title: Beneficial effects of physical exercise and an orally active mGluR2/3 antagonist pro-drug on neurogenesis and behavior in an Alzheimer’s amyloidosis model

first: Benjamin

last: Glicksberg

address: 1 Gustave Levy Place

department: Genetics and Genomics

institute: Icahn School of Medicine at Mt Sinai

summary: BCI-838 is a pro-drug whose active metabolite BCI-632 is an antagonist at the group II metabotropic glutamate receptor (mGluR2/3). Hippocampal dentate gyrus of four-month old mouse model of AD amyloid pathology (APP/PS1) were investigated via transcriptomics analysis following BCI-838 treatment and physical exercise. Findings demonstrate up-regulated brain-derived neurotrophic factor (BDNF), PIK3C2A of the PI3K-MTOR pathway, and metabotropic glutamate receptors, and down-regulated EIF5A of ketamine-modulating mTOR activity. Our study points to BCI-838 as a safe and orally active compound capable of mimicking the beneficial effect of exercise on AHN, learning behavior, and anxiety in a mouse model of AD neuropathology.

overall_design: APP/PS1 mice were divided into four groups: Group 1 no exercise / no drug; Group 2 exercise / no drug; Group 3 exercise + drug; and Group 4 no exercise / drug. Group 5 consisted of WT mice (C57BL6/J). Groups receiving exercise were given ad libitum access to a running wheel and treatment with drug or vehicle was continued for one month. Two cohorts of mice were used.  One cohort was used for behavioral analysis (n=12 mice per group) whereas a second was sacrificed for neurogenesis and biochemical studies (n=5 mice per group for each study).

first: Mesude

last: Bicak

first: Georgina

last: Perez-Garcia

last: Readhead

first: Michelle

last: Ehrlich

first: Gregory

last: Elder

first: Sam

last: Gandy


title: The Regulatory Network and Role of the circRNA-miRNA-mRNA ceRNA Network in the Progression and the Immune Response of Wilms Tumor based on RNA-seq

status: Public on May 25 2022

city: Chongqing

first: xiaomao

last: Tian

address: Zhongshan 2nd Road, Yuzhong District, Chongqing 400014, P.R. China

country: China

institute: Children’s Hospital of Chongqing Medical University, Chongqing, P.R. China

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNA (circRNA), which is a newly discovered non-coding RNA, has been documented to play important roles in miRNA sponges, and the dysregulation of which is involved in cancer development. However, circRNA expression profiles and their role in initiation and progression of Wilms tumor (WT) remain largely unclear at present. Here, we used paired WT samples and high-throughput RNA sequencing to identify differentially expressed circRNAs.

overall_design: we used 4 paired WT samples and high-throughput RNA sequencing to identify differentially expressed circRNAs.  A complete circRNA-miRNA-mRNA network was then constructed by miRanda prediction tool. Besides these, we selected a key circRNA, circEYA1, for function validation.

first: Xiao-Mao

first: Bin

last: Xiang

first: Feng

last: Liu

first: Guang-Hui

last: Wei


title: APIP5 functions as a transcription factor and an RNA-binding protein to modulate cell death and immunity in rice.

city: Beijing

first: Fan

last: Zhang

address: No. 2 Yuanmingyuan West Road, Haidian District

institute: Chinese Academy of Agricultural Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Many transcription factors (TFs) in animals bind to both DNA and mRNA, regulating transcription and mRNA turnover. However, whether plant TFs function at both the transcriptional and posttranscriptional levels remains unknown. The rice (Oryza sativa) bZIP TF AVRPIZ-T-INTERACTING PROTEIN 5 (APIP5) negatively regulates programmed cell death and blast resistance and is targeted by the effector AvrPiz-t of the blast fungus Magnaporthe oryzae. We demonstrate that the nuclear localization signal of APIP5 is essential for APIP5-mediated suppression of cell death and blast resistance. APIP5 directly targets two genes that positively regulate blast resistance: the cell wall-associated kinase gene OsWAK5 and the cytochrome P450 gene CYP72A1. APIP5 inhibits OsWAK5 expression and thus limits lignin accumulation; moreover, APIP5 inhibits CYP72A1 expression and thus limits reactive oxygen species production and defense compounds accumulation. Remarkably, APIP5 acts as an RNA binding protein to regulate mRNA turnover of the cell death- and defense-related genes OsLSD1 and OsRac1. Therefore, APIP5 plays dual roles, acting as TF to regulate gene expression in the nucleus and as an RNA-binding protein to regulate mRNA turnover in the cytoplasm, a previously unidentified regulatory mechanism of plant TFs at the transcriptional and posttranscriptional levels.

overall_design: In vitro ChIP-seq profiles of GST-APIP5 and GST


title: Hypoxia-reprogrammed regulatory group 2 innate lymphoid cells promote immunosuppression in pancreatic cancer [HMC-1]

city: shanghai

first: Xianjun

last: Yu

address: 270 Dong An Road, Shanghai

department: Department of Pancreatic Surgery

institute: Fudan University Shanghai Cancer Center

type: Expression profiling by high throughput sequencing

summary: Humans mast cell line-1 (HMC-1) cultured with or without hypoxia for indicated time period were analysed

overall_design: Examination of HMC-1 cells cultured with or without hypoxia

first: Longyun

last: Ye


title: Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos (ChIP-Seq)

status: Public on May 26 2022

first: Jin

last: Sun

department: life science and technology

institute: Tongji University

summary: Assisted reproductive technology (ART), especially in vitro fertilization (IVF) and embryo transfer have been widely applied in the treatment of human infertility. However, the accumulating evidences indicate that IVF is associated with low pregnancy rate, placental defect and the metabolic diseases in offspring. Here, we identify ectopic histone H3K4me3 in extraembryonic ectoderm (ExE) as an important reason for embryo implantation failure and extra-embryonic development abnormalities of IVF embryos. IVF manipulation notably disrupt extra-embryonic tissue-specific gene expression, 334 epiblast (Epi)-specific genes and 24 Epi-specific transcription factors were abnormally expressed in ExE of IVF embryos at embryonic day 7.5 (E7.5). Combined histone modification analysis reveal that ectopic H3K4me3 modification at the Epi-active promoter resulted in increased expression of these genes in ExE of IVF embryos at E7.5. By konckdown the expression of H3K4me3 recruited regulator Kmt2e, which highly expressed in IVF embryos, can improve the development of IVF embryo and reduce the abnormal gene expression in ExE. Therefore, our research identifies the abnormal H3K4me3 modification occupied in extra-embryonic tissue may be an important reason for implantation failure and abnormal placental development of IVF embryo.

overall_design: To precisely dissect the histone changes of IVF embryos, we generated a H3K4me3 and H3K27me3 landscapes of morula, E3.5 blastocyst (TE, ICM), E7.5 embryos (ExE, Epi) respectively from IVF and NM embryos by ULI-NChIP

first: Dandan

last: Bai

first: Wenqiang

first: Cizhong

last: Jiang

first: Shaorong

last: Gao


title: Time-course embryonic transcriptomes and improved genome annotation for the amphipod crustacean Parhyale Hawaiensis

city: Woods Hole

first: Nipam

middle: H

last: Patel

state: MA

address: 7 Mbl Street

country: USA

institute: Marine Biological Laboratory

summary: We performed RNA-Seq across multiple time points of development (stages 13, 19, 21, 23) in Parhyale hawaiensis and generated an improved genome annotation.

overall_design: Assembled transcriptomes, differential expression, and improved genome annotation using the Mikado pipeline for four developmental timepoints of Parhyale embryogenesis.

first: Dennis

middle: A

first: Jessen

middle: V

last: Bredeson

first: Heather

middle: S

last: Bruce


title: MCG 101 tumors implanted on prostaglandin receptor EP2 wildtype and EP2 knockout mice

city: Göteborg

first: Britt-Marie

last: Iresjö

address: Forskningsmottagning Kirurgi, Vita Stråket 12, plan 2, Sahlgrenska Universitetssjukhuset

department: Inst. of Clinical sciences/Dep. of Surgery

country: Sweden

institute: University of Gothenburg

summary:
Wild type tumor cells, producing high levels of prostaglandin E2 (MCG101, EP2 +/+), were inoculated on EP2 knockout (EP2 -/-) and EP2 wild type (EP2 +/+) mice. Solid tumors were dissected into tumor- and tumor-stroma tissue compartments for RNA expression microarray screening, followed by metabolic pathway analyses.
The study aims to evaluate simultaneous gene pathway expressions in separate tissue compartments, such as isolated tumor tissue and tumor stroma respectively.

overall_design: 32 samples; consisting of 8 wt tumor,8 EP2 knock tumor, 8 wt stroma, 8 EP2 knockout stroma


title: Lip-1 induces cell cycle arrest, apoptosis, and pyroptosis in K562 cells

status: Public on May 31 2022

city: Nanning

first: Haiqun

last: Dong

address: Shuangyong road 20

department: Department of Hematology

institute: The First Affiliated Hospital of Guangxi Medical University

summary: summary  (1)Objective: To investigate the antileukemic role of Lip-1 in K562 leukemia cells.  (2)Methods: We performed CCK-8, flow cytometry, microscopy, western blotting assay, next generation sequencing, PCR assays to evaluate the effect of Lip-1 in K562 leukemia cells.  (3)Results: Lip-1 inhibited K562 cell proliferation in a dose- and time-dependent manner. RNA sequencing revealed several pathways that were affected by Lip-1, such as the G1/S transition of the mitotic cell cycle and extrinsic or intrinsic apoptotic signaling pathways. The results of flow cytometry indicated that Lip-1 arrests the cell cycle. K562 cells were characterized by swelling and plasma membrane rupture. The expression of the hallmark of pyroptosis, the cleaved N-terminal GSDME, increased. Endoplasmic reticulum stress and autophagy were involved in Lip-1-induced cell death.  (4)Conclusion：Lip-1 induces cell cycle arrest, apoptosis, and secondary pyroptosis in K562 leukemia cells, which provides new hope for the treatment of leukemia.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for K562 cells treated with or without Lip-1

first: Hai-Qun

first: Peng

last: Cheng


title: Therapeutic potential for reversing miR-634-mediated cytoprotective processes to improve the efficacy of chemotherapy against oral squamous cell carcinoma

city: Tokyo

first: Jun

last: Inoue

address: Yushima 1-5-45, Bunkyo-ku

department: Molecular Cytogenetics

country: Japan

institute: Tokyo Medical & dental univ.

summary: For advanced oral squamous cell carcinoma (OSCC), increasing sensitivity to chemotherapy is a major challenge in improving treatment outcomes, and targeting cytoprotective processes that lead to the chemotherapy resistance of cancer cells may be therapeutically promising. Tumor-suppressive microRNAs (miRs) can target multiple cancer-promoting genes concurrently, and are thus expected to be useful seeds for cancer therapeutics. We revealed that miR-634-meditated targeting of multiple cytoprotective process-related genes, including cellular inhibitor of apoptosis proteins 1 (cIAP1), can effectively increase cisplatin (CDDP)-induced cytotoxicity and overcome CDDP resistance in OSCC cells. The combination of topical treatment with miR-634 ointment and administration of CDDP was synergistically effective against OSCC-tumor growth in a xenograft mouse model. Furthermore, the expression of miR-634 target genes is frequently upregulated in primary OSCC tumors. Our study suggests that reversing miR-634-mediated cytoprotective processes activated in cancer cells is a potentially useful strategy to improve CDDP efficacy against advanced OSCC.

overall_design: We identified transcripts enriched in RNP immunoprecipitation (RIP) assays using an antibody against AGO2 in cells overexpressing miR-634 in SAS cells by microarray analysis (RIP-chip analysis). Cells were transfected with 10 nM miR-NC or miR-634 and then lysed after 24 h. The lysates were precleared and incubated with AGO2 antibody-immobilized beads or normal rabbit IgG antibody-immobilized beads for RIP. Each bead complex was washed, and RNA was isolated. RNA from AGO2-RIP (RIP) and total RNA (input) were labelled and hybridized on the Agilent 8 × 60K array. Each experiment was performed in duplicate. In both miR-NC-overexpressing cells and miR-634-overexpressing cells, the enrichment (RIP/Input) was calculated. Then, the fold change of enrichment (miR-634/miR-NC) was calculated.

first: Tran

middle: X

last: Phuong

first: Hiroyuki

last: Harada

first: Johji

last: Inazawa


title: The DNA/RNA helicase DHX9 contributes to the transcriptional program of Androgen Receptor in prostate cancer.

city: Rome

first: Marco

last: Pieraccioli

address: Largo Francesco Vito 1

country: Italy

institute: Catholic University of the Sacred Heart rome

summary: Prostaste cancer (PC) is the most commonly diagnosed male malignancy and an important cause of mortality. Androgen signaling plays a key role in  PC pathogenesis and the understanding of the mechanisms involved in the regulation of AR function might pave the ground for the development of more efficacious and long-lasting therapeutic strategies for PC patients. DNA/RNA helicases are emerging as important regulators of many cellular processes. Among them, DHX9 has been implicated in the control of genomic stability, transcription and DNA replication. To investigate the role of DHX9 in PC we perform RNA-sequencing analysis in androgen-sensitive LNCaP cells affects upon DHX9 silencing.

overall_design: RNA-seq study of androgen-sensitive LNCaP cells knocked down for DHX9 to reveal DEGs upon DHX9 silencing.

first: Lidia

last: Chellini

first: Claudio

last: Sette

first: Maria

middle: P

last: Paronetto


title: Stella regulates the development of female germline stem cells by modulating chromatin structure and DNA methylation [RNA-Seq]

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: The expression profile data was obtained by RNA-Seq data.

overall_design: the expression profile of Stella-knockout and Stella-overexpression FGSCs

first: Changliang

last: Hou


title: Transcriptomic profiles of consistent risk-taking behaviour across time and contexts in European sea bass

city: Rennes

first: Bastien

last: Sadoul

address: 65 rue de Saint Brieuc

country: France

institute: Institut Agro

summary: Boldness is known to be a key driver of accessibility to food or reproduction, but also of increased risk including of being predated. Boldness is supposed consistent across time and contexts but studies investigating stability of this trait in variable environments, including in terms of stress load and over long periods of time are scarce. Moreover, underlying molecular components are poorly studied. Here, we report that boldness of 1154 European sea bass, evaluated using group risk-taking tests, is consistent over 7 months and for individuals subjected to multiple environments, including a stressful environment. Differences in risk-taking behaviour were strengthened by differences observed in the responses to a novel environment test; shy individuals displaed higher group dispersion, higher thigmotaxic behaviour and lower activity. Transcriptomic analyses performed on extreme phenotypes revealed that bold individuals display greater expression for genes involved in social and exploration behaviour, and memory in the pituitary, and genes involved in immunity and response to stimulus in the head kidney. This study demonstrates that personality traits come with underpinning molecular signature, especially in organs involved in the endocrine and immune systems. As such, our results may help to depict the state-behaviour feedback, previously proposed as key in shaping personality.

overall_design: Risk-taking behavior is assessed in 4 separated tests performed over 7 months in European sea bass. At the end of the experiment, 10 individuals were selected based on their extreme behavioral phenotype (either extremely bold or extremely shy) based on their first 3 tests and euthanized to sample the whole brain, the pituitary and the head kidney. These 30 tissues were snap-frozen until the RNA extraction.

first: Sébastien

last: Alfonso

first: Conor

last: Goold

first: Marine

last: Pratlong

first: Stéphanie

last: Rialle

first: Benjamin

last: Geffroy

first: Marie-Laure

last: Bégout


title: DNA methylation patterns in monocytes associate and evolve with prognosis in undifferentiated arthritis

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

type: Methylation profiling by genome tiling array

summary: The identification of predictive markers in an early undifferentiated arthritis (UA) patients is pivotal for selecting appropriate therapies to avoid a poor prognosis. In this work, we investigated the association between clinical features and DNA methylation patterns in monocytes from UA patients to seek potential prognostic biomarkers.

overall_design: We obtained DNA methylation profiles of blood and synovial fluid (SF) monocytes from UA patients and blood monocytes from healthy donors (HD) at baseline and in a following visit. These data were used to interrogate their relationship with prognostic status, to identify predictive biomarkers of poor prognosis.

first: Carlos

last: de la Calle-Fabregat

first: Javier

last: Rodríguez-Ubreva

first: Laura

last: Ciudad

first: Julio

last: Ramírez

first: Raquel

last: Celis

first: Ana

last: Belén Azuaga

first: Andrea

last: Cuervo

first: Eduard

last: Graell

first: Carolina

last: Pérez-García

first: César

last: Díaz-Torné

first: Georgina

last: Salvador

first: José

last: Gómez-Puerta

first: Isabel

last: Haro

first: Raimon

last: Sanmartí

first: Juan

middle: D

last: Cañete


title: Exploring the underlying mechanism of autophagy in liver cancer cells under hypoxia

city: shijiazhuang

first: jian

last: Dou

address: No.139 Ziqiang Road

department: Department of Hepatobiliary Surgery

institute: The Third Hospital of Hebei Medical University

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

overall_design: Refer to individual Series


title: PHF13 interacts with EZH2 in Panc1 cells

city: Shenyang

first: Wanhua

last: Xie

address: Huanghe North Street 146

institute: Shenyang Medical college

overall_design: Examination of PHF13 and EZH2 in Panc1 cells

first: Xie

last: Wanhua


title: DNA methylation patterns in monocytes associate and evolve with prognosis in undifferentiated arthritis [MACs]

first: Esteban

last: Ballestar

summary: Ontogenic origin of monocytic cells in the synovial fluid is currently under discussion. Also, the polarization of these cells have been described to a play a role in the pathogenic joints of arthritis patients. To answer these questions, we analyzed data from blood and SF monocytes and compared them with those of in vitro-generated monocyte-derived macrophages. All conditions were compared, and differences were characterized, considering experimental condition (MO, M-CSF or GM-CSF), compartment (blood or SF) and patient prognosis (good or poor).

overall_design: Peripheral blood monocytes were purified using CD14 magnetic-activated cell sorting (MACS © MicroBeads, Miltenyi Biotec) and cultured in RPMI 1640 in the presence of macrophage colony-stimulating factor (M-CSF) or macrophage-granulocyte colony-stimulating factor (GM-CSF) for 5 days.

first: Carlos

last: de la Calle-Fabregat

first: Javier

last: Rodríguez-Ubreva


title: Corticosteroid Sensitivity and the Effect of Th1 and Th17 Cytokines on Gene Expression in Human Airway Smooth Muscle

city: Columbus

first: Rodney

last: Britt

state: Oh

address: 575 Childrens Crossroad

department: Center for Perinatal Research

institute: Nationwide Children's Hospital

summary:
Purpose: Using RNA-sequencing, determine the effect of corticosteroids on human airway smooth muscle cells (ASM) exposed to Th1 and/or Th17 cytokines. Effects of cytokines and/or corticosteroids on gene expression was assessed.
Methods: Pediatric human ASM (ages 0-21; n=4/treatment group) were serum starved for 48 h and then treated with 10 ng/mL TNFα, IFNγ, IL-17A, TNFα/IFNγ, or IFNγ/IL-17A in the presence of vehicle (0.01% DMSO) or 10 nM fluticasone propionate (FP). Cells were harvested after 18 h for RNA isolation, QC, library prep, and RNA sequencing on the Illumina HiSeq4000 platform. RNA quality and integrity was determined by gel electrophoresis and  Agilent 2100 Bioanalyzer. Following sequencing. FASTQ files were processed and analyzed to generate counts files and perform differential expression analysis.
Results: Our analyses show that cytokines, particularly TNFα, IFNγ, and TNFα/IFNγ had significant effects on gene expression. Differentially expressed genes were largely related to pro-inflammatory responses. Interestingly, we found that IL-17A had only modest effects on gene expression. Corticosteroids (FP) reduced or inhibited the effects of pro-inflammatory cytokines. However, these anti-inflammatory effects were reduced in cells treated with TNFα/IFNγ or IL-17A/IFNγ.
Conclusions: These studies highlight the differential effects of pro-inflammatory cytokines and corticosteroids on gene expression in human ASM.

overall_design: Gene expression in human ASM

last: Britt Jr


title: Stella regulates the development of female germline stem cells by modulating chromatin structure and DNA methylation

first: Ji

last: Wu


title: Stella regulates the development of female germline stem cells by modulating chromatin structure and DNA methylation [MeDIP-seq]

type: Methylation profiling by high throughput sequencing

summary: Genome-wide DNA methylation was assessed by methylated DNA immunoprecipitation

overall_design: Genome-wide DNA methylation was obtained form Stella-knockout and Stella-overexpression FGSCs

first: Changliang

last: Hou


title: Effects of gestational exposure to air pollution on placental transcriptome

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

summary: We report the expression pattern of placental transcriptome by Next Generation Sequencing from Gestational D19 mouse exposed to Air -Pollutant material with or without prior treatment with Fish Oil.

overall_design: Examination of Gene expression pattern in mouse placenta during gestational exposer to Air pollutant material and impact of fish oil treatment.

first: Anela

last: Tosevska

first: Amit

last: Ganguly

first: Matteo

last: Pellegrini

first: Sherin

last: Devaskar


title: placental transcriptome


title: Examination of cell type specific gene expression pattern in placenta of mouse exposed to Air-pollutant material during gestation.

summary: We  are reporting  the expression pattern of placental transcriptome in a celltype specific manner from Gestational D19 mouse exposed to Air -Pollutant material.

overall_design: Placenta was collected from gestational Day19 (D19) of C57BL/6J mouse either exposed to air pollutant material or sterile PBS during the entire gestation period (from D1 of conception to D18). Three different compartments of placenta (Decidua, Junction and Labyrinth) were separated under the microscope and single cell suspension was prepared to make scRNA sequencing library.


title: Stella regulates the development of female germline stem cells by modulating chromatin structure and DNA methylation [Hi-C]

summary: We use in situ Hi-C to report the most comprehensive survey to date of chromatin organization in female germline stem cells

overall_design: Examination of the chromatin architecture in female germline stem cells


title: Transcriptional Characterisation of Proliferative Vitreoretinopathy

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

summary: Purpose: The development of vitreoretinal scars remains an unsolved challenge in clinical practice and often leads to repeated revision surgery and blindness due to lack of efficient therapy. The aim of this study was to characterize the cellular and molecular environment in vitreoretinal scar tissue from patients with proliferative vitreoretinopathy (PVR) in comparison to membranes of the vitreoretinal junction, in order to subsequently identify potential drug treatment options using bioinformatics techniques.  Methods: A total of 23 patients undergoing vitrectomy for retinal detachment due to proliferative vitreoretinopathy (PVR, n = 15), idiopathic macular hole (MH, n = 10) or idiopathic macular pucker (MP, n = 8), were included in this study. Vitreoretinal samples were analysed by RNA sequencing, MS-CyTOF proteomic and by conventional immunohistochemistry. The cellular microenvironment was assessed by bioinformatics cell type enrichment analysis. Drug target screening was performed by using a transcriptome-based drug-repurposing approach using drug-exposure transcriptome data from public available databases.  Results: RNA sequencing of vitreoretinal tissue samples showed distinct transcriptional differences of PVR, ERM and ILM samples allowing an accurate clustering according to the tissue types. The cellular microenvironment of PVR membranes was characterized by the enrichment of melanocytes, astrocytes and various immune cell types, such as M2 macrophages. Differential gene expression (DEG) analysis revealed XX up- and XX downregulated genes in PVR compared to ILM. Among them, FN1 (fibronectin1), SPARC (osteonectin) and various collagens were among the most upregulated factors in PVR, contributing to biological processes such as the organization of extracellular structures, the regulation of cell adhesion and the morphogenesis of blood vessels. Finally, we identified 13 drugs that induce a gene expression profile complementary to the PVR signature and thus represent potential therapeutic options for PVR, including aminocaproic acid and various topoisomerase 2A inhibitors such as doxorubicin, etoposide and mitoxantrone.  Conclusion: The present study reveals significant differences in the transcriptional signature of vitreoretinal scar tissue including PVR, MP and ILM tissue. Among a plethora of differentially expressed genes, FN1 and SPARC appeared to be central mediators underlying PVR development. Based on the transcriptome analyses, aminocaproic acid and topoisomerase-2 inhibitors, such as doxorubicin, etoposide and mitoxantrone, were identified as compatible drugs for the treatment of PVR.

overall_design: RNA sequencing of 10 human PVR membranes, 10 macular pucker and 7 macular hole samples

first: Yannik

last: Laich

first: Julian

last: Wolf

first: Stefaniya

last: Boneva

first: Rozina

last: Hajdu

first: Henrik

last: Faatz

first: Anja

last: Schlecht

first: Felicitas

last: Bucher

first: Andreas

last: Stahl

first: Albrecht

last: Lommatsch

first: Günther

last: Schlunck

first: Hansjürgen

last: Agostini


title: Next Generation Sequencing identifies differentially expressed genes regulated by overexpression of tRF AS-tDR-007333 in A549 cells

city: Shenzhen

first: Rihong

last: Zhai

state: Guangdong

address: 1066 Xueyuan Ave.

institute: Shenzhen University School of Medicine

summary: Our previous study identified that a novel tRNA-derived fragment (tRF)  termed AS-tDR-007333 was up-regulated in non-small cell lung cancer (NSCLC), but the molecular mechanisms of  AS-tDR-007333 in NSCLC were unclear. Here, we used RNA-seq for high-throughput profiling of transcriptomes in A549 cells transfected with AS-tDR-007333, in order to find differentially expressed  genes regulated by AS-tDR-007333.

overall_design: Comparison of mRNA expression profiles between AS-tDR-007333-overexpression in A549 cells  and control cells.

first: Qianqian

last: Chen


title: Exploring the underlying mechanism of autophagy in liver cancer cells under hypoxia based on miRNA sequencing

first: jian

last: Dou

summary:
We established cell models of hypoxia, and the number of autophagic vacuoles was observed by electron microscopy. Autophagy associated proteins and invasion were evaluated. RNA sequencing was used to identify DEmRNAs and DEmiRNAs to study the mechanism of hypoxia-induced autophagy in liver cancer cells.
Results: We found that hypoxia might promote liver cancer cell invasion by inducing autophagy. In addition, a total of 407 shared DEmRNAs and 57 shared DEmiRNAs were identified in both HCCLM3 autophagy group and SMMC-7721 autophagy group compared with normal controls. Furthermore, 278 DEmRNAs were identified cancer autophagy-specific DEmRNAs and 24 DEmiRNAs were identified cancer autophagy-specific DEmRNA and DEmiRNAs. Finally, we obtained 19 DEmiRNAs with high degree based on the DEmiRNA-DEmRNA interaction network. Among them, hsa-miR-483-5p, hsa-miR-4739, has-miR-214-3p and has-miR-296-5p may be potential gene signatures related to liver cancer autophagy.

overall_design: HCCLM3, SMMC-7721 and LX2 cells were used as the research objects, and they were divided into autophagy group and control group. Total RNA was extracted from cells using TRIzol reagent (Life Technologies, CA, USA) according to the manufacturer’s protocol. Spectrophotometric and agarose gel electrophoresis was used to evaluate the quality and quantity of total RNA. Sequencing of miRNA was carried out using BGIseq-500 platform (BGI, China).

first: Jian


title: Exploring the underlying mechanism of autophagy in liver cancer cells under hypoxia based on RNA sequencing

overall_design: HCCLM3, SMMC-7721 and LX2 cells were used as the research objects, and they were divided into autophagy group and control group. Total RNA was extracted from cells using TRIzol reagent (Life Technologies, CA, USA) according to the manufacturer’s protocol. Spectrophotometric and agarose gel electrophoresis was used to evaluate the quality and quantity of total RNA. Illumina Hiseq Xten platform (Illumina, San Diego, CA, USA) was performed to conduct sequencing of mRNA.


title: Next generation sequencing identifies differentially expressed tRNA-derived fragments (tRF) in the plasma of patients with non-small cell lung cancer (NSCLC)

summary: We report the application of small RNA sequencing for high-throughput profiling of circulating tRF in the pre- and post-operation plasma from patients with NSCLC

overall_design: Comparison of  tRF expression profiles between paired pre- and post-operation plasma samples in patients with NSCLC


title: Whole larval transcriptional changes due to nlrc3l deficiency in larval zebrafish.

city: Chapel Hill

first: Celia

middle: E

last: Shiau

state: NC

address: 4344 Genome Sciences Building

institute: UNC Chapel Hill

summary: We conducted a whole genome transcriptome analysis to examine significant gene expression changes in whole zebrafish larvae at 4 dpf between nlrc3l st73 mutants compared with their control siblings.

overall_design: RNAseq dataset from pooled 10-12 whole larvae at 4dpf were used to extract total RNA from nlrc3l st73 heterozyous/wt animals and nlrc3l st73 homozygous mutants that were sorted based on microglia phenotype using neutral red staining.


title: Exceptionally high sequence-level variation in the transcriptome of Plasmodium falciparum

city: Pune

first: Krishanpal

last: Karmodiya

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Center of Excellence in Epigenetics

country: India

institute: Indian Institute of Science Education and Research

summary: Single-nucleotide variations (SNVs) in RNA, arising from co- and post-transcriptional phenomena including transcription errors and RNA-editing, are well studied in a range of organisms. In the malaria parasite Plasmodium falciparum, stage-specific and non-specific gene-expression variations accompany the parasite’s array of developmental and morphological phenotypes over the course of its complex life cycle. However, the extent, rate and effect of sequence-level variation in the parasite’s transcriptome are unknown. Here, we report the presence of pervasive, non-specific SNVs in the P. falciparum transcriptome. SNV rates for a gene were not correlated to the AT-content of that gene. Global SNV rates for the P. falciparum lines we used, and for publicly available P. vivax and P. falciparum clinical isolate datasets, were of the order of 10-3 per base, ~10x higher than rates we calculated for bacterial datasets. These variations may reflect an intrinsic transcriptional error rate in the parasite, and RNA editing may be responsible for a subset of them. This seemingly characteristic property of the parasite may have implications for clinical outcomes and the basic biology and evolution of P. falciparum and parasite biology more broadly, and we anticipate that our study will prompt further investigations into the exact sources, consequences and possible adaptive roles of these SNVs.

overall_design: Variant-calling using REDItools 2.0 (https://github.com/tizianoflati/reditools2.0) done for 3 drug-resistant lines of P. falciparum; and also for a lab-adapted 3D7 line which was subjected separately to temperature stress and drug stress. Single-nucleotide variation rates were calculated from this data.

first: Abhishek

last: Kanyal


title: Analysis of lung transcriptomes after arginine treatment and Mycobacterium infection

city: Seoul

first: June-young

last: Lee

department: Dept. of Biology

country: South Korea

institute: KyungHee University

summary: Lung tissue mRNA profile above arginine treatment and/or Mycobacterium infection

overall_design: 4 samples

first: Youngjae

last: Kim

first: Sangmin

last: Jeon

first: Jin-Woo

last: Bae

first: Eun-Kyeong

last: Jo


title: Stella regulates the development of female germline stem cells by modulating chromatin structure and DNA methylation [ChIP-Seq]

first: Ji

last: Wu

summary: We use ChIP-seq to report the most comprehensive survey to date of chromatin organization in female germline stem cells

overall_design: Examination of STELLA binding sites in FGSCs

first: Changliang

last: Hou


title: A Characterization of the Chromatin Landscape and the Glucocorticoid Receptor Cistrome in Mouse Cerebral Cortical Embryonic Neural Stem and Progenitor Cells

city: Pittsburgh

first: Donald

middle: B.

last: DeFranco

state: PA

address: 7041 Biomedical Sciences Tower 3

department: Department of Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: The goals of this study are to use assays for transposase accessible chromatin and dual-crosslinking immunoprecipitation, each followed by genome-wide sequencing (ATAC-seq and ChIP-seq, respectively) to measure chromatin accessibility and genomic GR binding patterns in vehicle-treated and dexamethasone-treated primary embryonic neural and progenitor stem cell cultures.

overall_design: (1) ATAC-seq on female primary embryonic (E14.5) neural and progenitor stem cell neurosphere cultures. 2 conditions: ethanol-treated and dexamethasone-treated (10-7M) for a total of 4 hours.There are three individual biological replicates for each condition. (2) ChIP-seq on female primary embryonic (E14.5) neural and progenitor stem cell neurosphere cultures. 2 conditions: ethanol-treated and dexamethsone-treated (10-7M) for a total of 4 hours. 1-2 seperate embryos were pulled evenly between treatment conditions to obtain sufficient cell counts. There are three technical replicates for each condition.

first: K

middle: J

last: Berry

first: I

last: Rogatsky

first: U

middle: R

last: Chandran

first: M

last: Fangping

first: D

middle: B


title: A Myb transcription factor, PgMyb308-like, enhances the level of shikimate, aromatic amino acids, and lignins, but represses the synthesis of flavonoids and hydrolyzable tannins, in pomegranate (Punica granatum L.)

city: Kiryat Shmona

first: Rachel

last: Amir

address: Tarshis 2

department: Plant Science

country: Israel

institute: Migal

summary: We cloned and characterized a subgroup S4 R2R3 Myb transcription factor, PgMyb308-like. Overexpressing PgMyb308-like in pomegranate hairy roots. Transcriptome analysis of PgMyb308-like-overexpressing hairy roots revealed reprogramming of cell wall-related genes, while overexpression of PgMyb308-like in Arabidopsis thaliana plants uncovered its distinct role in a different genetic and metabolic background. The results suggest that PgMyb308-like activates genes in the shikimate pathway and lignin biosynthesis, but suppresses those involved in the production of HTs and flavonoids.

overall_design: Examination of 3-month old transgnic pomegranate hairy roots

first: Amir

last: Rachel

first: Dhakarey

last: Rohit


title: Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos

city: shanghai

first: Jin

last: Sun

institute: Tongji University

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

overall_design: Refer to individual Series


title: Gene expression data of EMT-TFs overexpressing ovarian cancer cell lines

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Recent findings show that EMT in cancer is dynamic and display a number of intermediate stages along the transition to obtain a high phenotypic and functional cellular plasticity. To comprehend transcriptional regulation among major EMT-transcription factors (EMT-TFs) along the EMT spectrum, we performed gene expression profiles of EMT-TFs (SNAI1/2, ZEB1/2, TWIST1) overexpressing epithelial (PEO1, OVCA420) and intermediate epithelial (OVCA429) ovarian cancer cell clones. Our results show that these factors generate an unidirectional repressive regulation in cells with epithelial phenotype (PEO1, OVCA420), whereas a bidirectional activation regulation in cells with intermediate epithelial phenotype (OVCA429). Microarray data analysis of these EMT-TFs overexpression clones revealed a distinct signature of gene expression for each phenotype and the overlapping gene set show a strong negative correlation with EMT scores, indicating that loss of this gene set is essential to trigger EMT.

overall_design: Stable clones overexpressing the core EMT-TFs: SNAI1 (S1), ZEB1 (Z1), ZEB2 (Z2), and TWIST1 (T1) were generated in two epithelial cell lines, PEO1 and OVCA420 (420) and one IE cell line OVCA429 (429), with the empty vector (EV) as controls. After antibiotic selection, ZEB1-PEO1 and all SNAI2-overexpression clones failed to survive. All samples were prepared as biological duplicates.

first: Tan

last: Ming

first: Vignesh

last: Sundararajan

first: Tuan

middle: Z

first: Ruby

middle: Y

last: Huang


title: T helper 2-biased transcriptional profile predicts HIV envelope-specific polyfunctional CD4+ T cells that correlated with reduced risk of infection in RV144 trial

city: Seattle

first: Yuan

last: Tian

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: Despite the critical role antigen-specific T cells play in containing viral infections, their aggregate frequencies in peripheral blood have not correlated with clinical protection during HIV infection. However, a subset of HIV-specific T cells, which are capable of simultaneously producing multiple effector cytokines, termed polyfunctional T cells, have correlated with delayed disease progression. HIV-specific polyfunctional T cells have been enumerated and characterized using the intracellular cytokine staining (ICS) assay, which allows for simultaneous multiplexed analysis of cytokine expression at the single-cell level. In addition, using an unbiased computational analysis of ICS data generated through the RV144 HIV vaccine case-control study, we identified vaccine-induced HIV envelope (Env)-specific polyfunctional CD4 T cells as a novel correlate of reduced risk of HIV infection. However, very little is known about these cells and what differentiates them from other vaccine-elicited T cells.  In addition, the use of sample fixation in the ICS assay prevents those cells from being further interrogated for transcriptional differences.  Thus, we developed a novel live-cell multiplexed cytokine capture assay which allows for identification, sorting and transcriptional profiling of individual antigen-specific polyfunctional T cells by single-cell RNA-sequencing (scRNA-seq).  We applied these methods to peripheral blood samples from participants who had received the RV144 vaccine regimen as part of the HVTN 097 clinical trial.  Using this approach, we discovered transcriptional signatures that specifically identify the single-cell Env-specific CD4 T-cell functional profiles which had correlated with reduced risk of HIV infection in RV144.  Interestingly, this signature is particularly characterized by upregulation of Th2 cytokines, supporting the hypothesis that the vaccine-induced Env-specific CD4 T cells likely contributed to the reduced risk of infection by providing T cell help to the Env-specific antibody responses.  By interrogating the gene signatures that correlated with polyfunctionality, we have identified potential mechanisms of how vaccine-elicited polyfunctional T cells may contribute to reduced risk of HIV infection.

overall_design: • Developed novel ex vivo multiplexed cytokine capture assay to enumerate and sort live polyfunctional T cells for downstream analyses  • Polyfunctional T cells were specifically detected among the vaccine-stimulated T cells  • Sc-RNA sequencing analysis identified novel surface markers enriched among vaccine-specific polyfunctional CD4 T cells  • Identified Th2 transcriptional signature that predicts polyfunctional CD4 T cell profile which correlated with reduced risk of HIV infection in the Rv144 HIV efficacy trial

first: Kristen

middle: W

last: Cohen

first: Robert

last: Amezquita

first: Aaron

last: Seese

first: Casey

last: Thayer

last: McElrath

first: Stephen

last: De Rosa

first: Raphael

last: Gottardo


title: Transcriptomic analysis of attenuated Salmonella Typhimurium infected chicken primary macrophages

city: Greenfield

first: Bijit

middle: Kumar

last: Bhowmik

state: IN

address: 2500 Innovation Way

department: Discovery Bacteriology & Microbiome

institute: Elanco Animal Health

summary: Salmonella enterica is one of the most important foodborne pathogens that infect a variety of animals and birds. In humans, S. Typhimurium causes gastroenteritis, leading to vomiting, diarrhea, fever, and abdominal cramps. We mainly get infected with Salmonella by ingesting comminated poultry products. Therefore, developing an oral live attenuated vaccine for the poultry industry is our best bet against Salmonella infection. In this article, we investigated the potential of the next generation of Salmonella vaccines. We generated a library of potentially attenuated S. Typhimurium mutants and compared fitness to that of a commercial vaccine. We also investigated the invasion and survival potential of these mutants in chicken macrophages. Our data indicate that although these mutants had no significant growth defects, they were much sensitive to macrophage attack. Analyzing the transcriptome data from infected primary chicken macrophages, we concluded that these mutants elicit a robust immune response by activating several immunoregulatory pathways. Our data also indicates that by combining phoPQ deletion with an already existing cya-crp deletion in MeganVac1, a much stronger immune response can be generated.

overall_design: Transcriptome profile of attenuated Salmonella infected primary macrophages

middle: K

first: Dharanesh

middle: M

last: Gangaiah

first: Arvind

last: Kumar


title: The effects of primary cilia on endothelial gene expression exposed to flow

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: Biomechanical forces such as wall shear stress induced by flowing blood influence the behavior of vascular cells and have been shown to be  crucial in the onset of vascular disease. Primary cilia are increasingly recognized as important biological sensors of low WSS. The goal of the study was to investigate gene expression profile of endothelial cell under low flow (2 dynes/cm2) as compared to physiological flow (30 dynes/cm2) in presence or absence of primary cilia.

overall_design: For flow experiments, cells were seeded in Ibidi μ-Slide VI0.4 slides coated with 0.1% gelatin and grown till confluence. Cells were serum starved for 24h prior exposure to flow. Laminar shear stress of 30 or 2 dynes/cm2  was applied for 48h. For each set of flow experiments, control cells were kept under static condition.

first: Mannekomba

last: Diagbouga

first: Brenda

last: KWAK


title: Changes in DNA methylation upon gain and loss of Prdm16 function

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: Cortical neurogenesis requires the fine tuning of gene expression, modulated by genetic and epigenetic mechanisms during the entire process. Among the epigenetic factors expressed by the proliferative radial glia cells, Prdm16 has been shown to play a key role in cell proliferation. We found Prdm16 to be expressed exclusively by radial glia cells and to be rapidly turned off in newborn neurons. Predictably, Prdm16-null mice displayed a decrease in cortical thickness as a consequence of an impairment in self-renewal of radial glia cells. Conversely, Prdm16-overexpressing neural progenitors showed an increase in self-renewal activity and failed to complete differentiation. Lineage restriction in differentiating stem cells is achieved by chromatin modifications such as histone modifications and DNA methylation along the promoters of stemness-related genes. We found the expression of the DNA methyltransferase Dnmt3b to be inversely correlated to that of Prdm16. Loss and gain of Prdm16 function leaded to an up- and down-regulation of Dnmt3b, respectively. Functional analysis confirmed Prdm16 competence to repress Dnmt3b expression. Finally, IUE of Prdm16 together with Dnmt3b rescued the increase in radial glia cells self-renewal observed with Prdm16 alone. Thus, Prdm16 may play a crucial role in ensuring neural progenitor self-renewal, mainly through the maintenance of the unmethylated state of stemness-related genes.

overall_design: Examination of the DNA methylation levels in 4 cell types

first: Alessandro

last: Sessa

first: Serena

middle: G

last: Giannelli

first: Federica

last: Ungaro

first: Gaia

last: Colasante

first: Vania

last: Broccoli


title: PHF13 Activates Enhancers to Promote TGFb-Induced Epithelial-to-Mesenchymal Transition [ChIP-Seq]

first: Wanhua

last: Xie

summary: We investigated the role of PHF13 in TGFβ-induced Epithelial-to-Mesenchymal Transition and found PHF13 is essential for TGFβ-promoted broadest H3K4me3 domains and super-enhancers activation.

overall_design: Examination of H3K4me3, H3K27me3, and H3K27ac in PANC-1 cells  in the following conditions: siControl, siControl+TGFb, siPHF13+TGFb.

first: Yating

last: Sun

first: Dan

last: Li


title: Changes in DNA methylation upon gain and loss of Prdm16 function (MeDIP-seq)

overall_design: Examination of the DNA methylation levels in 3 cell types

first: Davide

last: Cittaro


title: PRD class homeobox genes in bovine early embryos: function, evolution and overlapping roles

status: Public on May 24 2022

city: Oxford

first: Thomas

middle: Lewin

last: Lewin

state: Oxfordshire

address: 11a Mansfield Road

department: Department of Biology

country: United Kingdom

institute: Thomas Lewin

summary: ETCHbox genes are mammalian-specific PRD class homeobox genes with conserved expression in the preimplantation embryo but fast-evolving and highly divergent sequences. We ectopically expressed bovine ARGFX and LEUTX ETCHbox genes, both tagged with 3xFLAG tags, in bovine foetal fibroblasts and completed transcriptome seqencing. We compared the transcriptome of cells with ARGFX or LEUTX ectopic expression with control transfected cells. For ARGFX, we expressed the WT version of the gene and a mutant allele containing a 13bp frameshift deletion.

overall_design: Ectopic expression of bovine ARGFX and LEUTX homeobox genes in bovine foetal fibroblasts followed by transcriptome sequencing. 4 conditions (control, WT ARGFX, mutant ARGFX, LEUTX, each with 3 or 4 biological replicates).

first: Ali

middle: A

last: Fouladi-Nashta

first: Peter

last: Holland


title: DREAM Interrupted: Severing LIN-35-MuvB association in Caenorhabditis elegans impairs DREAM function but not its chromatin localization

city: Houghton

first: Paul

middle: Donald

last: Goetsch

address: 1400 Townsend Drive

department: Biological Sciences

institute: Michigan Technological University

summary: The highly conserved DREAM transcriptional repressor complex contains an RB-like pocket protein, an E2F-DP transcription factor heterodimer, and the 5-subunit MuvB complex. Using CRISPR/Cas9 targeted mutagenesis, we disrupted the interaction between the sole Caenorhabditis elegans pocket protein LIN-35 and the MuvB subunit LIN-52. A triple alanine substitution of LIN-52's LxCxE motif (3A) severed LIN-35-MuvB association and caused classical DREAM mutant phenotypes, including synthetic multiple vulvae, high-temperature arrest, and ectopic expression of germline genes in the soma. We performed RNA-seq in lin-52(3A) mutant late embryos (4 replicates) compared to lin-52(WT) wild-type late embryos (4 replicates) to assess the genome-wide effects on gene expression that result from severing LIN-35-MuvB association.

overall_design: We examined 4 biological replicates each of RNA samples (8 total samples) from lin-52(bn139[lin-52::GFP::3xFLAG]) (WT) and lin-52(bn151(lin-52[L42A,C44A,E46A]::GFP::3xFLAG)) (3A) late embryos. Gene expression was compared between 3A and WT to identify misexpressed genes following loss of LIN-35-MuvB association.

first: Susan

last: Strome


title: Enteroendocrine cell types that drive food reward and aversion

city: San Francisco

first: Zachary

last: Knight

address: 1550 Fourth St

institute: UCSF

summary: Animals must learn through experience which foods are nutritious and should be consumed, and which are toxic and should be avoided. Enteroendocrine cells (EECs) are the principal chemosensors in the GI tract, but investigation of their role in behavior has been limited by the difficulty of selectively targeting these cells in vivo. Here we describe an intersectional genetic approach for manipulating EEC subtypes in behaving mice. We show that multiple EEC subtypes inhibit food intake but have different effects on learning. Conditioned flavor preference is driven by release of cholecystokinin whereas conditioned taste aversion is mediated by serotonin and substance P. These positive and negative valence signals are transmitted by vagal and spinal afferents, respectively. These findings establish a cellular basis for how chemosensing in the gut drives learning about food.

overall_design: For Sample 1, we isolated Neurog3-Cre+ cells from the intestinal epithelium of mice by flow cytometry. We then processed single cells using the GemCode Single Cell Platform (10x Genomics) and sequeced single-cell cDNA libraries using an Illumina Highseq 4000. For Sample 2, we isolated CCK-Cre+ and CCK-Cre- cells from the intestinal epithelium of mice by flow cytometery. Half the mice were overnight fasted and the others were fasted and then allowed to refeed Ensure before sacrifice. Total RNA was prepared from CCK-Cre+ and CCK-Cre- cells from each mouse and then sequenced using an Illumina HiSeq 2500.

first: Ling

last: Bai

first: Shenliang

last: Yu


title: The molecular characteristics of low-grade and high-grade areas in desmoplastic infantile astrocytoma / ganglioglioma [RNA-seq]

city: Memphis

first: Jason

last: Chiang

state: Tennessee

address: 262 Danny Thomas Pl

department: Pathology

institute: St. Jude Children's Research Hospital

summary: A distinctive feature of the histopathology of desmoplastic infantile astrocytomas and gangliogliomas (DIA/DIGs) is a combination of low-grade and high-grade areas. In this study, we test the hypothesis that low-grade and high-grade areas in DIA/DIGs have distinct molecular characteristics. Tissue samples from microdissected low-grade and high-grade areas in 12 DIA/DIGs were analyzed by DNA methylome profiling, whole exome sequencing, RNA sequencing, and immunohistochemistry. Copy number variants among the tumours and between the two morphologically distinct areas were infrequent. No recurrent genetic alterations were identified across the tumor series, and high-grade areas did not have additional genetic alterations to explain their distinct morphology or biological behaviour. However, high-grade areas showed relative hypomethylation in genes downstream of the transcription factors SOX9 and LEF1 and evidence of a core SOX9 transcription network alongside activation of the BMP, WNT, and MAPK signalling pathways. This study contributes to our knowledge of molecular genetic alterations in DIA/DIGs, uncovers molecular differences between the two distinct cell populations in these tumours, and suggests potential therapeutic targets among the more proliferative cell population in DIA/DIGs.

overall_design: RNA-seq from the microdissected low-grade and high-grade areas of 12 DIA/DIG FFPE samples

first: David

last: Ellison

first: Xiaoyu

first: Hongjian

last: Jin

first: Gang

last: Wu

first: Tong

last: Lin


title: ZDHHC2-mediated AGK S-palmitoylation inactivates PTEN to reduce sensitivity to sunitinib in ccRCC

city: Changsha

first: Jin

last: xin

state: Hunan

address: 139 Renmin Zhong Lu, Changsha, Hunan, China

department: Department of Urology

institute: The Second Xiangya Hospital, Central South University

summary:
To investigate the role of ZDHHC2 in regulating the sensitivity of ccRCC to TKIs, we established 786-O cell lines in which each target gene has been knocked down by siRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 786-O cells and its KD derivatives (siZDHHC2).

first: Zhu

last: Liang


title: Single-cell analysis of stromal AR deletion on the progression of mouse prostate tumors induced by hormonal carcinogenesis

city: Beijing

first: jiawen

last: wang

address: Beijing

institute: NIBS

summary: Using the single-cell sequencing technology, the authors aim to make a globally construction of single-cell cell atlases comparing mouse prostate tumors induced by T+E2 treatment between the wildtype background and the stromal-AR-deletion background.

overall_design:
Adult mice of two genotypes were treated with T+E2 for 8 months and their prostate cells were captured and analyzed using the 10× Chromium platform.
Adult mice of two genotypes were tamoxifen-induced and waited for 12 months before their prostate cells were captured and analyzed using the 10× Chromium platform.

first: Yueli

last: Liu

first: Jiawen

last: Wang

first: Corrigan

last: Horton


title: The molecular characteristics of low-grade and high-grade areas in desmoplastic infantile astrocytoma / ganglioglioma [methylation array]

overall_design: Genome-wide methylation profiling microarray

last: Li


title: Myeloid FoxO1 in Nonalcoholic Steatohepatitis

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

summary: Our objective is to determine the role of myeloid FoxO1 in regulating hepatic lipid metabolism and its contribution to nonalcoholic steatohepatitis (NASH) in mice. We generated mice with conditional FoxO1 depletion in myeloid cells, using the FoxO1-LoxP/LysM-Cre system. We then fed myeloid cell-conditional FoxO1-knockout and wild-type male mice a NASH-inducing diet for 25 weeks. Then mice in both groups were euthanized and the liver tissues were procured for the preparation of total RNAs, which were subjected to RNA-seq assay. While myeloid FoxO1 was upregulated in animal models and human subjects with NASH, the underlying mechanism is poorly understood. We found that myeloid cell conditional FoxO1-knockout mice were protected from developing NASH, culminating in the reduction of hepatic inflammation, steatosis and fibrosis. Mechanistically, FoxO1 counteracts Stat6 to skew macrophage polarization from M2 toward M1 signatures to perpetuate hepatic inflammation in NASH. FoxO1 appears as a pivotal mediator of macrophage activation in response to overnutrition and a therapeutic target for ameliorating hepatic inflammation to stem the disease progression from benign steatosis to NASH.

overall_design: We used myeloid conditional FoxO1-knockout (n=4, male, 6-week old) and WT littermates (n=4, male, 6-week old) in this study. After feeding a NASH-inducing diet for 25 weeks, we euthanized mice in both groups (n=4/group) after 16-h fasting. Liver tissues were collected from euthanized mice and total liver RNAs were prepared for bulk RNA-seq analysis.

first: Sojin

last: Lee

first: Taofeek

middle: O

last: Usman

first: Jun

last: Yamauchi

first: Goma

last: Chettri

first: Xingchun

first: Gina

last: Coudriet

first: Cuiling

last: Zhu

first: Jingyang

last: Gao

first: Riley

last: McConnell

first: Kyler

last: Krantz

first: Sucha

last: Singh

first: Jon

last: Piganelli

first: Alina

last: Ostrowska

first: Alejandro

last: Soto-Gutierrez

first: Satdarshan

middle: P

last: Monga

first: Aatur

last: Singhi

first: Radhika

last: Muzumdar

first: Allan

last: Tsung

first: H

middle: H

last: Dong


title: Single cell RNA-sequencing of Zip8 knockout cells

city: Los Angeles

first: DIANHUA

last: JIANG

address: 8700 BEVERLY BLVD

institute: CEDARS SINAI

summary: 10-12 weeks SPC-CreERT2-Slc39a8 mice and littermate control mice were first treated 4 doses of tamoxifen, 2 weeks later, lung cells were isolated, magnetic enriched CD45 negative cells were used for single cell RNA sequencing

overall_design: We investigated single cell RNA sequencing of CD45 negative cells from lungs of SPC-CreERT2-Slc39a8 and control mice

first: Guanling

last: Huang

first: Jiurong

last: Liang

first: Paul

last: Noble

first: Dianhua

last: Jiang


title: Runx3 drives a tissue-residency program that is absent in CD4+ T cells

city: Melbourne

first: Luke

middle: C

last: Gandolfo

state: Victoria

address: 1G Royal Parade Parkville

department: Bioinformatics

country: Australia

institute: WEHI

overall_design: Refer to individual Series


title: Runx3 drives a tissue-residency program that is absent in CD4+ T cells [RNA-seq]

summary: Pattens of tissue-residency differs between CD4+ and CD8+ memory T cells in evironmentally exposed organs. The lineage-controlling transcription factor Runx3, expressed in CD8+ T cells, is responsible for shaping a tissue-resident gene network in response to the cytokine TGF-b. While the lack of Runx3 by CD4+ T cells precludes these transcriptional changes, Runx3-overexpression in CD+ T cells enable phenotypical, transcriptional and functional changes to allow residency.

overall_design: Effector CD4+ and CD8+ T cells were transduced with Control and Runx3-expressing retrovirus. Cells were co-transferred to HSV infected mice and isolated from the skin for RNA sequencing 14 days post HSV infection.

first: Raissa

last: Fonseca

first: Laura

last: Mackay


title: PHF13 Activates Enhancers to Promote TGFb-Induced Epithelial-to-Mesenchymal Transition

city: Shenyang

first: Wanhua

last: Xie

address: Huanghe North Street 146

institute: Shenyang Medical college


title: PHF13 Activates Enhancers to Promote TGFβ-Induced Epithelial-to-Mesenchymal Transition [RNA-Seq]

overall_design: mRNA profiles of PANC1 cells following TGFβ treatment and PHF13 knockdown. The mRNA-seqencing was performed  in duplicates including the following conditions: siControl, siPHF13, siControl+TGFβ, siPHF13+TGFβ.

first: Yating

last: Sun

first: Dan

last: Li


title: The BMP2/SMAD pathway is a key regulator of TP53-altered erytholeukemia [scRNA-seq]

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: Acute Myeloid Leukemia (AML) which occurs after an antecedent myeloproliferative neoplasm (MPN) has a dismal clinical prognosis and is not curative outside of the rare subset of patients who undergo successful allogeneic stem cell transplantation.  As such, there is a pressing need for new mechanistic insights into how MPNs transform into AML and to use these insights to credential novel therapeutic approaches.  The most common somatic mutational event which occurs in transformation from MPN to AML is mutation in TP53. However, the impact of TP53 allelic state on the ability to potentiate leukemic transformation, as well as the pathways involved in this process, have largely remained unresolved. Here we report the development of genetically accurate models of Jak2/Tp53 mutant MPN which undergoes progressive leukemic transformation with chromosomal instability similar to that observed in the clinical context. These models result in a fulminant erythroleukemia phenotype. We identify that leukemic transformation requires homozygous inactivation of TP53, and does not occur with heterozygous loss of Tp53. We further identify that the megakaryocyte erythroid progenitor (MEP) population is expanded prior to and after leukemic transformation, is characterized by progressive genomic instability (compared to other stem/progenitor compartments), and is capable of propagating the disease in vivo. Thus, the leukemia-initiating population is contained in the MEP compartment. Using gene-expression profiling we demonstrate that the BMP2/SMAD pathway (which is involved in self-renewal and DNA damage repair) is aberrantly activated in the leukemic phase of the disease. Importantly, attenuation of Bmp2 results in decreased self-renewal of leukemic cells in vitro and increased survival of leukemic mice in vivo, thus credentialing a biologic role for this pathway in leukemic transformation. Finally, given the loss of Tp53 function and associated disruption of DNA repair pathways, we hypothesized and subsequently identified that leukemic transformation is characterized by increased DNA damage. Using a synthetic-lethality strategy of targeting remaining DNA-repair pathways, using small-molecule inhibitors, in order to provoke biologically intolerable DNA damage and mitotic catastrophe, we demonstrate that Jak2/Tp53 mutant is highly sensitive to combined inhibition of WEE1 and PARP. This combination results in prolonged survival of mice and attenuates the leukemic phenotype. Collectively, these observations yield new mechanistic insights into the process of leukemic transformation resulting from TP53 alterations, and offer new, clinically-translatable, therapeutic options.

overall_design: Single cell RNA-sequencing of mouse c-Kit+ hematopoietic populations in the context of a Jak2/Tp53 MPN-AML model

first: Bing

first: Raajit

last: Rampal


title: The BMP2/SMAD pathway is a key regulator of TP53-altered erytholeukemia [Bulk RNA-seq]

overall_design: Bulk RNA-seq of stem and myeloid progenitor populations in the context of Jak2 and Tp53 mutations


title: Chemokines form nanoparticles with DNA and can superinduce TLR-driven immune inflammation

first: David

last: Oliver

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: Chemokines are chemotactic cytokines that control the migratory patterns and positioning of immune cells. Many chemokines have been associated with systemic autoimmune diseases that have chronic IFN signature. We now describe that a series of chemokines, including CXCL4, CXCL10, CXCL12 and CCL5, can superinduce type I IFN (IFN-I) by TLR9-activated plasmacytoid DCs (pDCs), independently of their respective known chemokine receptors. Mechanistically, we show that chemokines such as CXCL4 mediate transcriptional and epigenetic changes in pDCs, mostly targeted to the IFN-I pathways. We also describe that chemokines physically interact with DNA to form nanoparticles which promote clathrin-mediated cellular uptake and delivery of DNA in the early endosomes of pDCs. Using two mouse models of skin inflammation, we observed the presence of CXCL4 associated with DNA in vivo. These data thus reveal a non-canonical role for chemokines to modulate TLR signaling, and extend our understanding on the mechanism associated with the chronic expression of IFN-I by pDCs in autoimmune diseases.

overall_design: One hundred thousand purified pDCs were cultured in 96 U-bottom well plate with medium, CXCL4 (10μg/ml), CpG (0.25μM) alone or with CXCL4 (10μg/ml) for 6h. Total RNA was isolated using RNeasy Plus Mini kit. SMART-Seq v3 Ultra Low Input RNA Kit (Clontech) followed by Nextera library preparation were used to prepare Illumina-compatible sequencing libraries. Quality of all RNA were evaluated with BioAnalyser 2100 (Agilent). Single-end reads were obtained on an Illumina HiSeq 2500 in the Weill Cornell Epigenomics Core Facility at the depth of 21-37 million fragments per sample. Sequencing quality was measured with fastp (Chen et al., 2018). Reads were then mapped reads in genes counted against the human genome (hg38) with STAR aligner and Gencode v21(Dobin et al., 2013; Frankish et al., 2019). Differential gene expression analysis was performed in R(Team, 2020) using the edgeR package (Robinson et al., 2010).

first: YONG

last: DU

first: Marie

middle: D

last: Ah Kioon

first: Franck

middle: J

last: Barrat


title: Transcriptional profiles of CD27 negative and positive MAIT cells from PBMC of diabetic obese patients

city: Guangzhou

first: Jin

last: Wang

address: Zhongshan 2nd Road

institute: Sun yat-sen University

summary: Our previous observation found CD27 negative MAIT cell subset is associated with T2D progression in overweight/obese patients. To identify the difference of functional properties between CD27 negative and positive MAIT subsets under obesity related T2D condition, we isolated circulating CD27+ or CD27- CD3+ CD161+ TCR Va7.2+ MAIT cells from PBMC of three diabetic obese patients and performed bulk RNA-seq based on Smart-seq2 protocol. By the comparison of CD27- and CD27+ MAIT cells, we found CD27- MAIT cell exhibit an increased mitochondrial mass and decreased response to bacterium transcriptional pattern compared to CD27+ MAIT cells in diabetic obese patients, indicating the imbalanced cell-bacteria interaction might contribute to T2D progression in overiweight/obese people.

overall_design: CD27 negative and positive MAIT cell mRNA profiles of three diabetic obese patients

first: Yan

last: Lu


title: The BMP2/SMAD pathway is a key regulator of TP53-altered erytholeukemia

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


title: Transcriptional Profile and Chromatin Accessibility in Zebrafish Melanocytes and Melanoma Tumors

city: Saint Louis

first: Charles

last: Kaufman

state: MO

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St. Louis


title: Ribosome Profiling Reveals Novel Regulation of C9ORF72 GGGGCC Repeat-Containing RNA Translation

city: Worcester

first: Heleen

last: van 't Spijker

state: Massachusetts

address: 55 Lake Avenue North

institute: University of Massachusetts Medical School

summary: Using dynamic ribosome profiling, we identified three translation initiation sites in the intron upstream of GGGGCC; these sites are detected irrespective of the presence or absence of the repeat.

overall_design: Identification of translation initiation sites for C9ORF72 in iPSCs and HEK cells expressing a C9ORF72 reporter

first: Joel

last: Richter

first: Emily

last: Stackpole


title: Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA-seq]

summary: With high genetic heterogeneity in melanoma, understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes, pathways, and epigenetic regions influencing melanoma development. We performed RNA-seq and ATAC-seq on fluorescently-isolated melanocytes and melanoma cells from a zebrafish melanoma model.

overall_design: RNA-seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish (D. rerio).

first: Eva

middle: T

last: Kramer


title: Chromatin Accessibility in Zebrafish Melanocytes and Melanoma Tumors [ATAC-seq]

overall_design: ATAC-seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish (D. rerio).


title: Single-cell RNA-sequencing of mouse and human lung Lin–EpCAM+ cells

first: DIANHUA

last: JIANG

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

These datasets include RNA transcriptomics of bleomycin-injured mouse lungs, day 0, day 4 and day 14; and corresponding controls; as well as RNA transcriptomics of lungs from six healthy donors and six patients with IPF.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Single-cell RNA-sequencing of human lung Lin–EpCAM+ cells

summary: Healthy donor and idiopathic pulmonary fibrosis (IPF) patient lung tissues were digested, Lin–EpCAM+ cells were isolated with FACS, and then single-cell RNA-seq was performed.

overall_design: We investigated human lung epithelial cell subpopulation between healthy and IPF patients.

first: Guanling

last: Huang

first: Jiurong

last: Liang

first: Paul

last: Noble

first: Dianhua

last: Jiang


title: Characterization of chromatin and gene expression changes during fasting and refeeding in mouse liver [RNA-Seq]

city: NEW YORK

first: Domenico

last: Accili

state: NY

address: 1150 ST NICHOLAS AVENUE, RM238

department: Medicine

institute: Columbia University

summary: The discovery of FoxO1 as an effector of insulin action on gene expression filled a gap in our knowledge of insulin signaling. The metabolic impact of hepatic FoxO1 has been demonstrated in genetic mouse models showing that FoxO1 inhibition can reverse diabetes. However, the gamut of FoxO1 targets is unknown, due to the lack of robust genome-wide chromatin occupancy data. To elucidate the genomic architecture of the FoxO1 effect on liver metabolism, we integrated genome-wide ChIP-seq and RNA-seq. During the physiological transition from fasting to refeeding, hepatic FoxO1 translocated from the nucleus to the cytoplasm. At the same time points, cistrome analysis demonstrated that 60% of FoxO1 target sites were cleared by refeeding. RNA-seq from mice following acute liver-specific FoxO1 ablation allowed us to integrate the data in a comprehensive FoxO1 regulome. We identified four distinct classes of FoxO1 targets. Class I targets are enriched in genes regulating cell homeostasis, have FoxO1 sites clustered in promoters and do not show regulation with fasting/refeeding. Class II is comprised of canonical FoxO1 metabolic targets coordinately regulated with other fasting-inducible TFs, such as PPARA, CREB, and GR through promoters. Class III is enriched in glucose metabolic genes regulated through active enhancers, as detected by H3K4me1 and H3K27ac histone marks. Class IV is comprised of triglyceride (TG) and lipoprotein metabolism genes, regulated through intron sites, and characterized by an uneven response to fasting/refeeding regulation.

overall_design: mRNA profiles of liver tissues from constitutive or acute liver specific FoxO1 knockout mice during 4h fasted or 4 hr fasted/1 hr refed. For constitutive liver-specific FoxO1 knockouts, we crossed FoxO1lox/lox and Albumin-cre transgenic mice. Acute liver-specific FoxO1 knockout mice were generated by injection of 1×1011 purified viral particles (AAV8.TBG.eGFP or AAV8.TBG.Cre) per mouse via tail vein. We collected samples on day 21 post-injection.

first: Takumi

last: Kitamoto

first: Atsushi

last: Okabe

last: Kaneda


title: Single-cell RNA-sequencing of bleomycin-injured young and old mice

summary: Young and old mice were first injected with bleomycin. At day 0, day 4 and day 14, the lungs were harvested and digested, and Lin-Epcam+ cells were isolated with FACS, single-cell RNA-seq was performed with the FACS-sorted cells.

overall_design: We investigated lung epithelial cell subpopulation at day 0, day 4 and day 14 bleomycin-injured young and old mice lung.


title: Characterization of chromatin and gene expression changes during fasting and refeeding in mouse liver [ChIP-Seq]

overall_design: characterization of liver FoxO1 binding and histone acetylation during 4h fasted or 4 hr fasted/1 hr refed using chromatin immunoprecipitation


title: Characterization of chromatin and gene expression changes during fasting and refeeding in mouse liver


title: Foodomics study on the anti-proliferative activity mechanisms on HT-29 colon cancer cells in response to banana passion fruit (Passiflora mollissima) seeds PLE-extract

city: Madrid

first: Alberto

last: Valdés

state: Madrid

address: C\Nicolás Cabrera, 9

department: Bioactividad y Análisis de Alimentos

institute: Instituto de Investigación en Ciencias de la Alimentación

summary:
Passiflora mollissima commonly known as “banana passion fruit” is usually consumed as fresh food or processed products, being seeds and peel the main by-products of the industrial processing. The potentially bioactive metabolites from banana passion fruit PLE-extract seeds have been recently characterized by HPLC-HRMS after sequential pressurized liquid extraction (PLE)
To apply a Foodomics approach to study the effects of a banana passion fruit seeds PLE-extract (with high antioxidant capacity and enriched in phenolic-type compounds) on the transcriptome and metabolome of HT-29 colon cancer cells.

overall_design: Transcriptome and metabolome analyses of HT-29 colon cancer cells untreated or treated with a banana passion fruit seeds PLE-extract for 48 hours. Three biological replicates were included in the experiment.

first: D

last: Ballesteros-Vivas

first: G

last: Alvarez-Rivera

first: C

last: León

first: S

last: Morantes

first: E

last: Ibánez

first: F

last: Parada-Alfonso

first: A

last: Cifuentes


title: Foodomics study on the anti-proliferative activity mechanisms on HT-29 colon cancer cells in response to golden berry (Physalis peruviana L.) calyx extracts

summary:
Different research works have described goldenberry calyx as a source of bioactive compounds, but limited information is available about its effects at the transcriptome and metabolome levels
To apply a Foodomics approach to study the effects of a goldenberry calyx PLE-extract on the transcriptome and metabolome of HT-29 colon cancer cells.

overall_design: Transcriptome and metabolome analyses of HT-29 colon cancer cells untreated or treated with a goldenberry calyx PLE-extract for 48 hours. Three biological replicates were included in the experiment.


title: Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [ChIP-Seq II]

status: Public on May 23 2022

first: Ana

middle: Karina

last: Morao

address: 29 Washington Place

department: Biology

institute: New York University

summary: Condensin complexes are evolutionarily conserved molecular motors from the structural maintenance of chromosomes (SMC) family, that use ATPase activity to translocate along DNA and form loops. Condensin and topoisomerase II (TOP-2) are essential for the structure and function of mitotic chromosomes. While condensin-mediated DNA looping is thought to direct TOP-2 chain-passing activity to separate sister chromatids, it is not known if TOP-2 in turn regulates loop formation. Here we used an X chromosome specific condensin that represses transcription for dosage compensation in C.elegans, to determine how DNA topology affects SMC translocation in vivo. We applied auxin-inducible degradation of topoisomerases I and II to determine their effect on condensin DC binding and function. We found that both topoisomerases colocalize with condensin DC and control its movement at different genomic scales. TOP-2 depletion hindered condensin DC spreading over long distances, resulting in accumulation around its X-specific recruitment sites and shorter Hi-C interactions. In contrast, TOP-1 depletion did not affect long-range spreading but resulted in accumulation of condensin DC within gene bodies, specially of highly expressed and long genes. Both TOP-1 and TOP-2 depletion resulted in X chromosome upregulation indicating that condensin DC translocation at both scales is required for its function in transcriptional repression. Together our work reveals distinct DNA topological requirements for two modes of condensin DC association with chromatin: long-range linear translocation that requires decatenation and unknotting of DNA and short-range binding to genes that requires resolution of transcription-induced supercoiling.

overall_design: ChIP-seq data in WT, controls and topoisomerases I and II depleted conditions . Depletion was performed by Auxin inducible degradation. All experiments were performed in two biological replicates. L2/L3 larvae were used for most experiments. TOP-2 ChIP-seq in embryos and adults are also included.

first: Jun

last: Kim

first: Daniel

last: Obaji

first: Siyu

last: Sun

first: Sevinc

last: Ercan


title: Microarray of skin innate lymphoid cells (ILCs) of CCR10+/EGFP and Rag1-/-CCR10+/EGFP mice

city: HELOTES

first: Ming

last: Xu

state: TX

address: 9754 Magic Cedar

department: MIMG

institute: UTHSCSA

summary:
We previously found that while CCR10+ ILCs are dominant in the healthy skin, they differentiate into CCR10- ILCs in the skin of mice with various dysregulated or inflammatory conditions, such as T/B cell-deficient Rag1-/- mice. These suggest that CCR10- ILCs are activated effector cells in response to altered skin environments. To gain clues about the functional mechanism and regulation of the ILC activation in the skin, we compared gene expression profiles of CCR10+ skin ILCs of wild-type (WT) mice versus CCR10- or CCR10low skin ILCs of WT and Rag1-/- mice using microarray analyses.
Skin innate lymphoid cells were isolated by BD FACSAria sorting system. The microarry was perfomanced by Immunological Genome Project using Affymetrix arrays and used for analysis of gene expresssion of CCR10+ ILCs and CCR10- ILCs in different mice species as indicated.

overall_design: Skin CCR10+ and CCR10- ILCs from CCR10+/EGFP and Rag1-/-CCR10+/EGFP mice were sorted and the microarry was done to compare the gene expression of CCR10+ ILCs and CCR10- ILCs in different mice species.

last: Xiong


title: Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [Hi-C]

overall_design: Hi-C data in controls and topoisomerase II depleted conditions . Depletion was performed by Auxin inducible degradation. All experiments were performed in two biological replicates. L2/L3 larvae were used.


title: Characterization of Immature Macrophages in Mouse Colon

city: Seoul

first: Myung Jun

state: Jongno-gu

address: 103 Daehak-ro

department: College of Medicine

institute: Seoul National University

summary: To define the genetic characteristics of immature macrophages in the mouse colon, we isolated and sequenced monocytes and immature macrophages, and mature macrophage populations from WT mice

overall_design: mRNA profiles of intestinal macrophages and monocytes from WT mice were generated by sequencing

first: YiRang

first: Daun

last: Jung

first: MyungJun


title: Cell function and identity revealed by comparative scRNA-seq analysis in human nasal, bronchial and epididymis epithelia. [RNA-Seq]

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: The evolutionary relationship of cells within tissues having a similar function but located in different anatomical sites is of considerable biological interest. The development of single-cell RNA sequencing (scRNA-seq) protocols has greatly enhanced opportunities to address this topic. Here we focus on cells in the epithelium which lines two regions of the human respiratory tract and the male genital ducts to delineate the shared, differentiated functions of the different cell populations. Transcriptomic data were used to assess the gene expression profiles of human bronchial, nasal, and epididymal epithelium (HBE, HNE, and HEE). Bulk RNA-seq showed many shared genes expressed in cells from the nasal and bronchial epithelium and highlighted their divergence from the epididymal epithelium. ScRNA-seq in HBE and HNE cells demonstrated overlapping gene expression patterns within basal and secretory cell populations. Moreover, the distribution of cell types was altered in HNE cells derived from donors with cystic fibrosis (CF) when compared to cells from healthy donors. Next, the HBE and HNE datasets were merged and confirmed intersection of cell type gene expression profiles from the two sites, but that secretory and ciliated cells were the most abundant type in the HBE samples, while more basal cells were seen in the HNE. We then merged single-cell data from the epididymis to determine if overlapping functions of these cells corresponded to those in the airway. Of note, only the pulmonary ionocytes/epididymis clear cells showed a strongly conserved identity, which was confirmed by imputation in bulk RNA-seq datasets from the same cells.

overall_design: RNA-seq and single-cell RNA-seq of human bronchial or nasal epithelial tissue

first: Alekh

last: Paranjapye

first: Shih-Hsing

last: Leir

first: Felix

last: Huang

first: Jenny

middle: L

last: Kerschner


title: An essential role for PTIP in mediating Hox gene regulation along PcG and trxG pathways

city: Nangjing

last: Fang

state: jiangsu

address: 2 Sipailou Road

institute: Southeast University

summary: During Drosophila development, Polycomb-group and Trithorax-group proteins function to ensure correct maintenance of transcription patterns by epigenetically repressing or activating target gene expression. To get a deep insight into the PcG and trxG pathways, we investigated a BRCT domain-containing protein called PTIP, which was generally identified as a transcriptional coactivator and belongs to the TRR complex. At the genome scale, we sorted given PTIP binding peaks into two groups: PTIP/TRR-cobound and PTIP/PC-cobound peaks. In particular, we found that PTIP mediates the molecular switch between H3K4me3/H3K27ac and H3K27me3 histone modifications at TRR or PC occupied regions. Thus, we suggest that PTIP is a mediator rather than a dedicated co-activator along PcG and trxG pathways. Our hypothesis is further supported by the genetic assay: PTIP interacts genetically with either PcG or TrxG in a dosage-dependent manner, suggesting that PTIP functions as a co-factor of PcG/TrxG proteins. In addition, in accordance with the analysis of ChIP-seq, these genetic interactions correlate with modified ectopic HOX protein levels in imaginal discs, which reveals an essential role for PTIP in PcG-mediated Hox gene repression. Hence, we reveal a novel role for PTIP in the epigenetic regulation of gene expression along PcG and trxG pathways.

overall_design: PTIP ChIP was generated according to standard procedures. Genomic DNA was extracted from embryos (AEL4-6H) using PCR purification reagent (QIAGEN). ChIP-seq data for PTIP was obtained by the service provided by Novogene (Beijing, China) from their deep sequencing platform built on the Illumina Hiseq-PE150.

first: Qian

last: Cheng

first: Hao

last: Xie


title: Cell function and identity revealed by comparative scRNA-seq analysis in human nasal, bronchial and epididymis epithelia. [scRNA-Seq]


title: Proximal tubule cells in blood and urine have potential as biomarkers for kidney disease biopsies

city: Foshan

first: Dan

last: Zhou

address: Shiwan Street, Chancheng District, Foshan City

institute: Center, First People's  Hospital of Foshan

summary: Early diagnosis and treatment is pivotal to the management of kidney disease, whereas the pathological mechanisms and minimally invasive diagnostic method still need to be investigated. In the present study, single-cell RNA sequencing (scRNA-seq) was used to evaluate the heterogeneity of kidney diseases in single cell level. Cellular gene expression profiles of cells of renal tissue, peripheral blood mononuclear cells (PBMCs) and urine from four nephritis patients were performed. Our analysis revealed 12 subsets of renal cells and leukocytes, including fibroblast cells, mesangial cells, epithelial cells, proximal tubule cells (PTCs), and 6 types of immune cells, CD8+ T cell, macrophages (MC), nature killer cells (NK), dendritic cells (DC), B cell and neutrophils. PTCs were detected in both PBMC and urine, while PTC was negative in healthy blood sample. Multiple populations of fibroblast cells, mesangial cells and PTCs demonstrated pro-inflammatory or pro-apoptotic responses. Gene expression analysis suggested that chemotactic and activating effect of inflammatory PTCs and fibroblasts on neutropils were critical for the development and progress of nephritis, which was supported by the widely overexpressed pro-inflammatory genes in these cells. Gene expression profiles of inflammatory PTCs in PBMC, urine and kidney are highly correlated, indicating the high possibility of urine and PBMC PTCs in serving as a surrogate for kidney biopsies.

overall_design: In the present study, we aim to find out novel biomarkers from blood or urine by analysis cells from blood and urine using scRNA-seq, which may provide alternative minimally or noninvasive diagnostic method for kidney diseases.

first: Yan

last: Zeng

first: Fanna

last: Liu

first: Guoqiang

last: Chen


title: Bridging the muscle genome to phenome across multiple biological scales

city: Lowell

first: Matthew

last: Gage

address: 265 Riverside St

department: Chemistry

institute: University of Massachusetts Lowell

summary: Muscle is highly hierarchically organized, with functions shaped by genetically controlled expression of protein ensembles with different isoform profiles at the sarcomere scale. However, it remains unclear how isoform profiles shape whole-muscle performance. We compared two mouse hindlimb muscles, the slow, relatively parallel-fibered soleus and the faster, more pennate-fibered tibialis anterior (TA), across scales: from gene regulation, isoform expression and translation speed, to force-length-velocity-power for intact muscles. Expression of myosin heavy-chain (MHC) isoforms directly corresponded with contraction velocity. The fast-twitch TA with fast MHC isoforms had faster unloaded velocities (actin sliding velocity, Vactin; peak fiber velocity, Vmax) than the slow-twitch soleus. For the soleus, Vactin was biased towards Vactin for purely slow MHC I, despite this muscle's even fast and slow MHC isoform composition. Our multi-scale results clearly identified a consistent and significant dampening in fiber shortening velocities for both muscles, underscoring an indirect correlation between Vactin and fiber Vmax that may be influenced by differences in fiber architecture, along with internal loading due to both passive and active effects. These influences correlate with the increased peak force and power in the slightly more pennate TA, leading to a broader length range of near-optimal force production. Conversely, a greater force-velocity curvature in the near-parallel fibered soleus highlights the fine-tuning by molecular-scale influences including myosin heavy and light chain expression along with whole-muscle characteristics. Our results demonstrate that the individual gene, protein and whole-fiber characteristics do not directly reflect overall muscle performance but that intricate fine-tuning across scales shapes specialized muscle function.

overall_design: Comparative study of transcriptomes of slow-twitch Soleus and fast-twitch TA muscle tissues.

first: SaiLavanyaa

last: Sundar

first: Barbora

last: Rimkus

first: Prabath

middle: S

last: Meemaduma

first: Samuel

last: deLap

first: Nicholas

last: LaFave

first: Alice

middle: W

last: Racca

first: Pabodha

last: Hettige

first: Jeffrey

last: Moore

first: Andrea

last: Shehaj

first: Nicolai

last: Konow


title: Robust transcriptional indicators of plant immune cell death revealed by spatio-temporal transcriptome analyses

city: Bellaterra

first: Jose

last: Salguero Linares

state: Barcelona

address: Carrer de la Vall Moronta s/n

institute: Centre for Research in Agricultural Genomics

summary: We aim to monitor global transcriptomic changes during the HR in Arabidopsis Col-0 leaf upon localized infiltration of Pst DC3000 (avrRpm1) (5*107cfu/mL) and mock (10 Mm MgCl2) in a spatio-temporal manner. The infiltrated cells were harvested in parallel with the immediately adjacent uninfected cells. Samples were collected at 0,1,2,4,6 post-inoculation in three biological replicates.

overall_design: Leaf  tissue  was  separately  collected  from  the  IN  and  OUT  area  of  infiltration at 5 different time points: 0, 1, 2, 4 and 6 hours by making use of a sterile scalpel Leaf tissue was stored in 2 mL Eppendorf tubes and snapped-frozen in liquid nitrogen until the time of RNA extraction. Each sample collected consisted of tissue from six leaves derived from three different plants. For generation of three biological replicates from each condition (area, treatment and time), three independent experiments were performed. total sum of 60 samples -2  treatments  (mock/infected),  5  time  points  (0,  1,  2,  4  and  6  hpi),  2  areas  (IN/OUT)  and  3 biological replicates- were used for RNA-sequencing.

last: Salguero-Linares

first: Irene

last: Serrano

first: Nerea

last: Ruiz-Solani

first: Marta

last: Salas-Gómez

first: Ujjal

last: Phukan

first: Víctor

last: González

first: Martí

last: Bernardo-Faura

first: Marc

last: Valls

first: David

last: Rengel

first: Nuria

last: Coll


title: Cell function and identity revealed by comparative scRNA-seq analysis in human nasal, bronchial and epididymis epithelia.

first: Ann

last: Harris

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

overall_design: Refer to individual Series


title: Histone variant macroH2A1 is a stronger regulator of hippocampal transcription and memory than macroH2A2 in mice

city: Mississauga

first: Iva

middle: Toronto

last: Zovkic

state: Ontario

address: 3359 Mississauga Road North, CCT Building Room 4071

country: Canada

institute: University of Toronto Mississauga

summary: Our work and that of others (Zovkic et al 2014 Nature, Maze et al 2015 Neuron) recently established histone variants as novel regulators of memory, whereby enrichment of H2A.Z, a variant of histone H2A, impairs memory formation. However, H2A has several structurally and functionally distinct members whose function in memory has never been studied. macroH2A (mH2A) is of special interest because it has been implicated as a risk factor for neurodegenerative diseases, particularly Huntington’s (Hu et al 2011 PNAS), but its functional role in the brain is not known. Here, we conducted ChIP sequencing against macroH2A1 (mH2A1) and macroH2A2 (mH2A2) in the mouse hippocampus and showed that both proteins are enriched on transcriptionally silent genes, suggesting that mH2A has a repressive effect on transcription in the brain. However, only mH2A1 binding was dynamically reduced during learning, such that mH2A1 removal was associated with increased gene expression in response to fear conditioning. Additionally, viral vector mediated depletion of mH2A1 protein resulted in extensive dysregulation of gene transcription, whereas mH2A2 depletion had minimal transcriptional consequences. To determine if these differential downstream transcriptomes are functionally relevant, we showed that mH2A1, but not mH2A2 depletion resulted in impaired fear memory. These results suggest that mH2A1 is required for memory and that its dynamic removal during learning promotes training-induced gene expression. In concert with our prior evidence for a suppressive effect of H2A.Z on memory, these data suggest that unique H2A variants have distinct effects on memory formation and as such, implicate altered nucleosome composition as a novel regulator of neuroplasticity.

overall_design:
3 Sequencing data sets: 1) ChIP sequencing against macroH2A1 or macroH2A2, along with inputs with and without fear conditioning; 2) RNA seq in control mice and 1h after contextual fear conditioning; 3) RNA seq in mice with macroH2A1 or macroH2A2 knockdown in area CA1, along with mice receiving scramble control virus;
Additional Sequencing data sets: 1) ChIP sequencing against macroH2A1 and macroH2A2, along with inputs with and without fear conditioning at 1 hour time-point; 2) ChIP sequencing against macroH2A1, along with inputs with and without fear conditioning at 6 hour time-point;
NEW data set: RNA seq in mice with macroH2A1 or macroH2A1 knockdown in CA1, half untrained and half fear conditioned. Brains were collected 1h after training.


title: Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [RNA-Seq II]

first: Ana

last: Morao

overall_design: RNA-seq  in  controls and topoisomerases I and II depleted conditions . Depletion was performed by Auxin inducible degradation. All experiments were performed in two biological replicates. L2/L3 larvae were used for most experiments.

middle: K

first: Jun

last: Kim

first: Daniel

last: Obaji

first: Siyu

last: Sun

first: Sevinc

last: Ercan


title: RNA-seq analysis of HCC and hepatocytes

first: zhiwu

last: jiang

address: 190 Kai Yuan Avenue, Science Park

institute: GIBH

summary: mRNA from primary PHH or iHCC was prepared according to the TruSeqTM RNA Sample Preparation Guide, and sequencing was performed on BGISEQ-500 (BGI, Wuhan, China).

first: Zhiwu

last: Jiang

first: Peng

last: Li


title: RNAseq comparison between D1.1 and B2.7 Jurkat Cells

city: Belle Mead

first: Bitha

last: Narayanan

state: New Jersey

address: 241 Berkley Ave

institute: Rutgers

summary: RNA was extracted from D1.1 and B2.7 cells transfected with shCtrl or shPTB cDNA

overall_design: D1.1 vs B2.7 Jurkat cells

first: Diego

last: De Maio

first: Usha

last: Ganapathy

first: Lori

last: Covey


title: Characterization of two lung alveolar macrophages in bronchoalveolar lavage fluid (BALF) cells in non-fumer healthy, fumer and COPD patients

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

institute: PhyMedExp INSERM U1046

summary:
Rationale: Alveolar macrophages (AM) are functionally important innate cells involved in lung homeostasis and immunity. However, it remains unclear whether ontogenically and functionally distinct subpopulations of AM can be found in healthy human airways, and to what extent conditions like smoking or chronic obstructive pulmonary disease (COPD) trigger changes in the AM compartment.
Objective: To explore the phenotypical, ontological, transcriptional and functional diversity of human AM isolated from healthy non-smokers, healthy smokers and COPD patients.
Methods: We analyzed bronchoalveolar lavage fluid (BALF) cells by flow cytometry, bulk and single-cell(sc) RNA-sequencing (RNA-seq).
Main Results: We found that BALF CD206 + macrophage subpopulations could be distinguished based on their level of auto-fluorescence. CD206 + autofluorescent high (AF hi ) AM were identified as classical self-proliferative AM, while autofluorescent low (AF lo ) AM originated from monocytes and were expressing both monocyte- and classical AM-related genes. Of note, monocyte-derived AF lo AM were equally represented in each category of subjects and exhibited a functionally distinct immunoregulatory profile, including the ability to secrete the immunosuppressive cytokine interleukin-10 (IL-10). Finally, we provide evidence that the monocyte-associated marker CCR2 can be used by flow cytometry to distinguish AM according to their origin.

overall_design: Analysis of CD14+ blood monocytes, autofluorescence hi (alveolar macrophages) and autofluorescence lo (regulatory macrophages) CD45+ CD206+ macrophages in bronchoalveolar lavage fluids (BALF) from 3 groups of patients: healthy non-smokers, healthy smokers and COPD patients.

last: Bai

first: Maude

last: Liégeois

first: Laurence

last: Fievez

first: Dimitri

last: Pirottin

first: Thomas

last: Marichal

first: Fabrice

last: Bureau


title: Deconstruction of the immune microenvironment identifies tumor-, immune- and stroma-specific subtypes of intrahepatic cholangiocarcinoma

first: Daniela

last: Sia

address: 1425 Madison Avenue

department: Liver Diseases

institute: Icahn school of Medicine at Mount Sinai

summary:
We have profiled by RNA-sequencing healthy livers and 4 distinct murine intrahepatic cholangiocarcinoma (iCCA) models to compare their molecular profile to the identified human STIM clusters of iCCA.
Results: Comparative analysis indicated high molecular similarity between the KRAS/p19 model and the human Inflammatory stroma cluster while the other models resembled the Hepatic stem-like cluster.

overall_design: Livers from healthy mice, and from mice injected with 4 distinct plasmids combinations (KRAS/p19, NICD1/AKT1, YAP1/AKT1 and FBXW7/AKT1) were collected in triplicates and processed for RNA extraction and subsequent RNA-sequencing. Molecular class prediction, single sample enrichment analysis and Deseq analysis were performed to compare the murine tumors to the human disease and to the 5 proposed human clusters.

first: Miguel

middle: M

last: Torres


title: Characterisation of resident alveolar macrophages in bronchoalveolar lavage fluid (BALF) in non-fumer healthy, fumer and COPD patients


title: Single-cell RNAseq analysis (10X Genomics Chromium) of residual bronchoalveolar lavage fluids in healthy, fumer and COPD patients

overall_design: Analysis of bronchoalveolar lavage fluid (BALF) cells from 3 groups of patients: healthy non-smokers, healthy smokers and COPD patients.