title: Effect of V. cholerae biofilm formation and hemolysin production on human macrophages

city: Basel

first: Lucia

last: Vidakovic

address: Spitalstrasse 41

institute: Biozentrum, University of Basel

summary: In this study we determined the gene expression of THP-1 derived macrophages during the interaction with V. cholerae wildtype cells, biofilm-deficient or hemolysin-deficient mutants.

platform_organism:
Vibrio cholerae O1 biovar El Tor
Homo sapiens

overall_design: V. cholerae wildtype, ∆mshA∆tcpA, ∆hlyA or ∆mshA∆tcpA∆hlyA was exposed to THP-1 derived macrophages in 12-well plates and RNA-samples were taken at different time points after start of the V.cholerae-macrophage interaction. Three independent biological replicates for each sampled time point are provided. As a control, samples containing only macrophages were taken.

first: Valerya

last: Nisnevich

first: Noa

last: Bossel Ben-Moshe

first: Roi

last: Avraham

first: Knut

last: Drescher


title: Real-time quantitative PCR analysis of human induced T regulatory cells (Tregs) for metabolic enzymes

status: Public on Apr 30 2023

city: Rochester

first: Adebowale

last: Bamidele

state: Minnesota

address: Medicine, 200 First Street SW, Guggenheim 10

department: Medicine

country: USA

institute: Mayo Clinic

summary: Human naïve CD4 T cells were purified from healthy volunteers' blood and were differentiated into induced Tregs in vitro by culturing for 5 days in the presence of anti-CD3 and CD28 antibodies (2 µg/ml each), IL-2 (100 units/ml) and TGF-β1 (5 ng/ml) for 5 days, then in presence of anti-CD3 and CD28 antibodies for 2 days. Human iTregs were harvested on day 7 post differentiation, then treated with either vehicle or IL-21 (100 ng/ml) in serum-free RPMI media for 18 hours.

overall_design: qPCR gene expression profiling.  Tregs from three donors were used and treated separately as indicated in the summary. Equal amount total RNA from each donor was used for gene expression analysis.

middle: O

first: Petra

last: Hirsova


title: Gene Expression Changes after Coumestrol Stimulation of Human Trophoblast Cells

city: Chapel Hill

first: Kathleen

middle: M

last: Caron

state: NC

address: 111 Mason Farm Road, CB7545

department: Cell Biology and Physiology

institute: University of North Carolin

summary: Coumestrol is a potent isoflavone found in spinach and soy. To examine whether consuming large amounts of coumestrol during pregnancy affects the development of the placenta, human trophoblast cells (HTR8/Svneo) were treated with vehicle or coumestrol. Upon treatment, 3,079 genes were differentially regulated.

overall_design: Human trophoblast cell lines (HTR8/Svneo) were grown up and plated into 6-well plates. Upon reaching 70% confluency, cells were treated with media containing vehicle or 65µM coumestrol for 24 hours. At the time of harvest, cells were washed with sterile PBS and then RNA was isolated for downstream microarray analysis.

first: Margeaux

middle: W

last: Marbrey


title: p19-WT and p19-T111BpyAla treatment of extracted small RNAs

status: Public on Apr 28 2023

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: Ontario

address: 140 Louis Pasteur Private

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

summary: small RNA fractions were treated with either p19-WT or T111BpyAla to evaluate the catalytic ability of p19-T111BpyAla compared to the WT protein in degrading miRNAs

overall_design: Small RNA fractions were isolated using NucleoSpin miRNA (Macherey-Nagel).  RNA was then treated with purified protein (p19 WT or T111BpyAla) and Nanostring profiling was performed

middle: P

first: Noreen

last: Ahmed


title: Development of gene expression signatures for cisplatin resistance in gastric cancer cells

city: Hangzhou

first: Lifeng

last: Feng

state: Zhejiang

address: No.3 East Qingchun Road

country: China

institute: Zhejiang University, School of Medicine, Sir Run Run Shaw Hospital

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

summary: To further development of our gene expression approach to chemotherapy resistance, we have employed whole genome microarray expression profiling as a discovery platform to identify genes implicated in cisplatin resistance in gastric cancer cells.

overall_design: Constructed cisplation resistant gastric cancer cells BGC-R and SGC-R, and their pantental sensitive cells BGC823 and SGC7901 were harvested for RNA extraction. And Arraystar_Human_LncRNA_8x60k v3.0 microarray was applied to measure the gene expression profiles.

first: Hongchuan

last: Jin


title: Recruitment of ETS1 to activated accessible regions promotes cilia genes transcriptional program in ciliopathy [WES]

status: Public on Apr 26 2023

city: Zhanjiang

first: Yun-Miao

last: Guo

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

institute: Central People's Hospital of Zhanjiang

type: Genome variation profiling by high throughput sequencing

summary: Defects in cilia genes that is critical in cilia formation and function can cause complicated ciliopathy syndromes involving multiple organs and tissues; however, the underlying regulatory mechanisms of cilia gene networks in ciliopathy are largely unknown. Here, we define the genome-wide redistribution of chromatin accessibilities and extensive divergence of cilia genes expression programs happened in ciliopathy. Mechanistically, the distinct ciliopathy-activated accessible regions (CAAs) are characterized to positively regulate robust changes of flanking cilia genes, which are a key transcriptional feature of cilia required for the response to developmental signals. Moreover, the single transcriptional factors, ETS1, can be recruited to CAAs thus prominently reconstructing chromatin accessibility in ciliopathy. CAAs collapse driven by ETS1 suppression subsequently cause defective cilia formation and impaired developmental signal transduction, which eventually develops ciliopathy phenotypes of short fins and pericardium edema in larval fishes. Therefore, our results depicted a dynamic landscape of chromatin accessibility in ciliopathy, and uncover an insightful role of ETS1 in controlling global cilia genes transcriptional program by reprogramming widespread chromatin state.

overall_design: Whole exome sequencing

first: Dong-Hui

last: Zhang

first: Yi-Ting

last: Guan


title: Single-cell RNA sequencing of murine hearts for studying the development of the cardiac conduction system

city: 泸州

first: Xianhong

last: Ou

state: 四川

address: 四川省泸州市

department: Institute of Cardiovascular Research

institute: Southwest Medical University

type: Expression profiling by high throughput sequencing

summary: The development of the cardiac conduction system (CCS) is essential for correct heart function. However, critical details on the cell types populating the CCS in the mammalian heart during the development remain to be resolved. Using single-cell RNA sequencing, we generated a large dataset of transcriptomes of ~0.5 million individual cells isolated from murine hearts at six successive developmental corresponding to the early, middle and late stages of heart development. The dataset provides a powerful library for studying the development of the heart's CCS and other cardiac components. Our initial analysis identified distinct cell types between 20 to 26 cell types across different stages, of which ten are involved in forming the CCS. Our dataset allows researchers to reuse the datasets for data mining and a wide range of analyses. Collectively, our data add valuable transcriptomic resources for further study cardiac development, such as gene expression, transcriptional regulation and functional gene activity in developing hearts, particularly the CCS.

overall_design:
We isolated and collected the single cells from embryos or hearts at six developmental stages, including E8.5, E10.5, E12.5, E14.5, E16.5 and postnatal P3，two biological replicates per period using the standard enzymatic method.Single cells were prepared following 10× Genomics, Inc (Pleasanton, CA) protocol.

Please note that processed data files generated from two replicates (i.e. E16_5_1_1_7*, p3_* samples) are linked to the first replicate records (i.e. E16_5_1_7, p3_1).

first: Huiying

last: Ren

first: Xiaolin

last: Zhou

first: Jun

last: Yang

first: Kun

last: Kou

first: Tangting

last: Chen

first: Zhaoli

last: Pu

first: Kejun

last: Ye

first: Xuehui

last: Fan

first: Dan

first: Xinjiang

last: Kang

first: Zhongcai

first: Ming

last: Lei

first: Tianyi

last: Sun

first: Xiaoqiu

last: Tan


title: Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes

city: Vancouver

first: Sheila

last: Teves

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

institute: Life Science Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A large number of transcription factors have been shown to bind and interact with mitotic chromosomes, which may promote the efficient reactivation of transcriptional programs following cell division. Although the DNA-binding domain (DBD) contributes strongly to TF behavior, the mitotic behaviors of TFs from the same DBD family may vary. To define the mechanisms governing TF behavior during mitosis in mouse embryonic stem cells, we examined two related TFs: Heat Shock Factor 1 and 2 (HSF1 and HSF2). We found that HSF2 maintains site-specific binding genome-wide during mitosis, whereas HSF1 binding is somewhat decreased. Surprisingly, live-cell imaging shows that both factors appear excluded from mitotic chromosomes to the same degree, and are similarly more dynamic in mitosis than in interphase. Exclusion from mitotic DNA is not due to extrinsic factors like nuclear import and export mechanisms. Rather, we found that the HSF DBDs can coat mitotic chromosomes, and that HSF2 DBD is able to establish site-specific binding. These data further confirm that site-specific binding and chromosome coating are independent properties, and that for some TFs, mitotic behavior is largely determined by the non-DBD regions.

overall_design: Cleavage Under Target and Tagmentation (CUT&Tag) for transcription factors Sox2, HSF1, and HSF2 in asynchronous and mitotic JM8 mouse embryonic stem cells.

first: Rachel

last: Price

first: Marek

middle: A

last: Budzyński

first: Junzhou

last: Shen

first: Jennifer

middle: E

last: Mitchell

first: James

middle: J

last: Kwan

middle: S


title: Effects of the treatment of osteomodulin on gene expression in cultured human primary trabecular osteoblasts

city: Liège

first: Christelle

last: Sanchez

address: Quai G. Kurth 45

country: Belgium

institute: ULiege

summary: The RNA-seq revealed that only 35 genes (with padj<0.05) were differentially expressed after the OMD 10 ng/ml treatment, and with relatively modest fold-changes to expression. GSEA analysis using webgestalt on GO terms revealed an increase of some genes linked to the response to acid chemicals (genes AKR1C1, AKR1C2, AKR1C3) and a decrease of few genes involved extracellular structure organization (GO:0043062) and ossification (genes ACAN and IBSP), and of the molecular function of actin binding. The Reactome database revealed an up-regulation of genes responsible of collagen network degradation and a down-regulation of ECM proteoglycans, ECM organization, collagen formation, and integrin cell-surface interactions.

overall_design: RNA-Seq on primary human OA osteoblasts mRNA cultured 72h in the presence or not of osteomodulin (OMD) 10 ng/mL

first: Jeremie

last: Zappia

first: Yves

last: Henrotin

first: Marc

last: Muller


title: Transcriptional repressor FOXD3 safeguards genome integrity in embryonic stem cells

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

institute: UCSF

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

overall_design: Refer to individual Series


title: Gene Expression Changes in Soleus Muscle in Mice after Pericytes-Deletion

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary:
Pericytes(PCs) are  mural cells embedded in the capillary basal lamina. Some PC populations exhibit multipotency, similar to mesenchymal stem cells. Here, the the process of adaptation was investigated by determining changes in transcript profiles when NG2 positive PCs were deleted.
PC-deletion was induced by using NG2CreER(+/-)/diphtheria toxin flagment A(DTA) transgenic mice. Cre recombinase was induced by tamoxifen(Tam) treatment(intraperitoneally, 100mg/kg body weight per day) for 5days. Samples were collected at 1month after Tam treatment.

overall_design: Analysis used RNA of NG2Cre(-/-)/DTA mice with Tam treat as control sample for comparison to the experimental samples. Each RNA was extracted from four soleus muscles of two mice.

first: Takamitsu

last: Tatsukawa

first: Jun-ichi

last: Kawabe


title: Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies

city: La Jolla

first: Collin

last: Joyce

state: California

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: We used scRNAseq to profile memory B cells in logitudinal PBMC samples

overall_design: class-switched memory B cells were isolated via magnetic activated cell sorting (MACS) and analyzed using scRNAseq. Some samples contain the memory b cell depleted fraction (Non-Mem)

first: Elise

last: Landais

first: Dennis

middle: R

last: Burton


title: Characterization of pain-related behaviors and gene expression profiling of peripheral sensory ganglia of a mouse model of acute ankle sprain

status: Public on Apr 25 2023

first: Chengyu

last: Yin

address: 548 Binwen Road, Binjiang District, Hangzhou

department: The Third Clinical Medical College

institute: Zhejiang Chinese Medical University

summary: Lateral ankle sprain (LAS) is a very common type of joint injury.Unfortunately, a certain proportion of individuals who once developed LAS may suffer persistent ankle pain and recurrent sprains. However, the molecular pain mechanisms underlying LAS are still not well understood. To investigate the potential mechanisms of pain in LAS model mice, we performed RNA- Seq of ipsilateral DRG of sham and LAS model group mice. GO analysis found that the mostly enriched biological process include immune response and positive regulation of gene expression. Immune response can trigger neuroinflammation, a critical process for peripheral sensitization and contributes to chronic pain mechanisms. Furthermore, our RNA-Seq analysis indicated that LAS modulated the expression of multiple genes and gene networks in the DRGs. Our work may help to further advance the understandings of the molecular pain mechanisms underlying LAS and help to identify novel targets for LAS.

overall_design:
To investigate the potential mechanisms of pain in LAS model mice, we performed RNA- Seq of ipsilateral DRG of sham and LAS model group mice.
Examination of 2 different groups mRNA profiles in DRG：Sham group and LAS group.

first: Yushuang

last: Pan

first: Boyi

last: Liu


title: FAM3A Reshapes Vascular Smooth Muscle Cell Fate Specification in Abdominal Aortic Aneurysm by Regulating KLF4 Ubiquitination

status: Public on Apr 23 2023

city: Beijing

first: Yuehong

last: Zheng

address: No. 1 Shuaifuyuan, Dongcheng District

department: Department of Vascular Surgery

institute: Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences

summary: Vascular smooth muscle cell (VSMC) differentiation reprogramming plays an essential role in abdominal aortic aneurysm (AAA). However, the underlying mechanisms are still indistinct. FAM3A (family with sequence similarity 3, member A) is a newly identified metabolism regulator. We examined FAM3A expression and the downstream pathways affected by FAM3A in AAA, and how FAM3A regulated VSMC differentiation. We found that overexpression or supplement of FAM3A significantly attenuated the progression of AAA, manifested by maintenance of VSMC well-differentiation state and inhibition of VSMC transformation towards macrophage-, chondrocyte-, osteogenic-, mesenchymal-, and fibroblast-like cell subpopulations. Importantly, FAM3A induced a decrease in Krüppel-like factor 4 (KLF4) phosphorylation (Ser254) level, leading to its ubiquitination and a weakened nuclear localization. Our findings identify FAM3A as a novel VSMC fate-shaping regulator in AAA and unveil the underpinning mechanism associated with KLF4 ubiquitination and stability, which could develop new strategies based on FAM3A to restore VSMC homeostasis in AAA.

overall_design: We infected mice with empty vector adenovirus and adenovirus that could induce FAM3A overexpression, respectively, and obtained mRNA level matrix of aorta tissue to observe the effect of FAM3A on gene expression of aorta cells.

first: Chuxiang

last: Lei

first: Haoxuan

last: Kan

first: Xiangyu

last: Xian


title: Gene expression profiles at the single cell level of cochlear cells from C57BL/6J mice at both embryonic day 15 and postnatal day 7

status: Public on May 18 2023

city: Baltimore

first: Kevin

last: Rose

address: 670 West Baltimore Street

department: OTO-HNS

institute: University of Maryland, Baltimore

summary: Otic Mesenchyme Cells (OMCs) are the numerous cell type during cochlear development. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of OMCs during cochlear development

overall_design: Whole cochleae were harvested from either E15 or P7 C57BL/6J mice and single cell transcriptomics was completed with the 10x Genomics platform.

first: Ronna

last: Hertzano

first: Thomas

last: Coate

first: Yang

last: Song


title: Transcriptome analysis upon lymphatic endothelial cells (LEC) and cancer cells (Haca4) co-culture

status: Public on Apr 21 2023

city: Copenhagen

first: Mirna

last: Perez-Moreno

address: Universitetsparken 13

department: Department of Biology

country: Denmark

institute: University of Copenhagen

summary: To investigate the mechanisms underlying the connection between LEC and cancer cells and their potential roles in tumorigenesis we co-cultured LEC and HaCa4 cells for 24 hours and compared the transcript levels of both FACS-isolated HaCa4 cells and LEC from co-cultures with those from individual cell cultures

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LEC and HaCa4 cells and FACS-sorted HaCa4 cells and LEC after 24 hours co-culture

first: Anna

last: Cazzola


title: Genome-wide identification of nitrate-responsive microRNAs by small RNA sequencing in the rice restorer cultivar Nanhui 511

status: Public on Apr 20 2023

city: Chongqing

first: Xiaojian

last: Qin

state: --- Select One ---

address: No.37, Daxuecheng Middle Road, Shapingba District, Chongqing

institute: Chongqing Normal University

type: Non-coding RNA profiling by high throughput sequencing

summary: Rice productivity relies heavily on nitrogen fertilization, and improving nitrogen use efficiency (NUE) is important for hybrid rice breeding. Reducing nitrogen inputs is the key to achieving sustainable rice production and reducing environmental problems. Here, we analyzed the genome-wide transcriptomic changes in microRNAs (miRNAs) in the indica rice restorer cultivar NH511 (Nanhui 511) under high (HN) and low nitrogen (LN) conditions. The results showed that NH511 is sensitive to nitrogen supplies and HN conditions promoted the growth its lateral roots at the seedling stage. Furthermore, we identified 483 known miRNAs and 128 novel miRNAs by small RNA sequencing in response to nitrogen in NH511. We also detected 100 differentially expressed genes (DEGs), including 75 upregulated and 25 downregulated DEGs, under HN conditions. Among these DEGs, 43 miRNAs that exhibited a 2-fold change in their expression were identified in response to HN conditions, including 28 upregulated and 15 downregulated genes. Additionally, some differentially expressed miRNAs were further validated by qPCR analysis, which showed that miR443, miR1861b, and miR166k-3p were upregulated, whereas miR395v and miR444b.1 were downregulated under HN conditions. Moreover, the degradomes of possible target genes for miR166k-3p and miR444b.1 and expression variations were analyzed by qPCR at different time points under HN conditions. Our findings revealed comprehensive expression profiles of miRNAs responsive to HN treatments in an indica rice restorer cultivar, which advances our understanding of the regulation of nitrogen signaling mediated by miRNAs and provides novel data for high-NUE hybrid rice cultivation.

overall_design: Comparative miRNA expression profiling analysis of RNA-seq data for rice cultivar Nanhui511 under HN and LN conditions

first: Xiaowei

last: Li

first: Cuiping

first: Yuntong

first: Qian

last: Wu

first: Huan

last: Wen

first: Dan

last: Jiang

first: Tingting

last: Tang

first: Wenbin

first: Yongshu

last: Liang

first: Hanma

last: Zhang


title: A single-cell atlas of the tumor, stromal and immune microenvironments in pancreatic cancer liver metastasis

city: Nanjing

first: Dijun

last: Chen

state: Jiangsu

address: Xianlin

department: Life Sciences

institute: Nanjing University

summary: Pancreatic ductal adenocarcinoma (PDAC) remains one of the most aggressive and lethal malignant tumors all over the world, with a 5-year survival rate of less than 10%1,2. Usually diagnosed at an advanced stage, PDAC is highly resistant to current therapies, partly due to an extremely high rate of distant metastasis (>80%) at first diagnosis. The liver is the most frequent site of distant metastases for PDAC. Current therapeutic options for PDAC patients with liver metastasis are extremely limited3. Thus, understanding the molecular mechanisms underlying hepatic metastasis of PDAC is urgently needed to help us develop more effective treatments and improve survival for these patients with advanced disease.

overall_design:
Four primary untreated pancreatic ductal adenocarcinoma (PDAC) tumor, three hepatic metastasis along with one adjacent normal tissues were included in this cohort.

Sample codes:
ZC: normal pancreatic tissue
YF: pancreatic tumors
ZY: hepatic metastases

Raw scRNA-seq data from this study have been deposited in the Genome Sequence Archive for Human (GSA-Human) in the National Genomics Data Center under accession no. HRA004625 (https://ngdc.cncb.ac.cn/gsa-human/browse/HRA004625).

first: Shu

first: Wen

last: Fang


title: Transcriptome of  Helicobacter pylori in presence or absence of the cagPAI

city: Muenchen

first: Christine

last: Josenhans

address: Pettenkoferstrasse 9a

department: Max von Pettenkofer Institute

country: Germany

institute: LMU Munich

summary: To investigate the impact of the cagPAI on transcript regulation of H. pylori, RNA-seq was performed on bacterial samples with presence or absence of the cagPAI.

overall_design: RNA-seq samples were generated from H. pylori Su2 wt and cagPAI mutant grown for 20 hours on blood agar plates.

first: Martina

last: Hauke


title: Transplanted Human Intestinal Organoids: A Resource for Modeling Human Intestinal Development

status: Public on Apr 24 2023

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: We used a timecourse of tHIO development to model human fetal intestinal development.

overall_design: Single nucleus RNA sequencing was performed on 2wk, 4wk, 6wk, and 8wk tHIOs, as well as epithelial/mesenchymal cells from a patient sample for comparison.

first: Akaljot

last: Singh

first: Holly

last: Poling


title: Saracatinib synergizes with enzalutamide to downregulate androgen receptor activity in castration resistant prostate cancer

city: Minneapolis

first: Ralph

last: White

state: MN

address: 420 Delaware Street SE

institute: University of Minnesota

summary: We performed RNA-seq to evaluate the consequence of saracatinib's effects on androgen receptor residue Y534 as it pertains to Androgen Receptor gene signatures

overall_design: Performed gene expression profiling analysis using data obtained from RNA-seq of 1 cell line at 4 treatment groups. In duplicate

last: White III

first: Abderrahman

last: Day

first: Hannah

last: Bergom

first: Justin

last: Hwang

last: Drake

first: Maxwell

last: Bannister


title: RNA-seq analyses of human dental pulp stem cells (DPSC) transfected with siRNAs for MXRA5

city: Okayama

first: Shigeki

last: Suzuki

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Operative Dentistry

institute: Okayama University

summary: To explore the functions of MXRA5 for DPSC proliferation and migration, we established DPSC in which MXRA5 has been knocked down by 2 independent siRNAs.We then performed gene expression profiling analysis using data obtained from RNA-seq of DPSC-si-control, DPSC-siMXRA5-1, and DPSC-siMXRA5-2.

overall_design: Comparative gene expression profiling analyses between DPSC-si-control and DPSC-siMXRA5-1, and DPSC-si-control and DPSC-siMXRA5-2.


title: The effect of diacylglycerol lipase alpha (DAGLA) on mRNA expression in hepatocellular carcinoma

city: Jinan

first: Yu-Chuan

last: Yan

state: Shandong

address: 107 West Wen Hua Road

institute: Qilu Hospital of Shandong University

summary: To investigate the biological function of DAGLA in HCC progression, we downregulated DAGLA expression in Hep3B cells by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of control and shDAGLA cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hep3B-NC (infected with empty vector) and Hep3B-KD (infected with shRNA) cells, three biological replicates  for each group.

first: Yuchuan

first: Guangxiao

last: Meng

first: Zhaoru

last: Dong

first: Tao

last: Li


title: A familial natural short sleep mutation promotes healthy aging and extends lifespan in Drosophila

city: Baton Rouge

first: Kerr

last: Wall

state: LA

address: 202 Life Science Bldg

department: Biological Sciences

institute: Louisiana State University

summary: Sleep is a conserved physiological process, and sleep loss typically imposes negative effects on animal health. However, natural short sleepers, who sleep less without the usual negative effects of sleep deprivation, exist in the human population. One example are individuals that possess rare genetic mutations in the human dec2 gene; these individuals sleep on average ~6hrs/day rather than the typical 8hrs/day. Like many natural short sleepers, humans harboring the dec2P384R mutation do not exhibit any obvious adverse phenotypes typically associated with sleep loss, suggesting that these individuals may require less total sleep/day to achieve the same physiological outcomes. Potentially, the dec2P384R mutation could activate compensatory mechanisms that allow these individuals to thrive with less sleep. To test this directly, we used a dec2P384R short sleep Drosophila model to understand the effects of the dec2P384R mutation on animal health and dissect the genetic mechanisms that might drive these physiological changes. We found that expression of the mammalian dec2P384R mutation in fly sleep neurons was sufficient to mimic the short sleep phenotype observed in mammals. Remarkably, dec2P384R lived significantly longer with improved health and memory despite having a short sleep phenotype. The improved physiological effects in dec2P384R mutants were enabled, in part, by enhanced mitochondrial fitness and upregulation of multiple stress response pathways. Moreover, we provide evidence that the improved health in dec2P384R mutants may also contribute to the short sleep phenotype, and this may extend to other pro-longevity mutants.

overall_design: Differential gene expression analysis of RNA seq data for GR23E10-gal4;+, GR23E10-gal4;UAS-dec2WT and GR23E10-gal4;UAS-dec2P384R

first: Alyssa

last: Johnson


title: Whole genome transcriptomics of pre-access veins and hemodialysis arteriovenous fistula (AVF) samples from two-stage AVF patients with different maturation outcomes (matured vs failed)

status: Public on Apr 19 2023

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: We report the RNA expression profiles of native veins used for AVF creation and of remodeled AVF samples obtained 7-16 weeks later at the time of transposition (if vein matured) or salvage procedure (if vein failed). We perfomed RNA-seq on native veins and AVFs with different maturation outcomes (matured vs. failed). The "matured" and "failed" subgroups were similar in terms of demographics (age range, sex distribution, ethnicity distribution), clinical characteristics (proportion of diabetes mellitus and coronary artery disease, previous hemodialysis access history), and time interval between first-stage and second-stage surgeries.

overall_design: This case-control study was designed to evaluate longitudinal changes in gene expression during the vein to AVF transformation and those associated with maturation failure. Additional patients are found in GSE119296.

first: Roberto

middle: I

last: Vazquez-Padron

first: Laisel

last: Martinez


title: Proteomics of immune cells from liver tumors reveals immunotherapy targets

status: Public on Apr 18 2023

city: Bellinzona

first: Roger

last: Geiger

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine

summary: Elucidating the mechanisms by which immune cells become dysfunctional in tumors is critical to developing next-generation immunotherapies. We profiled proteomes of cancer cells, as well as monocyte/macrophages, and CD4+ and CD8+ T cells isolated from tumors, livers, and blood of 48 patients with hepatocellular carcinoma. We found that tumor macrophages induce the sphingosine-1-phospate-degrading enzyme SGPL1, which dampened their inflammatory phenotype and anti-tumor function in vivo. We further discovered that the signaling scaffold protein AFAP1L2 is upregulated in chronically activated CD8+ T cells in tumors but is not present during the canonical   T cell activation program. Ablation of AFAP1L2 in CD8+ T cells increased their viability upon repeated stimulation and enhanced their antitumor activity synergistically with PD-L1 blockade in mouse models. Our data revealed new targets for immunotherapy and provide a resource on immune cell proteomes in liver cancer (www.immunomics.ch/liver).

overall_design: Primary human CD8 T cells were stimulated with plate bound antibodies to CD3 and CD28 plus IL2 for 14 days (Chronic stimulation). In addition, CD8 T cells were activated for 72h and then cultured in complete medium with IL2 for 9 days (Transient activation) or T cells were activated for 72h, cultured for 8 days with IL2 and then re-stimulated for 72h (Re-activated).


title: Glc7/PP1 dephosphorylates histone H3T11 to regulate autophagy and telomere silencing in response to nutrient availability

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

institute: Hubei university

summary: How cells adapt their gene expression to nutritional changes remains poorly understood. Histone H3T11 is phosphorylated by pyruvate kinase to repress gene transcription. Here, we identify the protein phosphatase 1 (PP1), Glc7 as the enzyme that specifically dephosphorylates H3T11. We also characterize two novel Glc7-containing subcomplexes and reveal their roles in regulating gene expression upon glucose starvation. Specifically, the Glc7-Sen1 subcomplex dephosphorylates H3T11 to activate the transcription of autophagy-related genes. The Glc7-Rif1-Rap1 subcomplex dephosphorylates H3T11 to derepress the transcription of telomere-proximal genes. Upon glucose starvation, Glc7 expression is up-regulated and more Glc7 translocates into the nucleus to dephosphorylate H3T11, leading to induction of autophagy and derepressed transcription of telomere-proximal genes. Furthermore, the functions of PP1/Glc7 and the two Glc7-containing subcomplexes are conserved in mammals to regulate autophagy and telomere structure. Collectively, our results reveal a novel mechanism to regulate gene expression and chromatin structure in response to glucose availability.

overall_design: ChIP-Seq analysis. Yeast strain were grown in 200 ml YPD or SD-C media at 30°C until OD600 of ~0.7-1.0. The crosslinking was performed in 1% formaldehyde and quenched by adding 10 ml of 2.5 M glycine. Cells were harvested, washed once with cold TBS + PMSF, lysed in FA-SDS buffer (40 mM HEPES-KOH pH7.5, 1 mM EDTA pH8.0, 0.1% SDS, 1% Triton X-100, 0.1% Na deoxycholate, 1 mM PMSF, 2 μg/ml leupeptin, 1 μg/ml pepstatin A, protease inhibitor cocktail, phosphatase inhibitor cocktail). Chromatin was sonicated to an average size of ~500 bp and then subjected to immunoprecipitation with antibodies pre-bound to Protein G Dynabeads (Invitrogen) at 4°C overnight. The beads were washed successively with FA buffer, FA buffer + 1 M NaCl, FA buffer + 0.5 M NaCl, TEL buffer (10 mM Tris pH8.0, 1 mM EDTA, 0.25 M LiCl, 1% NP-40, 1% Na deoxycholate) and TE buffer (10 mM Tris pH7.4, 1 mM EDTA). The eluted DNA/protein complex was treated with 20 µg Proteinase K at 55°C for 1 h followed by treatment at 65°C overnight. After removing RNA by RNase (Roche), the DNA was purified with ethanol precipitation and sequenced . Yeast strains WT (BY4741 in Open Biosystem) and Rif1-FLAG were the in same group, yeast strains Sen1-FLAG and Glc7-FLAG cultured both in YPD medium and SD-C medium were the other group.

first: Xinyu

last: Zhang


title: Proteomics of immune cells from liver tumors reveals immunotherapy targets [tumor]

overall_design: Fresh tumor tissue samples were collected. Tumors were enzymatically digested. Cell suspensions were filtered through, and mononuclear immune cells were separated from tumor, stromal cells and red blood cells by Ficoll gradient centrifugation. Mononuclear immune cells were stained with antibodies to CD45 and CD14, plus antibodies to CD8, CD4, CD56 to exclude other cell types and sorted. Cell pellets were washed and snap frozen in liquid nitrogen.


title: Transcriptomic profile at single cell level of Age-associated B cells (ABCs) from individuals with different health conditions

status: Public on Apr 17 2023

city: Cambridge

first: Zhaleh

last: Hosseini

address: MRC Toxicology Unit, Tennis Ct Rd

country: United Kingdom

institute: University of Cambrdige

summary: Age-associated B cells are considered a homogenoeus B cell sub-population whose accumulation has been linked to a altered immune response. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity ABCs from different health conditions.

overall_design: B cell population was magnetically enriched from frozen PBMCs. Samples were next labelled with oligonucleotide-tagged antibodies to identify Age-associated B cells and analyzed using scRNAseq.

first: Nonantzin

last: Beristain-Covarrubias

first: Rebecca

last: Boston

first: Emili

last: Horner


title: A natural variation-based screen in mouse cells reveals USF2 as a regulator of the DNA damage response and senescence

city: Novato

first: Taekyu

last: Kang

address: 8001 Redwood Blvd

institute: Buck Institute

summary: Cellular senescence is a program of permanent cell cycle arrest, apoptosis resistance, and cytokine release induced by stress exposure in mammalian cells.  Landmark studies in laboratory mice have established master senescence regulators, including p16INK4a, p21, NF-kB, p53, and C/EBPβ.  To discover other molecular players in cellular senescence, we developed an approach that harnessed the natural divergence between distant mouse species.  We found that senescent primary cells from the Algerian mouse Mus spretus expressed a distinct, and largely muted, regulatory program relative to that of laboratory M. musculus.  We pinpointed which of these interspecies expression changes during senescence were under cis-regulatory control, via allele-specific expression profiling.  Then, in silico, we associated the latter with sequence variants in transcription factor binding sites.  Among the emergent candidate senescence regulators, we chose a little-studied cell cycle factor, USF2, for molecular validation.  In acute irradiation experiments, cells lacking USF2 exhibited compromised DNA damage repair and response.  Longer-term senescent cultures without USF2 mounted an exaggerated senescence regulatory program—shutting down cell cycle and DNA repair pathways, and turning up cytokine expression, more avidly than wild-type.  We interpret these findings under a model of pro-repair, anti-senescence regulatory function by native USF2.  Our study affords new insights into the mechanisms by which cells commit to senescence, and serves as a validated proof of concept for natural variation-based regulator screens.

sample_organism:
Mus musculus
Mus spretus
Mus musculus x Mus spretus

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Mus musculus, M. spretus, and F1 hybrid primary cells and its KD derivatives (shUSF2).


title: Transcriptional profiling of Myd88 L252P germinal center B-cells

status: Public on Apr 16 2023

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: A third of patients with diffuse large B-cell lymphoma (DLBCL) present with extranodal dissemination, which is associated with inferior clinical outcomes. MYD88L265P is a hallmark extranodal DLBCL mutation that supports lymphoma proliferation. Yet extranodal lymphomagenesis and the role of MYD88L265P in transformation remain mostly unknown. Here, we show that B cells expressing Myd88L252P (MYD88L265P murine equivalent) activate, proliferate, and differentiate with minimal T-cell costimulation. Additionally, Myd88L252P skewed B cells toward memory fate. Unexpectedly, the transcriptional and phenotypic profiles of B cells expressing Myd88L252P, or other extranodal lymphoma founder mutations, resembled those of CD11c+T-BET+ aged/autoimmune memory B cells (AiBC). AiBC-like cells progressively accumulated in animals prone to develop lymphomas, and ablation of T-BET, the AiBC master regulator, stripped mouse and human mutant B cells of their competitive fitness. By identifying a phenotypically defined prospective lymphoma precursor population and its dependencies, our findings pave the way for the early detection of premalignant states and targeted prophylactic interventions in high-risk patients.

overall_design: RNAseq

first: Leandro

last: Venturutti

first: Ari

last: Melnick


title: DSF effects on Arabidopsis

status: Public on Apr 15 2023

city: Shijiazhuang

first: Fang

last: Liu

state: HeBei

address: 46th, South Street of Friendship

department: Biology Institute

institute: Biology Institute, Hebei Academy of Sciences

summary: To investigate the effects of DSF on Arabidopsis in Xcc infecction, we used 2 μM DSF pretreated the roos of Arabidopsis for 48h and then inoculated with Xcc, We then performed gene expression profiling analysis using data obtained from RNA-seq of pretreated/unpretreated  at two time points (inoculated with Xcc or not)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DSF pretreated or unpretreated and inoculated with Xcc or not

first: Qian

last: Zhao

first: Shuishan

last: Song

first: Tingting

last: Zhai


title: Regulatory architecture of housekeeping genes is driven by promoter assemblies

first: Marion

middle: Dejosez

last: Zwaka

address: 1425 Madison Ave

department: Black Family Stem Cell Institute

institute: Icahn School of Medicine at Mount Sinai

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

overall_design: Refer to individual Series


title: Reduced Mitochondrial Calcium Uptake in Macrophages is a Major Driver of Inflammaging

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: Chronic low-grade inflammation is a hallmark of aging, but its etiology is not well understood. Mitochondrial dysfunction has been linked to both cellular senescence and age-related inflammation or inflammaging but fundamental mechanisms underlying these links are unclear. We analyzed age-related gene expression in different human tissues and discovered that in blood, the mRNA expression of Mitochondrial Calcium Uniporter (MCU) and its regulatory subunit MICU1 correlated inversely with age. MCU is the pore-forming subunit of a Ca2+-selective ion channel complex residing in the mitochondrial inner membrane and is the main conduit for Ca2+-influx into the mitochondrial matrix. Based on these findings we tested the simple hypothesis that mitochondrial Ca2+ uptake capacity of macrophages decreases with age. We found a significant reduction in the mitochondrial Ca2+-uptake capacity of macrophages derived from aged (80-90 weeks) mice. Notably, these macrophages display amplified cytosolic Ca2+ elevations and increased inflammatory output. To test the salience of mitochondrial calcium uptake in regulating macrophage inflammatory output, we deleted Mcu selectively in macrophages. The Mcu-/- macrophages of young mice (<25 weeks) express more inflammatory genes at baseline and show a hyper-inflammatory response when stimulated. We show that reduced mitochondrial Ca2+ amplifies cytosolic Ca2+ oscillations and potentiates downstream NFkB activation, which is central to inflammation. The regulation of inflammatory response by mitochondrial Ca2+ uptake is also seen readily in human macrophages. The siRNA-mediated knockdown of MCU in human blood derived macrophages recapitulates the phenomenon – the mitochondrial Ca2+-uptake is greatly reduced, cytosolic Ca2+ elevations are more pronounced, and the macrophages are hyper-inflammatory. Our findings pinpoint the MCU complex as a keystone molecular apparatus that links age-related changes in mitochondrial physiology to macrophage-mediated inflammation. Resident macrophages are intrinsic to every organ system and the steady erosion of their mitochondrial Ca2+-uptake capacity may play a germinal or exacerbating role in many age-related neurodegenerative, cardiometabolic, renal and musculoskeletal diseases that afflict us.

overall_design: Bone-Marrow Derived Macrophages generated from Mcu-/- and Wt mice. 3-5 biological replicates for Untreated, Zymosan 3hr (1:2 cells/particles), Zymosan + BAPTA-AM (10uM)

first: Philip

middle: V

last: Seegren

first: Pankaj

last: Kumar

first: Bimal

middle: N

last: Desai


title: Dynamically regulated transcription factors are encoded by highly unstable mRNAs in the Drosophila larval brain

city: Oxford

first: Ilan

last: Davis

address: South Parks Road

institute: University of Oxford

summary: The level of each RNA species depends on the balance between its rates of production and decay. Although previous studies have measured RNA decay across the genome in tissue culture and single-celled organisms, few experiments have been performed in intact complex tissues and organs. It is therefore unclear whether the determinants of RNA decay found in cultured cells are preserved in an intact tissue, and whether they differ between neighboring cell types and are regulated during development. To address these questions, we measured RNA synthesis and decay rates genome wide via metabolic labelling of whole cultured Drosophila larval brains using 4-thiouridine. Our analysis revealed that decay rates span a range of more than 100-fold, and that RNA stability is linked to gene function, with mRNAs encoding transcription factors being much less stable than mRNAs involved in core metabolic functions. Surprisingly, among transcription factor mRNAs there was a clear demarcation between more widely used transcription factors and those that are expressed only transiently during development. mRNAs encoding transient transcription factors are among the least stable in the brain. These mRNAs are characterized by epigenetic silencing in most cell types, as shown by their enrichment with the histone modification H3K27me3. Our data suggests the presence of an mRNA destabilizing mechanism targeted to these transiently expressed transcription factors, which would allow their levels to be regulated rapidly with high precision. Our study establishes a general method for measuring mRNA transcription and decay rates in intact organs or tissues, offering insights into the role of mRNA stability in the regulation of complex developmental programs.

overall_design: We estimated RNA synthesis, processing, and decay rates using metabolic labeling with 4-thiouridine in the Drosopihila larval brain.

first: Mary

middle: K

last: Thompson

first: Arianna

last: Ceccarelli

first: David

last: Ish-Horowicz


title: Identification of differentially expressed genes and molecular pathways involved in osteoclastogenesis using RNA-seq

status: Public on Apr 14 2023

city: Perth

first: Sarah

last: Rashid

state: WA

address: Nedlands

department: School of Biomedical Sciences

country: Australia

institute: The Univeristy of Western Australia

summary: In order to explore genes involved in osteoclastogenesis, we performed a differential gene expression analysis comparing human osteoclast (OC)-like cells with their precursor peripheral blood mononuclear cells (PBMC).

overall_design: Differential gene expression analysis of RNA-seq data from 8 PBMC samples and 8 OC-like cell samples.

first: Rashid

last: Sarah

first: Wilson

last: Scott

first: Kun

last: Zhu

first: Walsh

last: John

first: Xu

last: Jiake

first: Mullin

last: Benjamin


title: Regulatory architecture of housekeeping genes is driven by promoter assemblies [Pol2]

summary: Pol2 ChIA-PET in control and Ronin KO ES cells.

overall_design: ChIA-PET (Chromosome interaction analysis by paired-end tags) targeting Pol2-associated interactions in control and Ronin-KO mouse embryonic stem cells.

last: Dejosez Zwaka

first: Abraham

last: Weintraub

first: Denes

last: Hnisz

first: Richard

last: Young

first: Thomas


title: Gene expression profile of circRNA in spleen tissue of Meishan pigs at different time points

status: Public on Apr 11 2023

city: Yangzhou

first: Chao

last: Xu

address: Hanjiang

institute: Yangzhou University

summary: Numerous circular RNAs (circRNAs) have been recently identified in porcine tissues and cell types. Nevertheless, their significance in porcine spleen development is yet unelucidated. Herein, we report an extensive overlook of circRNA expression profile during Meishan pig spleen development at 1, 7, 14, 21, 28, 35, 120, and 180 days of age. Overall, 39,641 circRNAs were identified from 6,914 host genes. Among them, many circRNAs are up- or down-regulated at different time points of pig spleen development. Using WGCNA analysis, we revealed two essential modules for protein-coding genes and circRNAs. Subsequent correlation analysis revealed 67 circRNAs/co-expressed genes that participated in immnue-associated networks. Furthermore, a competing endogenous RNA (ceRNA) network analysis of circRNAs revealed that 12 circRNAs modulated CD226, MBD2, SAMD3, SIT1, SRP14, SYTL3 gene expressions via acting as miRNA sponges. Moreover, the circRNA_21767/miR-202-3p axis regulated SIT1 expression in a ceRNA manner, which is critical for the immune-based regulation of spleen development in Meishan pigs.

overall_design: Spleen tissue of Meishan pig at different time points

first: Yifu

last: Wang


title: DUX4 orchestrates translational reprograming by broadly suppressing translation efficiency [polysome-seq]

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: DUX4, an embryonic transcription factor normally silenced in somatic tissues, was recently shown to reduce major histocompatibility complex I (MHC-I) and promote immune evasion in numerous cancer types. We report that transient expression of DUX4 results in the long-term suppression of interferon-gamma induction of MHC-I and the immunoproteasome. Brief expression of transcriptionally active DUX4 leads to a prolonged decrease in protein synthesis, altering the activity of translation initiation regulators eIF2a, eIF4E, 4EBP1, and translation elongation factor eEF2. Translational profiling identified mRNAs susceptible to DUX4-induced inhibition of translation initiation and elongation, including mRNAs encoding antigen presentation factors. We show that DUX4 orchestrates translational reprogramming by broadly attenuating protein synthesis while inducing the expression of RNAs encoding early embryonic proteins that are translationally up regulated and predicted to be less vulnerable to translational inhibition. Endogenous expression of DUX4 and its target genes in FSHD muscle cells and SuSa germinoma cells also correlates with suppression of protein synthesis and reduced MHC-I presentation. Our findings reveal a novel role of DUX4 in modulating translational control to reshape the cellular translatome with important implications for development and disease.

overall_design: Comparative polysome profiling RNA-seq analysis for MB135iDUX4 myoblasts treated with a DUX4 pulse+IFNg harvested at 68h or with IFNg treatment alone.

first: Danielle

middle: C

last: Hamm

first: Ellen

last: Paatela

first: Sean

last: Bennett

first: Chao-Jen

last: Wong


title: RNA-seq of YAP's role in hDPCs

status: Public on Apr 08 2023

city: Chengdu

first: Fanyuan

last: Yu

state: Sichuan

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

department: Endodontics

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

summary: We report the application of RNA sequencing technology for high-throughput profiling of gene expression in YAP knockdown (siYAP) adult human dental pulp stromal cells (hDPCs).To knockdown YAP in hDPCs we transfected cells with YAP specific siRNAs and the scrambled RNAs. Cells were derived from a 18~22-year-old healthy male human donor. To induce pulp inflammation we used LPS to treat cells. Total mRNA was collected using TRIzol ® (Invitrogen, CA, USA) solution. Then all the extraction procedures were conducted according to manufacture’s instructions for RNA extraction from homogenized tissues.  After quality checks they were subjected to the high-throughput RNA-sequencing. Every group consists of 2 replicates which were from 2 independent experimental repeats.

overall_design: Examination of RNA expression in hDPCs after YAP knockdown or LPS treatment respectively.

first: Lin

last: Yao


title: Monoclonal antibodies binding to different epitopes of CD20 differentially sensitizes DLBCL to different classes of chemotherapy

status: Public on Apr 07 2023

city: Chicago

first: Brian

last: Lee

state: IL

address: 500 N Lake Shore Dr, Apt 601

institute: Northwestern Feinberg School of Medicine

summary: To investigate the differential gene expression profiles induced by rituximab and ofatumumab, we treated DLBCL cell lines U2932 and TMD8 with these monoclonal antibodies and analyzed their gene expression profiles

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U2932 and TMD8 treated with rituximab or ofatumumab

first: Tim

last: Pierpont

first: Avery

last: August

first: Kristy

middle: L

last: Richards


title: STAT4 increases the phenotypic and functional heterogeneity of tissue-resident memory T cells

status: Public on Apr 05 2023

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: We identified STAT4 as a regulator of tissue-resident memory T cell differentiation after infection. Single cell RNA sequencing was used to define the heterogeneity in gene expression among T cells in the lamina proprian and more clearly identify populations that are lost in a STAT4-deficient setting.

overall_design: Examine the gene expression profiles of wild-type and STAT4-deficient intestinal Trm cells after infection.

first: Bergsbaken

last: Tessa


title: Maternal N-acetyltransferase 10 (NAT10) orchestrates oocyte meiotic cell-cycle progression and maturation in mice

status: Public on Apr 04 2023

city: Hefei

first: Caoling

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

institute: University of Science and Technology of China

summary: Nat10 is required for sculpting the maternal transcriptome through timely degradation of polyA tail mRNAs during the Maternal-to-Zygotic transition(MZT)

overall_design: We used WT and ZP3 conditional knockout samples for Ribo-seq through tamoxifen injection for 3 days. For WT RIP-seq we used C57BL/6J

first: Xue

last: Jiang

first: Yuzhang

last: Zhu

first: Jianqiang

last: Bao


title: Altered non-coding RNA profiles of seminal plasma extracellular vesicles of men with poor semen quality undergoing In Vitro fertilization treatment

status: Public on Apr 02 2023

city: Amherst

last: Pilsner

state: Massachusetts

address: 686 N PLEASANT

department: Environmental Health Sciences

institute: University of Massachusetts Amherst

summary:
EVs are known to contain important cargo of biologically active and regulatory molecules including ncRNAs. EVs in seminal plasma, play an important role in sperm functions , including motility and fertilization. However, less is known about the comprehensive profile of spEV ncRNAs in clinical cohort and if these profiles differ by semen quality status.
We assessed sperm-free spEV ncRNA profiles from semen samples of male partners receiving IVF treatment. Men were classified into having normal (n = 59, Status 0)  or poor (n = 32, Status 1) semen quality based on WHO semen parameter guidelines.

overall_design: Small RNA-seq reads were mapped to standard biotype-specific transcriptomes in the order miRNA>tRNA>piRNA>rRNA> “other” RNA>circRNA>lncRNA using STAR. Differential expression of normalized ncRNA read counts between groups was conducted by EdgeR (Fold change ≥1.5 & FDR<0.05)

first: Oladele

last: Oluwayiose

first: J


title: Changes in gene expression and mechanisms underlying activation of tumor invasion and spread at the early steps of squamous cervical carcinoma progression.

status: Public on Apr 01 2023

city: Houston

first: Pavel

middle: Vladimirovich

last: Dobrynin

email: pdobrynin@gmail.com, pdobrynin2@uh.edu

state: Texas

address: 3620 SOUTHMORE BLVD APT 20

department: Psychology

institute: University of Houston

summary:
The development of an HPV-associated cervical cancer usually takes a long time (years, decades) and comprises stepwise change of intraepithelial (preclinical) neoplastic forms, but after invasive carcinoma is established it demonstrates extremely aggressive behavior and heterogenic molecular profile.
Women with pre-invasive neoplastic lesions or early-stage invasive cervical cancer who underwent treatment in the Republican Oncological Dispensary were enrolled in our study (all were HPV-positive).
Tissue samples were excised during surgery before any other treatment. Comparative transcriptomic analysis of invasive cancers (with an emphasis to the earliest stages) versus non-invasive precursor lesions was performed by means of RNA sequencing.

overall_design: Using RNA-seq we profiled 16 surgically obtained tissue samples, which comprised high-risk HPV(+) cervical intraepithelial neoplasia grades 1-3 (including carcinoma in situ, n=5), invasive squamous cell carcinoma at FIGO IA1-IIB stages (n=9, including 4 cases of microinvasive carcinoma), and morphologically normal epithelium (n=2).

first: Kurmyshkina

last: Olga

first: Kovchur

last: Pavel

first: Dobrynin

first: Ilyukha

last: Vladimir

first: Volkova

last: Tatyana


title: Integrative Single-cell Transcriptomics and Single-cell Epigenomics Mapping the Developmental Dynamics of Fetal Retina

status: Public on Mar 31 2023

city: Chongqing

first: Meryl

last: Liu

address: The First Affiliated Hospital of Chongqing Medical University

summary: The underlying mechanisms that determine gene expression and chromatin accessibility in retinogenesis are poorly understood. Here, we performed scRNA-seq and scATAC-seq on human embryonic retina samples from 9 to 26 post-conceptional weeks, explored the heterogeneity of retinal progenitor cells (RPCs) and neurogenic RPCs (NPCs), and verified the differentiation trajectory from RPCs to seven major types of retinal cells. Additionally, we identified cell-lineage-determining transcription factors (TFs) and refined their gene regulatory networks (GRNs) at transcriptomic and epigenomic levels. The inhibitor of RE-1 silencing transcription factor (REST) on retinospheres was found to have led to more neurogenesis with regular arrangement, whereas a decrease of Müller glial cells was observed. We also described the classification of developing RPC-derived cells and their correlation with pathogenic genes of multiple ocular diseases. Overall, we provided a framework for integrated exploration of the developmental dynamics of the human primary retina at the single-cell resolution.

overall_design: We conducted both scRNA-seq and scATAC-seq on developing human embryonic eyes at 9 time points (9, 10, 11, 14, 15, 18, 20, 23, 26) from post-conceptional weeks (PCW) 9 to 26. Therein, PCW26 fetal retina was separated into neuroretina and others two parts. Separate runs of scATAC-seq were performed at PCW11 (one biological replicate) and PCW19. After the initial data processing and quality control, we collected 74,571 single-cell transcriptomes with a median of 2277 genes per cell, and 75,197 single-cell epigenomes with a median of 7604 peak fragments per cell. The matrices obtained were further analyzed using Signac/Seurat (Hao et al., 2021), Chromvar (Schep et al., 2017) and Monocle (Cao et al., 2019;  Trapnell et al., 2014).

first: Ruonan

last: Li

first: Jiangyi

first: Ping

last: Yi

first: Xianli

last: Yang

first: Shengping

last: Hou


title: Galectin-3 activates microglia in arthritic pain: a process defective in Alzheimer’s disease mice

city: London

first: George

last: Sideris-Lampretsas

address: 20 Newcomen Street

department: Wolfson CARD

institute: King's College London

summary: Musculoskeletal chronic pain is prevalent in individuals with Alzheimer’s Disease (AD) however, remains largely untreated in these patients, raising the possibility that pain mechanisms are perturbed in AD. Here we utilised the TASTPM transgenic mouse model of AD with the K/BxN serum transfer (ST) model of inflammatory arthritis. We show that inflammatory allodynia in WT is associated with release of galectin-3 (Gal-3) by nociceptive fibres in dorsal horn and a distinct TLR4-dependent transcriptional profile and upregulation of P2Y12 in microglia.  In contrast, TASTPM show attenuated inflammatory allodynia which is not affected by a Gal-3 inhibitor and correlates with emergence of a subset of P2Y12- TLR4- microglia in the dorsal horn. We suggest that in WT, extracellular Gal-3, which is a TLR4 ligand, facilitates inflammatory allodynia through TLR4-regulated release of pro-nociceptive mediators by microglia. However, Gal-3 is not pro-nociceptive in TASTPM due to absence of TLR4 in microglia.

overall_design: Bulk RNA-seq of microglia (CD45low CD11b+ CX3CR1+ cells) from the dorsal lumbar spinal cord of six-month-old WT and TASTPM mice after Control and K/BxN Serum Transfer (ST)

first: Archana

last: Bajpai

first: Gopuraja

last: Dharmalingam

first: David

last: Collier

first: Marzia

last: Malcangio


title: Expression and Possible Mechanism of circular RNA rno_CIRCpedia_1953 in Deep Venous Thrombosis

city: Nantong

first: baolan

last: sun

address: 20 Xisi Road

institute: Affiliated Hospital of Nantong University


title: Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease

city: Boston

first: Xianjun

last: Dong

state: MA

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

summary: We identify and validate 11,039 circular RNAs with high confidence in dopamine and pyramidal neurons --- the preferentially vulnerable prototypical neurons in Parkinson’s and Alzheimer’s --- in 190 human brains using laser-capture RNA sequencing that combines ultra-deep sequencing of polyadenylated and non-polyadenylated RNA with cell-type enrichment afforded by light microscopy.

overall_design: To systematically profile the transcriptome of human brain neurons, we have developed the lcRNAseq method to deeply sequence ribo-depleted total RNAs from laser-captured neurons for human post-mortem brains in the BRAINcode project. In brief, dopaminergic neurons (DA) from the midbrain substantia nigra pars compacta of 104 high-quality human brains (DA; HC: n = 59; ILB: n = 27; PD: n = 18), pyramidal neurons from layers V/VI of the middle temporal gyrus of 83 brains (TCPY; HC: n = 40; AD: n = 43) and from the primary motor cortex of three brains (MCPY) were laser-captured. Human fibroblasts from four (FB) and peripheral blood mononuclear white cells from three individuals (PBMC) were analyzed as non-CNS cell types using the same pipeline.


title: Expression and Possible Mechanism of circular RNA rno_CIRCpedia_1953 in Deep Venous Thrombosis (RNA)

summary:
Purpose:  To explore the possible pathogenesis of venous thromboembolism from the perspective of circRNAs.
Methods: The thrombus model of inferior vena cava in SD rats was established by stenosis method. Peripheral blood samples of DVT rats were collected at 1h, 6h,12h and 3d, which were sequenced with Illumina circRNAs and mRNA. The differential circRNAs and mRNA were analyzed by STEM analysis software. Clusters that can reflect the evolution of thrombus were selected for in-depth analysis, and circRNAs and mRNA were screened according to the pathway enrichment analysis of the selected clusters. Real time fluorescent quantitative PCR (qPCR) was used to verify and determine the candidate circRNAs and mRNA. The function of target circRNA was verified in DVT rats. The interacting miRNAs of circRNAs and mRNA were predicted by online database respectively. Candidate miRNAs were identified by integrating the related information of miRNAs and verified by qPCR.
Results:The SD rat model of deep venous thrombosis was successfully established by the stenosis method. In model group, there were 736, 3691, 3406 and 2639 circRNAs up-regulated and 944, 327, 318 and 397 circRNAs down-regulated at 1h, 6h, 12h and 3d, respectively. Compared with Sham group, 169, 885, 298 and 500 mRNA were up-regulated and 231, 291,75 and 73 mRNA were down-regulated at 1h, 6h, 12h and 3d in model group, respectively. STEM analysis found that cluster 45 was similar to thrombus development. The pathway related to platelet function was selected in cluster 45, and 10 circrRNAs and 4 interacting mRNAs were selected for qPCR verification by combining the gene in platelet pathway and annotation gene of cluster 45 and mRNA-circRNA interaction network. According to qPCR results and whether ID is found in rat circRNA database (CIRCpedia-V2), CBT15_circR_3235 (ID in circpedia-v2: rno_CIRCpedia_1953) is determined as the target circRNA. In vivo，knockdown of rno_CIRCpedia_1953 attenuates the formation of DVT in rats. The potential target miRNAs of rno_CIRCpedia_1953 and Tuba4a were predicted by using online miRDB and miRWalk databases respectively, and rno-miR-3543, rno-miR-320-5p and rno-miR-26b-3p are preliminarily identified as potential target miRNAs that rno_CIRCpedia_1953 may combine to play the ceRNA mechanism.
Conclusions: Animal model of DVT in rats was successfully established by stenosis method. High-throughput sequencing analysis of circRNAs showed that circRNAs participated in the evolution of DVT. According to STEM functional analysis of mRNA sequencing, a target circRNA rno_CIRCpedia _1953 was screened, verified and identified. rno_CIRCpedia_1953 may participate in the development of DVT by acting as miRNA molecular sponge.

overall_design: DVT rat circRNA and mRNA profiles of 1h, 6h, 12h and 3d after modeling were generated by deep sequencing, in triplicate, using Illumina Xten.

first: Baolan

last: Sun

first: Yuquan

last: Zhang


title: Expression and Possible Mechanism of circular RNA rno_CIRCpedia_1953 in Deep Venous Thrombosis (circular RNA)


city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

type: Methylation profiling by genome tiling array

summary: HER3 (ErbB3) belongs to a family of receptor tyrosine kinases together with the known oncogenes EGFR and HER2. Recently, antibody drug conjugates (ADCs) targeting these receptors showed promising clinical activity in extracranial malignancies of breast and lung cancer. We aimed to investigate HER3 expression in breast and lung cancer brain metastases (BM) as the basis for future clinical trial design. Illumina MethylationEPIC 850k microarrays were used to analyze genome-wide DNA methylation patterns of HER3-positive (n=43) and HER3-negative (n=28) BM.

overall_design: Compare DNA methylation pattern between patients with HER3+ and HER3- brain metastases.

first: Erwin

last: Tomasich

first: Anna

last: Berghoff


title: BuTT-Seq: a new method for facile profiling of transcription

status: Public on Mar 30 2023

city: Waltham

first: Albert

middle: Dayuan

last: Yu

address: 415 South St.

department: Molecular and Cell Biology

institute: Brandeis University

summary: A wide range of sequencing methods have been developed to assess nascent RNA transcription and resolve the single-nucleotide position of RNA polymerase genome-wide. These techniques are often burdened with high input material requirements and lengthy protocols. We leveraged the template-switching properties of thermostable group II intron reverse transcriptase (TGIRT) and developed BuTT-Seq (BUlk analysis of nascent Transcript Termini sequencing), which can produce libraries from purified nascent RNA in 6 hours and from as few as 10,000 cells – an improvement of at least 10-fold over existing techniques. BuTT-Seq shows that inhibition of the superelongation complex (SEC) causes promoter-proximal pausing to move upstream in a fashion correlated with subnucleosomal fragments. To address transcriptional regulation in a tissue, BuTT-Seq was used to measure the circadian regulation of transcription from fly heads. All the results indicate that BuTT-Seq is a simple and powerful technique to analyze transcription at a high level of resolution.

overall_design: Comparing transcriptional pausing and elongation with or without treatment with Superelongation Complex inhibitor in S2 Cells as well as assaying Circadian transcription around the clock in Drosophila.

middle: D

first: Michael

last: Rosbash


title: A live-cell image-based machine learning strategy for reducing variability in iPSC differentiation systems

city: Beijing

first: Xiaochun

state: China

address: Equipment No.2, Peking University, Beijing, China

department: College of Future Technology

institute: Peking University

summary: The differentiation of induced pluripotent stem cells (iPSCs) into diverse functional cell types provides a promising solution to support drug discovery, disease modeling, and regenerative medicine. However, functional cell differentiation is currently limited by the substantial line-to-line and batch-to-batch variability, which severely impede the progress of scientific research and the manufacturing of cell products. For instance, iPSC-to-cardiomyocyte (CM) differentiation is vulnerable with great sensitivity to inappropriate doses of CHIR99021 (CHIR) that are applied in the initial stage of mesoderm differentiation. Here, by harnessing live-cell bright-field imaging and machine learning (ML), we realize real-time cell recognition in the entire differentiation process, e.g., CMs, cardiac progenitor cells (CPCs), iPSC clones, and even misdifferentiated cells. This enables non-invasive prediction of differentiation efficiency, purification of ML-recognized CMs and CPCs for reducing cell contamination, early assessment of the CHIR dose for correcting the misdifferentiation trajectory, and evaluation of initial iPSC colonies for controlling the start point of differentiation, all of which provide a more invulnerable differentiation method with resistance to variability. Moreover, with the established ML models as a readout for the chemical screen, we identify a CDK8 inhibitor to further improve the cell resistance to the overdose of CHIR. Together, this study indicates that artificial intelligence is able to guide and iteratively optimize iPSC differentiation to achieve consistently high efficiency across cell lines and batches, providing a better understanding and rational modulation of the differentiation process for functional cell manufacturing in biomedical applications.  With the assistance of RNA sequencing, we transcriptomically characterize the image-recognized CPCs (IR-CPCs), the cells treated with different CHIR doses at stage I, iPSC-CM treated with or without BI-1347, and cells treated with or without BI-1347 at stage I.

overall_design:
1. A total of 12 samples of IR-CPC, non-CPC, CM, and iPSC (including three biological repetitions) were collected and analyzed together, in which IR-CPCs were purified through DACT-1 photoactivation method; non-CPC were the cells under inappropriate CHIR conditions on day 6.
2. A total of 10 samples of cells under different CHIR doses (iPSC; CHIR 2 μM 48h, 6 μM 24h, 6 μM 36h, 10 μM 24h, 8 μM 36h, 6 μM 48h, 12 μM 24h, 12 μM 36h, and 10 μM 48h) were collected before withdrawing CHIR.
3. A total of 9 samples of iPSC-CM with BI-1347, iPSC-CM without BI-1347, and iPSC (including three biological repetitions) were collected and analyzed together. iPSC-CM with BI-1347 (induced by CHIR 12 uM 48h and BI-1347 0.5 uM 48h) and iPSC-CM without BI-1347 (induced by CHIR 8 uM 48h) were collected after 12 days of cardiac differentiation.
4. A total of 14 samples were collected and analyzed for exploring the mechanism of BI-1347 (including two biological repetitions), including two iPSC samples and 6 sample pairs from 2 groups, in which CM was induced in the presence or absence of BI-1347 (0.5 μM, 48h) under the overdose CHIR (16 μM, 48h). Guided by this experimental design, cells were collected at three time points (24h, 48h, and 72h).

first: Guangyin

last: Xi


title: Analysis of Expression Profiles of long noncoding RNAs in A549 cells infected by H1N1 [lncRNA-seq]

city: hangzhou

first: Hu

last: boli

state: zhejiang

address: Yuhangtang Road No.866

institute: Zijingang Campus of Zhejiang University

summary: Although accumulating evidence has shown that long non-coding RNAs (lncRNAs) are involved in multiple biological processes, considerably less is known regarding their functions in influenza A virus (IAV) replication. Here, lncRNA expression profiles were determined by RNA sequencing in three pairs of influenza virus A/Puerto Rico/8/34 (H1N1)-infected or uninfected A549 cells.

overall_design: Expression profiles of long noncoding RNAs in A549 cells infected by H1N1 were generated by deep sequencing, in triplicate, using Illumina Hiseq 3000.

first: Zixiao

first: Tianqi

first: Jiyong

last: Zhou


title: Regulatory architecture of housekeeping genes is driven by promoter assemblies [Ronin]

city: New York

first: Marion

last: Zwaka

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Ronin ChIA-PET in R1 mouse ES cells.

overall_design: ChIA-PET (Chromosome interaction analysis by paired-end tags) targeting Ronin-associated interactions in mouse embryonic stem cells.

last: Dejosez Zwaka

first: Megan

last: Hogan

first: Abraham

last: Weintraub

first: Denes

last: Hnisz

first: Richard

last: Young

first: Thomas


title: Profiling the transcriptome of excitatory neuronal nuclei during pilocarpine-induced seizure

city: Singapore

first: Jessica

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

summary: The initial seizure-induced events in neuronal nuclei can lead to long-term changes in gene expression and cellular responses that likely contribute toward epileptogenesis. Using a transgenic mouse model to specifically isolate excitatory neuronal nuclei, we profiled the seizure-induced nuclear transcriptome by RNA-seq, as well as proteome via tandem mass tag mass spectrometry (available at ProteomeXchange via PRIDE; Accession ID: PXD030637). In the transcriptome, we observed robust induction of genes involved in multiple processes, including MAPK signalling, and downregulation of zinc finger genes harbouring Krüppel-associated box (KRAB) domains, which were strongly enriched for binding sites of the Thap11/Ronin transcriptional repressor. Additionally, we characterised gene expression in introns, which provided further insights into seizure-driven transcriptional regulation and dynamics, including repression of transcription mediated by zinc finger transcription factors. Our results provide a detailed snapshot of nuclear events induced by seizure activity and demonstrate a robust method for cell-type-specific nuclear profiling that can be applied to other cell types and models.

overall_design: Gene expression in immunopurified mouse forebrain excitatory neuronal nuclei 100 min following injection with scopolamine + pilocarpine (Pilo) or scopolamine + saline (Mock) to induce acute seizures

first: Hui

last: Soon

first: Toh

middle: H

last: Ch'ng


title: High-fidelity encoding of mechanostimuli by tactile food-sensing neurons requires an ensemble of ion channels

first: Niels

last: Ringstad

address: 435 E. 30th Street

department: Cell Biology and Neuroscience Institute

institute: NYU School of Medicine

summary:
Dopaminergic neurons (expressing Pdat-1::mStrawberry) and serotonergic neurons (expressing Ptph-1::GFP) were purified from C. elegans embryos and larvae.
We identified transcripts that were enriched in dopaminergic neurons compared to serotonin neurons.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from C. elegans dopaminergic and serotonergic neurons.

first: Alice

last: Fok


title: High-throughput profiling of Candida auris isolates reveals clade-specific metabolic differences

city: Paris

first: Philipp

last: Brandt

address: 25-28 Rue du Dr Roux

department: Mycology

country: France

institute: Institut Pasteur

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

sample_organism:
Candida albicans
Candidozyma auris

platform_organism:
Candida albicans
Candidozyma auris

overall_design: Refer to individual Series


title: FLASH-RT does not affect chromosome translocations and junction structures beyond that of CONV-RT dose-rates

status: Public on Mar 29 2023

city: Stanford

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

summary: The molecular and cellular mechanisms driving the enhanced therapeutic ratio of ultra-high dose-rate radiotherapy (FLASH-RT) over slower conventional (CONV) ionizing radiation (IR) dose-rate are not known. However, attenuated DNA damage and transient oxygen depletion are among a number of proposed models. Here, we tested whether FLASH-IR under physioxic (4% O2) and hypoxic conditions (≤2% O2) attenuates detection of genome-wide translocations relative to CONV dose rates and whether any differences identified revert under normoxic (21% O2) conditions. We employed high-throughput rejoin and genome-wide translocation sequencing (HTGTS-JoinT-seq), usingS. pyogenesandS. aureusCas9 “bait” DNA double strand breaks (DSBs), to measure differences in proximal deletions, inversions, and excision circles and their translocation to “prey” genome-wide DSBs generated by CONV (0.08-0.13Gy/s) and FLASH (1x102-5x106Gy/s) dose rates, under varying IR doses and oxygen tensions. Normoxic and physioxic IR exposure in HEK293T cells increased translocations at the cost of decreasing proximal repair but were indistinguishable between CONV and FLASH dose-rates. Although decreased numbers of translocations were recovered as cells transitioned to hypoxic (<2%) conditions, the combined decrease in oxygen tension with IR dose-rate modulation did not reveal significant differences in the level of translocations nor in junction structures, which, for proximal repair, were increased in direct and short microhomologies. We conclude that irrespective of oxygen tension, FLASH IR dose rates produce translocations and junction structures at levels that are indistinguishable from CONV dose rates.

overall_design: We employed saCas9:RAG1.1 and spCas9:RAG1B gRNA bait DNA double strand break to map translocation and rejoining outcomes post raditaion treatment (CONV-RT and FLASH-RT) at various oxygen tensions (Normoxia or Hypoxia). Each experimental parameter was tested in triplicate.

first: Paul

middle: G

last: Barghouth

first: Jonathan

last: Ollivier

first: Patrik

last: Gonçalves

first: Stavros

last: Melemenidis

first: Rakesh

last: Manjappa

first: Pierre

last: Montay-Gruel

first: Murat

last: Surucu

first: Amy

last: Yu

first: Karl

last: Bush

first: Lawrie

last: Skinner

first: Peter

last: Maxim

first: Billy

middle: W

last: Loo Jr

first: Marie-Catherine

last: Vozenin

first: Charles

last: Limoli


title: Transcriptome profile of OVCAR3 cells treated with DMSO or THZ531 (200nM) for 6hr

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Transcription-associated cyclin-dependent kinases (CDKs) regulate the transcription cycle through sequential phosphorylation of the RNA polymerase II (RNAPII). We report that dual inhibition of the highly homologous CDK12 and CDK13 impairs splicing of a subset of promoter-proximal introns characterized by weak 3’ splice sites located at larger distance from the branchpoint. Nascent transcript analysis indicated that these introns are selectively retained upon pharmacologic inhibition of CDK12/13 with respect to downstream introns of the same pre-mRNAs. Retention of these introns was also triggered by Pladienolide B (PdB), an inhibitor of the U2 snRNP factor SF3B1 that recognizes the branchpoint. CDK12/13 activity promotes the interaction of SF3B1 with the RNAPII phosphorylated on serine 2 and disruption of this interaction by treatment with the CDK12/13 inhibitor THZ531 impairs the association of SF3B1 with the chromatin and its recruitment to the 3’ splice site of these introns. Furthermore, by using suboptimal doses of THZ531 and PdB, we describe a synergic effect of these inhibitors on intron retention, cell cycle progression and cancer cell survival. These findings uncover a mechanism by which CDK12/13 couple RNA transcription and processing and suggest that combined inhibition of these kinases and the spliceosome represents an exploitable anticancer approach.

overall_design: Briefly, OVCAR3 cells were treated with DMSO or THZ531 (200nM) for 6hr. Each sample has 3 biological repeats.

first: Valentina

last: Panzeri

first: Marco

last: Pieraccioli

first: Claudio

last: Sette


title: The PRC2-dependent epigenetic remodeling exacerbates inflammation and severity of urinary tract infection 2

city: Los Angeles

first: Xue

last: Li

address: 8700 Beverly Blvd, Davis 3089

institute: Samuel Oschin Comprehensive Cancer Institute

summary: To identify genes from bladder urothelium that are affected after acute bacterial infection

overall_design: RNA-seq analysis of female mouse bladder mucosal layer. Experiment group consists of these that were infected with UPEC bacterial strain UTI89. Mice inoculated with phospho-buffer saline were used as negative controls.

first: Chunming

last: Guo

first: Mingyi

last: Zhao

first: Xinbing

last: Sui

first: Zarine

last: Balsara


title: The PRC2-dependent epigenetic remodeling exacerbates inflammation and severity of urinary tract infection


title: Transcriptome analysis of kidneys of cisplatin-induced AKI model

city: Jinhua

first: Weiqiang

last: Lin

state: Zhejiang

address: Shangcheng street N1

institute: The Fourth Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine

summary: This study was aimed to investigate the role and underlying mechanism of TRPM2 in cisplatin nephrotoxicity. Cisplatin-induced acute kidney injury (AKI) model was established in WT and TRPM2-KO mice. The transcriptome profiling of  the kidneys of WT and TRPM2-KO mice treated with cisplatin was compared to find differentially expressed gene which may be related to TRPM2 on cisplatin nephrotoxicity.

overall_design: RNA-Seq was applied to detect the differentially expressed gene between the kidneys of WT and TRPM2-KO mice. All mice were treated with 18 mg/kg cisplatin for 72h.


title: The muscle-enriched myokine Musclin impairs beige fat thermogenesis and systemic energy homeostasis via Tfr1/PKA signaling in male mice

status: Public on Mar 27 2023

city: Hangzhou

first: Lu

last: Jin

address: Yuhangtang Road

institute: Zhejiang Univeristy

summary: This work defines the temperature sensitive myokine Musclin as a negative regulator of adipose thermogenesis that exacerbates the deterioration of metabolic health in male mice through antagonizing Tfr1/PKA signaling in beige adipocytes, and thus provides a framework for the therapeutic targeting of this endocrine pathway.

overall_design:
(1) RNA-Seq analysis of 7 tissues (Tibialis anterior (TA) muscle, Heart, Liver, White adipose, Brown adipose, Small intestine (Intestine), Brain) from C57BL/6J wildtype mice fed with chow diet was performed. No biological replicate was included in this RNA-Seq.
(2) RNA-Seq analysis of iWAT from MCK-Musclin and control mice following cold exposure at 8oC for 1 week was performed. Three biological replicates in each group were included.
(3) RNA-Seq analysis of BAT from MCK-Musclin and control mice following cold exposure at 8oC for 1 week was performed. Three biological replicates in each group were included.

first: Zhuoxian

last: Meng

first: Ziyin

last: Zhang

first: Qintao

last: Wang

first: Xinyuan

last: Qiu

first: Zhuoying

last: Yang


title: Transcriptional profiling of Candida albicans SC5314 grown on different carbon and nitrogen sources

first: Philipp

last: Brandt

summary: Goal of this study was to investigate the metabolic adaptation of C. albicans to different carbon sources (malic acid, α-ketoglutarate, proline) and nitrogen sources (dipeptides). As a control medium with glucose as carbon source and ammonium sulfate as nitrogen source was used. Transcriptional profiles were compared after 4 h incubation at 37°C.

overall_design: Candida albicans cells were cultivated in SD medium at 37°C until early log-phase was reached and transferred to the indicated medium, and incubated for 4 h at 37°C.

first: Mohammad

last: Mirhakkak

first: Lysett

last: Wagner

first: Dominik

last: Driesch

first: Anna

last: Möslinger

first: Pauline

last: Fänder

first: Sascha

last: Schäuble

first: Gianni

last: Panagiotou

first: Slavena

last: Vylkova


city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Fatty acids are critical energy sources and structural components of cells. We investigate how CARM1 reprograms fatty acid metabolism to promote ovarian cancer

overall_design: CHIP-seq of CARM1 and H3R17me2a in WT cells

first: Rugang

first: Simona

last: Lombardi


title: The effect of Gemcitabine chemotherapy on lung intertiatial macrophages (IMs) from tumor-free mice

status: Public on Mar 22 2023

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Chemotherapy offers long-term clinical benefits to many cancer patients. However, several pre-clinical studies have demonstrated that certain cytotoxic drugs enhance metastasis via multiple mechanisms. These studies have mainly focused on tumor cell-derived inflammation. The importance of host responses triggered by chemotherapy in regulating cancer metastasis has not been fully explored. Our recent studies have showed that multi-dose Gemcitabine (GEM) treatment promoted breast cancer lung metastasis in a transgenic spontaneous breast cancer animal model. Both CCR2+ macrophages and monocytes were increased in the lungs of GEM-treated mice. Further, the increase of CCR2+ macrophages and monocytes were observed in naïve (tumor-free) mice after GEM treatment. These changes were largely caused by chemotherapy-induced reactive myelopoiesis that are biased toward monocyte development. Importantly, the host responses following chemotherapy promote tumor metastasis, which is dependent on CCL2/CCR2 axis. To understand how lung macrophages contribute to the pro-metastatic effect of chemotherapy, the expression profile of lung interstitial macrophages (IMs) from GEM treated and PBS control tumor-free mice was examined.

overall_design: Lung interstitial macrophages in triplicate from 4 times GEM treated tumor-free mice and lung intertiatial macrophages in triplicate from PBS control tumor-free mice

first: Caijun

last: Wu

first: Qian

last: Zhong

first: Rejeena

last: Shrestha

first: Jingzhi

first: Xiaoling

last: Hu

first: Hong

last: Li

first: Julia

last: Chariker

first: Jun

last: Yan

first: Chuanlin

last: Ding


title: Effect of depletion of Mapk7 on  gene expression during vertebral development in  chondrocyte

city: Guangzhou

first: WU

middle: CHENG

last: ZHI

address: Zhongshan 2nd Road

institute: Sun Yat-sen University

summary: To investigate the role of Mapk7 in vertebral developmemnt,  we constructed Col2a1-cre;Mapk7f/f transgenic mouse model to delete Mapk7 in cartilage

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of vertebral growth plate of P7 mice.

first: Chengzhi

first: Hengyu

last: Liu

first: Dongmei

first: Peiqiang

last: Su


title: Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation [RNA-seq]

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

institute: Chinese Academy of Sciences

summary: RNA-binding proteins (RBPs) bind at different positions of pre-mRNA molecules to promote or reduce the usage of a particular exon. Seeking to understand the working principle of these positional effects, we develop a capture RIC-seq (CRIC-seq) method to enrich specific RBP-associated in situ proximal RNA-RNA fragments for deep sequencing. We determine hnRNPA1-, SRSF1-, and PTBP1-associated proximal RNA-RNA contacts and regulatory mechanisms in HeLa cells. Unexpectedly, the 3D RNA map analysis shows that PTBP1-associated loops in individual introns preferentially promote cassette exon splicing by accelerating asymmetric intron removal, whereas the loops spanning across cassette exon primarily repress splicing. These “positional rules” can faithfully predict PTBP1-regulated splicing outcomes. We further demonstrate that cancer-related splicing quantitative trait loci can disrupt RNA loops by reducing PTBP1 binding on pre-mRNAs to cause aberrant splicing in tumors. Our study presents a powerful method for exploring the functions of RBP-associated RNA-RNA proximal contacts in gene regulation and disease.

overall_design: We developed a capture RIC-seq (CRIC-seq) method for the global mapping of RBP-associated in situ proximal RNA-RNA fragments. Two biological replicates of CRIC-seq libraries were generated for PTBP1 IP (+pCp), hnRNPA1 IP (+pCp), SRSF1 IP (+pCp), IgG IP (+pCp), PTBP1 IP (-pCp), hnRNPA1 IP (-pCp), and SRSF1 IP (-pCp) in HeLa cells. In addition, we also constructed two biological replicates of RIC-seq libraries for PTBP1 and hnRNPA1 knockdown cells to test the specificity of PTBP1- or hnRNPA1-associated RNA loops identified by CRIC-seq. To identify PTBP1 Cys23-mediated RNA loops and their influence on splicing regulation, we performed RNA-seq and CRIC-seq in the PTBP1-C23S mutant replaced (C23S+Dox) or not replaced (C23S-Dox) HeLa cells.

first: Rong

last: Ye

first: Naijing


title: Transcriptional profiling of Candida auris B8441 (CAU30) grown on different carbon and nitrogen sources

first: Philipp

last: Brandt

summary: Goal of this study was to investigate the metabolic adaptation of C. auris to different carbon sources (malic acid, α-ketoglutarate, proline) and nitrogen sources (dipeptides). As a control medium with glucose as carbon source and ammonium sulfate as nitrogen source was used. Transcriptional profiles were compared after 4 h incubation at 37°C.

overall_design: Candida auris cells were cultivated in SD medium at 37°C until early log-phase was reached and transferred to the indicated medium, and incubated for 4 h at 37°C.

first: Mohammad

last: Mirhakkak

first: Lysett

last: Wagner

first: Dominik

last: Driesch

first: Anna

last: Möslinger

first: Pauline

last: Fänder

first: Sascha

last: Schäuble

first: Gianni

last: Panagiotou

first: Slavena

last: Vylkova


title: Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation [RIC-seq]

last: Hu


title: Transcriptome Profiling of Intact Bowel Wall Reveals that PDE1A and SEMA3D are Possible Markers with Roles in Enteric Smooth Muscle Apoptosis, Proliferative Disorders, and Autonomic Nervous Abnormality in Crohn's Disease.

status: Public on Mar 28 2023

city: Chengdu

first: Yun

last: Yang

address: 37 Guoxue Lane

department: Colorectal Cancer Center, Department of General Surgery

institute: West China Hospital, Sichuan University

summary: To use surgical resection specimens of the intact bowel wall from inflammatory bowel disease (IBD) patients and perform RNA-seq, bioinformatics analysis, and validation by quantitative polymerase chain reaction (qPCR) and immunohistochemistry (IHC) to explore the subtle differences between Crohn's disease (CD) and ulcerative colitis (UC), with predominant focus on the smooth muscle cells (SMCs) and enteric autonomic nervous system (ANS).

overall_design: The intact colon specimens from IBD surgical patients were divided based on their inflammatory status into inflamed (6 iCD, 6 iUC) and non-inflamed (6 niBD: 3 niCD+3 niUC) groups

first: Lin

last: Xia

first: Ye

last: Shu

first: Xiaoting

last: Wu


title: Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct


title: Genome-wide mapping of NRF1 (NFE2L1) binding in HCT116 cells upon proteasome inhibition.

status: Public on Mar 19 2023

city: Kyotanabe

first: Akira

last: Kobayashi

address: 1-3 Tatara Miyakodani

institute: Doshisha University

summary: The maintenance of protein homeostasis is an essential characteristic of life. Transcription factor NRF1 (NFE2L1) has been reported to be activated by proteasome dysfunction, although the genome-wide target genes are poorly understood. Using ChIP-seq analysis, we found a potential association between NRF1 and autophagy. Our findings highlight the new activation mechanism of autophagy through gene regulation under proteasome dysfunction.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for transcription factor NRF1 in HCT116 cells treated with 1 µM MG132 for 16 h.

first: Atsushi

last: Hatanaka

last: Watanabe

first: Tsuyoshi

last: Waku


title: Expression data from NRF1 knockdown and/or MG132 treated HCT116 cells

status: Public on Mar 18 2023

summary:
Transcription factor NRF1 (NFE2L1) has been reported to be activated by proteasome disfunction, although the target genes are poorly understood.
We used microarrays to identify NRF3-regulated gene expression network related to proteostasis.

overall_design: For RNA extraction and hybridization on Affymetrix microarrays, we prepared HCT116 cells transiently transfected NRF1 or control siRNA, and treated DMSO or proteasome inhibitor 1 µM MG132 for 16 hr.


title: ELAC2 is a prostate cancer rheostat that regulates nuclear and mitochondrial RNA metabolism

status: Public on Mar 21 2023

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

institute: The Kids Research Institute Australia


title: Single-nucleus RNA-seq of mouse arcuate nucleus of the hypothalamus after DOCA-salt treatment

status: Public on Mar 20 2023

city: Wauwatosa

first: Valerie

middle: A

last: Wagner

state: Wisconsin

address: 8701 W Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

summary: We compared the transcriptomic changes in cell populations of the arcuate nucleus of the hypothalamus in 21 day treated DOCA-salt male mice versus sham male mice using high-throughput single-nucleus RNA-seq.

overall_design: Bilateral arcuate nucleus punches were obtained from each mouse, tissues were homogenized to isolate nuclei. Nuclei were then subjected to single-nucleus RNA-sequencing (10X Genomics)

first: Guorui

last: Deng

first: Kristin

middle: E

last: Claflin

first: Huxing

last: Cui

first: Pablo

last: Nakagawa

first: Curt

last: Sigmund

first: Lisa

last: Morelli

first: Justin

last: Grobe

first: Anne

last: Kwitek


title: Jakyak-gamcho-tang ameliorates dexamethasone (DEX)-induced muscle atrophy and muscle dysfunction [Gastrocnemius and Soleus]

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

summary: Jakyak-gamcho-tang (JGT) is a herbal medicine that has been traditionally prescrived for pain control including muscular pain.  Muscle atrophy is a disease that is characterized with a gradual muscle loss.  Muscle atrophy is clearly observed in experimental animals that receive a repeated high-dose of an artificial glucocorticoid, dexamethasone (DEX).    This transcriptome analysis aims to investigate the changes in global gene expression profiles in gastrocnemius (GA) and soleus (SO) muscle tissues from mice with DEX-induced muscle atrophy in the presence or absence of JGT co-treatment.

overall_design:
All study protocol involving experimental animals was peer-reviewed by the Institutional Animal Care and Use Committee of Korea Institute of Oriental Medicine (#22-048).  Ten weeks-old male C57BL/6N mice were acclimated for at least 1 week before study.  Mice received intraperitoneal (i.p.) injections of 25 mg/kg/day DEX for cosecutive 10 days to induce muscle atrophy. Non-treated normal mice received i.p. injections of vehicle (PBS) instead of DEX.    Thirty minutes after DEX injection, JGT at 100 or 400 mg/kg/day were administered to mice by oral gavage. Non-treated normal mice and DEX-only treated mice received oral gavage of PBS.  Mice of positive control received oral gavage of resveratrol (200 mg/kg/day) instead of JGT.  After 1 day of final drug injection, the GA and SO muscle tissues were isolated from hind legs of mice.  A total RNA was isolated from muscle tissues uisng a TRIzol solution and subjected to mRNA-seq analysis.
JGT02: Paeoniae radix and Glycyrrhizae radix et rhizoma at 2:1 weight ratio; JGT03: Paeoniae radix and Glycyrrhizae radix et rhizoma at 1:1 weight ratio; JGT04: Paeoniae radix and Glycyrrhizae radix et rhizoma at 1:2 weight ratio  The dried powders of Paeoniae radix and Glycyrrhizae radix et rhizoma was subjected to extraction in a 10-fold volume of hot distilled water for 3 h in a reflux extraction system.  The extract solution was filtered through a 53 micrometer mesh filter, concentrated in a rotary evaporator system and lyophilized in a freeze dryer to get a final JGT extract.  The JGT was resuspended in sterile 0.5% carboxymethylcellulose (CMC) in PBS on the day of drug administration.  DEX was dissolved in a sterile PBS  Resveratrol was dissolved in a sterile 0.5% CMC in PBS.

first: Seongwon

last: Cha

first: No

middle: S

last: Kim


title: Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation [CRIC-seq]

city: Beijing

first: Yuanchao

last: Xue

first: Rong

last: Ye

first: Naijing

last: Hu


title: Improvement of wound healing by capsaicin through suppression of the inflammatory response and amelioration of the repair process

city: Taipei

first: SU-YI

last: SU

address: No. 280, Sec. 4, Renai Rd.,

department: Department of Medical Research

country: Taiwan

institute: Cathay General Hospital

summary: To analyze the effects of capsaicin on wound healing using an in vivo animal model.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for capsaicin-terated  wounds and  non capsaicin-terated wounds at day 3 and day 6.

first: Yu-Hsiu

last: Yen

first: Chi-Jung

last: Huang

first: Su-Yi

last: Su

first: Chi-Ming

last: Pu

first: Shih-Lun

last: Lo

first: Cheng-Hung

last: Lee


title: Transcriptional profiling of skin tumor samples from mice with combintions of Braf, Alk5, p53, Tgfbr2 and Kras mutations

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

summary: Murine skin tumors following combintions of Braf, Alk5, p53, Tgfbr2 and  Kras mutation, under the control of Lgr5CreER.

overall_design: Expression data from skin tumors of the noted genotypes.

first: Gareth

last: Inman

first: Owen

last: Sansom

first: Rene

last: Jackstadt