title: Genomic variations combined with epigenetic modifications rewire open chromatin in rice

status: Public on Sep 02 2023

city: Nanjing

first: Mengqi

last: Li

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: NanJing Argricultural University

summary: Cis-regulatory elements (CREs) fine-tune gene transcription during normal growth and development and environmental stress responses in eukaryotes. CREs with sequence variations play vital roles in driving plant or crop domestication. However, how global genomic sequence and structural variations causative for multi-level changes between Indica and Japonica are still less studied. To answer this question, we here conducted MH-seq (MNase hypersensitive sequencing) for global profiling of open chromatin (MNase hypersensitive sites, MHSs) between two typical Oryza sativa cultivars, Nipponbare (NIP) and 93-11. We found that differential MHSs exhibited some distinct intrinsic genomic sequence features between NIP and 93-11. Moreover, MHSs can coordinate with DNA sequence or genomic structural variations in the regulation of differential gene expression between NIP and 93-11. Importantly, by applying MHS-GWAS association analyses, we found that CREs with sequence variations may act as the key determinant for controlling expression of genes responsible for some biological relevance in NIP and 93-11. Therefore, this study provides new insights into how sequence and genomic structural variations function in differential biological relevance and key crop agronomic traits between Indica and Japonica. It also provides some promising genomic editing targets for molecular breeding to improve favorable agronomic trait.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: Differential MHSs can regulate differential expression of overlapping genes, thereby affecting some biological processes in NIP and 93-11.

first: Yilong

last: Feng

first: Wenli

last: Zhang


title: Integrative analysis of differential circular RNA and long noncoding RNA profiles and associated competing endogenous RNA networks in esophageal squamous cell carcinoma

city: Shanghai

first: Ronhua

last: Liu

address: No.138, Yi Xue Yuan Rd.

country: China

institute: Department of Immunology, Fudan University

type: Expression profiling by high throughput sequencing

summary: We constructed a competing endogenous RNA (ceRNA) network of ESCC based on the bovementioned pathways. Our findings provide important insight into the role of lncRNAs and circRNAs in ESCC; the differentially expressed lncRNAs and circRNAs may represent potential targets for  ESCC diagnosis and therapy.

overall_design: We performed a comprehensive analysis of the expression of RNAs, lncRNAs, and circRNAs by RNA-seq in esophageal squamous cell carcinoma

first: Jiang-Feng

last: Shen


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

status: Public on Sep 01 2023

city: Wuhan

first: Chaoyang

last: Wang

address: Jiefang Avenue #1277

institute: Wuhan Union Hospital

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

overall_design: To investigate the effect of ginkgetin on liver fibrosis and the underlying mechanism, we performed bulk RNA Sequencing on the liver tissues from fibrotic rats treated with vehicle (control group) or ginkgetin (10mg/kg/day) (ginkgetin group).


title: A PRECISION MEDICINE APPROACH TO INTERROGATE GENE EXPRESSION PATTERNS IN AFRICAN MEN PRESENTING WITH EARLY STAGE PROSTATE CANCER.

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

country: USA

institute: Medical University of South Carolina

summary: In this study, we used a precision medicine approach to examine molecular profiles in AA and EA men: men undergoing prostate biopsy

overall_design: RNA-seq on 67 Samples

first: Stephen

middle: J

last: Savage

first: E

middle: S

last: Hazard

first: Willian

middle: A

last: da Silveira

first: Robert

middle: C

last: Wilson

first: Susan

last: Caulder

first: Linda

last: Ambrose

first: Lewis

last: Frey

first: Bethany

last: Wolf

first: Sebastiano

last: Gattoni-Celli

first: Chanita

middle: H

last: Halbert


title: Analyzing Flow Cytometry or Targeted Gene Expression Data Influences Clinical Discoveries — Profiling Blood Samples of Pancreatic Ductal Adenocarcinoma Patients

city: Rotterdam

first: Willem

last: de Koning

state: Zuid-Holland

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

summary: We investigated the immunological changes in the blood of pancreatic ductal adenocarcinoma patients treated with a single cycle of FOLFIRINOX chemotherapy combined with lipegfilgrastim. We compared the use of flow cytometry and targeted gene expression analysis to study these immunological changes in blood samples. Our findings showed that FFX-Lipeg treatment increased the number of neutrophils and monocytes. Interestingly, flow cytometry analysis revealed an increase in B and T cells after treatment, while targeted gene expression analysis indicated a decrease in the expression of B and T cell-specific genes. This suggests that different measurement techniques can influence observed immunological changes. Therefore, the careful selection of an appropriate technique is essential when studying treatment effects in PDAC patients.

overall_design: RNA was extracted from Tempus tubes (44 patients, before FFX-Lipeg n=44, after FFX-Lipeg n=44)

first: Casper

middle: W

last: van Eijck

first: Fleur

last: van der Sijde

first: Gaby

last: Strijk

first: Astrid

last: Oostvogels

first: Reno

last: Debets

first: Dana

last: Mustafa


title: Transcriptome analyses of Filifactor alocis ATCC35896 and Porphyromonas gingivalis W83 in mono-culture as compared to co-culture under hydrogen peroxide stress conditions

city: Loma Linda

first: Yuetan

last: Dou

state: CA

address: 11021 Campus Street AH114

department: Microbiology and Molecular Genetics

institute: Loma Linda University

summary: Oal anaerobic bacteria have to face constant oxidative stress in order to survive in the inflammatory environment of the periodontal pocket. In this study, we analyzed the transcriptome profiles of P. gingivalis and Filifactor in monoculture as compared to P. gingivalis+F.alocis coculture under H2O2 stress condtions, to analyze the genes responsible for enhanced survival of P. gingivalis in presence of F. alocis under oxidative-stress conditions.

sample_organism:
Porphyromonas gingivalis W83
Filifactor alocis ATCC 35896

overall_design: RNA-seq was used to study the expression profiles of P. gingivalis as compared to P. gingivalis+F. alocis under stress conditions, and expression profile of F. alocis as compared to P. gingivalis+F. alocis under stress conditions respectively. Other experiments also designed and performed.

first: Arunima

last: Mishra

first: Hansel

middle: M

last: Fletcher


title: Synthetic Introns Identify GPATCH8 as Required for Mis-splicing by SF3B1 Mutations [TRIBE-seq]

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

summary: Mutations in the RNA splicing factor SF3B1 are common across hematologic and solid cancers and result in widespread alterations in splicing but therapeutic means to correct this mis-splicing do not exist. Here we utilize synthetic introns uniquely responsive to mutant SF3B1 to identify trans factors required for aberrant mutant SF3B1 splicing activity. This revealed the G-patch domain containing protein GPATCH8 as required for mutant SF3B1-induced splicing alterations and impaired hematopoiesis. GPATCH8 is involved in quality control of branchpoint selection, interacts with the RNA helicase DHX15, and functionally opposes SUGP1, a G-patch protein recently implicated in SF3B1 mutant diseases. Silencing of GPATCH8 corrected one-third of mutant SF3B1 splicing defects and was sufficient to improve hematopoiesis in SF3B1 mutant mouse and human cells. These data identify GPATCH8 as a novel splicing factor required for mis-splicing by mutant SF3B1 and the therapeutic impact of correcting aberrant splicing in SF3B1 mutant cancers.

overall_design: To determine the RNA binding sites of GPATCH8 and SUGP1 transcriptome-wide we performed TRIBE-seq of HEK293T cells with expression of either GPATCH8-ADAR or ADAR-SUGP1 fusion proteins, where ADAR is the catalytic domain of the hyperactive Drosophila adenosine deaminase. After background subtraction of endogenous RNA editing events and editing events created by a control ADAR fusion protein (MCP-ADAR or ADAR-MCP) we identified RNA editing events that were conserved between both replicates of GPATCH8-ADAR or ADAR-SUGP

first: Salima

last: Benbarche

first: Jose

last: Maria Bello Pineda

first: Laura

last: Baquero Galvis

first: Bo

last: Liu

first: Jeetayu

last: Biswas

first: Eric

last: Wang

first: Kadeen

last: Lyttle

first: Ariana

last: Dahi

first: Alexander

last: Lewis

first: Martina

last: Sarchi

first: Sanjoy

last: Mehta

first: Ralph

last: Garippa

first: Juliana

last: Ortiz-Pacheco

first: Zhuoning

last: Li

first: Mara

last: Monetti

first: Robert

last: Stanley

first: Sergei

last: Doulatov

middle: K

last: Bradley

first: Omar

last: Abdel-Wahab


title: HSF-1 promotes longevity through ubiquilin-1 dependent mitochondrial remodelling

city: London

first: John

last: Labbadia

address: Darwin Building, Gower Street

department: GEE

country: United Kingdom

institute: UCL

summary: In this experiment, we aimed to determine the gene expression changes associated with loss of UBQL-1 in wildtype and in worms overexpressing HSF-1 (hsf-1 OE).

overall_design: C. elegans worms (N2 laboratory wild-type strain, ubql-1(tm1574), hsf-1 OE, and hsf-1 OE;ubql-1(tm1574)) were synchornised by egg-laying, grown at 20C and collected at Day1 of adulthood as young adults. Worms were collected and snap frozen before RNA was extracted using an RNeasy kit (Qiagen).

first: Annmary

middle: P

last: Erinjeri


title: RNA-seq analysis of CAMA1 breast cancer cells after treatment with estradiol or antiestrogens in estradiol-depleted media

city: SAN FRANCISCO

first: Alison

last: Parisian

state: California

address: 780 Brannan St

institute: Olema Pharmaceuticals

summary: The estrogen receptor (ER) is a well-established target for the treatment of breast cancer, with the majority of patients presenting as ER-positive (ER+). Endocrine therapy is a mainstay of breast cancer treatment but the development of resistance mutations in response to aromatase inhibitors, poor pharmacokinetic properties of fulvestrant, agonist activity of tamoxifen, and limited benefit for elacestrant leave unmet needs for patients with or without resistance mutations in ESR1, the gene that encodes the ER protein. Here we describe OP-1250, a novel, orally bioavailable complete ER antagonist and selective ER degrader. OP-1250, like fulvestrant, has no agonist activity on the ER and completely blocks estrogen-induced transcriptional activity. In addition, OP-1250 demonstrates favorable biochemical binding affinity, ER degradation, and antiproliferative activity in ER+ breast cancer models that is comparable or superior to other agents of interest. OP-1250 has superior pharmacokinetic properties relative to fulvestrant, including oral bioavailability and brain penetrance, as well as superior performance in wild-type and ESR1-mutant breast cancer xenograft studies. OP-1250 combines well with cyclin-dependent kinase 4 and 6 inhibitors in xenograft studies of ER+ breast cancer models and effectively shrinks intracranially implanted tumors, resulting in prolonged animal survival. With demonstrated preclinical efficacy exceeding fulvestrant in wild-type models, elacestrant in ESR1-mutant models, and tamoxifen in intracranial xenografts, OP-1250 has the potential to benefit patients with ER+ breast cancer.

overall_design: CAMA1 cells were plated in estradiol-depleted charcoal dextran stripped serum-containing media and dosed for 24 hours with 316 nM compound or 100 pM 17-beta estradiol.

middle: D

first: Susanna

last: Barratt

first: Leslie

last: Hodges-Gallagher

first: Fabian

middle: E

last: Ortega

first: Guadalupe

last: Peña

first: Judevin

last: Sapugay

first: Brandon

last: Robello

first: Richard

last: Sun

first: David

last: Kulp

first: Gopinath

last: Palanisamy

last: Myles

first: Peter

last: Kushner

first: Cyrus

middle: L

last: Harmon


title: Gene expression profile at  single cell level of adipocyte tissue macrophages from Apoe-null eWAT

city: Wauwatosa

first: Yiliang

last: Chen

address: 8727 W Watertown Plank

institute: Versiti

summary: Macrophages (ATM) are the predominant immune cells in WAT, but their heterogeneity and phenotypes are poorly defined during atherogenesis. The scavenger receptor CD36 mediates ATM crosstalk with other cells, driving chronic inflammation. Here, we conducted single-cell RNA sequencing on major WAT ATM subpopulations using a diet-induced atherosclerosis mouse model (Apoe-null).

overall_design: Apoe-null or Apoe/Cd36 double-null mice on chow diet or high fat diet for 10 weeks were sacrificed, eWAT were isolated and CD45+ cells were selected for scRNA-seq analysis using 10X Genomics platforms

first: Vaya

first: Jackie

last: Chang

first: Jue

last: Zhangg


title: Gene expression from HCT116 cells after LS 1 2 treatment

city: Beijing

first: Haizhao

last: Yi

address: No. 52 Fucheng Rd., Haidian District

institute: Peking University Cancer Hospital & Institute

summary: To determine the signaling pathway involved in LS-1-2-mediated tumor inhibition, we performed genome-wide gene expression by comparing HCT116 cells with and without LS-1-2treatment.

overall_design: Differentially expressed genes total 2324 were identified between control vs 0.1 μM LS-1-2 6h, control vs 0.1 μM LS-1-2 12h, and control vs 0.1 μM LS-1-2 24h.

first: Dengbo

last: Ji


title: Disfunction of arachidonic acid metabolism in vascular smooth muscle cells contributes to restenosis

city: 长沙市

first: 辉

last: 吴

state: 湖南省

address: 中南大学湘雅医学院新校区

department: 检验系

institute: 中南大学湘雅三医院

summary: We applied the transcriptome profiling (RNA-seq) for high-throughput profiling of genes changes in the phenotypic switch of VSMCs. Rat primary VSMCs were divided into 3 groups, control, PDGF-BB, PDGF-BB+PTUPB,and mRNA sequence were performed. We found that Cell cycle related genes and cellular senescence related genes were significantly upregulated by PDGF-BB and significantly reversed by PTUPB. Subsequently, we deleted PTTG1 as a key gene for PTUPB to reverse phenotypic switching in VSMCs. Our study provided the transcription changes by RNA-seq in VSMC phenotypic switch, and found that PTUPB played a crucial role in correcting the dysregulation of sEH/COX-2 derived ARA metabolism in VSMC phenotypic switch

overall_design: In order to understand how PTUPB reverses the phenotypic transition of PDGF-BB-induced VSMCs, we divided rat primary VSMCs into control, PDGF-BB (20 ng/mL) stimulation for 24 h, and PTUPB  pretreatment (0.5 μM,2h) followed by PDGF-BB stimulation for 24 h. We performed NGS RNAseq on these groups.Each group included three VSMCs.

first: Hui

last: Wu

first: Ren

last: Guo


title: Analysis of the effect of prenatal alcohol exposure on the Placenta—Cortex transcriptomic signature

city: Rouen

first: Anthony

last: Falluel-Morel

address: 22 Boulevard Gambetta

country: France

institute: Rouen University

summary: Although alcohol consumption during pregnancy is a major cause of behavioral and learning disabilities, most FASD infants are late- or even misdiagnosed due to clinician’s difficulties achieving early detection of alcohol-induced neurodevelopmental impairments. Neuroplacentology has emerged as a new field of research focusing on the role of the placenta in fetal brain development. Several studies have reported that prenatal alcohol exposure (PAE) dysregulates a functional placenta–cortex axis, which is involved in the control of angiogenesis and leads to neurovascular-related defects.   However, these studies were focused on PlGF, a pro-angiogenic factor. The aim of the present study is to provide the first transcriptomic “placenta–cortex” signature of the effects of PAE on fetal angiogenesis. Whole mouse genome microarrays of paired placentas and cortices were performed to establish the transcriptomic inter-organ “placenta–cortex” signature in control and PAE groups at gestational day 20. Genespring   comparison of the control and PAE signatures revealed that 895 and 1501 genes were only detected in one of two placenta–cortex expression profiles, respectively. Gene ontology analysis indicated that 107 of these genes were associated with vascular development, and String protein–protein interaction analysis showed that they were associated with three functional clusters. PANTHER functional classification analysis indicated that “intercellular communication” was a significantly enriched biological process, and 27 genes were encoded for neuroactive ligand/receptors interactors.   Protein validation experiments involving Western blot for one ligand–receptor couple (Agt/AGTR1/2) confirmed the transcriptomic data, and Pearson statistical analysis of paired placentas and fetal cortices revealed a negative correlation between placental Atg and cortical AGTR1, which was significantly impacted by PAE. In humans, a comparison of a 38WG control placenta with a 36WG alcohol-exposed placenta revealed low Agt immunolabeling in the syncytiotrophoblast layer of the alcohol case. In conclusion, this study establishes the first transcriptomic placenta–cortex signature of a developing mouse. The data show that PAE markedly unbalances this inter-organ signature; in particular, several ligands and/or receptors involved in the control of angiogenesis. These data support that PAE modifies the existing communication between the two organs and opens new research avenues regarding the impact of placental dysfunction on the neurovascular development of fetuses. Such a signature would present a clinical value for early diagnosis of brain defects in FASD.

overall_design: From gestational day (GD)15 to GD20, twelve pregnant mice received a daily subcutaneous injection of sodium chloride (NaCl 9‰) or alcohol (3g/kg, Fisher Scientific) diluted in NaCl (50%, v/v). At GD20, placentas and paired fetal cortices were collected, immediately frozen in liquid nitrogen and stored at −80 °C until use.

first: Camille

last: Sautreuil

first: Maryline

last: Lecointre

first: Céline

last: Derambure

first: Carole

last: Brasse-Lagnel

first: Philippe

last: Leroux

first: Annie

last: Laquerrière

first: Gaël

last: Nicolas

first: Sophie

last: Gil

first: Daniel

last: Savage

first: Stéphane

last: Marret

first: Florent

last: Marguet

first: Bruno

last: Gonzalez


title: Transcriptional changes in human haematopoietic stem and progenitor cells（HSPCs） from umbilical cord blood in response to the corticotropin releasing hormone（CRH）

city: Hefei

first: mingming

last: wu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

summary: Corticotrophin-releasing hormone (CRH) is a key regulator involved in the stress pathway, yet its functions in the direct regulation of human stem/ progenitor cells (HSPCs) are poorly understood. Here we report that human CD34+ HSPCs constitutively expressed CRH receptor1. Treatment with CRH increased the motility and deformability of human HSPCs. Intravital two-photon imaging of bone tissues showed that CRH stimulated migration and bone marrow homing of HSPCs in vivo. Pretreatment of human HSPCs promoted homing and long-term engraftment when transplanted into primary and secondary NSG mice. Mechanistically, CRH modulates cell mechanics by extracellular matrix (ECM) remodeling, correlating with increased expression of the ECM protein THBS2 and activities of the Rho family small GTPases. Collectively, these findings show that CRH, a neurotransmitter, regulates biomechanics, which is correlated with its new functions in HSPSs migration, homing and engraftment, designating CRH as a promising drug candidate to facilitate clinical HSC transplantation.

overall_design: To explore the specific mechanism of CRH  regulation of hematopoietic stem cells, we isolated and purified HSPCs derived from umbilical cord blood and treated them with CRH for 16 hours. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different donors .Comparative gene expression profling analysis of RNA-seq data for freshly isolated HSPCs  treat with or without CRH.

first: Mingming

first: Haoxiang

last: Yang

first: Tingting

last: Liang

first: Yan

last: Wang

first: Fang

last: Ni


title: Single-cell analysis of Rohon-Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva]

city: Portland

first: Alex

last: Nechiporuk

state: OR

address: 3181 SW Sam Jackson Park Road

institute: Oregon Health and Science Univ

summary: Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish, this function is mediated by Rohon-Beard somatosensory neurons (RBs). RBs are optically accessible and amenable to experimental manipulation, making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however, the number and molecular make up of these potential RB subtypes have not been well defined. Using a single-cell RNA sequencing (scRNA-seq) approach, we demonstrate that larval RBs in zebrafish fall into three, largely non-overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross-species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A-fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities, including mechanical stimulation and chemical irritants. We leveraged our scRNA-seq data to determine that the fibroblast growth factor (Fgf) pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover, this phenotype can be phenocopied by treatment with an FDA-approved Fgf inhibitor dovitinib, which is used in clinic and causes peripheral neuropathy. Importantly, dovitinib-mediated axon loss can be suppressed by loss of Sarm1, a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug.

overall_design: About 150 7-day old larva were euthanized in 0.02% tricaine, and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase (Life Sciences) in a buffer containing 134 mM NaCl, 2.9 mM KCl, 1.2 mM MgCl2, 2.1 mM CaCl2, and 10 mM Na-HEPES (pH 7.8) at 28 °C for 2 hr, with intermittent trituration using a p200 pipette aid at 0, 0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue, the final triturations were done using fire-polished Pasteur pipettes with decreased opening sizes (300, 200, 100 μm respectively). Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution (in 1xPBS containing 1 mM EDTA) at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution (L15 with 1% fetal bovine serum). The tissue was collected by spinning at 400 g for 3 min at 4°C, washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire-polished Pasteur pipettes with 80-100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count, Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing

first: Adam

last: Tuttle

first: Lauren

last: Miller

first: Lindsey

last: Royer

first: Hua

last: Wen

first: Jimmy

last: Kelly

first: Nicholas

last: Calistri

first: Laura

last: Heiser

middle: V


title: RNA-seq analysis of MCF7 xenografts after treatment with OP-1250 and/or CDK4/6 inhibitors palbociclib or ribociclib

first: Alison

last: Parisian

overall_design: MCF7 cells were implanted into immuno-deficient mice supplemented with estradiol and mice were treated by oral gavage with OP-1250, palbociclib, ribociclib, OP-1250+palbociclib or OP-1250+ribociclib for 30 days prior to study termination and sample collection.

first: Susanna

last: Barratt

first: Leslie

last: Hodges-Gallagher

first: Fabian

last: Ortega

first: Guadalupe

last: Peña

first: Judevin

last: Sapugay

first: Brandon

last: Robello

first: Richard

last: Sun

first: David

last: Kulp

first: Gopinath

last: Palanisamy

last: Myles

first: Peter

last: Kushner

first: Cyrus

last: Harmon


title: Transcriptomic profiling of differentially expressed mRNA, lncRNA, miRNA and circRNA in liver tissue of acetaminophen induced liver injury mice [miRNA_APAP]

city: Hangzhou

first: CHAO

last: CHEN

state: Zhejiang

address: The First Affiliated Hospital, College of Medicine, Zhejiang University, NO.79 Qingchun Road, Hangzhou, Zhejiang 310003, China

institute: zhejiang university

summary: Acute liver failure is a serious clinical manifestation resulting from sudden liver injury, which can be triggered by various factors. One of the most frequent causes of acute liver failure is excessive ingestion of acetaminophen (APAP), which is known to damage hepatocytes directly by reducing glutathione levels in cells, ultimately leading to hepatocyte death.PGE2 can play a dual role in inflammation, either promoting or inhibiting the inflammatory response, depending on the cell type, local concentration, receptor type, and tissue microenvironment. Early studies have shown that PGE2 significantly alleviated acute liver failure induced by galactosamine/lipopolysaccharide, APAP, and carbon tetrachloride. However, the precise mechanism by which PGE2 alleviates APAP-induced acute liver failure remains unclear. The aim of this study is to investigate the mechanisms underlying the protective effects of PGE2 against APAP-induced hepatocyte injury.

overall_design: RNA-seq was conducted on total RNA isolated from livers of AILI mice treated with 500 mg/kg APAP or dmPGE2 300μg/kg for 6 h; n = 3 per group.

first: Chao

last: Chen

first: Xinyu

last: Gu

first: Qingfei

last: Chu

first: Jun

last: Guan

first: Haihong

last: Zhu


title: Transcriptomic profiling of differentially expressed mRNA, lncRNA, miRNA and circRNA in liver tissue of acetaminophen induced liver injury mice [mRNA_APAP]


title: Transcriptomic profiling of differentially expressed mRNA in liver tissue of Dgaln/LPS induced liver injury mice [mRNA_Dgaln]

summary: Acute liver failure is a serious clinical manifestation resulting from sudden liver injury, which can be triggered by various factors. Early studies have shown that PGE2 significantly alleviated acute liver failure induced by galactosamine/lipopolysaccharide(Dgaln/lps), APAP, and carbon tetrachloride. However, the precise mechanism by which PGE2 alleviates Dgaln/lps-induced acute liver failure remains unclear. The aim of this study is to investigate the mechanisms underlying the protective effects of PGE2 against Dgaln/lps-induced hepatocyte injury.

overall_design: RNA-seq was conducted on total RNA isolated from livers of AILI mice treated with D-GalN 500mg/kg, LPS 5μg/kg or dmPGE2 300μg/kg for 6 h; n = 3 per group except dmPGE2+Dgaln/LPS group. The number of samples in dmPGE2+Dgaln/LPS group is 4.


title: Active learning of enhancer and silencer regulatory grammar in photoreceptors

city: Saint Louis

first: Michael

middle: Aaron

last: White

state: MO

address: 660 South Euclid Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

summary: We performed iterative rounds of massively parallel reporter assay experiments in ex vivo retinas to generate training data for machine learning models of the photoreceptor cis-regulatory grammar.

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design: A series of libraries of barcoded reporter gene plasmids were transfected into mouse retinas in triplicate. We measured barcoded reporter gene activity by RNA-seq, normalized by the DNA-seq reads of the input plasmid pool.

first: Ryan

middle: Z

last: Friedman

first: Barak

last: Cohen


title: Transcriptomic profiling of differentially expressed mRNA, lncRNA, miRNA and circRNA in liver tissue of acetaminophen induced liver injury mice [circRNA_APAP]


title: Targeting conditioned media dependencies and FLT-3 in chronic lymphocytic leukemia

city: Boston

first: Salma

last: Parvin

state: MA

address: 440 Brookline ave

institute: Dana Farber Cancer institute

summary: The importance of the stromal microenvironment in chronic lymphocytic leukemia (CLL) pathogenesis and drug resistance is well established. Despite recent advances in CLL therapy, identifying novel ways to disrupt interactions between CLL and its microenvironment may identify new combination partners for the drugs currently in use. To understand the role of microenvironmental factors on primary CLL cells, we took advantage of an observation that conditioned media (CM) collected from stroma was protective of CLL cells from spontaneous cell death ex vivo. The cytokine in the CM-dependent cells that most supports CLL survival in short term ex-vivo culture was CCL2. Pre-treatment of CLL cells with anti-CCL2 antibody enhanced venetoclax-mediated killing.  Surprisingly, we found a group of CLL samples (9 of 23 cases) that are less likely to undergo cell death in the absence of CM support. Functional studies revealed that CM-independent (CMI) CLL cells are less sensitive to apoptosis than conventional stroma-dependent CLL. Additionally, a majority of the CMI CLL samples (80%) harbored unmutated IGHV. Bulk-RNA Seq analysis revealed upregulation of the focal adhesion and Ras signaling pathways in this group, along with expression of FLT3 and CD135 expression. Treatment with FLT3 inhibitors caused a significant reduction in cell viability among CMI samples.  In summary, we were able to discriminate and target two biologically distinct subgroups of CLL based on CM dependence with distinct microenvironmental vulnerabilities.

overall_design: To investigate the difference between CMD verses CMI CLL samples, we then performed gene expression profiling analysis using data obtained from Bulk RNA-seq of 5 CMD samples (CMD1, CMD2, CMD3, CMD4,CMD5) and 5 CMI samples (CMI1, CMI2, CMI3, CMI4,CMI5). Each sample is viably frozen CLL PBMC

first: Shanye

last: Yin


title: Somatic Cell Contamination as an Inhibitor of Proper Sperm Methylation Analysis

city: Provo

first: Timothy

middle: G

last: Jenkins

state: UT

address: 4005 Life Sciences Building

department: Cell Biology and Physiology

institute: Brigham Young University

summary: The purpose of this data set was to identify the affects of somatic cell introduction of the methylation results of the sperm samples. This data was then used to help build a computational tool to properly identify somatic cell contamination within a sperm sample.

overall_design: 4 samples were taken and 12 biological replicates were taken of each for a total of 48 samples. Samples were then spiked with various amounts of somatic cells, and either processed immediately or run through a purification protocol to test for accuracy.

first: Tim

first: Chad

last: Pollard

first: Kelaney

last: Stalker

first: Ki

last: Aston


title: RNA-Seq profiling of circular RNAs in colorectal cancer and circST7L as a potential biomarker

city: Suqian

first: Xiaoming

last: Ma

address: No.138 Huanghe Road, Suqian

institute: The affiliated hospital of xuzhou medical university

type: Non-coding RNA profiling by high throughput sequencing

summary: Aberrant expression of circular RNAs (circRNAs) has been reported in a variety of cancers. CircRNAs may serve as candidate biomarkers and have implications for cancer diagnosis and treatment. RNA-sequencing (RNA-seq) was applied to detect circRNA expression in five CRC and paired normal tissues. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed to measure circRNA expression, and the receiver operating characteristic curve was used to assess the diagnostic value of circRNA as a biomarker in 50 patients. A total of 1602 circRNAs were differentially expressed, including 743 upregulated and 859 downregulated circRNAs in CRC. CircST7L (hsa_circ_0110464) has a high diagnostic value for CRC. The expression of circST7L was closely associated with tumor size (P=0.024), grade (P=0.017), depth of invasion (P=0.034) and lymph node metastasis (P=0.001). In addition, prediction of circRNA-miRNA interactions identified miR-6821-5p, miR-1908-3p, and miR-6748-5p as pivotal targets of differentially expressed circRNAs. Finally, we predicted 7 miRNAs that may bind to circST7L and 13 target genes for these miRNAs. This study demonstrated that circRNAs were differentially expressed between CRC and normal tissues, and suggested that circST7L might be a promising diagnostic biomarker for CRC.

overall_design: Comparative circular RNA expression profiling analysis of RNA-seq data for colorectal cancer tissues and adjacent normal tissues in human

first: Haixing

last: Pan

first: Hailong

last: Huang

first: Mingzuo

last: Zhao


title: Genetic and chemical targeting of the ATPase complex TIP48 and 49 impairs acute myeloid leukemia

city: Kyoto

first: Ayuna

last: Hattori

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo

country: Japan

institute: Kyoto University

summary: The chromatin-associated AAA+ ATPases Tip48 and Tip49 are the core components of various complexes implicated in diverse nuclear events such as DNA repair and gene regulation. Although they are frequently overexpressed in many human cancers, their functional significance remains unclear. Here, we show that loss of Tip49 triggered p53-dependent apoptosis and inhibited leukemia development in vivo. To examine the impact of chemical inhibition of this complex on leukemia, we have developed the novel compound DS-4950, which interferes with the ATPase activity of the Tip48/49. Administration of DS-4950 was well-tolerated in healthy mice, and the drug effectively reduced tumor burden and improved survival. We also provide evidence that the dependency on Tip48/49 is widely conserved in non-hematologic malignancies with wild type p53. These results demonstrated that the Tip48/49 ATPases are functionally necessary and therapeutically targetable for the treatment of human cancers.

overall_design: To test Tip48/49 function in leukemia, we established Tip48/49 cKO mice and their chemical inhibitor.


title: Analysis of light induced secondary seed dormancy in Aethionema arabicum, Cyprus accession

city: Wien

first: Zsuzsanna

last: Mérai

address: 1030 Wien Dr. Bohr-Gasse 3.

country: Austria

institute: Gregor Mendel Institute

summary: Light inhibits the seed germination in the Cypriot accession (CYP) of Aethionema arabicum. Extended light illumination also induces a secondary seed dormancy that inhibits the germination even if the seeds were transferred back to darkness. This analysis aims to compare the seed transcriptome before or after the dormancy was established by light illumination (100 µmol/m2s; white light). One day light treatment (1dL) inhibits the germination but the seeds are not yet dormant. Seven day (7dL) or 14-day (14dL) long light treatment induces dormancy, and the seeds stay dormant after 7 dal-light plus 7 day-dark (7dL7dD) treatment.  To understand the dormancy establishment, transcriptome was compared between non-dormant (1dL) and dormant (7dL, 14dL, 7dL7dD) seed samples.

overall_design: Imbibed seeds of CYP accession were exposed to white light (100 µmol m-2s-1) for 23 hours (1dL), 7 days, 14 days or 7 days followed by a 7-day dark period. mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. In total, 12 samples were analyzed (4 conditions x 3 repetitions)

first: Kai

last: Graeber

first: Ortrun

last: Scheid

first: Gerhard

last: Leubner-Metzger

first: Katarina

last: Lalatovic


title: Transcriptomic profiling between HSC-3 and HSC-3-S5 cells

city: Toyoake

first: Kouhei

last: Sakurai

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Department of Joint Research Laboratory of Clinical Medicine, School of Medicine

institute: Fujita Health University

summary: This study aimed to evaluate the gene expression signature of HSC-3 cells and its subline adapted to suspension culture (HSC-3-S5). Total RNAs were isolated from HSC-3 cells and HSC-3-S5 cells, and gene expression signatures were examined using gene expression microarray.

overall_design: Total RNA was isolated from HSC-3 cells and HSC-3-S5 cells for gene expression profiling.


title: Mechanisms of Tissue Susceptibility to FMDV Persistent Infection Based on Genes Differentially Expressed between Target and Non-target Tissues

city: Orient Point

first: James

middle: Jiangtao

last: Zhu

state: NY

department: Plum Island Animal Disease Center

institute: USDA-ARS

summary: Comparison of the transcriptiomic profiles using DNA microarray analysis betwween the pharyneal (target of FMDV acute and persistent infection) and lung (target of FMDV acute infection) tissues of cattle

overall_design: Six adult Holstein steers were used in this study. Three steers were aerosol-inoculated with FMDV-A24-Cruzeiro and three were mock inoculated. All steers were euthanized at 72 hours post infection. Necropsies and tissue collections were performed immediately after euthanasia. Eight tissues including the dorsal soft palate (DSP), dorsal nasal pharynx (DNP), mid anterior lung (LNG), nasal turbinate epithelium (NTE), interdigital cleft skin (IDC), coronary band (CB), tongue epithelium (TONG) and the metacarpal skin (MCS) were collected from each animal. Total RNA was extracted from the tissues using Qiagen total RNA isolation kit and used in microarray analysis using DNA microarrays (Agilent array design ID: 019963; Design Format: IS-45220-4-V1 or 4 X 44k per slide). Low input RNA two color labeling kit (Agilent Technologies) was used to labeled cRNA. RNA isolated from MCS was labeled with Cy5 as universal control, all individual samples were labeled with Cy3. One Cy3 labeled sample was co-hybrided with the Cy5 labeled control in one hybridization chamber. After hybridization and washing, the arrays the arrays were scanned with a GenPix 4000B and the images were saved as tiff files. All procedures followed protocols provided by Agilent Technologies. The expression data were extracted with Genpix 7.0 software for statistical analysis using R with libraries (limma, MASS, statmod, splines). LOESS method was applied to normalize inter-array variation with a background subtraction of 15. The cow gene sequences were mapped to human genes with BLAST and manual annotation using information displayed on the UCSC Genome Browser.


title: Analysis of differential gene expression in Regorafenib resistant human HCC cells either expressing or lacking Axl

city: Vienna

first: Wolfgang

last: Mikulits

address: Borschkegasse 8A

institute: Medical University of Vienna

summary: Human HCC cell line SNU449 and SNU449-Axl-KO were cultured in increasing concentrations of Regorafenib (Rego) to generate resistance. Treatment naive cells (SNU449-ctrl and SNU449-Axl-KO-ctrl) and resistant ones (SNU449-Rego and SNU449-Axl-KO-Rego) were sent for RNA-seq.

overall_design:
Differential gene expression analysis was performed based on RNA-seq data of SNU449-ctrl, SNU449-Axl-KO-ctrl, SNU449-Rego and SNU449-Axl-KO-Rego. Analysis was done in technical triplicates for each cell line.
SNU449_wt_parental_r1 to r3 = SNU449-ctrl as there is no Axl KO and no resistance induced. Three replicates for sequencing (r1-r3).
SNU449_wt_plusRego_r1 to r3 = SNU449-Rego. No Axl KO but Regorafenib resistance. Three replicates for sequencing (r1-r3).
SNU449_AxlKO_parental_r1 to r3 = SNU449-Axl-KO-ctrl as there is a Axl KO but no resistance induced. Three replicates for sequencing (r1-r3)
SNU449_AxlKO_plusRego_r1 to r3 = SNU449-Axl-KO-Rego as there is a Axl KO and Regorafenib resistance.. Three replicates for sequencing (r1-r3)

first: Kristina

last: Breitenecker

first: Viola

last: Hedrich

first: Franziska

last: Pupp

first: Doris

last: Chen


title: Transcriptome analysis of wild type, slbd40 and slwrky37 tomato seeds after imbibition.

first: Jialong

last: Zhang

address: Malianwa Street

institute: China Agricultural University

summary:
In order to study the role of SlLBD40 and WRKY37 in seed germination, we established two gene knockout lines respectively.
We then used RNA-seq data from seeds 6 h after imbibition of WT and two gene knockout lines for gene expression profiling.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WRKY37 and SlLBD40 knockout lines and WT seeds  after 6h of imbibition.

first: Zhirong

last: Wang


title: The brain tumor classifications based on machine learning models trained with older version of methylation microarray chip compatible with the new EPIC v2 illumina’s chip.

city: BETHESDA

first: Rust

last: Turakulov

state: MD

address: 10 Central rd

department: NCI

institute: NIH

type: Methylation profiling by genome tiling array

summary: Methylation profiling is a critical tool for brain tumor classification, and the Illumina methylation EPIC microarrays have been the dominant platform used for this purpose. The version 1 of the EPIC beadchips released in 2015 covers approximately 850k CpG sites, while version 2, released this year, has coverage over 950k CpG sites. Most probes on both chips overlap. However, the vendor has replaced over 15% of probes in v2 to address issues such as underlying SNPs, non-unique mapping, and off-target hybridization [1]. Moreover, EPIC v2 has over 200K additional new probes designed to enhance coverage of poorly covered genomic regions like enhancers and open chromatin regions. The EPICv2 lacks about 144k old probes present in the original content, comprising 16.5% of the old array content (Figure 1). If some of these missing probes were heavily used in predictors, they could potentially affect classifier results. The impact of changes in chip content on classifiers' predictions is uncertain. Herein, we validated the new methylation array to show that the new chip design does not affect tumor classification, although we found it may affect the classification score.

overall_design:
Two approaches were used for the validation:
1.	We performed technical DNA replicates on both chip types. This involved reprocessing and hybridizing DNA from 16 FFPE samples of various brain tumors previously run on the Illumina EPICv1 methylation chips. For the missing probes in new design (EPICv2), we replaced beta values or intensities with sample mean. We conducted prediction tests using four available classifiers and found no differences in tumor class calls in all samples and all tested classifiers. However, the new chip design had a significant effect on prediction scores in some classifiers. The figure 2 illustrates the correlation of class prediction scores between the chips and a calibrated scores between chip types on box plots. Furthermore, we examined the effect of probe imputation on the prediction of tumor content using three previously published algorithms: RFpredict.ABSOLUTE, RFpredict.ESIMATE, LUMP, and the prediction of MGMT promoter methylation using an R package. Our analysis revealed that replicates on both array types are highly correlated and produce compatible results.
2.	For the second approach we conducted an in silico assay. Here we modified the original results of EPICv1 and 450k chips where we replaced methylation beta values for the 485 probes with median beta values from the entire sample. These 485 cpg probes are used amongst 10k in CNS classifier v12b6 developed by DKFZ in Heidelberg. Simulation done on 22,504 real brain tumor samples which were re-run on the v11b6 classifier and compared with the original results: the unmodified beta values. We found no differences in the predicted brain tumor classification between the original and simulated data. The calibrated prediction scores were highly correlated (R>0.98). However, there was a small but highly significant drop in the prediction calibrated score (Paired t-test p-value <2.2E-16).

first: Zied

last: Abdullaev

first: Kenneth

last: Aldape


title: Low input RNA-seq of endothelial cells sorted from tail of zebrafish larvae

city: Guangzhou

first: Xinyi

state: Guangdong

address: Guangzhou

institute: SUN YAT-SEN MEMORIAL HOSPITAL

summary:
To characterize the mechanism by which AML derived  extracellular vesicles(EV) impaired the vascular architecture and function, EV or PBS injected flk:GFP zebrafish larvae were used for sorting endothelial cells and performing RNA-Seq.
Vascular niches sustain hematopoietic stem and progenitor cells (HSPC) and are drastically remodeled in myeloid leukemia to support pathological progression. By utilizing the leukemia-xenografted zebrafish model, we identified that myeloid leukemia secreted extracellular vesicles (EVs) to impair HSPC proliferation, survival and differentiation towards lymphoid/erythroid lineages. The leukemia EVs delivered arginase-1 into venous vasculature to deplete L-arginine and cause NOS uncoupling, which catalyzes production of ROS instead of NO. The oxidative stress caused endothelial cell loss, vascular constriction and failure of secreting niche factors and supporting hematopoiesis. Our findings indicate that myeloid leukemia impaired the vascular function of supporting hematopoiesis by delivering arginase in EVs and arginase inhibition has the potential to improve normal hematopoiesis in myeloid leukemia.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for endothelial cells sorted from tails of  MV4-11 derived EV or PBS injected flk:GFP zebrafish larvae.

first: Linjia

last: Jiang

first: Weijian


title: Loss of function of CDK7 is Synthetically Lethal with Fatty Acid Oxidation Inhibition in Glioblastoma

city: New York

first: Markus

last: Siegelin

department: Pathology and Cell Biology

institute: Columbia University

summary: CDK7 has been identified as a potential drug target for glioblastoma (GBM), a highly lethal primary brain tumor. However, resistance to therapy develops quickly, which may be facilitated by drug-induced reprogramming of metabolism. By combination of a transcriptome and metabolite screening analyses followed by carbon tracing (U-13C-Glucose, U-13C-Glutamine and U-13C-Palmitic acid) and extracellular flux analysis, we demonstrated that both genetic and pharmacological (YKL-5-124 and THZ1) CDK7 inhibition elicited substantial metabolic reprogramming. Specifically, CDK7 inhibition elicited an increase of oxygen consumption rate fueled by enhanced fatty acid oxidation (FAO) manifested by enhanced labeling of citric acid cycle intermediates from palmitic acid. Consistently, the combination treatment of CDK7 inhibitors with blockers of FAO (etomoxir) exerted substantial synergistic growth inhibition in patient derived xenograft as well as neurosphere GBM cultures, which was mainly driven by a collapse of oxidative energy metabolism. In turn, exogenous administration of adenosine triphosphate partially rescued from the cell death induced by the combination treatment. Finally, the combined administration of YKL-5-124 and etomoxir extended overall in an orthotopic patient-derived xenograft model of GBM. In summary, these data support that simultaneous targeting of CDK7 and FAO might be a potential novel therapy against GBM.

overall_design: GBM43 cells were treated with DMSO, THZ1, Etomoxir or combination of both for 24h. Cells were collected and were extracted for total RNA by using miRNAeasy Mini Kit from QIAGEN. RNA samples were sequences and analyzed for gene set enrichment.

first: Trang

last: Nguyen


title: The SOS2–SERRATE module maintains miRNA homeostasis under salt stress

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

summary: MicroRNAs (miRNAs) are master regulators that act in response to development signals or environmental stimuli by mediating the cleavage of their target mRNAs or repressing their translation; however, the mechanisms by which miRNA dynamics are precisely regulated under salt stress are yet to be fully elucidated. SOS2 modulates the reconstruction of the salt-responsive transcriptome by post-translationally modifying SE.

overall_design: Comparative gene expression profiling analysis of RNA-seq and small RNA-seq data for gl1 and sos2-2 mutant.

first: Jinrong

last: Niu

first: Yijun

last: Qi

first: Yan

last: Guo


title: Transcriptome sequencing of the hnRNPA2B1 knockout Huh7 cell line

city: shanghai

first: Weijie

last: Hao

state: shanghai

address: 1630 Dongfang Road, Shanghai, China

institute: shanghai jiaotong university

summary: To investigate the role of hnRNPA2B1 in the progression of hepatocellular carcinogenesis, we established a Huh7 cell line in which the hnRNPA2B1 gene was knocked out by crisper/cas9.

overall_design: Comparative gene expression profiling of RNA-seq data from Huh7 cells and their KO derivative (sg-hnRNPA2B1).


title: Transcriptome analysis of avocado embryogenic cultures selected for resistance to Rosellinia necatrix exudates

city: Malaga

first: Clara

last: Pliego

state: Malaga

address: Cortijo de la Cruz

department: Department of Genomics and Biotechnology

country: Spain

institute: IFAPA

summary: Embryogenic cultures derived from a zygotic embryo of the avocado cv. Anaheim, were selected for resistance to the culture filtrate (CF) of Rosellinia necatrix, the causal agent of avocado white root rot. Cultures were obtained through recurrent selections in progressively increasing concentrations of fungal CF (from 20% up to 80%).

overall_design: RNA-Seq technology was used to compare the transcriptomic profiles of the avocado callus tolerant line L3 (capable to survive in the presence of 80% CF) and control line AN-9 (not exposed to CF), after 24 hours of growth in a medium containing 40% CF.

first: Ana

last: Moreno-Pérez

first: Adela

last: Zumaquero

first: Elsa

last: Martínez-Ferri

first: Araceli

last: Barceló-Muñoz

first: Carlos

last: Lopez-Herrera

first: Fernando

last: Pliego-Alfaro

first: Elena

last: Palomo-Ríos


title: Dynamic single-cell regulomes characterize human peripheral blood ILC subpopulations [scRNA-seq]

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Innate lymphoid cells (ILCs) are highly plastic immune cells that have been separated into 3 main subsets, characterized by distinct phenotypic and functional profiles. Using single cell approaches, heightened heterogeneity of mouse ILCs has been recently appreciated, imprinted by tissue signals that shape their transcriptome and epigenome. Intra-subset diversity has also been observed in human ILCs. However, combined transcriptomic and epigenetic analyses of single ILCs in humans are lacking.  Here we show high transcriptional and epigenetic heterogeneity among human circulating ILCs in healthy individuals. We describe phenotypically distinct subclusters within main circulating ILC populations. We show diverse chromatin accessibility within main ILC subsets, compatible with differentially poised states. We validate the use of this healthy donor-based analysis as resource dataset to infer ILC changes occurring in disease conditions. Overall, our work provides new insights in the complex human ILC biology. We anticipate our work to be a starting point to facilitate hypothesis-driven studies in patients, without the need to perform single cell OMICs using precious patients’ material

overall_design: We sorted total innate lymphoid cells from peripheral blood of 3 healthy human donors, and subjected them to single-cell RNA sequencing analysis using the 10x Genomics technology

first: Maryline

last: Falquet

first: Ziyang

last: Su

first: Camilla

last: Jandus


title: Cell microparticles loaded with tumor antigen and resiquimod reprogram tumor-associated macrophages and promote stem-like CD8+ T cells to boost anti-PD-1 therapy

city: Wuhan

first: Zhaohan

last: Wei

address: Luoyu Road 1037

institute: Huazhong University of Science and Technology

summary: Tumor microenvironment profoundly affects the therapeutic efficacy of ICB. In view of the fact that inbred mouse strains bearing monoclonal cancer cell line-derived tumors respond in a dichotomous manner to ICB, to gain insight into the mechanisms of ICB resistance in HCC, the anti-PD-1 antibody-responsive and nonresponsive mice were used for analyzing the difference in gene expression using bulk RNA sequencing (RNA-seq).

overall_design: The orthotopic Hepa1-6 tumor-bearing mice were intraperitoneally injected with anti-PD-1 antibody or PBS every four days for five times and then the three PBS-treated tumors, anti-PD-1-treated three smallest tumors (deemed as anti-PD-1 antibody-responsive tumors) and the anti-PD-1-treated three largest tumors (deemed as anti-PD-1 antibody-nonresponsive) were used for analyzing the difference in gene expression using bulk RNA sequencing (RNA-seq).

first: Xiaoqiong

last: Zhang

first: Lu

last: Gan

first: Xiangliang

last: Yang


title: Dynamic single-cell regulomes characterize human peripheral blood ILC subpopulations.

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Atypical K6-linked ubiquitylation marks toxic RNA-protein crosslinks induced by formaldehyde

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Straße 40

department: Institute of Pathology

country: Germany

institute: University Medical Centre Göttingen

summary: Reactive aldehydes are produced during cellular metabolism and can accumulate in specific tissues particularly when aldehyde clearance mechanisms are impaired. Reactive aldehydes induce DNA-DNA and DNA-protein crosslinks (DPCs) that are repaired by different DNA repair pathways. Cellular toxicity of endogenous formaldehyde has been attributed to the damage of the genomic DNA and consequent inhibition of transcription. However, whether damage to other cellular macromolecules and interference with additional metabolic processes contributes to formaldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces toxic RNA-protein crosslinks (RPCs) in mRNA that inhibit translation and induce a specific RPC stress response pathway that is characterized by linkage-specific ubiquitylation. RPCs in the mRNA are recognized by stalling ribosomes and marked by K6-linked ubiquitylation that promotes their clearance by the ubiquitin-dependent unfoldase VCP.

overall_design: Comparative gene expression profiling analysis of factory-RNA-seq data for U2OS cells without (DMSO) or with FA treatment (PFA).

first: Petra

last: Beli

first: Yajie

last: Zhu


title: Dynamic single-cell regulomes characterize human peripheral blood ILC subpopulations [scATAC-seq]

overall_design: We sorted total innate lymphoid cells from peripheral blood of 3 healthy human donors, and subjected them to single-cell ATAC sequencing analysis using the 10x Genomics technology


title: Synthetic Lethal Interaction Between Loss of Function of OGDH and Bcl-xL in Glioblastoma

first: Markus

last: Siegelin

summary: Glioblastoma (GBM) remains an incurable disease, requiring more effective therapies. Through CRISPR and RNAi library screening interrogation we identified several TCA-cycle enzymes as essential for GBM growth. By combining a transcriptome and metabolite screening analyses we discovered that loss of function of OGDH by the clinically validated drug compound, CPI-613, is synthetically lethal with Bcl-xL inhibition (genetically and through the clinically validated BH3-mimetic, ABT263) in patient-derived xenograft as well neurosphere GBM cultures. CPI-613 mediated energy deprivation drives an integrated stress response with an up-regulation of the BH3-only domain protein, Noxa in an ATF4 dependent manner as demonstrated by genetic loss of function experiments. Consistently, silencing of Noxa rescued from cell death induced by CPI-613 in model systems of GBM. In patient-derived xenograft models of GBM in mice, the combination treatment of ABT263 and CPI613 suppressed tumor growth more potently than each compound on its own. Therefore, combined inhibition of Bcl-xL along with interference of the TCA-cycle might be a novel treatment strategy for GBM.

overall_design: KNS42 GBM cells were treated with DMSO or CPI-613 for 24h. Cells were collected and were extracted for total RNA by using miRNAeasy Mini Kit from QIAGEN. RNA samples were sequences and analyzed for gene set enrichment.

first: Trang

last: Nguyen


title: Association between HPK1 expression and T-cell exhaustion

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: We aimed to investigate the association between HPK1 expression and exhausted status of tumor.

overall_design: Bulk RNA-seq was performed on fresh-frozen tissue samples of renal cell carcinoma.

first: Yong

middle: J

last: Lee

first: Seung

first: Minyong

last: Kang

first: Seong

middle: I

last: Seo

first: Su-Hyung

last: Park

first: Eui-Cheol

last: Shin


title: Effect of HPK1 inhibitor on exhausted CD8 T cells

summary: We aimed to compare the effects of HPK1 inhibitor on CD8 T cells according to the exhaustion status.

overall_design: Progenitor exhausted CD8+ T cells (TPEX, PD1+CD28+Tim3-) and terminally exhausted CD8+ T cells (TTEX, PD1+Tim3+) were sorted from single cell suspension of renal cell carcinoma. The cells were stimulated with anti-CD3/CD28-coated beads and treated with HPK1 inhibitor or DMSO control.


title: ADAR1 Links R-Loop Homeostasis to ATR Activation in Replication Stress Response

city: Tianjin

first: Chunyong

state: Tianjin

address: Tianjin Medical University HepingNo.22, Qixiangtai Road

institute: TMU

summary: Unscheduled R-loops are a major source of replication stress and DNA damage. R-loop-induced replication defects are sensed and suppressed by ATR kinase, whereas it is not known whether R-loop itself is actively involved in ATR activation and, if so, how this is achieved. Here, we report that the nuclear form of RNA-editing enzyme ADAR1 promotes ATR activation and resolves genome-wide R-loops, a process that requires its double-stranded RNA-binding domains. Mechanistically, ADAR1 interacts with TOPBP1 and facilitates its loading on perturbed replication forks by enhancing the association of TOPBP1 with RAD9 of the 9-1-1 complex. When replication is inhibited, DNA-RNA hybrid competes with TOPBP1 for ADAR1 binding to promote the translocation of ADAR1 from damaged fork to R-loop region. There, ADAR1 recruits RNA helicases DHX9 and DDX21 to unwind R-loops, simultaneously allowing TOPBP1 to stimulate ATR more efficiently. Collectively, we propose that the tempo-spatially regulated assembly of ADAR1-nucleated protein complexes link R-loop clearance and ATR activation, while R-loops crosstalk with blocked replication forks by transposing ADAR1 to finetune ATR activity and safeguard the genome.

overall_design: The genome extracted from Hela cells expressing control siRNA or ADAR1 siRNA were treated with or without RNase H, then incubated with S9.6 antibody for immunoprecipitation and sequencing.


title: Effect of pharmacological BCL-2 inhibition with venetoclax on T cell homeostasis [RNA-seq]

city: Chicago

first: James

last: LaBelle

state: IL

address: 900 East 57th Street, KCBD 5122

institute: University of Chicago

summary: Venetoclax, a BCL-2 inhibitor, is being increasingly used in the clinic as a single agent or in combination. Thus far, there has been little to show how this drug affects the immune system. Research has been done to characterize the mechanisms of resistance of cancer cells to venetoclax, however, an immune subset of T cells called regulatory T cells has also shown resistence to apoptotic cell death via venetoclax administration. To investigate the effects of venetoclax on the transcriptional landscape of regulatory T cells (with some comparison to conventional T cells), we treated FOXP3-IRES-GFP mice for 14 days with 50mg/kg of venetoclax and analyzed their RNA profiles. We observed that Treg cells upregulate genes involved in Th17 effector cell differentiation, which was not observed in the Tcon counterparts.

overall_design: RNA-seq of CD4+ FOXP3- Tcons and CD4+ FOXP3+ Tregs following treatment with venetoclax

first: Rosy

last: Liao


title: Effect of pharmacological BCL-2 inhibition with venetoclax on T cell homeostasis

summary: Venetoclax, a BCL-2 specific inhibitor, has been show to confer transcriptional changes in T cell populations. In order to elucidate how these changes may be occuring, we sought to investigate whether there are epigenetic alterations that may offer a potential explanation. To begin to answer this question, we conducted ATAC-sequencing on Treg cells isolated from FOXP3-IRES-GFP mice treated  for 14 days with 50mg/kg of venetoclax and assessed for global accessibility changes.

overall_design: ATAC-seq of venetoclax treated CD4+ FOXP3+ Tregs isolated from the spleen


title: Single cell transcriptomic profile of human airway orgnaoids.

city: Seoul

first: Jong-Il

last: Kim

address: Daehakro 103

institute: Seoul National University

summary: We profiled transcriptome of human airway organoids with three different culture methods.

overall_design: Human airway organoids treated with vehicle or viruses are dissociated to analyze scRNA-seq.

first: Woochan

first: Seyoon

first: Jung-Ki

last: Yoon


title: Generation of Pre-Clinical Cardiac Organoids for Drug Testing and Transplantation

city: Shenzhen

first: Fujian

last: Wu

address: No.1017, Dongmen North Road, Luohu District

institute: Shenzhen People's Hospital

summary: To explore the events during the differentiation process and timelines of various cells developed in cardiac organoid differentiation,we collected cell spheres for bulk RNA sequencing at each stage of differentiation (days 0, 1, 2, 3, 4, 6, and 30)

overall_design: Comparative gene expression profiling analysis of RNA-seq data between each time points

first: Qian

last: He

first: Furong

last: Li

first: Xiaofei


title: Oncolytic virus M1 functions as a bi-functional checkpoint inhibitor to enhance the antitumor activity of DC vaccine

first: Jia

last: Dan

address: No.58 Zhongshan Road 2

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Although promising, dendritic cell (DC) vaccines still provide limited clinical benefits, mainly due to the immunosuppressive tumor microenvironment (TME) and the lack of tumor-associated antigens (TAAs). Oncolytic viruses are considered to be an ideal strategy to overcome immunosuppression and expose TAAs, therefore they may work synergistically with DC vaccines. In this study, we demonstrated that oncolytic virus M1 (OVM) can enhance the antitumor effects of DC vaccine in a variety of syngeneic tumor mouse models by increasing the infiltration of CD8+ effector T cells in the TME. Mechanically, we identified that tumor cells offset the function of DC vaccines through the myeloid immune checkpoint SIRPα-CD47, while OVM can downregulate the expression of SIRPα and CD47 in DCs and tumor cells, respectively. Based on the fact that OVM upregulates the expression of PD-L1 in DCs, PD-L1 blockade was introduced with the combination of DC vaccines and OVM, resulting in a further potentiation of antitumor activity. Overall, we revealed that OVM can strengthen the antitumor efficacy of DC vaccines by targeting the immune checkpoint SIRPα-CD47 axis, which exerts dominant immunosuppressive effects on DC vaccines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow-derived dendritic cells (iDC), DCs cocultured with B16-F10 tumor cells (tumorDC), M1 treated DCs cocultured with B16-F10 tumor cells (M1_tumorDC), and M1 treated DC (M1_DC)

first: Jing

last: Cai

first: Yingqian

last: Zhong

first: Chaoqun

last: Wang

first: Shanyu

last: Huang

first: Zhen

last: Fan

first: Cuiying

last: Xu

first: Linyi

last: Hu

first: Jiayu

last: Zhang

first: Jun

first: Xingwen

last: Su

first: Wenbo

first: Guangmei

last: Yan

first: Jiankai

last: Liang

first: Yuan

last: Lin


title: Gene expression profile and TCR sequencing data of CD45+ cells sorted from single cell suspensions of tumors after in vitro anti-CD3 stimulation and treatments

first: Seung Hyuck

last: Jeon

summary: We aimed to analyze the transcriptomic difference of tumor-infiltrating immune cells treated with anti-PD-1 blockade and/or HPK1 inhibitor.

overall_design: Single cell suspensions of tumors were stimulated with soluble anti-CD3 antibody or tumor-specific stimulation wirh or without HPK1 inhibitor or anti-PD-1 blocking antibody. The cells were incubated for 96 hours, and live CD45+ cells or CD8+ cells were sorted using flow cytometry. The sorted cells were processed into single cell RNA/TCR sequencing.

first: Yong

last: Lee

first: Seung

first: Minwoo

first: Heejin

last: Nam

first: Jee

middle: Y

last: Kim

first: Jeon

last: Jang

first: Chul-Ho

first: Shin

last: Hwang

first: Jae-Ho

last: Cheong

first: Byung

middle: S

last: Min

first: Minyong

last: Kang

first: Seong

last: Seo

first: Su-Hyung

last: Park

first: Eui-Cheol

last: Shin


title: EXPLORING GENE EXPRESSION PROFILES IN PRIMARY CENTRAL NERVOUS SYSTEM VASCULITIS

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: To explore the gene expression profile of primary CNS vasculitis (PCNSV) compared with normal controls

overall_design: Gene expression profiling analysis was performed from RNA extraxted from brain biopsy of patients with primary CNS vasculitis and normal brain tissue as control.

first: Carlo

last: Salvarani

first: Jonas

last: Paludo

first: Gene

last: Hunder

first: Stephen

last: Ansell

first: Caterina

last: Giannini

first: Joseph

last: Parisi

first: John

last: Huston III

first: Matthew

last: Koster

first: Kenneth

last: Warrington

first: Stefania

last: Croci

first: Robert

last: Brown Jr


title: The role of H3K4me3 of low temperature memory in Arabidopsis

city: Lanzhou

first: Zezhong

last: Su

address: YuZhong

institute: Lanzhou University

summary:
Plants experience a wide array of environmental stimuli to form a memory of adversity. Histone modification plays roles in plant stress memory, of which the mechanisms of H3K4me3 of low temperature memory in plants are poorly understood although H3K4me3 is a key histone modification. Combined with phenotypic analysis, chip-seq, and transcriptome analyses were performed to investigate the potential H3K4me3 contributions for different phases of recurring cold stresses Arabidopsis plants.
We then performed gene expression profiling analysis using data obtained from RNA-seq of  different low temperature treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for different low temperature treatments, cold memory (S1:4°C for 6 h, then at room temperature for 18 h; S4:4°C for 6 h, then at room temperature for 18 h, repeated four times), and then placed at 0°C for 6 h, and control groups with normal growth conditions.

first: Yuan

last: Song

first: Tianyi

last: Zhang


title: Clonal cooperation through soluble metabolite exchange facilitates metastatic outgrowth by modulating Allee effect

city: Milano

first: Kristina

last: Havas

address: Via Adamello 16

country: Italy

institute: IFOM-ETS AIRC Institute of Molecular Oncology

summary: Tumours feature substantial heterogeneity of phenotypically distinct lineages. Although intra-clonal interactions between co-existing lineages is emerging as major contributor shaping tumor evolution, the extent and nature of interactions remain largely unknown. Here, we show that Allee effect, i.e., growth dependency on population size, is pervasive, and that intra-clonal soluble metabolite exchange alleviates the Allee thresholds to growth. Additionally, we find clear evidence for cooperative ecological interactions between lineages in that all clones are alleviated by reconditioned medium from the whole population; pairwise combinations of clones typically show cooperative interactions, as do polyclonal combinations. In mouse xenograft models, polyclonal metastasis formed from groups of interacting clones displayed enhanced metastatic outgrowth highlighting the physiological role of metabolic cooperation in vivo. Our results bring forward intra-tumor metabolite exchange as a modulator of tumor ecology and metastasis.

overall_design: RNA-seq,  2 conditions (A and C), Condition A 6 clones (03CR, 10CR, 13CR, 22CR, 35CR, and 45CR), Condition C 3 clones (22CR, 35CR, and 45CR), 3 replicates (R1, R2, R3).

first: Benjamin

last: Hershey

first: Fabio

last: Iannelli


title: VPS34 regulates RAB7 activation and Retromer localization to autophagosomes and mitophagy in oocytes

city: NanJing

first: Wenya

last: Sun

address: 140 Hanzhong Rd,Gulou, Nanjing, 210029,China

institute: NanJing Medical University

summary: To investigate the role of Vps34 during oocyte development, we crossed female Vps34f/f mice with Gdf9-Cre and Zp3-Cre male transgenic mice for Cre recombinase specifically in oocytes at either primordial or early growing stages. Our results revealed that Vps34 plays a key role in oocyte cytoplasmic maturation. In order to reveal the changes in oocyte transcriptome level caused by Vps34 deletion, we conducted transcriptome sequencing on oocytes at GV stage, MII stage and 2cell embryo of ZcKO, and analyzed the changes in transcripts at these three stages. Transcriptome sequencing results showed that the oocytes and 2cell embryos of ZcKO were enriched with a large number of transcription and transport-related differential genes, and the 2cell stage had the most differential genes, which was the key period for the occurrence of major ZGA. Further analysis of transcription-related genes revealed that the enriched major ZGA genes were all down-regulated in 2cell of ZcKO mice. In addition, differential genes involved in autophagy were enriched in ZcKO 2cell, with HPG abnormally increased. Autophagy is the main degradation pathways of maternal proteins in early embryonic development, and degradation of maternal proteins is necessary for the normal process of ZGA, which occurs prior to major ZGA and even during oocyte maturation, when defects appear to be irremediable later. These results suggest that Vps34 deletion leads to degradation inhibition of maternal factors and impaired major ZGA, leading to embryonic development arrest.

overall_design: GV oocytes, MII oocytes, and 2cell embryos were collected from female mice with Zp3-cre (ZcKO) for oocyte conditional deletion and carrying floxed Vps34 (Vps34f/f) for single-cell RNA-seq for three biological replicates, respectively.

first: Wenwen

last: Liu

first: Lu

last: Wang


title: Cdt1 overexpression drives colorectal carcinogenesis through origin overlicensing and DNA damage

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

institute: University of Geneva

summary: To examine origin firing upon CDT1 overexpression, EdUseq-HU was performed in HCT116 cells with normal expression levels of CDT1 (OFF) and HCT116 cells with CDT1 overexpression (ON)

overall_design: Cells were collected by mitotic shake-off and allowed to progress through the cell cycle for 12 hours in the presence of 5-ethynyl2′-deoxyuridine (EdU) and hydroxyurea (HU). EdU-labelled DNA was then isolated and subjected to high-throughput sequencing (EdUseq-HU)

first: Michalis

last: Petropoulos

first: Vasilios

first: Thanos

last: Halazonetis

first: Zoi

last: Lygerou

first: Stavros

last: Taraviras


title: Dmrt1 maintains testicular immune homeostasis by activating Spry1 and inhibiting NF-κB signaling pathway [Spry1 KD RNA-Seq]

city: Yangling

first: Mengfei

state: Shaanxi

address: No.3rd, Taicheng Road

department: College of Veterinary Medicine

institute: Northwest A&F University

summary: To explore the function of Spry1 in testis, we constructed a mouse model with testicular specific KD of Spry1 through seminiferous tubule transplantation

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type testes and Spry1-KD testes

first: Jinlian

last: Hua

first: Donghui

last: Yang

first: Shicheng

last: Wan


title: Dmrt1 maintains testicular immune homeostasis by activating Spry1 and inhibiting NF-κB signaling pathway [ChIP-Seq]

summary: In order to explore the mechanisms of Dmrt1 in regulating testicular immune homeostasis, we performed ChIP-seq analysis on primary SCs infected with a lentiviral vector expressing FLAG-tagged Dmrt1

overall_design: Focusing on the regions that DMRT1 protein bound within 5 KB upstream and downstream of transcription start site (TSS) and transcription end site (TES)

first: Yudong

last: Wei

first: Xiaomin

last: Du


title: Differentially forms of nitrogen regulates the response of Microcystis aeruginosa to nanoplastics under environmentally relevant nitrogen concentration

city: Qingdao

first: Mei-Yan

state: Shandong

address: Aoshanwei Street

institute: Shandong university

summary: As an essential primary producer, cyanobacteria play an important role in the global cycle for both carbon and nitrogen in the ecosystems. Though the influence of nanoplastics on the carbon metabolism of cyanobacteria, especial Microcystis aeruginosa, a dominant species causing cyanobacterial blooms, is well studied, little is known about nanoplastics affecting the nitrogen metabolism.

sample_organism: Microcystis aeruginosa FACHB-905 = DIANCHI905

overall_design: we show that the amino-modified polystyrene nanoplastics (PS-NH2) promote the nitrogen consumption, microcystins synthesis and release of M. aeruginosa under environmentally relevant nitrogen concentration of nitrate, ammonium and urea.

first: Li-Juan

last: Feng

first: Xiao-Yu


title: Dmrt1 maintains testicular immune homeostasis by activating Spry1 and inhibiting NF-κB signaling pathway

last: Zhang

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

sample_organism:
Capra hircus
Mus musculus

platform_organism:
Capra hircus
Mus musculus

overall_design: Refer to individual Series


title: Oral combined contraceptives induce liver mitochondrial ROS and whole body metabolic adaptations in female mice.

city: College Station

first: Kartik

last: Shankar

email: kartik.shankar@cuanschutz.edu, kartikster@gmail.com, kartik.shankar@usda.gov, kartik.shankar@ag.tamu.edu

state: TX

address: 498 Olsen Blvd TAMU 2250 TAMU 2250

department: RAFSRU

institute: USDA ARS

summary: Compared to age-matched men, pre-menopausal women are protected against cardiovascular disease (CVD), hepatic steatosis, diabetes, and obesity - findings that are widely attributed to estrogen action. However pre-menopausal women who use oral combined contraceptives (OC) have 2-fold higher risk of cardiovascular disease (CVD), and OC use compounds with metabolic risk factors such as dyslipidemia, hypertension, or diabetes to further increase CVD susceptibility. While mitochondrial function in metabolically important tissues such as the liver and skeletal muscle is an emerging mechanism by which estrogen may confer its protection, effects of OC use on mitochondrial function and whole body metabolism in the context of disease risk has not yet been explored. To answer this question, female C57Bl/6J mice  were fed a high fat diet and treated with vehicle or OCs for 3, 12, or 20 weeks (n=6-12 per group). Liver and skeletal muscle mitochondrial function (respiratory capacity, H2O2, coupling) was measured along with clinical outcomes of cardiometabolic disease such as obesity, glucose tolerance, hepatic steatosis, and aortic atherosclerosis. Main findings include that regardless of duration of treatment, OCs induced robust increases in hepatic mitochondrial H2O2, likely due to diminished antioxidant capacity. Furthermore, OC use in female mice decreased wheel running, spontaneous physical activity, and total energy expenditure. Surprisingly, in the chronic studies (12, 20 wk) OC treated mice had lower adiposity and hepatic triglyceride content compared to control mice. Together, these studies describe tissue-specific effects of OC use on mitochondrial function as well as variable impacts on markers of metabolic disease susceptibility.

overall_design: RNA was extracted from liver tissue from individual mice in four groups (oral combined contraceptives, OC, or veh diet, with or without VWR, n = 5 per group)

first: John

last: Thyfault

first: Kelly

last: Fuller


title: Molecular basis of strain variations of a chlamydial pathogen of arthropods

city: Vienna

first: Matthias

last: Horn

address: Djerassiplatz 1

department: Division of Microbial Ecology

institute: University of Vienna, Center of Microbiology and Environmental Systems Science

summary: Variations between strains have been extensively studied in human pathogens mainly because even genomically highly identical strains can cause severely different phenotypes in their hosts. Here we investigate within-species diversity in Rhabdochlamydia porcellionis a pathogen infecting terrestrial isopods and a member of the phylum Chlamydia that also includes well-known human pathogens as Chlamydia trachomatis. Using an infection assay in Sf9 insect cell cultures we could show that albeit there are only few genomic variations, the strains 15C and ZGO cause different phenotypes. To investigate potential underlying mechanisms we carried out a global gene expression analysis and could show that changes in major metabolic pathways help strain 15C to replicate more efficiently in the host cells. In addition we found that genes shown to be involved in pathogenicity and host interaction of human pathogenic chlamydia i.e. genes encoding the type III secretion system and polymorphic membrane proteins are regulated differently by the strains.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the two strains of Rhabdochlamydia porcellionis 15C and ZGO.

first: Tamara

last: Halter

first: Astrid

last: Collingro

last: Loewenstern


title: Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli

city: Saint Louis

first: Yichao

last: Han

address: 1 Brookings Dr

department: Department of Energy, Environmental & Chemical Engineering

institute: Washington University in St Louis

summary: Elucidating genome-scale regulatory networks requires a comprehensive collection of gene expression profiles, yet measuring gene expression responses for every transcription factor (TF)-gene pair in living prokaryotic cells remains challenging. Here, we develop pooled promoter responses to TF perturbation sequencing (PPTP-seq) via CRISPR interference to address this challenge. Using PPTP-seq, we systematically measure the activity of 1372 Escherichia coli promoters under single knockdown of 183 TF genes, illustrating more than 200,000 possible TF-gene responses in one experiment. We perform PPTP-seq for E. coli growing under three different media. The PPTP-seq data reveal robust steady-state promoter activities under most single TF knockdown conditions. PPTP-seq also enables identifications of new TF auto-regulatory responses and complex transcriptional control on one-carbon metabolism. We further find context-dependent promoter regulation by multiple TFs whose relative binding strengths determined promoter activities. Additionally, PPTP-seq reveals different promoter responses under different growth media, suggesting condition-specific gene regulation. Overall, PPTP-seq provides a powerful method to examine genome-wide transcriptional regulatory networks and can be potentially expanded to reveal gene expression responses to other genetic elements.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We measured genome-wide promoter activity profiling under TF knockdown conditions by Fluorescence-activated cell sorting (FACS). CRISPRi was used to perturb every known TF gene in E. coli

first: Fuzhong


title: Dual-transcriptomic analysis of Nicotiana benthamiana and two compatible Pseudomonas strains

city: Tucson

first: David

last: Baltrus

state: AZ

address: 1140 E. South Campus Drive

institute: University of Arizona

summary: We sought to compare and contrast plant host and bacterial transcriptional changes during compatible infections that cause disease (albeit within different symptoms). We investigated the infection by the two Pseudomonas syringae sensu lato strains P. syringae pv. syringae B728a (Psy) and P. amygdali pv. tabaci 11528 (Pta) of Nicotiana benthamiana at an early time point post inoculation to understand how a plant host responds to two related bacteria with different infection strategies. Plant and bacterial transcriptomes were analyzed prior to and five hours post inoculation.

sample_organism:
Pseudomonas syringae pv. syringae
Pseudomonas amygdali pv. tabaci
Nicotiana benthamiana

overall_design: RNA was taken from six Nicotiana benthamiana plants before and five hours after syringe inoculation with Psy or Pta for assessing the plant transcriptome. For the bacterial transcriptomes, bacteria growing on King's B medium and from the leaf intercellular wash fluid five hours post inoculation were used for RNA isolation. For each organism and condition there are 3 replicates. To determine whether bacterial transcriptomes were impacted by pelleting before RNA collection, the Psy B728a has a pelleted (P) and not-pelleted (N) set of samples for the in vitro timepoint.

first: Morgan

last: Carter

first: Mary

last: Smith

middle: A

first: Brian

last: Kvitko


title: The neuropeptide neuromedin U directs eosinophils to promote epithelial cell differentiation and barrier immunity of the small intestine

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

summary: In this work we show that neuromedin U receptor 1 (NMUR1)-mediated signaling programs SI eosinophils to support epithelial cell differentiation and barrier immunity. The global transcriptional profiling of eosinophils from different tissues of mice revealed that Nmur1 was expressed in a subset of eosinophils specifically in the SI. Fate mapping analyses showed that NMUR1 expression in SI eosinophils was imprinted by local microenvironment and further enhanced by the inflammation. Genetic deletion of NMUR1 decreased the numbers of eosinophils, degranulation activity, and goblet cell differentiation in the SI. Chemogenetic manipulation of NMU-expressing cells significantly altered the goblet cell differentiation and mucus secretion. Eosinophil-organoid co-culture experiments demonstrated that NMU-mediated eosinophil activation directly promoted the growth of intestinal organoids and formation of budding domains and complex crypt–villus structures. Finally, the deficiency of NMUR1 compromised anti-parasite immunity. Thus, NMU regulates epithelial cell differentiation and function through stimulating NMUR1-expressing eosinophils in the SI, highlighting the importance of neuro-immune-epithelium crosstalk in maintaining tissue homeostasis.

overall_design: We flow-sorted total eosinophils from the small intestine, bone marrow, blood, spleen, lung, skin and colon of wildtype mice, or NMUR1+ and NMUR1- eosinophils from the NMUR1-TdT reporter mice at the steady state. The cells were then subjected to bulk RNA-seq or scRNA-seq as indicated. Libraries were pair-end (150+ 150 bp) sequenced on a Hiseq X Ten or NovaSeq (Illumina).

first: Yu

last: Li

first: Shaorui

last: Liu

first: Kewen

last: Zhou


title: RNAseq analysis of genes differentially expressed in SMMC7721 cells with SNRPE knockdown

city: Nanjing

first: Qipeng

last: Wu

state: Jiangsu

address: Tongjiaxiang No.24

institute: China Pharmaceutical University

summary: Hepatocellular carcinoma (HCC) is a malignant tumor with poor prognosis and lack of effective treatment targets is the major challenge in treating HCC. Previous studies have revealed significant changes in spliceosome-related genes in HCC. The unique expression pattern in tumor cells makes oncofetal proteins ideal candidate targets for cancer diagnosis and treatment. Therefore, we focused on the differentially expressed splicing factors in embryonic liver development and HCC. We identified an oncofetal splicing factor, small nuclear ribonucleoprotein polypeptide E (SNPRE).In order to better understand the effect of SNRPE in HCC, we knocked down SNRPE using siRNA (siSNRPE) assessed the gene expression pattern by RNA-Seq.

overall_design: Six samples obtained from smmc7721 cells including negative control (NC) and siSNRPE group were analyzed. Three independent samples were analyzed for each group.

first: Zhenzhou

last: Jiang

first: Luyong

last: Zhang


title: Dmrt1 maintains testicular immune homeostasis by activating Spry1 and inhibiting NF-κB signaling pathway [Dmrt1 RNA-Seq]

first: Mengfei

summary: To explore the potential function of Dmrt1 in spermatogenesis, we constructed a Dmrt1-deficiency mouse model by knockdown Dmrt1 in testicular seminiferous tubule specifically

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type testes and Dmrt1-KD testes

first: Jinlian

last: Hua

first: Yudong

last: Wei

first: Xiaomin

last: Du


title: Transcript buffering and 3ʹUTR lengthening are shaped during human neurodevelopment by shifts in mRNA stability and microRNA load

city: Toronto

first: Marat

last: Mufteev

address: 686 Bay St.

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: The change in abundance of individual mRNAs as cells differentiate through neurodevelopmental stages is generally attributed to transcription level alterations while the potential contribution of mRNA half-life is commonly overlooked. While some genes are regulated solely by transcription, others may be regulated by mRNA half-life only, or genes with changed transcription rates could be buffered by compensating half-life decreases or even boosted by amplifying half-life increases. In addition, during neurodevelopment there is widespread 3ʹUTR lengthening that could be shaped by differential shifts in the stability of transcript isoforms. Here we measure transcription rate and mRNA half-life changes during induced Pluripotent Stem Cell-derived neuronal development using RATE-seq at the resolution of gene isoforms. We found that during transitions to progenitor and neuron stages, transcript buffering occurs in up to half of all genes. Half-life only changes are observed in as many genes as transcription rate only changes, and almost 10% of genes exhibit transcript boosting. Global mRNA half-life decreases two-fold in neurons relative to iPSCs. The observed mRNA destabilization differentially affects gene isoforms and contributes to 3ʹUTR lengthening. Small RNA sequencing further captured an increase in microRNA copy number per cell. We propose that mRNA destabilization and 3ʹUTR lengthening are driven in part by an increase in microRNA load. Our findings identify mRNA stability mechanisms in human neurodevelopment that regulate gene and isoform level abundance and provide a precedent for similar post-transcriptional regulatory events as other tissues develop.

overall_design: Human iPSCs and iPSC-derived neuronal progenitor cells were subjected to RATE-seq and miRNA-seq to characterize changes in transcription rate and RNA stability.

first: Deivid

middle: C

last: Rodrigues

first: Olivia

last: Rissland

first: Michael

last: Wilson

first: James

last: Ellis


title: Identification of potential pathways whereby dietary high fat induced hepatic lipid metabolic disorder of Oreochromis niloticus through long non-coding RNAs

city: wuxi

first: Yi-Fan

last: Tao

state: jiangsu

address: 9 Shanshui East Road

institute: Freshwater Fisheries Research Center

summary: Genetically improved farmed tilapia (Oreochromis niloticus, GIFT) is prone to hepatic metabolic imbalance and suffer from fatty liver disease during the intensive farming. Long non-coding RNAs (lncRNAs) performed essential roles in varieties of biological processes, including lipid metabolism. However, the lncRNAs regarding hepatic lipid metabolism in tilapia have not been identified. In this study, Illumina sequencing and bioinformatic analysis was performed on the liver of male GIFT juvenile fed with high-fat diet (HFD, 18.5% lipid) or normal-fat diet (NFD, 8% lipid) for 56 days. RNA-seq analyses revealed 299 differentially expressed (DE)-mRNAs and 284 DE-lncRNAs between these two groups. The transcript expression of 16 candidates (eight DE-mRNA and eight DE-lncRNAs) was verified by qRT-PCR, and the results were consistent with those of RNA-seq. Furthermore, 65 cis targets and 3610 trans targets of DE-lncRNAs were predicted. Functional analyses suggested that multiple metabolic pathways was changed in response to high-fat intake, including PPAR signaling pathway, Fatty acid degradation and Fatty acid metabolism, among others. Co-expression networks was constructed and indicated that most lncRNAs interact with numerous mRNAs involved in lipid metabolism, and vice versa. Additionally, expression patterns analysis of three lncRNAs (MSTRG.14598.1, MSTRG.6725.3 and MSTRG.13364.2) and their potential targets (faldh, slc25a48 and fabp7a) associated with PPAR signaling pathway were investigated. Our study provides a basis for further explore the functions of lncRNAs associated with lipid metabolism in tilapia.

overall_design: mRNA and lncRNA profiles of GIFT fed with HFD NFD for 56 days  were generated by deep sequencing, in triplicate, using Illumina Novaseq™ 6000.

first: Tao

last: Yi-Fan

first: Lu

last: Si-Qi

first: Zheng

first: Li

last: Ming-Xiao

first: Qiang

last: Jun

first: Xu

last: Pao


title: Single cell sequencing of microglia in developing white matter

city: Edinburgh

first: Nizar

middle: N.

last: Batada

address: Crew Road

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

summary: Microglia were FACS-isolated from developing mouse corpus callosum at postnatal days 0, 7, and 21, then sequenced by 10X Genomics single-cell sequencing.

overall_design: C57Bl6J mice were anesthetised and perfused with phosphate buffered saline. Brains were extracted and placed on ice in HBSS with HEPES buffer. Corpus callosi were dissected out and homogenized in glass dounces and filtered. Following centrifugation, cells were resuspended in 10% fetal bovine serum and run through a Percoll gradient. Cells were collected in FACS buffer, spun, and resuspended in HBSS. Myeloid cells were sorted based on expression of Cd11b.

first: Veronique

last: Miron

first: Rebecca

last: Holloway

first: Graeme

last: Ireland

last: Millar


title: microRNA expression profiles of extracellular vehicles released from alveolar macrophage

city: Chang Sha

first: shan

middle: shan

last: Liu

state: Hunan

address: 139 Renmin Zhong Lu

institute: THE SECOND XIANGYA HOSPITAL OF CENTRAL SOUTH UNIVERSITY

summary: Interstitial lung diseases (ILDs) such as idiopathic pulmonary fibrosis (IPF) is diffuse parenchymal lung disorders characterized by varying degrees of inflammation and fibrosis of the lung interstitium. The failure of lung alveolar regeneration in IPF is critical for this incurable disease. Here we report that chronic lung injury causes a profibrotic phenotype of alveolar macrophages that release extracellular vehicles (EVs) to promote PF development through repressing the stemness traits of type 2 alveolar epithelial cells (AEC2s). We found that an increased expression of acetylases KAT5 interacts with and acetylates protein kinase MLKL, which directly promotes release of EVs from AMs following chronic lung injury. AEC2s takes up the EVs and releases miR-148a-3p to repress expression of endogenous b-catennin agonist Wnt10b and alveolar regeneration. Pharmacologic inhibition of the miR-148a-3p expression or interruption of the KAT5-MLKL interaction restores regenerative capacity of AEC2s and exhibits potent therapeutic efficacy against PF. Our study confers a potential strategy for the treatment of IPF and other interstitial lung diseases.

overall_design: miRNA profiles of extracellular vehicles secreted by alveolar macrophage from control and BLM-induced PF mice were generated by deep sequencing, in triplicate, using Illumina NextSeq 500.

first: Shanshan

first: Jiali

last: Min


title: Osteoclast microRNA profiling to capture the erosive factor in rheumatoid arthritis

city: Sherbrooke

first: Sophie

last: Roux

state: Quebec

address: 3001, 12th avenue N

department: Division of Rheumatology

institute: Université de Sherbrooke

summary:
Background: In rheumatoid arthritis (RA), only a subset of patients develop an irreversible bone destruction. Our aim was to develop a microRNA (miR)-based osteoclast-related signature to predict erosiveness in RA.
Results: We identified 5 miRs from PBMC-derived osteoclasts differentially expressed in RNASeq also in qPCR assessment.
Conclusion: We found 5 miRNAs differentially refulated in erosive rheumtoid arhtritis compare to no erosve patient. This study could improve the current approach to identify RA subjects at risk of erosions, by adding biomarker signatures based on the profile of miRs in the osteoclasts.

overall_design: Blood samples were obtained from 8 patients with erosive and  8 with no erosive RA sex- and age- matched controls. Peripheral blood mononuclear cells (PBMCs) were differentiated into osteoclasts in 3-week in-vitro cultures and osteoclast samples were sent to be sequenced using multiplex sequencing on a HiSeq (Illumina) instrument (Genome Quebec).

first: Hoang

last: Nguyen

first: Audrey

last: Lortie

first: Leopold

last: Mbous Nguimbus

first: Javier

last: Marrugo

first: Hugues

last: Allard-Chamard

first: Luigi

last: Bouchard

first: Gilles

last: Boire

first: Michelle

last: Scott


title: RNA sequencing of sham-operated and unilateral ureteral obstruction (UUO)-operated mouse kidneys in Pax8Cre+ and Kdm6afl/Y Pax8Cre+ knockout mice

first: Andrew

last: Advani

state: Ontario

address: 6-151 61 Queen Street East

department: Medicine

institute: St. Michael's Hospital

summary: RNA-sequencing of mouse left kidneys for which the left ureter was obstructed (UUO) or not obstructed (sham) animals, isolated 7 days after the surgery in normal mice and mice in which the Kdm6a gene was deleted from tubule epithelial cells

overall_design: Whole left kidneys were collected from either sham or UUO kidneys of mice and bulk kidney tissue RNA was isolated for sequencing

first: Harmandeep

last: Kaur

first: Sri

last: Nagarjun Batchu


title: Retinoid X Receptor Gamma Dictates Reactivity of Intestinal Group 2 Innate Lymphoid Cells and Constrains Type 2 Inflammation

first: Heping

last: Xu

summary: In this work we report that retinoid x receptor gamma (Rxrg) was highly expressed in small intestinal ILC2s, but rapidly suppressed by alarming cytokines. Genetic deletion of Rxrg didn’t impact ILC2 development, but significantly facilitated ILC2 responses and type 2 inflammation induced by IL-25 or helminths. RXRγ maintained the expression of its target genes that support cholesterol efflux in ILC2s. Chemical inhibition of HMG-CoA reductase rescued the abnormal responses of RXRγ-deficient ILC2s. Furthermore, RXRγ expression in ILC2s protected the host from the intestinal mastocytosis induced by skin injury. We propose that the dynamic regulation of RXRγ expression and it mediated genomic states functions as a cell-intrinsic circuit to determine ILC2 reactivity in the small intestine.

overall_design: Small intestinal ILC2s were flow-sorted from Rxrg+/+ (WT) or Rxrg-/-(KO) mice at the steady state, or treated with IL-25 or PBS for two days. The cells were then subjected to bulk RNA-seq, ATAC-seq or CUT&Tag-seq as indicated. Libraries were pair-end (150+ 150 bp) sequenced on a Hiseq X Ten (Illumina).

first: Yang

last: Zang

first: Shaorui


title: Differential gene expression in MEF SEC24D knockout cells with additional SEC24s knockdown

city: Ames

first: Jinoh

last: Kim

state: IA

address: 515 Morrill Rd

department: Biomedical Sciences

institute: Iowa State University

summary: We transfected MEF SEC24D KO cells with SEC24B siRNA for a double KD or combined SEC24s siRNA (SEC24a, 24B and 24C) for a quadruple KD. Cells were transfected with siRNA or Scramble siRNA (control) for 2 days then total RNA for each knockdown sample was extracted and purified for RNA-seq to evaluate the change in transcriptome.

overall_design: Examination of gene expression in Sec24D knockdown

first: Chung-Ling

last: Lu