title: Sperm-inherited H3K27me3 epialleles are transmitted transgenerationally in cis

status: Public on May 31 2022

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

country: USA

institute: UC Santa Cruz

type: Expression profiling by high throughput sequencing

summary: The role that gamete-inherited chromatin states serve in regulating gene expression across generations is poorly understood. To interrogate how histone marks inherited on parental genomes influence gene expression in offspring, we profiled different tissue contexts in worms that inherited the sperm genome lacking the repressive mark H3K27me3. We found that worms that inherited the sperm genome lacking H3K27me3 upregulated genes in all tissues profiled, which included hermaphrodite and male germlines and mixed soma. We found that most upregulated genes were upregulated specifically from sperm alleles and in a tissue-specific manner, highlighting the importance of cellular context in determining which genes are sensitive to upregulation when H3K27me3 repression is absent. To determine whether chromatin states can impact gene expression transgenerationally, i.e. across 3 generations, we profiled gene expression and chromatin states in the germlines of worms that inherited the sperm genome lacking H3K27me3 (F1 generation) and in the germlines of their offspring (F2 generation). We found that genes upregulated in F1 germlines maintained the H3K27me3(-) state of sperm alleles and that the upregulated and H3K27me3(-) state of sperm alleles was maintained in the germlines of their offspring (F2 generation). These findings demonstrate that histone marks can serve as a transgenerational carrier.

overall_design: We generated genetically identical worms that inherited the sperm genome with H3K27me3 (K27me3 M+P+) or without H3K27me3 (K27me3 M+P-) by mating wild-type females with males heterozygous or homozygous mutant for the PRC2 component MES-3, respectively. We used single nucleotide polymorphisms (SNPs) between the oocyte-inherited (Hawaii/CB4856 genetic background) and sperm-inherited (Bristol/N2 genetic background) genomes to distinguish from which parental genome RNA-sequencing and CUT&RUN (H3K27me3 and H3K36me3) sequencing reads came. We profiled transcripts from 3 tissues in K27me3 M+P- and K27me3 M+P+ worms: hermaphrodite and male germlines and mixed soma.   To assess chromatin and gene expression patterns in germlines across 3 generations, we profiled transcripts and the chromatin marks H3K27me3 and H3K36me3 via CUT&RUN (Skene and Henikoff 2017; Skene et al. 2018) in him-8 males (a surrogate for wild-type fathers), K27me3 M+P- and K27me3 M+P+ offspring (F1 generation) hermaphrodites, and their genetically identical hermaphrodite grandoffspring, K27me3 GM+GP- & K27me3 GM+GP+ (F2 generation).  All germline analysis was performed from distal halves of germlines from day 1 adults. Mixed soma samples were prepared from newly hatched, never starved L1 larvae. For transcript analysis, libraries were prepared from polyA-selected RNA and sequenced to acquire paired-end 50 bp or 75 bp reads on NovaSeq or NextSeq Illumina sequencing platforms. 50 bp reads were mapped (75 bp reads were trimmed to 50 bp) to the ce10 genome in 2 ways: single-end for SNP analysis and paired-end for differential gene expression analysis.   For chromatin analysis, libraries were prepared from DNA associated with H3K27me3 and H3K36me3 collected using the CUT&RUN method and sequenced to acquire paired-end 50 bp or 75 bp reads on NovaSeq or NextSeq Illumina sequencing platforms. 50 bp reads were mapped (75 bp reads were trimmed to 50 bp) to the ce10 genome.

first: Kiyomi

middle: R

last: Kaneshiro

first: Thea

middle: A

last: Egelhofer

first: Andreas

last: Rechtsteiner

first: Chad

last: Cockrum


title: RNA-Sequencing Facilitates Quantitative Analysis of Control and Mettl3 Knockdown LPS-induced Macrophage Transcriptomes

city: Guangzhou

first: Ruiqing

last: Yu

state: Guangdong

address: 56 Ling Yuan Xi Road

country: China

institute: Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University

summary: The goal of this study is to investigate the potential role of Mettl3 in the innate immune response by RNA-seq

overall_design: The RAW264.7cells were transfected with shMettl3 to knock down Mettl3 expression, and RNA-seq was performed for cells after LPS stimulation for 24 h

first: Yongjie

last: Cai

first: Qiong

last: Xu


title: Research on the mode of action of a novel 2-cyclopropyl-4-aminopyrimidine hydrazine compound (4k) for control of cyanobacteria

city: Wuhan

first: Meng

state: Hubei

address: NO.152 Luoyu Road

institute: Central China Normal University

summary: We reported the transcriptomics files of cyanobacteria treated by compound 4k, which exhibited a good algicidal activity. The results revealed that the transcription of genes in the photosynthesis pathways, such as thylakoid and PSI pathway, were affected by 4k, which was validated by the qPCR results. Photosynthesis parameters was further measured and showed that photosynthesis were significantly affected by 4k treatments.

overall_design: mRNA profiles of Synechocystis sp. PCC6803 cells treated by 1 μM and 3 μM of 4k, using DMSO treatment as a control. Three independent biological replicates were performed for each treatment.

first: Yingying

last: Qin

first: Yuan

last: Zhou

first: Hongwu

last: He


title: Senolytics rescue blunted muscle hypertrophy in old mice

status: Public on May 29 2022

city: Lexington

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

summary: With aging, skeletal muscle plasticity is attenuated in response to exercise. Here, we report that senescent cells, identified using senescence markers senescence-associated β-Galactosidase (SA β-Gal) and p21 are very infrequent in resting muscle but emerge approximately two-weeks after a bout of resistance exercise in humans. We hypothesized that these cells contribute to blunted hypertrophic potential in old age. Using synergist ablation-induced mechanical overload of the plantaris muscle to model resistance training in adult (5-6 month) and old (23-24 month) male C57BL/6J mice, we found increased senescent cells in both age groups during hypertrophy. Consistent with the human data, there were negligible senescent cells in adult and old sham controls, but old mice had significantly more senescent cells 7- and 14-days following overload relative to young. Old mice had blunted whole muscle hypertrophy when compared to adult mice, along with smaller muscle fibers, specifically glycolytic Type 2x+2b fibers. To ablate senescent cells using a hit-and-run approach, old mice were treated with vehicle or a senolytic cocktail consisting of 5 mg/kg dasatinib and 50 mg/kg quercetin (D+Q) on day 7 and 10 during 14-days of overload; control mice underwent sham surgery with or without senolytic treatment. Old mice given D+Q had larger muscles and muscle fibers after 14 days of overload, fewer senescent cells when compared to vehicle-treated old mice, and changes in the expression of genes (i.e., Igf1, Ddit4, Mmp14) that are associated with hypertrophic growth . Our data collectively show that senescent cells emerge in human and mouse skeletal muscle following a hypertrophic stimulus, and that D+Q improves muscle growth in old mice.

overall_design: Mice (N=5 per group) were treated with vehicle or senolytics 7 and 10 days following synergist ablation (mechanical overload) surgery. Mice were then euthanized 14 days following surgery. Control (sham) mice were treated with vehicle or senolytics 7 and 14 days following a sham surgery.

first: Dungan

last: Cory


title: Dual Morphologic Subtypes of High-Grade Serous Ovarian Cancer

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

summary: We identified novel, gross morphology-based subtypes of high-grade serous ovarian cancer, with unique clinical features and molecular signatures.

overall_design: We performed RNAseq analysis of untreated high-grade serous ovarian cancer samples and correlated gene expression with morphological and histological information

first: Katelyn

middle: F

last: Handley

first: Travis

middle: T

last: Sims

first: Nicholas

middle: W

last: Bateman

first: Dean

last: Glassman

first: Katherine

middle: I

last: Foster

first: Sanghoon

last: Lee

first: Jun

last: Yao

first: Hui

first: Bryan

middle: M

last: Fellman

first: Jinsong

last: Liu

first: Zhen

last: Lu

first: Kelly

last: Conrads

first: Brian

middle: L

last: Hood

first: Waleed

last: Barakat

first: Li

last: Zhao

first: Jianhua

last: Zhang

first: Shannon

middle: N

last: Westin

first: Joseph

last: Celestino

last: Rangel

first: Sunil

last: Badal

first: Pereira

last: da Silva

first: Prahlad

last: Ram

first: George

last: Maxwell

first: Livia

middle: S

last: Eberlin

first: Andrew

middle: P

last: Futreal

first: Robert

middle: C

last: Bast

first: Nicole

middle: D

last: Fleming

first: Thomas

first: Anil

middle: K

last: Sood


title: Regulation of erythropoiesis in the spleen by Desert Hedgehog (Dhh)

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

summary: Dhh negatively regulates multiple stages of erythrocyte differentiation. In Dhh-deficient bone marrow, the common myeloid progenitor (CMP) population was increased, but differentiation from CMP to granulocyte/macrophage progenitor was decreased, and the mature granulocyte population was decreased, compared with wild-type (WT). In contrast, differentiation from CMP to megakaryocyte/erythrocyte progenitor was increased, and the megakaryocyte/erythrocyte progenitor population was increased.  In Dhh-deficient spleen and bone marrow, BFU-Es and erythroblast populations were increased compared with WT. During recovery of hematopoiesis after irradiation, and under conditions of stress-induced erythropoiesis, erythrocyte differentiation was accelerated in both spleen and bone marrow of Dhh-deficient mice compared with WT.  To investigate possible mechanisms for its regulation of erythropoiesis we carried out RNAsequencing on Facs-sorted erythroblast population II (CD71+Ter119+) cells from Dhh-/-, Dhh+/- and WR mice.

overall_design: Splenocyte suspensions were prepared from 4 week old Wildtype (WT), Dhh heterozygous (Dhh+/-) and Dhh knockout (Dhh-/-) mice spleen.  Cells were stained against Ter119 and CD71 and facs sorted to purify CD71+Ter119+ cells.  RNA was extracted from this CD71+Ter119+ cells defined as erythroblast population II.

first: Sonia

last: Norris


title: RNA-Seq of pancreatic cancer cell line CAPAN-2 with or without SIRT4 overexpression

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

summary: We profile gene expression with or without SIRT4 overexpression in pancreatic cancer cell line CAPAN-2 to find the different genes and pathways regulated by SIRT4.

overall_design: The gene expression changes are analyzed by comparing SIRT4 group to ctrl group in CAPAN-2 cells.

first: Juan

last: Li


title: Exploring Relevant mRNAs and miRNAs in Injured Urethral Tissues of Rats with High-Throughput Sequencing

city: Kunming

first: Han

last: Lin

state: Yunnan

address: No. 295, Xichang Road

department: Department of Urology

institute: The First Affiliated Hospital of Kunming Medical University

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Exploring Relevant mRNAs and miRNAs in Injured Urethral Tissues of Rats with High-Throughput Sequencing [miRNA-seq]

summary: Acute urethral injuries caused by urethral endoscopy and other mechanical injuries are the main reasons for secondary infection and late urethral stricture. However, there are no studies to explore the transcriptomic changes in urethral injury and the molecular mechanism of urethral injury, which is important for the treatment and cure of urethral injury. Therefore, we used RNA-seq and sRNA-seq profiles from normal and injured urethral tissues to identify and characterize differentially expressed mRNAs and miRNAs. In total, we found 166 differentially expressed mRNAs, of which 69 were upregulated, and 97 were downregulated in injured urethral tissues. The differentially expressed mRNAs were mainly involved in the positive regulation of epithelial cell differentiation, focal adhesion, cell adhesion molecules, protein activation cascade, complement activation, complement and coagulation cascades, and chemokine-mediated signaling pathway. Additionally, we found six upregulated and four downregulated miRNAs, respectively, in the injured urethral tissues. Notably, their target genes were involved in the vascular endothelial growth factor receptor 2 binding, PI3k-Akt signaling pathway, and Notch signaling pathway. In summary, our results suggest that the cell damage response induced by mechanical injury activates the pathological immune response in a variety of ways in injured urethral tissues.

overall_design: MiRNA profiles of urethral tissues in Sprague-Dawley Rats (Rattus norvegicus) were generated by deep sequencing.


title: Study on the role and mechanism of lupeol in acute myeloid leukemia

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

institute: Henan University

summary: We investigated the mechanism of action of lupanol on THP-1 cells and further determined the effect of lupanol on PI3K/AKT signaling pathway

overall_design: Detection of transcription level in THP-1 cells treated with lupeol

first: Qingling

last: Ma

first: Yaru

last: Ye


title: Comparative transcriptomes of WT or jasmonic acid oxidase 2-1 (jao2-1) rosette leaves before or after inoculation with Botrytis cinerea spores

city: Strasbourg

first: Thierry

last: HEITZ

address: 12 rue du General Zimmer

department: IBMP

country: France

institute: CNRS

summary:
The deficiency of Jasmonic Acid Oxidase 2 (JAO2) disrupts a metabolic sink in jasmonate hormonal pathway. Consequently, higher flux towards hormone JA-Ile is observed and some leaf JA responses have elevated basal levels relative to wild-type (WT) leaves.
We report the compared transcriptomes of WT and jao2-1 rosette leaves, before and 48h after inoculation with spores of the fungus Botrytis cinerea. The study reveals the set of jao2-deregulated genes before infection

overall_design: RNA from 6-week old rosette leaves cultivated under 12h light/12h dark photoperiod

last: Heitz

first: Valentin

last: Marquis

first: Stéfanie

last: Graindorge


title: The effect of 2HG level on transcriptome at different stages of male mouse meiosis

city: Jerusalem

first: Eli

last: Pikarsky

address: Ein Karem

department: The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University-Hadassah Medical School

summary: We found that L2-hydroxyglutarate (2HG) level is 15 times higher in pachytene-diplotene (PD) stage as compared to leptotene-zygotene (LZ) stage. Since 2HG shows epigenetic effects we asked if the addition of 2HG to LZ cells or the decrease of 2HG level in PD cells will cause changes in gene expression.

overall_design: LZ and PD cells were isolated using flow cytometry from mice expressing tdTomato in germ cells. LZ cells were cultured for 6 days without and with 0.3 mM cell-permeable L2HG. PD cells were cultured for 48 hours without and with 24 mM oxamate, which reduces 2HG level to that of LZ cells. Three independant experiments were performed. RNA was isolated using Qiagen kit and RNA seq was performed .

first: Nina

last: Mayorek


title: NanoString immune gene expression analysis of PARP inhibitor and STING agonist treated mouse breast tumors

city: Boston

first: Geoffrey

last: Shapiro

state: MA

address: Dana Farber Cancer Inst 450 Brookline Avenue Mayer 446

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: This study aimed to assess changes in immune gene expression and immune-related pathways in mouse tumors from syngeneic mice treated with combined PARP inhibitor and STING agonist therapy. The objective was to identify differentially expressed genes related to immune oncology in response to the combination treatment as compared to single treatments, in order to gain mechanistic insight into the enhanced anti-tumor efficacy of the combination treatment.

overall_design: Four treatment groups (Vehicle, ADU-S100, Olaparib, Olaparib+ADU-S100), 3 tumors per treatment group (total 12 samples). Control group is vehicle.

first: Constantia

last: Pantelidou

first: Heta

last: Jadhav


title: To explore the change of the gut microbiota in yki3SA tumor-bearing flies by metagenomics sequencing.

status: Public on May 30 2022

first: Yuchen

last: Chen

address: Donghu road 115

institute: Wuhan University

summary: To investigate the effect of gut microbiota on host wasting, we established a wasting model in fly by activation of Yki in adult midgut ISCs, in which the host flies present the sysytmeic organ wasting and metabolic abnormalities.

overall_design: We then performed species composition and diversity analysis, gene expression profiling analysis using data obtained from meta-seq of control and yki3SA tumor-bearing flies.Comparative species composition and diversity analysis,gene expression profiling analysis of meta-seq data for control and yki3SA tumor-bearing flies.


title: RNAseq of 6 cell populations along spermatogenesis

summary:
Purpose: Analysing gene expression changes along mose spermatogenesis
Method:The novel method  of the isolation of 6 populations of cells at sequantial developmental stages -from undifferentiated spermatogonia (Undiff.Spg), differentiating spermatogonia (Diff.Spg), preleptotene (PreL), leptotene/zygotene (LZ), pachytene/diplotene (PD) and  round spermatids (RS) was developed.
Results: Median sequencing depth was ~18 million reads per sample. Sequencing depth was homogenous across samples in the experiment. We found a profound shift in gene expression between LZ and PD populations.

overall_design: Germ cells mRNA profiles of 6 populations of cells isolated from adult male mice in triplicates.

first: Yousef

last: Mansour


title: Onepot-Seq: capturing single-cell transcriptomes simultaneously in a continuous medium via transient localization of mRNA

city: Seoul

first: Dongju

last: Shin

address: 50, Yonsei-ro

department: Chemistry

country: South Korea

institute: Yonsei University

summary: The development of single-cell RNA-seq has broadened the spectrum for biological research by providing a high-resolution analysis of cellular heterogeneity. However, the requirement for sophisticated devices for the compartmentalization of cells has limited its widespread applicability. Here, we develop Onepot-Seq, a device-free, well-based method, that harnesses the transient localization of mRNA after lysis to capture single-cell transcriptomes simultaneously in a continuous fluid medium. In mixed-species experiments, we obtained high-quality single-cell profiles. Further, cell-type-specific poly(A)-conjugated antibodies allow Onepot-Seq to effectively capture target cells in complex populations. Chemical perturbations to cells can be profiled by Onepot-Seq at single-cell resolution. Onepot-Seq should allow routine transcriptional profiling at single-cell resolution, accelerating clinical and scientific discoveries in many fields of science.

overall_design: single cell transcriptomes were captured in one pot

first: Jungwon

last: Choi

first: JiHyun

last: Lee

first: Duhee

last: Bang


title: DNMT3A mutations define a unique biological and prognostic subgroup associated with cytotoxic T-cells in PTCL-NOS [RNA-Seq]

city: Omaha

first: Chengfeng

last: Bi

state: Nebarska

address: 42nd and, Emile St

institute: University of Nebraska Medical Center

summary: Peripheral T-cell lymphomas (PTCLs) are heterogenous T-cell neoplasms often associated with epigenetic dysregulation. We investigated de novo DNA methyltransferase 3A (DNMT3A) mutations in common PTCL entities, including angioimmunoblastic T-cell lymphoma and novel molecular subtypes identified within PTCL-not otherwise specified (PTCL-NOS) designated as PTCL-GATA3 and PTCL-TBX21. DNMT3A-mutated PTCL-TBX21 cases showed inferior overall-survival, with DNMT3A mutated residues skewed towards the methyltransferase domain and dimerization motif (S881–R887). Transcriptional profiling demonstrated significant enrichment of activated CD8+ T-cell cytotoxic gene signatures in the DNMT3A-mutant PTCL-TBX21 cases, which was further validated using immunohistochemistry. Genome-wide methylation analysis of DNMT3A-mutant versus wild-type PTCL-TBX21 cases demonstrated hypomethylation in target genes regulating IFN-g, TCR signaling and EOMES, a master transcriptional regulator of cytotoxic effector cells. Similar findings were observed in a murine model of PTCL with Dnmt3a loss (in-vivo) and further validated in-vitro by ectopic expression of DNMT3A-mutants (DNMT3A-R882, -Q886, -V716, versus WT) in CD8+T-cell line, resulting in T-cell activation and EOMES upregulation. Furthermore, stable, ectopic expression of the DNMT3A-mutants in primary CD3+ T-cell cultures resulted in the preferential outgrowth of CD8+ T-cells with DNMT3AR882H mutation. Single-cell-RNA-seq analysis of CD3+ T-cells revealed differential CD8+ T-cell subset polarization, mirroring findings in DNMT3A-mutated PTCL-TBX21 and validating the cytotoxic and T-cell memory transcriptional programs associated with the DNMT3AR882H mutation.  Our findings indicate that DNMT3A mutations define a cytotoxic subset in PTCL-TBX21 with prognostic significance, thus may further refine pathological heterogeneity in PTCL-NOS and suggest alternative treatment strategies for this subset.

overall_design: T8ML1 cells were transduced with empty LeGO-iG2 or vector containing WT DNMT3A or DNMT3A mutants, sorted for GFP expression, expanded after sorting,  and then RNA-seq was conducted. Similar to how in the ScRNA description you specified they were cultured following sorting and then RNA-seq was performed

first: Tyler

last: Herek

first: Alyssa

last: Bouska

first: Waseem

last: Lone

first: Sunandini

last: Sharma

first: Catalina

last: Amador

first: Tayla

last: Heavican

first: Yuping

last: Li

first: Qi

last: Wei

first: Dylan

last: Jochum

first: Timothy

last: Greiner

first: Lynette

last: Smith

first: Stefano

last: Pileri

first: Andrew

last: Feldman

first: Andreas

last: Rosenwald

first: German

last: Ott

first: Soon

last: Lim

first: Choon

last: Ong

first: Joo

last: Song

first: Elaine

last: Jaffe

first: Greg

last: Wang

first: Louis

last: Staudt

first: Lisa

last: Rimsza

first: Julie

last: Vose

first: Francesco

last: d'Amore

first: Dennis

last: Weisenburger

first: Wing

last: Chan

first: Javeed

last: Iqbal


title: Exploring Relevant mRNAs and miRNAs in Injured Urethral Tissues of Rats with High-Throughput Sequencing [RNA-seq]

first: Han

last: Lin

overall_design: RNA profiles of urethral tissues in Sprague-Dawley Rats (Rattus Norvegicus) were generated by deep sequencing.


title: Murine lung transcriptomes of Neiserria subclava and Pseudomonas aeruginosa infection

city: Singapore

first: Hong Sheng

last: Cheng

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine,

country: Singapore

institute: Nanyang Technological University

summary: To characterize the dynamic changes and differences of lung transcriptomic profiles induced by intratracheal infection of Neiserria subclava and Pseudomonas aeruginosa over a 14-day course.

overall_design: For intratracheal mouse infection experiments, 6-10 week old C57BL/6 mice were anesthetized using 80 mg/kg body weight ketamine and 10 mg/kg body weight xylazine and infected via intratracheal delivery with the Neisseria subflava (isolate SG-KL01) and Pseudomonas aeruginosa at 2 x 107 CFU in sterile phosphate-buffered saline (PBS). Mice were euthanized on Day 0, 2, 4, 7 , and 14 and the lung tissues were harvested and snap frozen in liquid nitrogen for total RNA extraction.

first: Liang

last: Li

first: Micheál

last: Mac Aogáin

first: Hong-Sheng

first: Nguan-Soon

last: Tan

first: Sanjay-Haresh

last: Chotirmall


title: DNMT3A mutations define a unique biological and prognostic subgroup associated with cytotoxic T-cells in PTCL-NOS [meDIP-Seq]

first: Chengfeng

last: Bi

type: Methylation profiling by high throughput sequencing

overall_design: T8ML1 cells were transduced with  LeGO-iG2 vector containing WT DNMT3A or DNMT3A mutatants, sorted for GFP expression, and then RNA-seq was performed

first: Tyler

last: Herek

first: Alyssa

last: Bouska

first: Waseem

last: Lone

first: Sunandini

last: Sharma

first: Catalina

last: Amador

first: Tayla

last: Heavican

first: Yuping

first: Qi

last: Wei

first: Dylan

last: Jochum

first: Timothy

last: Greiner

first: Lynette

last: Smith

first: Stefano

last: Pileri

first: Andrew

last: Feldman

first: Andreas

last: Rosenwald

first: German

last: Ott

first: Soon

last: Lim

first: Choon

last: Ong

first: Joo


title: DNMT3A mutations define a unique biological and prognostic subgroup associated with cytotoxic T-cells in PTCL-NOS

first: Chengfeng

last: Bi


title: Gene expression in murine regulatory T cells in chronic lymphocytic leukemia

city: Luxembourg

first: Etienne

last: Moussay

address: 6 rue Nicolas-Ernest Barblé

department: Cancer Research

country: Luxembourg

institute: Luxembourg Institute of Health

summary: mRNA profiles were generated by 3'-sequencing, in triplicate from different regulatory T cells populations of 8-week-old Foxp3-EGFP mice, healthy (Ctrl) or leukemia-bearing (TCL1) .

overall_design: mRNA profiles of sorted Treg from Foxp3-EGFP mice (Ctrl) and with leukemia (subsets A CD44low CD69+ LAG3high and subset B CD44high CD69+ LAG3low)

first: Jerome

last: Paggetti


title: Low cost transcriptomic mapping of TMT associated neurotoxicity using human minibrains

city: Geneve

first: subashika

last: govindan

state: Geneve

address: chemins de mine 9

country: Switzerland

institute: HEPIA-HESO

summary: RNA sequencing was performed on minibrains exposed to distinct doses and treatment exposures of TMT using BRB sequencing.

overall_design: We collected transcriptome of minibrains (derived from human induced neural stem cells derived from iPScs) exposed to 0uM, 1uM, 2.5uM and 5uM for 1 day, 3 days and 1 week.

first: Subashika

last: Govindan

first: Adrien

last: Roux


city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

institute: University of Geneva

summary: Short- and long-distance extrinsic regulation of interneuron specification and migration.

overall_design: We performed single-cell RNA-seq on 60 days ventral and dorsal organoids (COs). From each condition, 5 COs were dissected and processed.

first: Fabrizia

last: Pipicelli

first: Silvia

last: Cappello

first: Natalia

last: Baumann


title: Phytochrome B regulates reactive oxygen signaling during stress in plants.

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: Plants are essential for life on Earth converting light into chemical energy in the form of sugars. To adjust for changes in light intensity and quality, and to become as efficient as possible in harnessing light, plants evolved multiple light receptors, signaling, and acclimation mechanisms. In addition to altering plant metabolism, development and growth, light cues sensed by some photoreceptors, such as phytochromes, are also impacting many plant responses to biotic and abiotic stresses. Central for plant responses to different stresses are reactive oxygen species (ROS) that function as key signaling molecules. Recent studies demonstrated that respiratory burst oxidase homolog (RBOH) proteins that reside at the plasma membrane and produce ROS at the apoplast play a key role in plant responses to different biotic and abiotic stresses. Here we reveal that phytochrome B (phyB) and RBOHs function as part of a key regulatory module that controls ROS production, transcript expression, and plant acclimation to excess light stress. We further show that phyB can regulate ROS production during stress even if it is restricted to the cytosol, and that phyB, RBOHD and RBOHF co-regulate thousands of transcripts in response to light stress. Surprisingly, we found that phyB is also required for ROS accumulation in response to heat, wounding, cold, and bacterial infection. Taken together, our findings reveal that phyB plays a canonical role in plant responses to biotic and abiotic stresses, regulating ROS production, and that phyB and RBOHs function in the same regulatory pathway.

overall_design: mRNA from 4 week old WT, phyB, rbohD and rbohF plants non-treated, after 10 min of white ligh or 10 min of red light (600-700nm)

first: Yosef

last: Fichman

first: Haiyan

last: Xiong

first: Rajeev

last: Azad

first: Julian

last: Hibberd

first: Emmanuel

last: Liscum

first: Ron

last: Mittler


title: Explore the gene expression files of HGECs after P. gingivalis persisters treatment via RNA sequencing

city: Hong Kong

first: Chuan

last: Wang

address: 34 Hospital Road, Sai Ying Pun

department: Faculty of Dentistry

country: Hong Kong

institute: The University of Hong Kong

summary: This study investigated how P. gingivalis persisters interacted with human gingival epithelial cells (HGECs) and affected the gene expression of cytokines, and the related signaling pathways, via RNA sequencing. P. gingivalis (ATCC 33277) was treated with metronidazole (100 μg/ml) for 6 hours to generate P. gingivalis persisters (M-PgPs). HGECs with or without IL-1β pretreatment were stimulated by M-PgPs and P. gingivalis for 24 hours, and those without any treatments served as the blank control (BL).

overall_design: HGECs were divided into 6 groups: HGECs without any treatments (BL), M-PgPs treated, P. gingivalis treated,  IL-1β treated (NC), IL-1β + M-PgPs treated,  IL-1β + P. gingivalis treated. Each group has 3 replications.

first: Xuan

last: Li

first: Tianfan

last: Cheng

first: Leilei

first: Lijian

last: Jin


title: Identification of HOTAIR target genes using RNA-seq after overexpression (OE) and downregulation (si) of HOTAIR in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GF) subcutaneous adipose tissue

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

summary: Human adipose serived stem cells (ASC) isolated from A and GF adipose tissue obtained from premenopausal women were used to overexpress and downregulate HOTAIR (respectively). RNA-seq was used to study the transcriptome of control and treated cells.

first: T

last: Osborne

first: S

last: Smith


title: Placental Interferon Signaling is Involved in Chronic Intervillositis of Unknown Etiology

city: VANCOUVER

first: Jefferson

last: Terry

state: British Columbia

address: 4480 Oak Street, Room 2H60

country: Canada

institute: Anatomical Pathology

summary: GeoMX digital spatial profiling is used to explore gene expression patterns in inflammatory and other pathways in chronic intervillositis of unknown etiology (CIUE).

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Gene expression patterns in placenta and intervillus macrophages in CIUE placenta (4 cases) are compared to normal placenta (4 cases) and granulomatous lymhpadenitis macrophages (4 cases) controls respectively using GeoMX DSP and nCounter sequencing.


title: PngCMs isolated exhibit better potential in cardiac repair and in CM subtype differentiation

city: Durham

first: Li

address: 111 T.W. Alexander Dr

institute: NIH

summary: CMs were isolated from Myh6-Cre/Esr1;R26-tdTomato mice at P1 and P7,which were permanently labeled with RFP upon treatment with tamoxifen immediately after birth, and injected resulting CMs into infarcted mouse hearts induced by LAD ligation. After two weeks, RFP+ cells were isolated by FACS and subjected to scRNA-Seq.

overall_design: Single cell RNA-Seq of mouse heart CMs labeled with RFP.

first: Fang

last: Yao

first: Zheng


title: Reduced placental expression of Regulator of G Protein Signaling-2 during preeclampsia

status: Public on May 28 2022

city: Iowa City

first: Justin

last: Grobe

state: IA

address: 2-300 Bowen Science Building, Iowa City, IA 52242

department: Pharmacology

institute: University of Iowa

summary: This experiment examined effects of reduced placental Regulator of G protein Signaling-2 (Rgs2) upon the placental transcriptome in C57BL/6J mice at gestational day 12.5.

overall_design: A selective breeding strategy in which wildtype C57BL/6J dams were mated with Rgs2-deficient (Rgs20KO) sires or with wildtype male littermates of these Rgs2-KO sires. These matings resulted in pregnant wildtype C57BL/6J dams carrying feto-placental units that were either heterozygous for Rgs2 or wildtype, respectively. Total RNA from whole placenta at GD 12.5 was isolated, and transcriptomes were assessed by RNAsequencing.

first: Katherine

middle: J

last: Perschbacher

first: Guorui

last: Deng

first: Jeremy

last: Sandgern

first: Donna

last: Santillan

first: Gary

last: Pierce

first: Curt

last: Sigmund

first: Mark


title: Combining LSD1 and JAK-STAT inhibition targets Down syndrome-associated myeloid leukemia at its core

status: Public on May 27 2022

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

summary:
We investigated the combination of the irreversible LSD1 inhibitor T-3775440 and the JAK1/JAK2 inhibitor ruxolitinib as novel therapeutic approach in ML-DS which is specifically designed to target key hallmarks of ML-DS leukemogenesis.
We observed synergistic anti-leukemic effects by combining both drugs. To elucidate the underlying molecular mechanisms we performed RNAseq in two independent patients samples treated with vehicle, LSD1 inhibitor or ruxolitinib monotherapy or the combination of both drugs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ML-DS samples of two different patients treated with DMSO, the LSD1 inhibitor T-3775440, ruxolitinib, or the combination of T-3775440 and ruxolitinib for 48 hours in vitro. Experiment was conducted with two replicates per condition.

first: Juliane

last: Grimm


title: The gene expressional profiles between A172 glioma cells and the derived TMZ-resistance cells

city: Tainan

first: Kwang-Yu

last: Chang

address: 367 Sheng-Li Road

country: Taiwan

institute: National Institute of Cancer Research, National Health Research Institutes

summary: We want to investigate whether there is an aquired resistance in glioma cells after TMZ treatment.

overall_design: We use the parental A172 cells and the resistant A172 clone cells selected by TMZ to examine the gene levels.

first: Chia-Hung

last: Chien

first: Shang-Hung

last: Chen


title: Hypoxia inhibits HUNK-mediated phosphorylation of GEF-H1 for epithelial-to-mesenchymal transition

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

summary: Hypoxia regulates epithelial to mesenchymal transition (EMT) of cancer cells. However, the mechanism underlying hypoxia-mediated EMT remains largely unknow. Here, utilizing colorectal cell carcinoma (CRC) as a model, we find that HUNK inhibits EMT and suppresses metastasis of CRC cells via its substrate GEF-H1 in a kinase-dependent manner. Mechanistically, HUNK directly phosphorylates GEF-H1 at ser645 site, which activates RhoA and consequently leads to a cascade of phosphorylation of LIMK1/CFL-1, thereby stabilizing F-actin and inhibiting EMT. Moreover, hypoxia suppresses HUNK activity and dephosphorylates GEF-H1 to promote EMT. Clinically, the expression levels of both HUNK and phosphorylation of GEH-H1 ser645 are not only downregulated in CRC tissues with metastasis compared to that without metastasis, but also positively correlated among these tissues. Our findings highlight the importance of hypoxia-regulated HUNK kinase activity and phosphorylation of GEF-H1 in regulation of EMT and metastasis of CRC.

overall_design: We conducted total RNA sequencing after HUNK genes were knocked out in SW480 cell lines. Totally 6 samples were generated.

first: Qinong

last: Ye

first: Xiaoqi

last: Han

first: Siyuan

last: Jiang

first: Yinmin

last: Gu

first: Enhao

last: Zhao

first: Dongxing

last: Cao

first: Xiaodong

last: Wang

first: Ya

last: Wen

first: Yongbo

last: Pan

first: Xin

last: Yan

first: Liqing

last: Duan

first: Yibo

last: Xi

first: Minxuan

last: Sun

first: Tao

last: Zhou

first: Lina

last: Shang

first: Yajuan

last: Liu


title: Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Rat]

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

summary:
Purpose: To reveal the differences on epithelial cell composition, functional assignments and pharmacokinetics among mammals intestine, we use single cell sequencing to examine the conserved and divergent features among species, providing a cross-species single-cell transcriptomic atlases of ileal epithelium
Methods:Alive ileum epithelial cells were sorted from three adult rats (3 months old). ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000. Raw reads were aligned to the Rnor_6.0 Rat genome, and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs). Raw aligned features were loaded and processed using the Seurat package (v4.0.2). Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes.
Results: After cells with low information content and a high fraction of mitochondrial RNAs were excluded, 3040 cells were analyzed.
Conclusions: Seven cell types were identified in rat ileum based on reported markers, including enterocytes, transient-amplifying (TA) cells, goblet cells, goblet progenitor cells, stem cells, enteroendorcine cells and tuft cells.

overall_design: Single cell profiles of ileum epithelial cells from adult rats

first: Ye-Guang

first: Haonan

last: Li

first: Xiaodan

first: Yalong

first: Mengxian

last: Zhang

first: Fan

last: Hong

first: Hong

first: Along

last: Cui

first: Jianguo

first: Weizhi

last: Ji


title: The circRNA expression profiles of reticulocytes for β-thalssemia carriers with high fetal hemoglobin

city: Nanning

first: Ketong

last: Lai

address: Shuangyong Road

department: Department of Pediatrics

institute: the First Affiliated Hospital of Guangxi Medical University

summary: To explore the involvement of circRNAs in β-thalassemia and their actions on fetal hemoglobin (HbF), we surveyed circRNA expression profiles using circulating reticulocytes isolated from individuals with β-thalassaemia carriers with high HbF.

overall_design: Reticulocytes were isolated from the peripheral blood of healthy controls (n=3) and β-thalassemia carriers with high HbF (n=3). All 6 samples were analyzed for circRNAs expression.

first: Ke


title: Intron retention and down-expression of defense response-related genes together affect the susceptibility of mutants pls4 to rice sheath bligh

city: Nanchang

first: shaochun

address: Jiaoqiao town

institute: Jiangxi Agricultural University

summary: Pls4 is a gene encoding a β -ketoacyl carrier protein reductase (KAR), which is mainly involved in biological processes such as cell membrane formation. However，the role of pls4 in rice sheath blight remains unclear. Our preliminary studies showed that rice pls4 mutants were highly susceptive to sheath blight in early development stage, and insensitive in adulthood. To explore the role of this gene in the occurrence of rice sheath blight, we compared the transcriptome profiles of rice pls4 mutant and wild-type by RNA-seq. The results showed that, 2569 differentially expressed genes (DEGs), and down-regulated genes were significantly enriched in defense response related biological stress. The expression pattern significantly changed in genes related to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), which were the main two innate immunity pathways in plants. The chitinase-related genes were mainly down-regulated, while both the disease-related genes and the related genes of the WRKY gene family were significantly up-regulated. Furthermore, 467 genes had significantly alternative splicing (AS) events. Among them, intron retention (IR) affected the gene expression levels and functions in vitamin B6 (VB6) metabolism pathway, which was related to sheath blight. This suggested that IR played an important role in sheath blight resistance of mutant pls4. In conclusion, these studies suggested that pls4 might be involved in the biological stress process of sheath blight by DEGs and the fine-tuning of IR, which would provide a molecular basis for the study of rice sheath blight resistance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type and pls4 mutant.

first: Shaochun

first: Jiamin

last: Hu

first: Dahu

first: Haihui

last: Fu


title: MtBZR1 plays an important role in nodule development in Medicago truncatula

city: qingdao

first: yang

last: zhao

address: binhai road72#

institute: shandong university

summary: Brassinosteroid (BR) is an essential hormone in plant growth and development. BR signaling pathway has been extensively studied, in which Brassinazole resistant 1 (BZR1) functions as a key regulator. Here, we carried out a functional study of the homolog of BZR1 in Medicago truncatula, whose expression was induced in nodules upon rhizobial inoculation. We identified a loss-of-function mutant mtbzr1-1 and generated 35S:MtBZR1 transgenic lines for further analysis at the genetic level. Both the mutant and the overexpressor lines of MtBZR1 showed no obvious phenotypic changes under normal growth condition. After rhizobial inoculation, however, the shoot and root dry mass was reduced in mtbzr1-1 compared with the wild-type, caused by partially impaired nodule development. The transcriptomic analysis identified 1,319 differentially expressed genes in mtbzr1-1 compared with wild-type, many of which are involved in nodule development and secondary metabolite biosynthesis. Our results demonstrate an essential role of MtBZR1 in nodule development in M. truncatula, shedding light on the potential role of BR in legume-rhizobium symbiosis.

overall_design: Five-day-old seedling of wild-type, mtbzr1-1, and were inoculated with 5 mL with Sinorhizobium meliloti 1021. The nodule tissue were harvested 28dpi. RNA samples were sequenced on a BGISEQ-500 platform as eukaryotes samples following the manufacturer’s instructions at BGI Genomics Institute (BGI-Shenzhen, China). About 22 million raw reads were generated for each sample. Adapter sequences, low-quality reads and reads containing more than 5% unknown nucleotide were first filtered out by trimmonmatic (v0.37).

first: Can

first: Limei

first: Hongfeng

last: Wang

first: Yiteng

last: Xu

first: Chuanen

first: Yang

last: Zhao


title: Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Pig]

first: Ye-guang

summary:
Purpose: To reveal the differences on epithelial cell composition, functional assignments and pharmacokinetics among mammals intestine, we use single cell sequencing to examine the conserved and divergent features among species, providing a cross-species single-cell transcriptomic atlases of ileal epithelium
Methods:Alive ileum epithelial cells were sorted from three adult pigs (6 months old). ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000. Raw reads were aligned to the Sscrofa11.1 Pig genome, and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs). Raw aligned features were loaded and processed using the Seurat package (v4.0.2). Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes.
Results: After cells with low information content and a high fraction of mitochondrial RNAs were excluded, 730 cells were analyzed.
Conclusions: Eight cell types were identified in pig ileum based on reported markers, including enterocytes, transient-amplifying (TA) cells, goblet cells, goblet progenitor cells, stem cells, enteroendorcine cells, CA7+ cells and tuft cells.

overall_design: Single cell profiles of ileum epithelial cells from adult pigs

first: Ye-Guang

first: Haonan

first: Xiaodan

first: Yalong

first: Mengxian

first: Fan

first: Hong

first: Along


title: Epigenome screen suggests DNA methylation may affect beef tenderness through signal transduction in Bos indicus

city: Sao Carlos

first: Simone

middle: C M

last: Niciura

state: Sao Paulo

address: Rodovia Washington Luiz, Km 234

country: Brazil

institute: Embrapa

summary: Beef tenderness is a complex trait of economic importance for the beef industry. Understanding the genetic and epigenetic mechanisms underlying this trait may help improve the accuracy of breeding programs and deliver a better product quality to consumers. However, little is known about epigenetic effects in the muscle of Bos taurus and their implications in tenderness, and no studies have been conducted in Bos indicus. Therefore, we analyzed Reduced Representation Bisulfite Sequencing (RRBS) to search for differences in the methylation profile of Bos indicus skeletal muscle with extreme values for beef tenderness (tender = 6 animals, tough = 6 animals).

overall_design: Reduced representation bisulfite sequencing (RRBS). Six muscle of animal showing higher shear force values (lower tenderness) and six muscle of animals showing lower shear force values (higher tenderness).

first: Marcela

last: de Souza

first: Marina

last: Rocha

first: Zhangyuan

last: Pan

first: Huaijun

first: Jennifer

last: Bruscadin

first: Wellison

last: Diniz

first: Juliana

last: Afonso

first: Priscila

last: de Oliveira

first: Gerson

middle: B

last: Mourao

first: Adhemar

last: Zerlotini

first: Luiz

last: Coutinho

first: James

middle: E

last: Koltes

first: Luciana

last: Regitano


title: Single-Cell RNA-seq of Postnatal Development of Cardiomyocyte

first: Li

summary: Postnatal heart maturation is the basis of normal cardiac function and provides critical insights into heart repair and regenerative medicine. While static snapshots of the maturing heart have provided much insight into its molecular signatures, few key events during postnatal cardiomyocyte maturation have been uncovered.Here we processed single cell RNASeq of Cardiomyocyte at different postnatal time points.

overall_design: Single cell RNA-Seq of postnatal mouse cardiomyocytes at different stages. The series includes single-cell RNA-seq of adult cardiomyocytes after knockdown of Jun or control sh_NT.

first: Fang

last: Yao

first: Zheng

last: Li


title: Targeting Krebs-cycle-deficient renal cell carcinoma with Poly ADP-Ribose Polymerase inhibitors and low-dose alkylating chemotherapy

city: Los Angeles

first: Paul

last: Boutros

address: 10833 Le Conte Ave

department: Human Genetics

institute: University of California, Los Angeles

summary: Loss-of-function mutations in genes encoding the Krebs cycle enzymes Fumarate Hydratase (FH) and Succinate Dehydrogenase (SDH) induce accumulation of fumarate and succinate, respectively and predispose patients to hereditary cancer syndromes including the development of aggressive renal cell carcinoma (RCC). Fumarate and succinate competitively inhibit αKG-dependent dioxygenases, including Lysine-specific demethylase 4A/B (KDM4A/B), leading to suppression of the homologous recombination (HR) DNA repair pathway. In this study, we evaluated novel treatment approaches in newly generated models of FH- and SDHB-deficient RCC.

overall_design: CRISPR/Cas9 was used to engineer isogenic Fh1- and Sdhb-deficient murine models of RCC. The efficacy of poly ADP-ribose polymerase inhibitors (PARPis) and temozolomide (TMZ), alone and in combination, was evaluated both in vitroand in vivo.

first: Daiki

last: Ueno

first: Juan

last: Vasquez

first: Brian

last: Shuch


title: Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium

first: Ye-guang

last: Chen

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

sample_organism:
Macaca mulatta
Sus scrofa
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Analysis of MiRNAs responsive to long-term Ca deficiency in tef (Eragrostis tef (Zucc.) Trotter)

city: Greensboro

first: Muhammad

last: Numan

state: North Carolina

address: 321 McIver Street

department: Biology

institute: University of North Carolina Greensboro

summary: miRNAs play an important role in growth, development, stress resilience and epigenetic modifications of plants. However, the effect of calcium nutrition on miRNA expression in orphan crops such as tef ((Eragrostis tef) remained unknown. In this study, we analyzed genome-wise miRNAs of roots and shoots in response to long-term calcium deficiency in tef. MiRNA-seq followed by bioinformatic analysis identified a large number of small RNAs with size ranging from 17bp to 35bp. A total 1380 miRNAs were identified in plants experiencing long-term Ca deficiency, while 1495 miRNAs were identified in the control plants. Among the miRNAs identified in this study, 161 miRNAs were known, and 348 miRNAs were novel while the remaining miRNAs were uncharacterized. Putative target genes and their functions were predicted for all the known and novel miRNAs. Based on gene ontology (GO) analysis, the target genes were found to have various biological and molecular functions including calcium uptake and transport. Pairwise comparison of differentially expressed miRNAs revealed that some of the miRNAs were specifically enriched in roots or shoots of low calcium treated plants as compared to control plants. Further characterization of the miRNAs and their targets detected in this study will help in identifying Ca deficiency responses not only in tef but also in related orphan crops

overall_design: two different calcium treatments, 1. low calcium treatment. 2. optimum calcium

first: Ayalew

last: Ligaba-Osena

first: Wanli

last: Guo


title: Arginine vasopressin infusion is sufficient to model preeclampsia in mice

first: Justin

last: Grobe

summary: Copeptin, the c-terminal fragment of arginine vasopressin (AVP), is considered a useful biomarker for the secretion of AVP.  Preeclampsia, a cardiovascular disorder of pregnancy, has been associated with elevated maternal plasma copeptin concentrations.  These findings led us to hypothesize that AVP secretion is elevated during preeclampsia, and may contribute to the pathogenesis of this disorder.  To examine the effect of increased circulating AVP upon placental development, exogenous AVP was infused into pregnant wildtype C57BL/6J mice, and the transcriptome of a single placenta per dam was assessed at gestational day 12.5 by RNAseq.

overall_design: Pregnant C57BL/6J mice were infused with arginine vasopressin (AVP, 24ng/hr, sc) or saline via osmotic pumps from three days before mating until tissues were collected on gestational day 12.5.  RNA from whole placenta was isolated, and transcriptomes were assessed by RNAsequencing.

first: Jeremy

middle: A

last: Sandgren

first: Guorui

last: Deng

first: Henry

last: Keen

first: Donna

last: Santillan

first: Gary

last: Pierce

first: Curt

last: Sigmund

first: Mark


title: AR cooperates with SMAD4 to maintain muscle homeostasis

city: Oxford

first: Thomas

last: Roberts

address: Paediatrics, University of Oxford, Le Gros Clark Building, South Parks Road

institute: University of Oxford

summary:
The goal of this study was to determine the mechanism of androgne in driving muscle hypertrophy programmes.
CONCLUSION: AR transcriptionally cooperates with SMAD4 and this affect is lost in the presence of expansion of the polyglutamine repeat in the AR gene.

overall_design: RNA-seq was performed in quadricpes femoris from SBMA (spinal bulbar muscular atrophy) AR100Q mice treated with AAV vectors expressing BMP7 or GFP mock control. Untreated wild-type mice (C57BL/6) were analysed in parallel as additional controls.

first: Mitra

last: Forouhan

first: Carlo

last: Rinaldi


title: Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Mouse]

summary:
Purpose: To reveal the differences on epithelial cell composition, functional assignments and pharmacokinetics among mammals intestine, we use single cell sequencing to examine the conserved and divergent features among species, providing a cross-species single-cell transcriptomic atlases of ileal epithelium
Methods:Alive ileum epithelial cells were sorted from three adult mice (10 weeks). ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000. Raw reads were aligned to the GRCm38/mm10 Mouse genome, and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs). Raw aligned features were loaded and processed using the Seurat package (v4.0.2). Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes.
Results: After cells with low information content and a high fraction of mitochondrial RNAs were excluded, 1060 cells were analyzed.
Conclusions: Eight cell types were identified in mouse ileum based on reported markers, including enterocytes, transient-amplifying (TA) cells, goblet cells, goblet progenitor cells, stem cells, Paneth cells, enteroendorcine cells and tuft cells.

overall_design: Single cell profiles of ileum epithelial cells from adult mice

first: Ye-Guang

first: Haonan

last: Li

first: Xiaodan

last: Wang

first: Yalong

first: Mengxian

last: Zhang

first: Fan

last: Hong

first: Hong

first: Along

last: Cui

first: Jianguo

last: Zhao

first: Weizhi

last: Ji


title: Applying transcriptomics to screen the significantly altered genes, cell function and signal transduction pathway of chicken trachea exposured to hydrogen sulfide

city: Harbin

first: Shiwen

last: Xu

address: NO.600 Changjiang Street, Xiangfang District, HarBin, China

department: College of Veterinary Medicine

institute: Northeast Agricultural University

summary: Hydrogen sulfide (H2S) is well known to cause irritation and damage to airway following inhalation, but the mechanism by which H2S contributes to airway toxicity is unclear. We apply  transcriptomics  to demonstrate the possible effects, obtain valuable information about adverse health effects following H2S exposure and to study the molecular mechanisms of the gas toxicity in trachea.

overall_design: lncRNA and miRNA profiles of 42-day old normal and hydrogen sulfide exposed chicken were generated by deep sequencing, in triplicate.

first: Xiaojing

first: Menghao

last: Chen


title: Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Macaque]

first: Ye-guang

summary:
Purpose: To reveal the differences on epithelial cell composition, functional assignments and pharmacokinetics among mammals intestine, we use single cell sequencing to examine the conserved and divergent features among species, providing a cross-species single-cell transcriptomic atlases of ileal epithelium
Methods:Alive ileum epithelial cells were sorted from two cynomolgus monkeys (14 years old). ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000. Raw reads were aligned to the Mmul_10 Macaque genome, and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs). Raw aligned features were loaded and processed using the Seurat package (v4.0.2). Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes.
Results: After cells with low information content and a high fraction of mitochondrial RNAs were excluded, 886 cells were analyzed.
Conclusions: Eight cell types were identified in macaque ileum based on reported markers, including enterocytes, transient-amplifying (TA) cells, goblet cells, goblet progenitor cells, stem cells, enteroendorcine cells, CA7+ cells and tuft cells.

overall_design: Single cell profiles of ileum epithelial cells from adult cynomolgus monkeys


title: Real-time quantitative PCR analysis of autophagy and apoptosis in Myelodysplastic syndromes (MDS)

status: Public on May 26 2022

city: Athens

first: georgia

last: tsekoura

address: Zografou

country: Greece

institute: National and Kapodistrian University of Athens

summary:
A large series of genes involved in autophagy and apoptosis process was screened in samples with different types of MDS (low/high grade of malignancy) versus samples from healthy individuals
qPCR gene expression profiling

overall_design: 3 control samples and 10 patient samples

first: Georgia

last: Tsekoura

last: Mporonikola


title: Single Cell transcriptomic atlas of mouse sex determination and gonadal differentiation

city: Geneve

first: Chloe

last: MAYERE

address: Michel Servet, 1

institute: UNIGE

summary:
Gonadal sex determination represents a unique model for studying cell fate decisions. However, a complete understanding of the different cell lineages forming the developing testis and ovary remains elusive. Here, we investigated the origin, specification, and subsequent sex-specific differentiation of a previously uncharacterized population of supporting-like cells (SLCs) in the developing mouse gonads. The SLC lineage is closely related to the coelomic epithelium and specified as early as E10.5, making it the first somatic lineage to be specified in the bipotential gonad. SLC progenitors are localized within the genital ridge at the interface with the mesonephros and initially coexpress Wnt4 and Sox9. SLCs become sexually dimorphic around E12.5, progressively acquire a more Sertoli- or pregranulosa-like identity and contribute to the formation of the rete testis and rete ovarii. Last, we found that WNT4 is a crucial regulator of the SLC lineage and is required for normal development of the rete testis.

In the present study, we built a transcriptomic atlas of the entire cell population of the developing female and male gonads during the process of mouse sex determination. We identified a previously uncharacterized population of supporting-like cells (SLC) and shed light on the origin and the developmental trajectory of this important cell lineage during the process of testis and ovary development.

overall_design: 20 10X single cell captures in duplicates at 5 stages (E10.5, E11.5, E12.5, E13.5 and E16.5) of gonadal ridges (E10.5, E11.5) and gonads in XX and XY CD1 mouse embryos

first: Chloé

last: Mayère

first: Violaine

last: Regard

first: Yasmine

last: Neirijnck

first: Pauline

last: Sararols

first: Isabelle

last: Stévant

first: Françoise

last: Kühne

first: Serge

last: Nef


title: Postnatal development of Cardiomyocyte

first: Li

last: Wang

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Postnatal heart maturation is the basis of normal cardiac function and provides critical insights into heart repair and regenerative medicine. While static snapshots of the maturing heart have provided much insight into its molecular signatures, few key events during postnatal cardiomyocyte maturation have been uncovered.Here we processed bulkRNASeq and ChIPSeq of Cardiomyocyte at different postnatal time points.

sample_organism:
Mus musculus
Rattus rattus

platform_organism:
Mus musculus
Rattus rattus

overall_design: RNA-Seq of mouse/rat cardiomyocytes in postnatal; ChIP-Seq of H3K4me1, H3K4me3, H3K27me3, H3K27ac and Pol II in mouse cardiomyocytes in postnatal

first: Fang

last: Yao

first: Zheng

last: Li


title: Phytohormone-triggered Transcriptional Reprograming Reveals β-glucosidase as a Key Player for Polysaccharide Metabolism in Dendrobium catenatum

city: Shenzhen

first: Zhicai

state: guangdong province

address: N.889, wangtong RD, Luohu district

institute: Orchid conservation and research center of Shenzhen

summary: Dendrobium catenatum (D. catenatum) has long been used as an important medicinal herb in oriental medicine. Polysaccharide, flavonoid, and alkaloid are the major active ingredients, the production and accumulation of which are frequently affected by many environmental factors including water, temperature, and mycorrhizal fungus. However, how phytohormones frequently used in orchid tissue culture regulate the production of active components in D. catenatum is far from clear. Here, major medicinal metabolites were comparatively analyzed in 2-month-old D. catenatum seedlings exposed to phytohormones (0.1 mg/L NAA and/or 1.0 mg/L 6-BA) for three weeks, and eight transcriptomes (two replicates each) corresponding to the treatments were generated. Results demonstrated that the phytohormones triggered transcriptional reprograming, analysis of which revealed a tight association of β-glucosidase (BGLU) expression with the accumulation of polysaccharide. Subsequently, a second RNA-sequencing was further conducted to reveal that a relatively short period (2 w) of varied concentrations of 6-BA application might initially reduce BGLU expression and polysaccharide content and then increase their levels with prolonged treatments (4 w). The RNA-seq data was reconfirmed by functional analysis that 6-BA induced polysaccharide production, while knockdown of BGLU2L resulted in decreased polysaccharide levels. Therefore, the present study clearly demonstrated that BGLU is a key regulator for polysaccharide production and that it is extremely susceptible to NAA and 6-BA treatments in D. catenatum.

overall_design:
1. Examination of the expression of medicinal components production related genes in response to  1.0 mg/L 6-BA and/or 0.1 mg/L NAA treatments for 3 w in Dendrobium catenatum
2. Examination of the expression of medicinal components production related genes in response to varied concentrations of 6-BA (0, 0.5, 1.0, and 2.0 mg/L) and treatment duration (2 w and 4w) in Dendrobium catenatum

first: Meina


title: Gut microbiome generated Phenylacetylglutamine from dietary phenylalanine is associated with Crohn's Disease and exacerbates colitis in mouse model possibly via platelet activation

city: Guangzhou

first: Yijun

last: Zhu

address: Zhongshan Er Lu

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

summary: Objectives: To better understand the interplay of diet and gut microbiota in Crohn’s disease (CD), taking advantage of a newly-onset treatment naïve CD cohort. We focus on phenylacetylglutamine (PAGln), a diet-derived meta-organismal prothrombotic metabolite.  Design: We collected fecal and serum samples prior to treatment in a newly-onset CD cohort (n=262). Plasma PAGln was quantified using LC-MS/MS. Platelet count and mean platelet volume were determined. Diet was assessed using food-frequency questionnaires. Human platelet rich plasma (n=5-6) was primed with PAGln, P-selectin and CD40L expression were determined after exposure to platelet agonists. Dextran sodium sulfate (DSS)-induced colitis mice (C57BL/6) were given phenylacetylglycine (PAGly, the mouse-prevalent metabolite) or saline, colitis severity and colonic tissue gene expression were examined. Mice (C57BL/6) were given isocaloric high protein and low protein diet for 18 days, followed by DSS administration in water. Plasma PAGly was quantified and colitis severity was examined. Bioinformatic analysis and bacterial culturing were performed to identify the main contributor of PAGln in CD.  Results: Phenylacetylglutamine (PAGln), a meta-organismal prothrombotic metabolite, is associated with CD. PAGln enhanced platelet activation and CD40L expression in platelet rich plasma ex vivo. Administration of PAGly exacerbated colitis in mouse model and upregulated coagulation-related biological processes. Further study revealed that high dietary protein intake and increased abundance of phenylacetic acid (PAA)-producing Proteobacteria mediated by phenylpyruvate decarboxylase act in concert to cause the elevated PAGln levels in CD patients.  Conclusion: Taken together, these results suggest that PAGln is a potential early diagnostic marker and therapeutic target of CD.

overall_design: Dextran sodium sulfate (DSS)-induced colitis mice (C57BL/6) were given phenylacetylglycine (PAGly, the mouse-prevalent metabolite) or saline for 9 days. Colonic tissue was collected and sequenced.

first: Rui

last: Feng

first: Zhenyi

last: Tian

first: Minhu


title: Distinct epigenetic profiles at the cytosine modification level define epithelial-to-mesenchymal cell-state transitions

city: Lebanon

first: Min Kyung

last: Lee

state: NH

address: 1 Medical Center Dr

institute: Geisel School of Medicine at Dartmouth

type: Methylation profiling by genome tiling array

summary:
Genome wide DNA methylation and hydroxymethylation profiling of 6 isolated single cell clones and the parental (SUM149-PT) cell line.  The Illumina Infinium  Human MethylationEPIC Beadchip was used to obtain DNA methylation and hydroxymethylation profiles across approximately 850,000 CpGs in 6 isolated single cell clones that represent the phenotypes of the epithelial-to-mesenchymal spectrum along with the parental (SUM149-PT) cell line.
Isolated single cell clones represent varying phenotypes of the epithelial-to-mesenchymal transition. Detailed isolation and characterization methods can be found in Brown et al, 2021. https://doi.org/10.1101/2021.03.17.434993

overall_design: Oxidative-Bisulfite converted DNA from the 7 cell types were hybridised to the Illumina Infinium Human MethylationEPIC Beadchip.

first: Min

first: Brock

last: Christensen


title: Dysfunction of the circadian clock in the renal tubule leads to enhanced renal gluconeogenesis and exacerbated hyperglycemia in diabetes

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

summary: In diabetes, the kidney contributes to the development of diabetic hyperglycemia by increasing glucose reabsorption from the primary urine and by upregulating gluconeogenesis in the proximal tubule. However, these two processes are also controlled by the circadian clock, a mechanism that synchronizes a large number of specific renal functions with environmental daily cycles. Here, we investigated the (patho)physiological role of intrinsic renal tubule circadian clocks in the diabetic kidney. We demonstrate that diabetic mice devoid of the circadian transcriptional regulator BMAL1 in the renal tubule exhibit additional enhancement of renal gluconeogenesis, exacerbated hyperglycemia, increased glucosuria, polyuria and renal hypertrophy. Collectively, our results suggest that diabetic hyperglycemia can be worsened by dysfunction or misalignment of intrinsic renal circadian clocks.

overall_design: We induced type I diabetes with the drug streptozotocin (STZ) in mice devoid of the circadian transcriptional regulator BMAL1 in the renal tubule (cKOt mice). We had four experimental groups (STZ-control, STZ-cKOt, PBS-control, PBS-cKOt) and nine animals per group.

first: Camille

last: Ansermet

first: Gabriel

last: Centeno

first: Andy

last: Garcia

first: Yohan

last: Bignon

first: Dmitri

last: Firsov


title: SMCHD1 variants induce variegated expression in Facio Scapulo Humeral Dystophy and Bosma Arhinia and microphtalmia syndrome. [ChIP-Seq]

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

institute: Aix-Marseille Université - Marseille Medical Genetics

summary: Determination of SMCHD1 epi-signature in type 2 Facio Scapulo Humeral Dystrophy (FSHD2) and Bosma Arhinia and Microphtalmia Syndrome (BAMS).

overall_design: By combining RNA Seq, DNA methylation profiling and ChIP-Seq, we showed that SMCHD1 regulates repressed chromatin but also cis-regulatory elements and enhancers.

first: Magdinier

last: Frederique

first: Laberthonnière

last: Camille

first: Chevalier

last: Raphael


title: Changes in gene expression profile caused by mechanical stress in the ligamentum flavum -short term rabbit model-

city: Osaka

first: Akinobu

last: Suzuki

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Orthopaedic surgery

country: Japan

institute: Osaka Metropolitan University

summary: To identify the changes in gene expression profile caused by mechanical stress in the ligamentum flavum, we performed resection of the L3-4 supraspinal muscle and L2-3, L4-5 posterolateral fusion with instrumentation to concentrate the mechanical stress with segmental instability at the L3-4 level. The control group underwent only surgical exposure as a sham operation. Both groups of rabbits were sacrificed at 16 weeks after surgery and total RNA were extracted from ligamentum flavum.

overall_design: mRNA profiles of rabbit ligamentum flavum obtained at the intervertebral stress concentration level (ISC level) , the fused level and the control level were generated by microarray.

first: Hayashi

last: Kazunori

first: Akito

last: Yabu


title: Multigenerational Effects of Dietary Benzo[a]pyrene Exposure on Behavior, Gene Expression, and DNA Methylation

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

institute: Woods Hole Oceanographic Institution

summary: Benzo[a]pyrene (BaP), a polycyclic aromatic hydrocarbon (PAH), is implicated in many developmental and behavioral adverse outcomes in offspring of exposed parents.  Following a dietary preconceptional exposure to BaP in zebrafish, the objective of this study was to compare parental sex-dependent adverse outcomes in F1 and F2 offspring with the transcriptomic and epigenetic changes in eggs, sperm, and 10-hour post fertilization (hpf) embryos. Adult wild-type (5D) zebrafish were fed 708 µg BaP/g diet (measured) at a rate of 1% body weight twice/day (14 µg BaP/g fish/day) for 21 days. Fish were spawned using a crossover design and parental (F0) behavior and reproductive indexes measured. In offspring behavioral effects were measured at 96 hours post fertilization (hpf) in F1 & F2 larvae, and again when F1s were adult. Compared to controls, there was no significant effect of BaP exposure on adult behavior in F0, but locomotor behavior was significantly increased in F1 adults of both sexes. Larval behavior (96 hpf, photomotor response assay) was significantly altered in both the F1 and F2 generations following parental BaP exposure. To assess parental sex-dependent molecular mechanisms, BaP-mediated differential gene expression and DNA methylation changes were measured using RNAseq and RRBS, respectively, on F0 sperm and eggs and the 10 hpf embryos from all four crosses in F1 generation. Embryos resulting from the BaP male and control female cross had the most differentially methylated regions (DMRs) and differentially expressed genes. Some DMRs were associated with genes encoding chromatin modifying enzymes suggesting regulation of chromatin conformation by DNA methylation. Parental dietary BaP exposure caused persistent behavioral changes wherein the male germline contributed most significantly to the multigenerational adverse outcomes.

overall_design: Sexually mature (120 dpf) 5D strain of zebrafish were fed either acetone alone or BaP-treated (25 μg/g fish equivalent to 1250 μg/g food, respectively) TetraMin® Tropical Flakes.  Paired (2x2) zebrafish in five replicate tanks per treatment group (N=5 replicate tanks for a total 20 fish/group) were allowed to acclimate for a week while maintained at 25.5-28°C and fed twice daily with untreated flakes and Gemma 300 micron food. During the exposure, fish were fed 1% body weight twice daily of the corresponding dose of BaP-treated flake food and once daily Gemma 300 micro food for 21 days. At the end of day 21, a cross-over breeding design was implemented to assess sex-specific contributions into the following groups: control males x control females, BaP females x control males, BaP males x control females, and BaP males x BaP females. On days 22 and 23 (no longer being exposed), eggs were collected to determine reproductive success. On day 24 (females) and day 25 (males), fish were euthanized, and gonad, liver, and brain were collected biobanked for future analysis. Furthermore, sperm or eggs from the BaP exposed and control fish, along with 10 hpf embryos from each cross (4 crosses) were collected for RNA-seq and DNA methylation analysis.

first: Kristie

last: Willett

first: Zacharias

last: Pandalides

first: Caroline

last: Sturgis

first: Cammi

last: Thornton


title: Molecular profiling in the Habenula of Rat Chronic Restaint Stress Model

city: Seoul

first: Hyeijung

last: Yoo

address: Goryeodaero 73

department: Department of anatomy

institute: Korea University College of Medicine

summary: Chronic stressful situations contribute to the risk of developing depression. Using Genome-wide gene expression analysis, we analyzed the habenula transcriptome of rats exposed to chronic restraint stress for 14 days. We selected 379 differentially expressed genes (DEGs) affected by chronic stress.  From 379 DEGs, neuroactive ligand-receptor interaction, cAMP signaling pathway, circadian entrainment and synaptic signaling on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, response to corticosteroid, positive regulation of lipid transport, anterograde trans-synaptic signaling, chemical synapse transmission on Gene Ontology (GO) pathway analysis was identified as significantly enriched pathways. We made a protein-protein interaction network of DEGs and analyzed subclusters, and neuroactive ligand-receptor interaction, circadian entrainment, and cholinergic synapse-related clusters were identified. To validate the findings, quantitative RT-PCR was done for significant genes. Identified DEGs and pathways could be important factors modulating habenular response to stress and lead to behavioral change. These data identify key molecular targets involved in chronic stress-induced depression within habenula and provides a valuable resource for future study.

overall_design: We randomly assigned male Sprague-Dawley rats into chronic stress and non-stress group. After 14 days of chronic restraint stress on stress group habenula tissues were dissected from 4 rats in each group and the whole-genome transcriptome was examined.

first: Hyun

last: Kim

first: Hyun-Woo

last: Lee

first: Hyun-Jung


title: Analysis of Long non-coding RNAs in Adipose Tissue of Pigs Fed Resveratrol-supplemented Diet

city: Nanning

first: Sanbao

last: Zhang

address: No.100,Daxue East Road

institute: Guangxi University

summary: Fat is an important energy store in animals, especially pigs, because of their high fat deposition ability. In animal husbandry, fat content is closely related to animal's lean meat rate and other important economic traits. Long-chain non-coding RNA regulates numerous biological processes, including lipid metabolism. Resveratrol (RES) has been reported to have anti-obesity effects. However, it is unclear whether RES can control fat deposition in pigs by regulating the activities of long-chain non-coding RNAs (lncRNA). The aim of this study was to examine the expression of lncRNA in subcutaneous fat tissues of pigs fed RES-supplemented diet. A total of 12 Duroc × Landrace × Yorkshire hybrid pigs were randomly assigned to two diets, the control diet and the experimental diet containing 400 mg/kg RES. At the end of the study, RNA sequencing was carried out, and the results indicated the expression of lncRNA in the adipose tissues of pigs from the two groups. A total of 499 lncRNAs were identified. Eighty-two (82) differentially expressed genes, including 5 lncRNAs and 77 mRNAs, were also identified. We also observed that the lncRNAs, MSTRG.12490 and MSTRG.13223 targeted the mRNAs, THBS4 and SFPR2, respectively. Results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that the differentially expressed genes were mainly involved in adipocytokine signaling pathway, Wnt signaling pathway, PI3K-Akt signaling pathway, and MAPK signaling pathway, which are associated with glycolipid metabolism.Results from this study contributes to the knowledge of the genes and pathways involved in fat metabolism in pigs and the role of RES in the diet of pigs.

overall_design: Profiles of mRNAs and non-coding RNAs during the control diet and the experimental diet containing 400 mg/kg RES of Duroc × Landrace × Yorkshire hybridsubcutaneous fat tissues

first: Qinyang

last: Jiang

first: Yanna

last: Huang


title: Analysis of microRNAs from osteoblast and osteoclast derived small extracellular vesicles using high through-put miRNA sequencing

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

summary: To gain insight into the microRNA expression profile of small extracellular vesicles derived from bone metabolism related cell types and to verify their mechanism, we utilized the miRNA sequencing technology to analyze the miRNA profiles of different mouse osteoblast and osteoclast cell derived small extracellular vesicles.

overall_design: We collect the small extracellular vesicles from the supernatant of osteoclast and osteoblst cells using ultracentrifugation method. The small extracellular vesicles were then extracted for small RNAs to perform high through-put sequencing

first: Huajiang

last: Chen

first: Wen

last: Yuan


title: Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos [RNA-Seq 3]

city: shanghai

first: Jin

last: Sun

department: life science and technology

institute: Tongji University

summary: To further investigate the relationship between abnormal accumulation of H3K4me3 modification and abnormal embryo development. We injected Kdm5b siRNA, which is an H3K4me3 eraser, at the zygote (PN3-PN4) stage of NM embryos and then examined the transcriptome of extraembryonic ectoderm at E7.5.

overall_design: Examination of the transcriptome of extraembryonic ectoderm with sikdm5b or water.

first: Dandan

last: Bai


title: Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos (RNA-Seq 2)

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

overall_design: To explore if interference Kmt2e could corrected the extra-embryonic tissue gene expression of IVF embryos, we fist analysed the E7.5 ExE transcriptome data of IVF control and siKmt2e embryos which produced by Smartseq2 RNA-seq method.

first: Wenqiang

last: Liu

first: Cizhong

first: Shaorong

last: Gao


title: beta catenin in CCA cell lines and patient samples

city: Regensburg

first: Alexander

last: Scheiter

state: Bavaria

address: Franz-Josef-Strauss Allee 11

department: Institute of Pathology

institute: University of Regensburg

summary: test the activation of beta catenin in APC and CTNNB1 mutated samples (CCA cell lines and patient samples) versus WT

overall_design: 3 mutant cell lines (1x CTNNB1, 1x APC, 1x RNF43) versus 2 non-mutant. 4 mutant patient CCA samples (3x APC, 1x CTNNB1) versus 3 non mutant.


title: Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos [ChIP-Seq 2]

summary: To further investigate the relationship between abnormal accumulation of H3K4me3 modification and abnormal embryo development. We injected Kdm5b siRNA, which is an H3K4me3 eraser, at the zygote (PN3-PN4) stage of NM embryos and then examined the H3K4me3 modification of extraembryonic ectoderm at E7.5.

overall_design: Examination H3K4me3 modification of extraembryonic ectoderm with sikdm5b or water.


title: Global miRNA sequencing upon HDAC inhibition in HCC

city: Hannover

first: Britta

last: Skawran

address: Carl-Neuberg-Straße 1

institute: Hannover Medical School

summary: Global miRNA expression upon HDAC inhibition was analyzed using miRNA sequencing in HCC cell lines (HLE, HLF, Huh7, HepG2, Hep3B) and normal liver cell lines (THLE-2, THLE 3)

overall_design: Global miRNA expression

first: Nicole

last: Huge


title: Ectopic histone modification in extra-embryonic tissues influence implantation and placenta development of IVF embryos (RNA-Seq 1)

overall_design: We performed RNA-seq transcriptomic analysis of NM and IVF embryos at the stage of 2-cell, morula, E3.5 blastocyst (trophectoderm, TE; inner cell mass, ICM), E7.5 embryos (Epiblast, Epi; Extraembryonic ectoderm, ExE)


title: Global gene expression changes in osteoblasts from fluoride-tolerant mice

status: Public on May 25 2022

city: Hangzhou

first: Yi

state: Zhejiang

address: 166 North Qiutao Rd

department: Department of Endodontics

institute: Zhejiang University

summary: In order to define the underlying mechanism of fluoride resistance in mammals and provide a theoretical basis for fluorosis treatment, high-throughput sequencing was applied to map the genetic changes of fluoride-resistant mouse osteoblasts. Fluoride-tolerant MC3T3-E1 cells were developed by gradient fluoride exposure. The differentially expressed genes of fluorine-resistant MC3T3-E1 cells were identified by high-throughput sequencing. High-throughput RNA sequencing identified 2702 differentially expressed genes (DEGs) showed more than 2-fold difference in 30ppm FR MC3T3-E1 cells, of which 17 DEGs were associated with ferroptosis.

overall_design: Wild-type MC3T3-E1 (WT MC3T3-E1) cells were continuously exposed to a gradient of 10 ppm F- to induced them survive in fluorinated medium. During cell adaptation, the cell proliferation was continuously monitored using Cell Counting Kit-8 (CCK-8) kit until a normal cell proliferation rate was confirmed. The above procedure was repeated for all other MC3T3-E1 clones to develop desired fluorine resistance. The differentially expressed genes of fluorine-resistant MC3T3-E1 cells were identified by high-throughput sequencing.

first: Yimin

last: Fang

first: Shen

last: Zhao

first: Jialong

last: Wu

first: Chenkang

last: Lu

first: Lai

first: Shujun

last: Ran

first: Jia

last: Wang

first: Fei

first: Bin


title: Prenatal exposure to a climate-related disaster results in changes of the placental transcriptome and infant temperment

city: New York

state: NY

address: 85 Saint Nicholas Ter

department: Neuroscience

institute: CUNY Advanced Science Research Center

summary: Maternal stress during pregnancy exerts long-term effects on the mental well-being of the offspring. However, the long-term effect of prenatal exposure on the offspring’s mental status is only partially understood. The placenta plays a vital role in connecting the maternal side to the fetus, thereby serving as an important interface between maternal exposure and fetal development. Here, we profiled the placental transcriptome of women who were pregnant during a hurricane (Superstorm Sandy), which struck New York City in 2012. The offspring were followed longitudinally and their temperament was assessed during the first 6-12 months of age. The data identified a significant correlation between a Superstorm Sandy stress factor score and infant temperament. Further, analysis of the placental transcriptomes identified an enrichment of functional pathways related to inflammation, extracellular matrix integrity and sensory perception in the specimen from those infants with “Slow-to-Warm-up” temperament during the first year of life. Together, these findings provide initial evidence that maternal exposure to climate-related disasters results in altered placental transcriptome, which may be related to long-term emotional and behavioral consequences.

overall_design: RNA-seq of placental specimens from 24 human subjects


title: Stella regulates the development of female germline stem cells by modulating chromatin structure and DNA methylation [Hi-C_2]

first: Ji

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

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

overall_design: Examination of the chromatin architecture in female germline stem cells, Stella-KO.

first: Changliang

last: Hou


title: Single-cell transcriptomic profiling of ~1500 K562 cells expressing dCas9-KRAB to compare Illumina and Ultima sequencing platforms.

city: Cambridge

first: Joseph

last: Replogle

state: Massachussetts

address: 455 Main St

institute: UCSF / Whitehead Institute / MIT

summary: ~1500 K562 cells expressing dCas9-KRAB were profiled on the 10x Genomics 3' v3 droplet-based scRNA-seq platform. The resulting library was sequenced on the Illumina and Ultima sequencing platforms.


title: Gene expression  signatures of the PRMS tumors.

city: Tsu

first: Noboru

last: Suzuki

state: Mie

address: 2-174 Edobashi

department: Department of Animal Functional Genomics of Advanced Science Research Promotion Center

institute: Organization for Research Initiative and Promotion at Mie University

summary: Several groups identified CSCs in solid tumors, including breast, brain, thyroid, melanoma, colon, pancreatic, liver, prostate, lung, head and neck, ovarian, and stomach cancers, by adopting many biomarkers. Here, we examined PRMS by gene expression microarray analysis for them. As a result, the tumor expressed various specific genes in each CSCs, SCs, FAPs, and PICs.

overall_design: Gene expression of the tumors by subcutaneous injection of the PRMS cell line, RMS3.


title: Jak2V617F Reversible Activation Shows an Essential Requirement for Jak2V617F in Myeloproliferative Neoplasms

city: Philadelphia

first: Robert

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

summary: Janus kinases (JAKs) mediate cytokine signaling, cell growth and hematopoietic differentiation. Gain-of-function mutations activating JAK2 signaling are seen in the majority of  myeloproliferative neoplasm (MPN) patients, most commonly due to the JAK2V617F driver allele. While clinically-approved JAK inhibitors improve symptoms and outcomes in MPNs, remissions are rare, and mutant allele burden does not substantively change with chronic JAK inhibitor therapy in most patients. This has been postulated to be due to incomplete dependence on constitutive JAK/STAT signaling, alternative signaling pathways, and/or the presence of cooperating disease alleles; however we hypothesize this is due to the inability of current JAK inhibitors to potently and specifically abrogate mutant JAK2 signaling. We therefore developed a conditionally inducible mouse model allowing for sequential activation, and then inactivation, of Jak2V617F from its endogenous locus using a Dre-rox/Cre-lox dual orthogonal recombinase system. Deletion of oncogenic Jak2V617F abrogates the MPN disease phenotype, induces mutant-specific cell loss including in hematopoietic stem/progenitor cells, and extends overall survival to an extent not observed with pharmacologic JAK inhibition. Furthermore, reversal of Jak2V617F in MPN cells with antecedent loss of Tet2 abrogates the MPN phenotype and inhibits mutant stem cell persistence suggesting cooperating epigenetic-modifying alleles do not alter dependence on mutant JAK/STAT signaling. Our results suggest that mutant-specific inhibition of JAK2V617F represents the best therapeutic approach for JAK2V617F-mutant MPN and demonstrate the therapeutic relevance of a dual-recombinase system to assess mutant-specific oncogenic dependencies in vivo.

overall_design: Gene expression profiling was performed on sorted lineage negative, Sca1+, Kit+ (LSK) and megakaryocyte-erythroid progenitor cells (MEPs). These were cells were sorted from JAK2 V617F mice where tamoxifen (TAM)-mediated Cre activation results in loss of the JAK2 V617F allele. LSKs and MEPs were sorted from either vehicle treated mice, after 3 days of TAM, after 7 days of TAM, or after 7 days of JAK2 inhibition with Ruxolitinib.

first: Andrew

last: Dunbar

first: Ross

last: Levine


title: Gut epithelial barrier damage caused by dishwasher detergents and rinse aids

city: Davos

first: ISMAIL

last: OGULUR

address: Herman-Burchard-Strasse 9

institute: Swiss Institute of Allergy and Asthma Research

summary: We investigated the effects of professional dishwasher detergents and  rinse aid on cytotoxicity, barrier function and the transcriptome in gastrointestinal epithelial cells. RNA-seq was used for checking transcriptome.

overall_design: Monolayered Caco-2 cells were treated with rinse aid in 1:10000 and 1:40000 dilutions for 24 hours. Then, RNA samples were isolated, RNA-seq performed and comparative gene expression analysis done.

first: Ismail

last: Ogulur

first: Tamer

last: Aydin


title: Investigating effect of TMEM184B mutation on hippocampal gene expression in 5 month and 15 month old mice

city: Tucson

first: Martha

last: Bhattacharya

state: AZ

address: 1040 E 4th Street

institute: University of Arizona

summary: The objective of this study was to determine whether TMEM184B influenced the expression of genes important for neuronal function or memory.

overall_design: We isolated hippocampus tissue from 3-4 mice of wild type or TMEM184B gene trap mutant mice at 5 months and 15 months of age. We then isolated total RNA and performed paired-end bulk RNA sequencing

middle: R

first: Erik

middle: G

last: Larsen

first: Elizabeth

last: Wright

first: Hannah

last: Hart


title: cGAS maintains basal antiviral state

city: Berlin

first: Julia

last: Kazmierski

address: Charitéplatz 1

institute: Charité Universitätsmedizin Berlin

summary: Upon recognition of aberrantly located DNA, the innate immune sensor cGAS activates STING/IRF-3-driven antiviral responses. Here we characterized the ability of a specific variant of the cGAS-encoding gene MB21D1, rs610913, to alter cGAS-mediated DNA sensing and viral infection. rs610913 is a frequent G>T polymorphism resulting in a P261H exchange in the cGAS protein. Data from the International Collaboration for the Genomics of HIV suggested that rs610913 nominally associates with HIV-1 acquisition in vivo. Molecular modeling of cGAS(P261H) hinted towards the possibility for an additional binding site for a potential cellular co-factor in cGAS dimers. However, cGAS(WT) or cGAS(P261H)-reconstituted THP-1 cGAS KO cells shared steady-state expression of interferon-stimulated genes (ISGs), as opposed to cells expressing the enzymatically inactive cGAS(G212A/S213A). Accordingly, cGAS(WT) and cGAS(P261H) cells were less susceptible to lentiviral transduction and infection with HIV-1, HSV-1, and Chikungunya virus as compared to cGAS KO- or cGAS(G212A/S213A) cells. Upon DNA challenge, innate immune activation appeared to be mildly reduced upon expression of cGAS(P261H) compared to cGAS(WT). Finally, DNA challenge of PBMCs from donors homozygously expressing rs610913 provoked a trend towards a slightly reduced type I IFN response as compared to PBMCs from GG donors. Taken together, the steady-state activity of cGAS maintains a base-line antiviral state rendering cells more refractory to ISG-sensitive viral infections. rs610913 failed to grossly differ phenotypically from the wild-type gene, suggesting that cGAS(P261H) and wild-type cGAS share a similar ability to sense viral infections in vivo.

overall_design: Total RNA samples extracted from THP-1 cGAS KO cells reconsituted with individual cGAS variants

first: Christine

last: Goffinet


title: Modeling clonal evolution and oncogenic dependency in vivo in the context of hematopoietic transformation

summary: Cancer evolution is a multifaceted process involving the acquisition of somatic mutations and progressive epigenetic dysregulation of cellular fate. Both cell-intrinsic mechanisms and environmental interactions provide selective pressures capable of promoting clonal evolution and expansion, with single-cell and bulk DNA sequencing offering increased resolution into this process. Advances in genome editing, single-cell biology and expressed lentiviral barcoding have enabled new insights into how transcriptional/epigenetic states change with clonal evolution. Despite the extensive catalog of genomic alterations revealed by resequencing studies, there remain limited means to functionally model and perturb this evolutionary process in experimental systems. Here we integrated multi-recombinase (Cre, Flp, and Dre) tools for modeling reversible, sequential mutagenesis from premalignant clonal hematopoiesis to acute myeloid leukemia. We demonstrate that somatic acquisition of Flt3 activating mutations elicits distinct phases of acute and chronic activation resulting in differential cooperativity with Npm1 and Dnmt3a disease alleles. We next developed a generalizable allelic framework allowing for the reversible expression of oncogenic mutations at their endogenous loci. We found that reversal of mutant Flt3 resulted in rapid leukemic regression with distinct alterations in cellular compartments depending upon co-occurring mutations. These studies provide a path to model sequential mutagenesis and deterministically investigate mechanisms of transformation and oncogenic dependency in the context of clonal evolution.

overall_design: Gene expression profiling was performed on sorted lineage negative, Sca1+, Kit+ (LSK) and granulomyeloid progenitor cells (GMPs). These cells were sorted from Flt3 mutant mice, harboring either a single Flt3 mutant, or combination mutations with Npm1 and Dnmt3a. Lineage negative hematopoietic stem and progenitor cells (HSPCs) were isolated from Flt3 mutant mice where tamoxifen (TAM)-mediated Cre activation results in loss of the Flt3 mutant allele.


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

first: Xianjun

last: Yu

address: 270 Dong An Road, Shanghai

department: Department of Pancreatic Surgery

institute: Fudan University Shanghai Cancer Center

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis

first: Nipam

middle: H

last: Patel

state: MA

address: 7 Mbl Street

institute: Marine Biological Laboratory

summary: Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-Seq, an improved form of the Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing (ATAC-Seq), to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis, and limb development. In addition, we use short- and long-read RNA-Seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We leverage a variety of bioinformatic tools to discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions, and correlate gene expression with accessibility.

overall_design: 30 samples were analyzed; two replicates each (A and B) for each of 15 developmental stages. Replicates are two groups of 5 sibling embryos each. Each sample was sequenced on two different lanes of Illumina NovaSeq.

first: Dennis

last: Sun

first: Jessen

middle: V

last: Bredeson

first: Heather

last: Bruce


title: Hypoxia-reprogrammed regulatory group 2 innate lymphoid cells promote immunosuppression in pancreatic cancer [ILC2]

summary: ILC2 cells from mice cultured with or without hypoxia for indicated time period were analysed

overall_design:
Examination of ILC2 cells from mice cultured with or without hypoxia.
Hypoxia protocol: Cells were exposed to hypoxia (1% O2) for the indicated time period.
Reoxygenation protocol: RNA was collected from ILC2 after 24h hypoxia culture (1% O2)  + 24h reoxygenation (20% O2).

first: Longyun

last: Ye