioblastoma stem cells

city: Mainz

first: Ella

middle: L

last: Kim

state: Select an option…

address: Langenbeckstraße 1

department: Neurosurgery

institute: University Medical Center Mainz

summary:
Tumour suppressor p53 regulates hundreds of genes by either activating or repressing their transcription. p53-dependent transcription is activated by stress factors such as DNA damage, reactive oxygen species, hypoxia or oncogenic signaling. Lysosomotropic agent and DNA intercalating agent chloroquine has been implicated in sensitizing glioblastoma to radiation via p53 pathway. This study evaluates the effects of chloroquine in glioblastoma stem cells differing for the status of TP53 by using an integrated approach encompassing in vitro, in vivo and in silico methodologies to characterize the impacts of chloroquine on cell vitality, tumor-propagating capacity and gene expression.
We used microarrays to identify the genes whose expression is influenced by DNA intercalator chloroquine (ClQ) in glioblastoma stem cells expressing wild type p53 (line #993), mutant p53 (line G112) or a p53 null line #1095. To compare chloroquine-associated transcriptomic changes with those induced by ionizing radiation (IR), samples of IR-treated line #993 ("#993_IR") were analyzed in parallel with ClQ-treated samples ("993_ClQ").

overall_design: Gene expression was analyzed in three lines of glioblastoma stem cell lines (#993, #1095 and G112) either untreated or treated with chloroquine (ClQ).  In addition to ClQ-associated gene expression, transcriptomic changes associated with exposure to ionizing radiation (IR) were also analyzed in line #993. For each line and each condition (treated or untreated), 3 replicates were analyzed (re1, rep2 and rep3).

first: Gabriela

last: Salinas

first: Lennart

last: Opitz


title: RNA-seq of glioblastoma stem cells with shRNA-mediated CCR7 knockdown

city: Shanghai

first: Zhixin

last: Qiu

address: Dongan Road

institute: Fudan University

overall_design: RNA-seq of glioblastoma stem cell line GSC2907 with shRNA-mediated CCR7 knockdown (2 replicates each)

first: Linjie

last: Zhao

first: Jeremy

last: Rich


title: Manipulating the 3D organization of the largest synthetic yeast chromosome [HiC]

first: Weimin

address: 435 E 30th street

department: Institute for Systems Genetics

institute: NYU Langone Health

summary: Whether synthetic genomescan power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we reportde novosynthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bpSaccharomyces cerevisiaechromosome resulting from extensive genome streamlining and modification. During the construction ofsynIV, we developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction and facilitated chromosome debugging. In addition to the drastic sequence changes made to synIV by rewriting it, we further manipulated the three-dimensional structure of synIV in the yeast nucleus to explore spatial gene regulation within the nuclear space. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of the largest synthetic yeast chromosome shed light on higher-order architectural design of the synthetic genomes.

overall_design: This submission includes the Hi-C data for synIV or control strains to compare the 3D structure of synIV with BY4741 control. Also examine the 3D structures of the inside-out synIV.

first: Jef

middle: D

last: Boeke


title: Characteristic gene expression in the liver monocyte-macrophage-DC system is associated with the progression of fibrosis in NASH

city: Beijing

first: Xiaoxiao

last: Wang

address: No.11 Xizhimen South Street

institute: Peking Univeristy People's Hospital

summary: The monocyte-macrophage-dendritic cell (DC) (MMD) system exerts crucial functions that may modulate fibrogenesis in nonalcoholic steatohepatitis (NASH). We explored the cell characteristics, distribution and developmental trajectory of the liver MMD system in NASH mice with fibrosis using single-cell RNA sequensing (scRNA-seq).

overall_design: Liver tissues of C57BL/6 mice were obtained from wild-type mice (N=2) and NASH mice with fibrosis (HFD+F+CCl4, N=3; WD+F+CCl4, N=3) and were transferred into a sterile RNase-free tube containing calcium-free and magnesium-free 1x phosphate buffered solution (PBS) on ice. Tissues were dissociated into single cells and analyzed using scRNA-seq.

first: Zilong

first: Baiyi

last: Liu

first: Rui

last: Jin

first: Yuyun

last: Song

first: Ran

last: Fei

first: Xu

last: Cong

last: Huang

first: Xiaohe

last: Li

first: Jia

last: Yang

first: Lai

last: Wei

first: Huiying

last: Rao

first: Feng


title: Profiling Drosophila third instar larval eye discs with disruptions in Hippo and Rbf pathways by 10X single-cell RNA-Sequencing

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary: We performed single-cell RNA-sequencing experiments to understand how the Rbf and Hippo pathways collaborate to maintain cell identity. Drosophila melanogaster photoreceptor neurons with dual mutation in Rbf[120a] and wts[x1] specify normally before abruptly dedifferentiating. We performed scRNA-Seq on w1118, Rbf[120a] single mutant, wts[x1] single mutant, and Rbf[120a] wts[x1] double mutant tissues to better understand the dedifferentiation phenotype. We identified transcriptional changes that were unique to double mutant tissue. We then validated these experiments using a novel dedifferentiation model expressing constitutively active yki[S111A,S168A,S250A] in Rbf[120a] mutant tissue using the GMR-GAL4 driver. We performed single-cell experiments on eye tissues expressing yki[S111A,S168A,S250A] in Rbf wildtype and mutant backgrounds, as well as tissues co-expressing Hth and yki. We then analyzed these experiments to determine the dedifferentiation transcriptional program.

overall_design: 10X single-cell RNA-sequencing on single cell suspensions from third instar larval eye discs dissected at the optic stalk and eye antennal border. In total 2 wildtype w1118, 2 Rbf[120a] mutant, 1 wts[x1] mutant, 1 Rbf[120a] wts[x1] double mutant, 1 GMR-GAL4>ykiS111A,S168A,S250A, 1 Rbf[120a];GMR>yki[S111A,S168A,S250A], and 1 GMR>Hth, yki[S111A,S168A,S250A], replicates were included to explore the role of the RB and Hippo pathways in maintaining photoreceptor specification.

first: Alexandra

middle: E

last: Rader

first: Maxim

last: Frolov


title: CCRL2 expression by specialized lung capillary endothelial cells controls NK  cells homing in lung cancer

city: Rome

first: Mattia

last: Laffranchi

address: Viale Regina Elena 291

department: Molecular Medicine

country: Italy

institute: La Sapienza University of Rome

summary: Patterns of chemotactic receptors regulate the homing of leukocytes to tissues. Here we report that the CCRL2/chemerin/CMKLR1 axis represent a selective pathway for the homing of NK cells to the lung. CCRL2 is a non-signaling seven-transmembrane domain receptor able to control lung tumor growth. Total or endothelial cell targeted CCRL2 deletion or the deletion of its ligand chemerin were found to promote tumor progression in a KrasG12D/+;p53LoxP  lung cancer model. This phenotype was dependent on the reduced recruitment of CD27-CD11b+ mature NK cells. Mining scRNA-seq databases identified CCRL2 expression as the hallmark of general alveolar lung capillary endothelial cells (gCaps). CCRL2 expression is epigenetically regulated in lung endothelium. In vivo administration of low doses of the demethylating agent 5-Aza induced CCRL2 upregulation, increased recruitment of NK cells and lung protection in a tumor model. These results identify CCRL2 as a NK cell lung homing molecule that might be exploited to promote NK cell-mediated lung immune surveillance.

overall_design: To investigate the role of Ccrl2 in lung NK cells recruitment, scRNA sequencing was performed in total ILCs (CD45 + NKp46 + CD127 + cells) purified from Kras G12D/+ /p53 LoxP TK WT and Ccrl2 deficient mice.

first: Francisco

last: Bianchetto

first: Nicola

last: Tamassia

first: Tiziana

last: Schioppa

first: Francesca

last: Sozio

first: Annalisa

last: Del Prete

first: Silvano

last: Sozzani


title: RNA-seq of glioblastoma stem cells with CCL21 treatment

first: Zhixin

last: Qiu

overall_design: RNA-seq of glioblastoma stem cell line GSC20 with CCL21 treatment or IgG control (3 replicates each)

first: Linjie

last: Zhao

first: Jeremy

last: Rich


title: SMART-Seq analysis of a lymphatic endothelial cell line

overall_design: A total of 24 single cells from a lymphatic endothelial cell line were analyzed using SMART-Seq at the single cell level.


title: Alternative splicing changes promoted by NOVA2 upregulation in endothelial cells and relevance for gastric cancer

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

country: United Kingdom

institute: UCL

summary: Angiogenesis is crucial for cancer progression and anti-angiogenic drugs are in use for its treatment. However, their clinical benefits are unsatisfactory. Thus, a deeper understanding of the mechanisms sustaining cancer vessel growth is crucial to identify better biomarkers and novel therapeutic targets. Alternative Splicing (AS) is an essential modifier of human proteome diversity. Nevertheless, its contribution to tumor vasculature development is poorly known. NOVA2 is an important AS regulator of angiogenesis and vascular development and it is up-regulated in tumor endothelial cells (ECs) of different cancers, thus representing a potential driver of tumor blood vessels aberrancies. Here, we identified novel AS transcripts generated upon NOVA2 upregulation in ECs, suggesting a pervasive role of NOVA2 in vascular biology. In addition, we report that NOVA2 is also upregulated in ECs of gastric cancer (GC), with its expression correlating with poor overall survival of the GC patients. We also found that the AS of the newly identified NOVA2 target RapGEF6 is altered in GC patients and associated with NOVA2 expression, tumor angiogenesis and poor patient outcome. Our findings provide a better understanding of GC biology and suggest that AS might represent a potential source of biomarkers and therapeutics for novel anti-angiogenic GC treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for endothelial cells (control n=2) with Nova2 overexpression (n=2) .

first: Anna

last: Di Matteo

first: Elisa

last: Belloni

first: Davide

last: Pradella

middle: M

last: Chiaravalli

last: Bugatti

first: Roberta

last: Alfieri

first: Chiara

last: Barzan

first: Elena

middle: F

last: Tena

last: Terenzani

first: William

last: Vermi

first: Manuel

last: Irimia

first: Claudia

last: Ghigna


title: Meteorin in macrophages regulates hematopoietic stem/progenitor cells

city: hangzhou

first: Xin-Jiang

last: Lu

address: Zijingang Campus, Zhejiang University, No.866, Yuhang Tang Road

department: Department of Physiology, and Department of Hepatobiliary and Pancreatic Surgery of The First Affiliated Hospital,

institute: Zhejiang University

summary: We show that meteorin (Metrn) from hypoxic macrophages restrains hematopoietic stem cells (HSCs) proliferation and mobilization.  In macrophages specific Metrn knockout mice, reactive oxygen species levels in HSCs were upregulated through activating phospholipase C signaling. Macrophage specific knockout mice for Metrn (Metrn-fl/fl*LysM-Cre) were generated. Transcriptome profiling (RNA-Seq) and differential gene expression analysis of bone marrow LSK (lin- sca-1+ c-kit+) cells from Metrn-fl/fl*LysM-Cre (Metrn-cKO) and Metrn-fl/fl mice was performed. Metrn cKO mice showed a regulatory role for HSPCs by macrophages.

overall_design: Total 4 LSK samples were analyzed in this study. 2 samples as Metrnf/f, 2 samples as Metrnf/f LysM


title: CCL21/CCR7 axis in regulating glioblastoma stem cell-lymphatic endothelial cell interaction

last: Qiu

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

overall_design: Refer to individual Series


title: RNA-seq of glioblastoma stem cells treated by CCR7 inhibitors.

overall_design: RNA-seq of glioblastoma stem cell line GSC2907 with CCR7 inhibitors (Cmp2105 and Navarixin) treatment (3 replicates each)

last: Zhao


title: Reconstruction of a Pan-regulon for Fur uncovers the conservation of its transcriptional regulation in E. coli

first: Ye

last: Gao

summary: Regulons for many transcription factors have been elucidated in model strains leading to an understanding of their role in producing physiological states.  Comparative analysis of a regulon and its target genes between different strains of the same species is lacking.  Ferric uptake regulator (Fur), involved in iron homeostasis, is one of the most conserved TFs, and is present in a wide range of bacteria. Using ChIP-exo experiments, we performed a comprehensive study of Fur binding sites in nine Escherichia coli strains with different lifestyles. 79 of the 431 target genes (18%) found belong to Fur’s core regulon, comprising genes involved in ion transport and metabolism, energy production and conversion, and amino acid metabolism and transport. 179 of the target genes (42%) comprise the accessory regulon, most of which were related to cell wall structure and biogenesis, and virulence factor pathways. The remaining target genes (173 or 40%) were in the unique regulon, with gene functions that were largely unknown. Furthermore, deletion of the fur gene led to distinct phenotypes in growth, motility, antibiotic resistance, and siderophore production. These results provide a more complete understanding of how Fur regulates a set of target genes with surprising variation in closely related bacteria.

sample_organism:
Escherichia coli
Salmonella enterica
Escherichia coli K-12
Escherichia coli O157:H7

overall_design: Expression profiling data for wild type E. coli and S. Typhimurium LT2 strains and their corresponding fur deletion strains were generated by RNA-seq, in duplicate

first: Ina

last: Bang


title: The Fur Pan-regulon in E. coli shows diversity in strain-specific sets of target genes

platform_organism:
Escherichia coli
Salmonella enterica
Escherichia coli K-12
Escherichia coli O157:H7

overall_design: Identification of genome-wide bindings for nine different E. coli strains using ChIP-exo technology


title: CPT1B regulates goat intramuscular preadipocyte lipid deposition through p38MAPK signaling pathway

status: Public on Aug 03 2023

city: chengdu

first: Yinggui

last: Wang

state: sichuan

address: 2-31, Jingwenyuan, South District, Airport Campus, Southwest University for Nationalities, Chengdu, Sichuan

institute: Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province

summary: CPT1B, as the major rate-limiting enzyme for fatty acid β-oxidation, involved in the regulation of adipose tissue lipid deposition, but its role in the regulation of goat intramuscular fat (IMF) remains unclear. Here, we conducted knockdown experiments targeting the CPT1B gene in goat intramuscular preadipocytes, resulting in a significant increase in intracellular triglyceride (TAG) content and lipid droplet accumulation. Conversely, the overexpression of CPT1B led to a significant decrease in intracellular TAG content and lipid droplet accumulation. Mechanistically, through RNA-seq analysis of CPT1B knockdown samples, we identified 285 differentially expressed genes (DEGs), including 71 up-regulated and 214 down-regulated genes. Notably, these DEGs were significantly enriched in various KEGG signaling pathways, such as fatty acid metabolism, focal adhesion, FoxO signaling, PI3K-Akt signaling, and MAPK signaling pathways. Gene Set Enrichment Analysis (GSEA) further confirmed the upregulation of the MAPK signaling pathway upon CPT1B knockdown in adipocytes. In rescue experiments, we demonstrated that the addition of a p38MAPK inhibitor (PD169316) to CPT1B-knockdown adipocytes counteracted the increase in lipid deposition caused by the loss of CPT1B function. These findings suggest that CPT1B inhibits lipid deposition in goat intramuscular preadipocytes via the p38MAPK signaling pathway. In addition, we observed a potential interaction between CPT1B and CPT1A through Protein-Protein Interaction Networks (PPIs). Interestingly, CPT1A exhibited a similar regulatory function to CPT1B, and they both were able to partially restore the changes in lipid deposition induced by each other. This observation supports the hypothesis of synergistic effects between CPT1B and CPT1A. Collectively, our results elucidate the role of CPT1B in the regulation of lipid deposition in goat intramuscular adipocytes through the p38MAPK signaling pathway, providing valuable insights for enhancing the quality of goat intramuscular fat.

overall_design: Differentially expressed genes were detected by RNA-seq sequencing in goat intramuscular adipocytes from knockdown CPT1B (si-CPT1B) and negative control (NC).

first: Jiangjiang

last: Zhu

first: Lian

last: Huang


title: Effects of Poly (ADP-ribose) Polymerase Inhibitor Treatment on the Repair Process of Ischemic Acute Kidney Injury

city: Seoul

first: Junseok

last: Jeon

state: Seoul

address: 81, Irwon-ro, Gangnam-gu

department: Internal Medicine

institute: Samsung Medical Center, Sungkyunkwan University School of Medicine

summary: The role of PARP inhibitors in the repair process of renal remains unclear. The effects of JPI-289, a novel PARP inhibitor, during the healing phase after renal ischemia-reperfusion injury were investigated.

overall_design: scRNAseq were perfomed with post-ischemic kidneys. JPI-289 100 mg/kg (n = 1) or saline (n = 1) was injected into the peritoneal cavity immediately before reperfusion during bilateral renal ischemia-reperfusion surgery. Mice were sacrificed at 24 h following bilateral ischemia-reperfusion surgery

first: Hye

last: Jang

first: Hyeonju

last: Ahn

first: Woong-Yang

last: Park

first: Wooseong

last: Huh


title: Combined application of whole transcriptome sequencing and ceRNA theory: lncRNA LOC110519952 participates in glucose transport under hypoxia stress in rainbow trout (Oncorhynchus mykiss) by regulating novel-m0023-5p/glut1a axis

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

summary: Hypoxia is a tricky and unavoidable environmental stressor for aquaculture with ongoing ecological deterioration and increasing stocking density, resulting in serious economic losses. Rainbow trout (Oncorhynchus mykiss), a commercially important fish species worldwide, exhibits extraordinarily poor tolerance to hypoxia; however, the regulatory mechanisms under hypoxia stress have not been elucidated. In this study, rainbow trout were separately subjected to moderate (Tm12L) and acute hypoxia for 12 h (Ts12L) and 12 h reoxygenation to investigate the changes of histology, biochemical parameters and transcriptomes (mRNA, miRNA and lncRNA) in liver, and interactions between LOC110519952-novel-m0023-5p-glut1a were further verified. The results showed that acute hypoxia resulted in more severe liver oxidative injury than moderate hypoxia, and anaerobic metabolism and lipid and protein metabolism were enhanced to some extent, especially in Ts12L. We also found that innate immune response was strengthened in Tm12L, while it was inhibited in Ts12L. In addition, dozens of hypoxia-related ceRNA networks derived from 1824 differentially expressed (DE) mRNAs, 427 DEmiRNAs and 545 DElncRNAs were identified, including LOC110519952-novel-m0023-5p-glut1a, LOC110520012-miR-206-y-vegfaa, LOC118965299-novel-m0179-3p-epoa and MSTRG.7382.2-miR-184-y-hmox. Further studies validated that LOC110519952 acted as a ceRNA that can positively regulate glut1a expression by adsorbing novel-m0023-5p. Overexpression of novel-m0023-5p could promote liver cell viability and proliferation, and introduction of LOC110519952 attenuated the effects.  The findings contribute to deepen our understanding of the adaptive mechanisms used by rainbow trout in response to hypoxia stress, and provide valuable information for hypoxia-tolerant varieties breeding.

first: Jinqiang

first: Shenji

last: Wu


title: Effects of ginkgetin on liver fibrosis by bulk RNA Sequencing

city: Wuhan

first: Chaoyang

address: Jiefang Avenue #1277

institute: Wuhan Union Hospital

summary: Ginkgetin could significantly attenuate liver fibrosis in a mouse model induced by TAA, including inhibiting hepatic inflammtion and fibrosis. In addition, the related signaling pathways and gene expression were also downregulated by ginkgetin by bulk RNA Sequencing analysis.

overall_design: To investigate the effect of ginkgetin on liver fibrosis and the underlying mechanism, we performed bulk RNA Sequencing on the liver tissues from fibrotic mice treated with vehicle (control group) or ginkgetin (5mg/kg/day) (ginkgetin group).

first: Bin

last: Xiong


title: Collagen VI sustains cell stemness and chemotherapy resistance in glioblastoma.

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary:
Microenvironmental factors are known fundamentals regulators of the phenotype and aggressiveness of glioblastoma (GBM), the most lethal brain tumor, characterized by fast progression and marked resistance to treatments. In this context, the extracellular matrix (ECM) is known to heavily influence the behavior of cancer cells from several origins, contributing to stem cell niches, influencing tumor invasiveness and response to chemotherapy, mediating survival signaling cascades, and modulating inflammatory cell recruitment.  Here we show that collagen VI (COL6), an ECM protein widely expressed in both normal and pathological tissues, has a distinctive distribution within the GBM mass, strongly correlating with the most aggressive and phenotypically immature cells. Our data demonstrate that COL6 sustains the stem-like properties of GBM cells and supports the maintenance of an aggressive transcriptional program promoting cancer cell proliferation and survival. In particular, we identified a specific subset of COL6-transcriptionally regulated genes, required for the response of cells to replicative stress and DNA damage, supporting the concept that COL6 is an essential stimulus for the activation of GBM cell response and resistance to chemotherapy, through the ATM/ATR axis.  Altogether, these findings indicate that COL6 plays a pivotal role in GBM tumor biology, exerting a pleiotropic action across different GBM hallmarks, including phenotypic identity and gene transcription, as well as response to treatments, thus providing valuable information for the understanding of the complex microenvironmental cues underlying GBM malignancy.
Collagen VI is over-expressed in the cancer stem cell niche in glioblastoma and protects them from differentiation stimuli and chemotherapy exposure.

overall_design: Gene expression was measured using Affymetrix platform in primary GBM cells transfected with a Negative Control siRNA or two different siRNAs against COL6A1.

first: Silvia

last: Bresolin

first: Luca

last: Persano


title: Functional Adaptations of Endogenous Retroviruses to the Drosophila host Reveal Principles of their Evolutionary Diversification

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences


title: De novo assembly and annotation of the singing mouse genome

first: Paul

last: Frazel

address: 435 E 30th St

institute: NYU Langone Medical Center

summary: We sequenced the genome and transcriptome of Alston’s singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types.

overall_design: Genomic and transcriptomic sequencing files from Alston's singing mouse, Scotinomys teguina

first: Samantha

last: Smith

first: Stephen

last: Phelps


title: Single-cell RNAseq uncovers cellular heterogeneity and provides a signature for pediatric sleep apnea

city: Columbia

first: Rene

last: Cortese

state: MO

address: 1 Hospital Dr. Room MA104E

department: Department of Child Health, School of Medicine

institute: Child Health Research Institute

summary: Obstructive Sleep Apnea (OSA) is a highly prevalent disease and a major cause of systemic inflammation leading to neurocognitive, behavioral, metabolic, and cardiovascular dysfunction in children and adults. However, the impact of OSA on the heterogeneity of circulating immune cells remains to be determined. scRNA-seq demonstrated OSA-induced heterogeneity in cellular composition and enabled the identification of previously undescribed cell types in PBMCs.

overall_design: The OSA group consisted of 11 patients who were polysomnographically diagnosed with OSA (Apnea Hypopnea Index (AHI) >5 events/hour sleep). The Control group consisted of 11 asymptomatic individuals without OSA (AHI < 1 events/hour sleep). Participants were recruited from individuals undergoing PSG due to suspected OSA at the Pediatic Sleep Clinics at the University of Missouri. Inclusion criteria were 2-16 years of age; male and female, all ethnic groups and all BMIs. Exclusion criteria were individuals younger than 2 years and older than 16 years of age, presence of genetic disorders: cerebral palsy, neuromuscular diseases, genetic or any underlying systemic congenital disease.

first: Taylor

last: Adams

first: Kylie

middle: H

last: Cataldo

first: Justin

last: Hummel

first: Naftali

last: Kaminski

first: Leila

last: Kheirandish-Gozal

first: David

last: Gozal


title: Study the  global mRNA translation changes between SKBR cells overexpressing VIRMA and eGFP control

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

summary:
In order to determine whether increased m6A abundance coupled with upregulation of transcripts regulating UPR also promote their translation, we first compared levels of key UPR signalling proteins in VIRMA FL-overexpressing SKBR3 cells and eGFP control. To our surprise, none of the key UPR signalling proteins measured showed increased levels in VIRMA FL cells compared to control
We then performed ribosome profiling analysis between SKBR cells overexpressing VIRMA FL and eGFP control

overall_design: Comparative translation analysis of Poly-ribo-seq data for VIRMA-overexpressing SKBR3 cells and eGFP control

last: Wong

first: Jessamy

last: Tiffen

first: Quintin

last: Lee

first: Renhua

last: Song


title: Effect of VIRMA amplification on gene expression in breast cancer cells

summary:
To confirm the contribution of elevated VIRMA levels towards cell proliferation and colony formation, we depleted VIRMA in four breast cancer cell lines, SKBR3, HS578T, MCF7 and MDAMB453 using short-hairpin RNAs (shRNAs).
We then performed gene expression profiling analysis using data obtained from RNA-seq data

overall_design: Comparative gene expression profiling analysis of RNA-seq data for VIRMA-overexpressing SKBR3 cells and eGFP control


title: RNA-sequencing (transcriptome analysis) of Desulfovibrio vulgaris Hildenborough during electron uptake process on a cathode.

city: Tsukuba

first: Xiao

last: Deng

state: Ibaraki

address: 1-1 Namiki

country: Japan

institute: National Institute for Materials Science

summary: Desulfovibrio vulgaris Hildenoborough was incubated in an H-type electrochemical reactor for 7 days on an indium-tin doped oxide electrode poised at −0.2 V (versus standard hydrogen electrode), which served as the sole electron donor. As a negative open circuit (without electrode) control, cells were incubated in a glass vial in the absence of an electrode. Total RNA was extracted from cells after incubation, and RNA fragments were purified and transcribed into cDNA. cDNA was sequenced by NovaSeq 6000 System.

overall_design: Gene expression profile of Desulfovibrio vulgaris Hildenborough incubated for 7 days on an −0.2 V (vs. SHE) electrode versus under an open circuit condition.


title: Mammalian SWI/SNF chromatin remodeling complexes promote tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer

city: New Haven

first: Fernando

middle: J.

last: de Miguel

state: Connecticut

address: 333 Cedar Street

department: Yale Cancer Center

institute: Yale University

summary: Acquired resistance to tyrosine kinase inhibitors (TKI), such as osimertinib used to treat EGFR-mutant lung adenocarcinomas, limits long-term efficacy and is frequently caused by non-genetic mechanisms. Here, we define the chromatin accessibility and gene regulatory signatures of osimertinib sensitive and resistant EGFR-mutant cell and patient-derived models and uncover a role for mammalian SWI/SNF chromatin remodeling complexes in TKI resistance. By profiling mSWI/SNF genome-wide localization, we identify both shared and cancer cell line-specific gene targets underlying the resistant state. Importantly, genetic and pharmacologic disruption of the SMARCA4/SMARCA2 mSWI/SNF ATPases re-sensitizes a subset of resistant models to osimertinib via inhibition of mSWI/SNF-mediated regulation of cellular programs governing cell proliferation, epithelial-to-mesenchymal transition, epithelial cell differentiation, and NRF2 signaling. These data highlight the role of mSWI/SNF complexes in supporting TKI resistance and suggest potential utility of mSWI/SNF inhibitors in TKI-resistant lung cancers.


title: TrACES of Time: Transcriptomic Analyses for the Contextualization of Evidential Stains – identification of RNA markers for estimating time-of-day of bloodstain deposition

city: Cologne

first: Annica

last: Gosch

address: Melatengürtel 60-62

department: Forensic Genetics

institute: Institute of Legal Medicine Cologne

summary: Obtaining forensically relevant information beyond who deposited a biological stain on how and under which circumstances it was deposited is a question of increasing importance in forensic molecular biology. In the past few years, several studies have been produced on the potential of gene expression analysis to deliver relevant contextualizing information, e.g. on nature and condition of a stain as well as aspects of stain deposition timing. However, previous attempts to predict the time-of-day of sample deposition based on the differential expression of a limited number of previously known circadian oscillators were of limited success.   Herein, we newly approached this goal by applying current sequencing technologies and statistical methods to identify novel candidate markers for forensic time-of-day predictions from whole transcriptome analyses. To this purpose, we collected whole blood samples from ten individuals at eight different time points throughout the day, performed whole transcriptome sequencing and applied biostatistical algorithms for differential gene expression in combination with forensically relevant filtering criteria to identify 81 mRNA markers with significantly differential expression as candidates to predict the time of day. In addition, we assessed the characteristics of a subset of 13 candidate predictors in dried and aged blood stains. While we demonstrated the general possibility of using the selected candidate markers to predict time-of-day of sample deposition, we also observed notable variation between different donors and storage conditions, highlighting the relevance of employing accurate quantification methods in combination with robust normalization procedures.   This study’s results are foundational and may be built upon when developing a targeted assay for time-of-day predictions from forensic blood samples in the future.

overall_design: Analysis of differential gene expression in human blood samples obtained at different time points of a day

first: Archana

last: Bhardwaj

first: Cornelius

last: Courts


title: BAFF and APRIL counterregulate susceptibility to inflammation-induced preterm birth

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Emerging clinical evidence points to a function for B cell activating factor (BAFF) in pregnancy. However, a direct role for BAFF-axis members including BAFF, the closely related a proliferation-inducing ligand (APRIL), and their respective receptors in pregnancy has not been examined. This study demonstrates that loss of BAFF results in decreased inflammatory responsiveness and decreased susceptibility to inflammation-induced preterm birth (PTB). In contrast, loss of APRIL increases inflammatory responsiveness and susceptibility to PTB. Consistent with overlapping receptor utilization by BAFF and APRIL, deletion of BAFF-axis receptors is not sufficient to modify susceptibility to PTB. Critically, therapeutic administration of BAFF/APRIL monoclonal antibodies or recombinant proteins is sufficient to manipulate susceptibility to inflammation-induced PTB. Further, macrophages are identified as the principle BAFF producing immune cells at the maternal-fetal interface and BAFF and APRIL divergently manipulate macrophage gene expression and inflammatory function. Genes linked to labor initiation are upregulated in WT and APRIL deficient macrophages while downregulated in BAFF deficient macrophages and correlate with myeloid gene expression in human placental samples during labor. Thus, BAFF and APRIL play important, but divergent, counterregulatory inflammatory roles in pregnancy and provide new therapeutic targets for mitigating the risk of PTB.

overall_design: Bulk RNA-Seq on macrophages from BAFF

first: Jessica

last: Doll

first: Maria

last: Moreno-Fernandez

first: Traci

last: Stankiewicz

first: Jennifer

last: Wayland

first: Adrienne

last: Wilburn

first: Claire

last: Chougnet

first: Daniela

last: Giordano

first: Monica

last: Cappelletti

first: Pietro

last: Presicce

first: Suhas

middle: G

last: Kallapur

first: Tamara

last: Tilburgs

first: Senad

last: Divanovic


first: Fernando

last: de Miguel

overall_design: RNAseq data of sensitive and osimertinib resistant cell lines and after SMARCA4 knock-down and osimertinib treatment in PC9-OR and YU-005C cells.


title: Gene expression profile at single cell level of cultuted bovine milk-derived cells (MiDCs)

city: Ithaca

first: Gerlinde

middle: R.

last: Van de Walle

address: 235 Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

summary: Bovine milk derived cells are a novel population with reported stem cell-like properties. We assessed these cells using scRNA-seq for markers of pluripotency and other features associated with the effects of their conditioned medium (CM).

overall_design: Fresh bovine milk was centrifuged to isolate cells and adherent cells were isolated by plating on tissue-culture plates. Upon isolation of colonies and formation of a monolayer, the cells were analyzed using scRNA-seq.

first: Nikola

last: Danev

first: Rebecca

last: Harman


title: Single Cell Transcriptomic Atlas of Lung Microvascular Regeneration after Targeted Endothelial Cell Ablation

city: Ottawa

first: Duncan

last: Stewart

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: In a model of ALI induced by lung endothelial cell (EC) ablation we show for the first that resolution of acute lung injury and EC regeneration is orchestrated by novel apelin-expressing, gCap endothelial stem-like cells by a mechanism dependent on apelin signaling.

overall_design: The study comprises twelve single cell RNA-seq samples from three pooled libraries (all twelve samples present in all three libraries) constructed using the MULTI-seq protocol. Raw data for MULTI-seq libraries includes paired-end sequences for the gene expression libraries and paired-end sequences for the sample barcode libraries. The individual sample information (including the MULTI-seq barcode, barcode ID for each sample) is provided in the sample_metadata.txt.

first: Rafael

middle: S

last: Godoy

first: David

middle: P

last: Cook

first: Nicholas

last: Cober

first: Emma

last: McCourt

first: Yupu

last: Deng

first: Liyuan

last: Wang

first: Kenny

last: Schlosser

first: Katelyn

last: Rowe


overall_design: WES data of sensitive and osimertinib resistant cell lines. New mutations in resistant cells were called using the sensitive counterparts as reference.


title: Effect of Overexpression of VIRMA on m6A-methylated mRNAs in breast cancer cells

first: RENHUA

last: SONG

summary: To identify m6A-regulated mRNA targets affected by VIRMA overexpression we compared m6A peak abundance measured via m6A RNA immunoprecipitation sequenc-ing in SKBR3 cells overexpressing full-length VIRMA and eGFP control

overall_design: m6A-RIP-sequencing was performed according to the recently published “Refined RIP-seq”  with several modifications. . 5 μg total RNA was fragmented into ~200 nucleotide long fragments via incubation with ZnCl2 at 70˚C for 3 minutes. Fragmented RNA was precipitated, and the RNA size distribution was assessed using RNA 6000 Nano Bioanalyzer kit

first: Justin

last: Wong

first: Jessamy

last: Tiffen

first: Quintin

last: Lee

first: Renhua

last: Song


title: Transcript analysis under calcium deficiency in 6 day old Marchantia polymorpha wildtype (Tak-1) and Gβ-null mutant (gpb1-2) gemmalings and inter-species comparison of M. polymorpha, Arabidopsis and lettuce under calcium deficiency

city: Singapore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Lifescience Laboratory

summary: Calcium deficiency response in liverwort, Arabidopsis and lettuce: (1) Marchantia polymorpha: M. polymorpha wildtype and Gβ-null mutant plants (Tak-1, gpb1-2) were grown in control liquid Yamagami media (2 mM Ca) for 6 days. For RNA-seq experiments, 6 day old gemmalings were transferred to calcium deficiency (0 mM Ca) media. Samples were collected at 48 h after the transfer. The transcriptomic profiles were collected from two independent batches. In total four biological replicates were used for each condition and each genotype for a total of 16 samples. (2) Arabidopsis thaliana: For Arabidopsis RNA-seq experiment, 6-day old seedlings grown on ½ strength MS media with sucrose were transferred to Yamagami media with 2 mM or 0 mM CaCl2 and treated for 7 days. (3) Lactuca Sativa: For lettuce RNA-seq, 4-day old seedlings grown on water agar (1%) were transferred to Yamagami media with 2 mM or 0.15 mM CaCl2 and treated for 7 days. In total four and three biological replicates were used for each condition for a total of 8 and 6 samples respectively for Arabidopsis and lettuce.

sample_organism:
Marchantia polymorpha
Arabidopsis thaliana
Lactuca sativa

overall_design: Transcript analysis of 6-day old M. polymorpha gemmalings under two conditions (2 mM Ca, 0 mM Ca) with wild type Tak-1 and gpb1-2. Transcript analysis of 6-day old (Arabidopsis) under two conditions (2 mM Ca, 0 mM Ca) and 4-day old (lettuce) wildtype seedlings under two conditions (2 mM Ca, 0.15 mM Ca).

first: Richalynn

last: Leong


first: Fernando

last: de Miguel

overall_design: ATAC-seq data in untreated PC9 cells and after SMARCA4 knock-down and osimertinib treatment in PC9-OR and YU-005C cells.

first: Wesley

last: Cai


title: Analysis of CD8+ T cell of BCD mice

city: Kyoto

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

institute: Graduate School of Medicine, Kyoto University

summary: The gut microbiome has garnered attention as an effective target to boost immunity and improve cancer immunotherapy. We found that B cell defective (BCD) mice, such as µ membrane targeted deletion (µMT) and activation-induced cytidine deaminase (AID) knockouts (KO), have elevated anti-tumor immunity under specific-pathogen-free but not germ-free conditions. Microbial dysbiosis in these BCD mice enriched the type I interferon (IFN) signature in mucosal CD8+ T cells, resulting in upregulation of the type I IFN-inducible protein stem cells antigen-1 (Sca-1). Among CD8+ T cells, naïve cells predominantly circulate from the gut to periphery, and those that had migrated from the mLN to the periphery had significantly higher expression of Sca-1. The gut-educated Sca-1+ naïve subset is endowed with enhanced mitochondrial activity and anti-tumor effector potential. The heterogeneity and functional versatility of the systemic naïve CD8+ T cell compartment was revealed by single cell analysis and functional assays of CD8+ T cell subpopulations. These results indicate one of the potential mechanisms through which microbial dysbiosis regulates anti-tumor immunity.

overall_design: 12 sample were included along with corresponding control (no replicates)

first: Tasuku

last: Honjo


title: MethylC-capture sequencing of control, osteoporotic, and Astragalus polysaccharides (APS)-treated osteoporotic SD rats

city: guangzhou

first: Ruiqiang

last: Yan

address: 黄埔大道西601号

institute: Jinan University

type: Methylation profiling by high throughput sequencing

summary: SD rats were intramuscular injected with dexamethasone to induce osteoporosis, and treated with APS. Then, colonic epithelia of control, osteoporotic and APS-treated osteoporotic rats were collected for MethylC-capture sequencing .

overall_design: examination of DNA methylation in colonic epithelia of  three groups of rats

first: Junsheng

last: Liu

first: Xichun

last: Peng


title: miRNA expression in tracheal aspirates [ICS-BPD vs. ICS-BPD-PH]

status: Public on Aug 02 2023

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

summary: Tracheal aspirate (TAs) samples were collected from intubated preterm infants with hemodynamically significant intracardiac shunt (ICS), and a diagnosis of ICS-BPD/ICS-BPD-PH. 36 TA samples were analyzed. Small RNAs were extracted and the expression miRNAs was detected with PCR arrays.

overall_design: We extracted RNA  from 0.5 mL of tracheal aspirates from premature neonates using the Plasma/Serum RNA Purification Kit (Norgen). The expression of 1,066 human miRNAs was quantified using the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z). Results (Ct values) were normalized to global means, and fold changes were calculated using the 2-ΔΔCT method.

first: Roopa

last: Siddaiah

first: Lucy

last: Emery


title: Transcription-factor-(TF)-dependence of ncRNA expression to define enhancers and enhancer-associated ncRNAs that are involved in a TF-dependent regulatory network

city: Chicago

first: Xinan

middle: Holly

last: Yang

state: IL

address: 900 East 57th Street, KCBD Room 5121

department: Pediatrics

institute: universty of Chicago

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

overall_design: Refer to individual Series


title: HapX-mediated H2B deub1 and SreA-mediated H2A.Z deposition coordinate in fungal iron resistance [ChIP-seq]

city: Hangzhou

first: SUN

last: Kewei

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Plant pathogens are challenged by host-derived iron starvation or excess during infection, but the mechanism through which pathogens counteract iron stress is unclear. Here, we found that Fusarium graminearum encounters iron excess during the colonization of wheat heads. Deletion of heme activator protein X (FgHapX), siderophore transcription factor A (FgSreA) or both attenuated virulence. Further, we found that FgHapX activates iron storage under iron excess by promoting histone H2B deubiquitination (H2B deub1) at the promoter of the responsible gene. Meanwhile, FgSreA is shown to inhibit genes mediating iron acquisition during iron excess by facilitating the deposition of histone variant H2A.Z and histone 3 lysine 27 trimethylation (H3K27 me3) at the first nucleosome after the transcription start site. In addition, the monothiol glutaredoxin FgGrx4 is responsible for iron sensing and control of the transcriptional activity of FgHapX and FgSreA via modulation of their enrichment at target genes and recruitment of epigenetic regulators, respectively. Taken together, our findings elucidated the molecular mechanisms for adaptation to iron excess mediated by FgHapX and FgSreA during infection in F. graminearum and provide novel insights into regulation of iron homeostasis at the chromatin level in eukaryotes.

overall_design: ChIP-seq on WT, FgSwc2 knockout and FgSwc6 knockout

first: K

last: SUN

first: Y

last: YIN


title: TBX5 Adult Knockout Atrial ncRNA Expression [2023_eRNA]

summary: We deep sequenced wildtype and Tbx5-mutant mouse atria, identifying ~2600 novel Tbx5-dependent ncRNAs. Tbx5-dependent ncRNA transcription provided a quantitative metric of Tbx5-dependent enhancer activity, correlating with target gene expression.

overall_design: Each sample is ribozero sequenced at high depth (single lane), same sample split into "oligodT" and "non-oligodT" fractions and the non-oligodT fractions were sequenced over 2 lanes, - 50bp single ended, library is directional.

first: Rangarajan

last: Nadadur

first: Ivan

last: Moskowitz


title: TBX5 Adult Knockout Right Atrial Gene Expression [RA_RNAseq]

summary: TBX5 removed from adult mice with R26CreERt2, right atrial RNA extracted and sequenced.

overall_design: To define the downstream gene expression changes that occur in the adult atria after removal of TBX5, we compared control right atrium (RA) with Tbx5 knockout RA.


title: Bcl6, Irf2 and Notch2 promote nonclassical monocyte development [RNA-Seq]

city: St. Louis

first: Kevin

middle: William

last: O'Connor

address: 4925 Children's Place

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: Ly6Clo monocytes are a myeloid subset that specializes in the surveillance of vascular endothelium.  Ly6Clo monocytes have been shown to derive from Ly6Chi monocytes.  NOTCH2 signaling has been implicated as a trigger for Ly6Clo monocyte development, but the basis for this effect is unclear.  Here, we examined the impact of NOTCH2 signaling of myeloid progenitors on the development of Ly6Clo monocytes in vitro.  NOTCH2 signaling induced by delta-like ligand 1 (DLL1) efficiently induced the transition of Ly6Chi TREML4– monocytes into Ly6Clo TREML4+ monocytes.  We further discovered two additional transcriptional requirements for development of Ly6Clo monocytes.  Deletion of BCL6 from myeloid progenitors abrogated development of Ly6Clo monocytes.  IRF2 was also required for Ly6Clo monocyte development in a cell-intrinsic manner.  DLL1-induced in vitro transition into Ly6Clo TREML4+ monocytes required IRF2 but unexpectedly could occur in the absence of NUR77 or BCL6.  These results imply a transcriptional hierarchy for these factors in controlling Ly6Clo monocyte development.

overall_design: Ly6Chi monocytes were obtained from wild-type, Nr4a1KO, Bcl6cKO, and Irf2KO mouse bone marrow and subjected to RNA sequencing.

middle: W

first: Kenneth

last: Murphy


title: The CRTC-1 transcriptional domain is required for COMPASS complex mediated longevity in C. elegans

city: Boston

first: William

middle: B.

last: Mair

state: MA

address: 665 Huntington Avenue

department: Molecular Metabolism

institute: Harvard T.H. Chan School of Public Health

summary: Loss of function during ageing is accompanied by transcriptional drift, altering gene expression and contributing to a variety of age-related diseases. CREB-regulated transcriptional coactivators (CRTCs) have emerged as key regulators of gene expression that might be targeted to promote longevity. Here, we define the role of the Caenorhabditis elegans CRTC-1 in the epigenetic regulation of longevity. Endogenous CRTC-1 binds chromatin factors, including components of the COMPASS complex, which trimethylates lysine 4 on histone H3 (H3K4me3). CRISPR editing of endogenous CRTC-1 reveals that the CREB-binding domain in neurons is specifically required for H3K4me3-dependent longevity. However, this effect is independent of CREB but instead acts via the transcription factor AP-1. Strikingly, CRTC-1 also mediates global histone acetylation levels, and this acetylation is essential for H3K4me3-dependent longevity. Indeed, overexpression of an acetyltransferase enzyme is sufficient to promote longevity in wild-type worms. CRTCs, therefore, link energetics to longevity by critically fine-tuning histone acetylation and methylation to promote healthy ageing.

overall_design: set-2 mutants [set-2] are long-lived due to changes in epigenetic modifications. CRTC-1 is required to promote this longevity phenotype since the double mutants set-2;crtc-1(CBD) [WBMB1036] show a normal lifespan. CRTC-1 regulates this set-2-dependent longevity through its CBD domain, which is important to modulate transcription. In order to identify the CRTC-1(CBD)-dependent transcriptional changes in the set-2 mutants, we performed an RNA-seq analysis in the following strains wild type [N2], set-2 [set-2], crtc-1(CBD) [WBM1041], and se-2;crtc-1(CBD) [WBM1036].

first: Carlos

last: Giovanni Silva-García

first: Laura

middle: I

last: Láscarez-Lagunas

first: Katharina

last: Papsdorf

first: Caroline

last: Heintz

first: Aditi

last: Prabhakar

first: Christopher

last: Morrow

first: Lourdes

last: Pajuelo Torres

first: Arpit

last: Sharma

first: Jihe

first: Monica

last: Colaiácovo

first: Anne

last: Brunet

middle: B


title: Sex differences in colonic gene expression in a mouse model of obesity-associated colorectal cancer

city: Seoul

first: Mi-Kyung

last: Sung

address: Cheongpa-ro 47 gil

institute: Sookmyung Women's University

summary: We evaluated the effects of sex hormones and genes as factors involved in sex differences in obesity-associated colorectal cancer.

overall_design: Microarray analysis was performed on 24 colon tissue samples (n = 4 per group). Three comparison groups of differentially expressed genes were generated: Male+Low fat diet vs. Male+High fat diet, Female+Low fat diet vs. Female+High fat diet, and Female(Ovariectomized)+Low fat diet vs.  Female(Ovariectomized)+High fat diet.

first: Yoo-Mee

last: Chang


title: A phenotypic screening platform for chronic pain therapeutics using all-optical electrophysiology

city: Cambridge

first: Caitlin

last: Lewarch

address: 179 Sidney Street

institute: Quiver Bioscience

summary: Chronic pain associated with osteoarthritis (OA) remains an intractable problem with few effective treatment options. New approaches are needed to model the disease biology and to drive discovery of therapeutics. Here, we present an in vitro model of OA pain, where dorsal root ganglion (DRG) sensory neurons were sensitized by a defined mixture of disease-relevant inflammatory mediators, here called Sensitizing PAin Reagent Composition or SPARC. OA-SPARC components showed synergistic or additive effects when applied in combination and induced pain phenotypes in vivo. To measure the effect of OA-SPARC on neural firing in a scalable format for drug discovery, we used a custom system for high throughput all-optical electrophysiology. This system enabled light-based membrane voltage recordings from hundreds of neurons in parallel with single cell resolution and a throughput of up to 500,000 neurons per day, with patch clamp-like single action potential resolution. A computational framework was developed to construct a multiparameter OA-SPARC neuronal phenotype and to quantitatively assess phenotype reversal by candidate pharmacology with different mechanisms of action. We screened ~3000 approved drugs and mechanistically focused compounds, yielding data from over 1.2 million individual neurons with detailed assessment of both functional OA-SPARC phenotype rescue and orthogonal “off-target” effects. Analysis of confirmed hits revealed diverse potential analgesic mechanisms including well-known ion channel modulators as well as less characterized mechanisms including MEK inhibitors and tyrosine kinase modulators, providing validation of the platform for pain drug discovery.

overall_design: p10 WT rat DRG cells cultured for 8 days (5 replicates).

first: Pin

last: Liu

first: Hongkang

last: Zhang

middle: A

last: Werley

first: Monika

last: Pichler

first: Steve

last: Ryan

first: Jane

last: Jacques

first: Jennifer

last: Grooms

first: John

last: Ferrante

first: Guangde

last: Li

first: Dawei

first: Nate

last: Bremmer

first: Adam

last: Barnett

first: Romina

last: Chantre

first: Amy

last: Elder

last: Cohen

first: Luis

last: Williams

first: Graham

middle: T

last: Dempsey

first: Owen

last: McManus


title: Identification of genes associated with the development of silk glands using transcriptomics in silkworm (Bombyx mori)

city: Zhenjiang

first: Sun

last: Lindan

address: 301 xuefu road

department: School of Life and Sciences

institute: Jiangsu University

summary: The silk gland development has a greater impact on silk yields in silkworms. Silk glands from three pure silkworm strains (A798, A306, and XH) with different silk gland weight phenotypes were compared using transcriptome, proteomics, and WGCNA. Five genes (BGIBMGA002524, BGIBMGA002629, BGIBMGA005659, BGIBMGA005711, and BGIBMGA010889)  may be strongly associated with the growth of silk glands to be confirmed. These DEGs encoded alkylglycerol monooxygenase (AGMO), glucose dehydrogenase (GDH), zonadhesin (ZAN), odorant binding protein (OBPs), and β-fructofuranosidase (INV), respectively. PCR and ELISA were used to verify the mRNA and protein expression of five genes in the silk glands and tissues of 18 silkworm strains. The GO results showed that four genes have higher levels of expression and participate in glycogen metabolism, fatty acid synthesis, and branched-chain amino acid metabolism, thus, promoting growth and silk proteins synthesis.

overall_design: We selected three pure silkworm strains (A798, A306, and XH) with different silk gland weight phenotypes to investigate the silkworm's development-related genes. Then, we carried out the gene expression levels using the data obtained from the RNA-seq of three pure silkworm strains. Comparative gene expression profiling analysis of RNA-seq data for A306 against A798 and XH against A798.

first: Lindan

last: Sun

first: Binbin

first: Liang

last: Chen

first: Qi

last: Ge

first: Keping


title: Conservation of chromatin organization within human and primate centromeres

city: Seattle

first: Andrew

middle: Ben

last: Stergachis

state: WA

address: 1959 NE Pacific St

department: Medical Genetics

institute: University of Washington

summary: The focal attachment of the kinetochore to the centromere core is essential for genome maintenance, yet the highly repetitive nature of human centromeres limits our understanding of their chromatin organization. We demonstrate that single-molecule chromatin fiber sequencing can uniquely resolve chromatin organization within centromeres at single-molecule and single-nucleotide resolution. We find that the centromere core contains a dichotomous chromatin organization not found elsewhere in the genome, which is characterized by highly accessible chromatin patches heterogeneously punctuated amongst tightly compacted nucleosome arrays. These highly accessible chromatin patches correspond to sites of kinetochore attachment, and clustered CENP-B occupancy within these patches phase nucleosome arrays to the alpha-satellite repeat. This dichotomous chromatin organization is conserved between humans despite the marked divergence of the underlying alpha-satellite organization and is similarly conserved in primate centromeres that lack alpha-satellite repeats, indicating that functional conservation within centromeres is mediated at the level of chromatin, not DNA.

sample_organism:
Homo sapiens
Hoolock leuconedys

platform_organism:
Homo sapiens
Hoolock leuconedys

overall_design: Fiber-seq on cell lines from different individuals. CHM13 cells and CHM1 cells are complete hydatidiform mole cell lines derived from separate humans. GM14385 cells are lymphoblastoid cells derived from a different human. HLE cells are lymphoblastoid cells derived from a gibbon. Fiber-seq was performed as indicated below.

first: Danilo

last: Dubocanin

first: Adriana

middle: E

last: Sedeño-Cortés

first: Gabrielle

last: Hartley

first: Jane

last: Ranchalis

first: Aman

last: Agarwal

first: Glennis

last: Logsdon

first: Katherine

last: Munson

first: Taylor

last: Real

first: Benjamin

middle: J

last: Mallory

first: Evan

last: Eichler

first: Rachel

last: O-Neill


title: A postnatal network of co-hepato/pancreatic stem/progenitors in the biliary trees of pigs versus humans

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

summary: A network of co-hepato/pancreatic stem/progenitors exists in pigs and humans in Brunner’s Glands (BGs) in the submucosa of the duodenum, in peribiliary glands (PBGs) of intrahepatic and extrahepatic biliary trees, and in pancreatic duct glands (PDGs) of intrapancreatic biliary trees, collectively supporting hepatic and pancreatic regeneration postnatally. The network is found in humans postnatally throughout life and, so far, has been demonstrated in pigs postnatally at least through to young adults. These stem/progenitors in vivo in pigs are in highest numbers in BGs and in PDGS nearest the duodenum, and in humans are in BGs and in PBGs in the hepato/pancreatic common duct, a duct missing postnatally in pigs. Elsewhere in PDGs in pigs and in all PDGs in humans are only committed unipotent or bipotent progenitors.

overall_design: Variety of immune cell sorts from various pig tissues to identify parallels in the networks of co-hepato/pancreatic stem/progenitors in pigs and humans

first: Wencheng

last: Zhang

first: Lola

last: Reid

first: Matt

last: Kanke


title: Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney

city: Los Angeles

last: McMahon

state: CA

address: 1975 Zonal Ave

department: Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

summary: Mammalian organs exhibit distinct physiology, disease susceptibility and injury responses between the sexes. In the mouse kidney, sexually dimorphic gene activity maps predominantly to proximal tubule (PT) segments. Bulk RNA-seq data analyses demonstrated sex differences were established from 4 and 8 weeks after birth under gonadal control. Hormone injection studies and genetic removal of androgen and estrogen receptors highlighted direct androgen receptor (AR) mediated regulation of gene activity in PT cells as the primary regulatory mechanism. Single-nuclear multiomic analysis identified putative cis regulatory regions and cooperating factors mediating PT responses to AR activity. In the human kidney, a limited set of genes showed conserved sex-linked regulation. Comparative analysis of the mouse liver underscored organ-specific differences in the regulation of sexually dimorphic gene expression. The organ-specific pathways of sexual differentiation identified here raise interesting questions on the evolution, physiological significance, and disease-linkage of sexually dimorphic gene activity.

overall_design: Whole kidneys were dissociated from adult male and female C57BL/6J mice and combined snRNA- and snATAC-seq was performed using the 10X Chromium multiome ATAC + gene expression kit. There were two genotypes: WT (Ar_c/y) and nephron-specific knockout of androgen receptor (Six2CRE/+, Ar_c/y).

first: Xiong

last: Lingyun

first: Liu

last: Jing

first: Han

last: Seung Yub

first: Koppitch

last: Kari

first: Guo

last: Jin-Jin

first: Rommelfanger

last: Megan K.

first: Gao

last: Fan

first: Hallgrimsdottir

last: Ingileif B.

first: Pachter

last: Lior

first: Kim

last: Junhyong

first: MacLean

last: Adam L.

first: McMahon

last: Andrew P.


title: Single-cell RNA-sequencing of the mouse Dorsomedial Hypothalamic Nucleus (DMH)

city: Dallas

first: Allan-Hermann

last: Pool

state: Texas

address: 6124 Harry Hines Blvd

department: Neuroscience

institute: University of Texas Southwestern Medical Center

summary: Single-cell RNA-seq data from the mouse Dorsomedial Hypothalamic Nucleus (DMH) was generated following a modified protocol from https://www.nature.com/articles/s41586-020-2821-8. Briefly, six 7.5 week old C57B6 mice (3 male, 3 female) were anaesthetized with isoflurane. Brains were rapidly extracted and dropped into ice-cold carbogenated NMDG-HEPES-ACSF. Brain sections (2 mm) containing DMH were cut with a razor blade on a stainless steel brain matrix (51392, Stoelting) and transferred to a dissection dish  on  ice  containing  NMDG-HEPES-ACSF.  DMH  was  bilaterally  microdissected  in  ~700·700·350 micron tissue block. Microdissected tissue was aggregated in a collection tube on ice containing NMDG-HEPES-ACSF  and  30  μM  actinomycin  D.  For  enzymatic  tissue  digestion,  NMDG-HEPES-ACSF  was replaced  by trehalose-HEPES-ACSF  containing papain  (50  U/ml;  P3125,  Sigma Aldrich,  pre-activated with 2.5 mM cysteine and a 30-min incubation at 34 °C and supplemented with 0.5 mM EDTA) and 15 μM actinomycin D. Extracted DMH tissue was incubated at room temperature with gentle carbogenation for 55 min. During enzymatic digestion the tissue was pipetted periodically every 10 min. At the end of enzymatic digestion, the medium was replaced with 200μl of room temperature trehalose-HEPES-ACSF containing  3  mg/ml  ovomucoid  inhibitor  (OI-BSA,Worthington)25  U/ml  DNase  I (90083,  Thermo Scientific) and 15 μM actinomycin D and tissue was gently triturated into a uniform single-cell suspension with fire-polished glass Pasteur pipettes. The resulting cell suspension volume was brought up to 1 ml with trehalose-HEPES-ACSF with 3 mg/ml ovomucoid inhibitor and pipetted through a 40μm cell strainer. Single-cell suspension was centrifuged down at 300g for 5 min at 4 °C and the supernatant was replaced with 1 ml fresh ice-cold trehalose-HEPES-ACSF and the cell pellet was resuspended. Cells were pelleted again  and  resuspended  in  100  μl  of  ice-cold  resuspension-ACSF.  Cell  suspensions  were  kept on  ice while cell densities were quantified with a haemocytometer and the final cell densities were verified to be in  the  range  of  300–1,000  cells/μl.  Cell  suspension  volumes  estimated  to  retrieve  ~10,000  single-cell transcriptomes were added to the 10x Genomics RT reaction mix and loaded to the 10X Next GEM Chip G  (2000177, 10x Genomics) per the manufacturer’s protocol. We used the Chromium Next GEM Single Cell 3’ Reagents Kit v3.1 (1000128, 10x Genomics) and the Single Index Kit Set A (100213) to prepare Illumina sequencing libraries downstream of reverse transcription following the manufacturer’s protocol. Resulting  scRNA-seq  sequencing  library  was  sequenced  on  an  Illumina  NovaSeq  6000  sequencers (paired-end 150). Sequencing  data  were  aligned  to  optimized  pre-mRNA  reference  transcriptome52  and  digital  gene-cell matrices were generated with the 10x Genomics Cell Ranger v.6.0.0 count pipeline. The resulting scRNA-seq  data  were  analyzed  in  R  (4.1.2)  using  Seurat  (v.4.1.0.9007)  as  previously  described51. Briefly, expression data were filtered to exclude cells with fewer than 1,000 unique transcripts as well as cells exhibiting  more  than  15%  of  mitochondrial  transcripts.  We  followed  the  standard  Seurat  workflow  to identify transcriptomic cell-types and assigned cel class identities based on canonical cell-type markers: Ndrg4 for neurons, Ntsr2 for astrocytes, Slco1c1 for endothelial cells, Fcer1g for microglia and Mag for oligodendrocytes. We digitally extracted neuronal clusters from our dataset resulting in expression data for 4587 DMH neurons that we used to establish an unbiased neuronal nomenclature for DMH.

overall_design: Two separate groups of mice (3 male, 3 female each per sample) were processed for tissue extraction from DMH and single cell suspension generation.

first: Yuki

last: Oka