title: RNA-seq on CD16Int versus CD16High in severe COVID-19 patients

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel viral pathogen that  causes a clinical disease called coronavirus disease 2019 (COVID-19). Approximately 20% of  infected patients experience a severe manifestation of the disease, causing bilateral pneumonia  and acute respiratory distress syndrome. Severe COVID-19 patients also have a pronounced  coagulopathy with approximately 30% of patients experiencing thromboembolic complications.  However, the cellular etiology driving the coagulopathy remains unknown. Here, we explore  whether the prominent neutrophilia seen in severe COVID-19 patients contributes to  inflammation-associated coagulation. We found in severe patients the emergence of a CD16Int  low-density inflammatory band (LDIB) neutrophil population that trends over time with changes  in disease status. These cells demonstrated spontaneous neutrophil extracellular trap (NET)  formation, higher phagocytic capacity, enhanced cytokine production, and associated clinically  with D-dimer, ferritin, and systemic IL-6 and TNF-α levels. Strikingly, LDIB neutrophils are the  major immune cells within the bronchoalveolar lavage (BAL) fluid with increased CXCR3 and  loss of CD44 and CD38 expression. We conclude that the LDIB subset contributes to COVID-  19-associated coagulopathy (CAC) and systemic inflammation and could be used as an adjunct  clinical marker to monitor disease status and progression. Identifying patients who are trending  towards LDIB crisis and implementing early, appropriate treatment could improve all-cause  mortality rates for severe COVID-19 patients.

overall_design: Three paired CD16Int and CD16High samples from severe COVID-19 patients were compared with each other, as well as with three healthy donor NDN samples.

first: Samantha

last: Morrissey

first: Anne

last: Geller

first: Xiaoling

last: Hu

first: David

last: Tieri

first: Elizabeth

middle: A

last: Cooke

first: Chuanlin

last: Ding

first: Matthew

last: Woeste

first: Zachary

middle: C

last: Martin

first: Huang-ge

last: Zhang

first: Rodrigo

last: Cavallazzi

first: Sean

middle: P

last: Clifford

first: James

last: Chen

first: Lu

last: Cai

first: Maiying

last: Kong

first: Corey

middle: T

last: Watson

first: Jiapeng

last: Huang

first: Jun

last: Yan


title: Drosophila attack inhibits hyphal regeneration and defense mechanisms activation for the fungus Trichoderma atroviride

status: Public on Jul 20 2021

city: IRAPUATO

first: Alfredo

last: Herrera-Estrella

state: GUANAJUATO

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: LANGEBIO

country: Mexico

institute: CINVESTAV

type: Expression profiling by high throughput sequencing

summary: Fungi as animals and plants conserves the ability to respond to stressful environmental conditions as biotic an abiotic stress. A correct injury response in Eukaryotes including fungi is carried out thought the activation of signaling pathways Ca2+ related dependent of DAMPs/MAPMPs recognizing for the activation of the innate immune system. During herbivory, plants, in addition to activating pathways related to injury, activates specific responses to combat its predator. Using a transcriptional approach, here, we reported the capacity of the filamentous fungus T. atroviride to activate or not a specific response to injury and predation to different predators also, we provide evidence of how fungivory by Drosophila melanogaster larvae inhibits the reported injury response for T. atroviride, although this predation negatively affects the hyphal regeneration thought the larval salivary compounds. Also, the activation of a putative alternate injury reproduction pathway is proposed.

overall_design: This paper presents the analysis of 42 RNA-seq libraries of T. atroviride mycelia under  three different conditions (injury, Fungivory by D. melanogaster larvae and Fungivory  by the collembola Orthonychiurus folsomi) at four time points, early times (30 and 90 minutes after treatment or insect interaction) and late times (4 and 8 h after treatment or insect interaction). Fungi mycelia at 30 min and 8h of the experiment without any stimuli (only oxygen exposed), were taken as control condition. In total three independent biological replicates ( each was a pool of three independent technical replicates) of each time point per condition were sequenced (42 RNA-seq libraries).

first: Karina

last: Atriztán-Hernández

middle: H


title: Granulocytic nuclear lobation.

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

summary: Changes in nuclear morphology during granulopoiesis are a characterising feature of human granulocytic immune system cells. The leading hypothesis for their specific function relates to cell extravasation and migration through extracellular space. Nevertheless, the mechanisms of polylobation are unclear, with the sole identified molecular determinant being lamin B-receptor. It has been long speculated that cytoskeletal forces, especially microtubule-networks, are the shaping force behind this process.

overall_design: Analysis of 3 different time points during 4 day granulocytic differentiation of HL60 cells. 4 biological replicates.

first: Sebastian

last: Martewicz

first: Nicola

last: Elvassore


title: Identification of a link between exercise and brain function in humans through mapping of skeletal muscle enhancers [RNA-Seq]

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Regular exercise improves health and prevents many chronic disorders such as obesity, cardiovascular and neurological diseases. Here, we hypothesized that skeletal muscle gene enhancers undergo epigenetic remodeling after exercise training and overlap with known disease variants from genome-wide association studies (GWAS). Overlapping exercise-remodeled enhancers with GWAS and cis-expression Quantitative Trait Loci data revealed enrichment with traits related to platelet function, cognitive traits and cardiovascular disease. We identify FBXW4 and PLEKHO2 as candidate genes regulated by variant-containing, exercise-responsive enhancers, and that are potentially involved in the distal modulation of brain function. Our results identify a list of genes differentially regulated after exercise training in humans, and which may cooperatively control brain function through the cardiovascular system.

overall_design: RNA-seq of human vastus lateralis biopsies before and after exercise.

first: Kristine

last: Williams

first: Germán

middle: D

last: Carrasquilla

middle: R

first: Mette

middle: Y

last: Hochreuter

first: Ida

last: Donkin

first: Soetkin

last: Versteyhe

first: Tuomas

middle: O

last: Kilpeläinen

first: Romain

last: Barrès


title: Identification of a link between exercise and brain function in humans through mapping of skeletal muscle enhancers

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Identification of a link between exercise and brain function in humans through mapping of skeletal muscle enhancers [ChIP-Seq]

overall_design: H3K27ac & H3K4me1 ChIP-seq of human vastus lateralis biopsies before and after exercise.


title: Impairment of methylglyoxal detoxification systems causes mitochondrial dysfunction and behavioral deficits

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

country: USA

institute: UT Southwestern Medical Center

summary: Methylglyoxal (MG) is a reactive alpha-dicarbonyl by-product of glycolysis. Several bio-defense systems to detoxify the highly toxic MG are equipped in our body, including an enzymatic system by glyoxalase (GLO) 1 and GLO2 and a scavenge system by vitamin B6 (VB6). We have reported that some population of patients with schizophrenia shows impairment of the MG detoxification systems. Although we have evidences showing a link between impairment of MG detoxification systems and development of schizophrenia, the molecular mechanism to connect them remains poorly understood. Here, we generated a novel mouse model for MG detoxification deficits by feeding Glo1 knockout mice with VB6-lacking diets (KO/VB6(-)), and evaluate effects of impaired MG detoxification systems on brain function. KO/VB6(-) mice showed the accumulation of MG in the prefrontal cortex (PFC), hippocampus, and striatum, and displayed schizophrenia-like behavioral deficits, such as social deficits, cognitive impairment, a sensorimotor deficit in the prepulse inhibition test. Furthermore, we found aberrant gene expression related to mitochondria function in the PFC of the KO/VB6(-) mice by RNA-seq and weighted gene correlation network analysis (WGCNA). Finally, we actually demonstrated respiratory deficits in mitochondria isolated from the PFC of KO/VB6(-) mice. These findings suggest that MG detoxification deficits might cause schizophrenia-like behavioral deficits via mitochondrial dysfunction in the PFC.

overall_design: Glo1 KO and wild-type mice were fed with a vitamin B6 (VB6)-lacking diet containing 5 micro g/100 g VB6 pellets from 8 to 12 weeks of age, while control mice in normal VB6 condition were fed with a normal diet, with 1.4 mg/100 g VB6 pellets. As the result,  we have four groups: WT/VB6(+), WT/VB6(-), KO/VB6(+) and KO/VB6(-). Each group contains 5 mice. RNA-seq were consucted using RNAs extracted from prefrontal cortex, striatum and hippocampus of these mice.

first: Kazuya

last: Toriumi

first: Stefano

last: Berto

first: Noriyoshi

last: Usui

first: Takashi

last: Dan

first: Toshio

last: Miyata

first: Masanari

last: Itokawa

first: Makoto

last: Arai


title: Single-cell RNA-seq to decipher the subpopulations of human decidual leukocytes in normal and RSA pregnancies

city: Beijing

first: Yan-Ling

last: Wang

state: Beijing

address: Beichen West Rd., Chaoyang, Beijing

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Maternal fetal immune tolerance is a biological event that plays a key role in pregnancy. In particular, the mechanism by which the maternal immune system does not exclude the semi-identical antigen of the fetus has not been fully answered so far. The most serious result of the maternal fetal immune tolerance balance is the recurrent spontaneous abortion (RSA). The fetus is rejected by the mother in the early pregnancy and cannot continue to develop in the uterus. Based on these scientific questions, we used single-cell sequencing technology to analyze nearly 30,000 leukocytes in the decidua of normal and RSA. A total of 13 immune cell subsets were found, of which dNK cells were more prominent, The lineage differentiation pathway of dNK cells was excavated, and the pathological role of dNK differentiation abnormality in the occurrence of RSA was analyzed. Our results deepen our understanding of the differentiation and function of human decidual leukocytes, especially dNK cells. We clearly recognize that the immune system has dynamic changes compared with normal pregnancy under pathological conditions, which is likely to occur in RSA. The important factors, we expect our results to provide a new basis for RSA's immune diagnosis and treatment strategy.

overall_design: Single cell sequencing on decidual immune cellss was performed from normmal pregnancy women and recurrent spontaneous abortion (RSA) patients. CD45+  leukocytes were sorted from decidua at early pregnancy period  through MoFLo XDP.

first: Feiyang


title: The impact of maternal age on trophectoderm gene expression profiles in human.

city: Leeds

first: Panagiotis

last: Ntostis

address: Clarendon Way

department: Medicine and Health

country: United Kingdom

institute: University of Leeds

summary:
Ageing is a crucial factor that affects embryonic development and implantation. Maternal age has an impact on the blastocyst's gene expression levels from the fertilised oocyte and throughout the development of the preimplantation embryo.
The current study reported differential gene expression analysis among trophectoderm samples that derived from young maternal age women (YMA - below 30 years), intermediate maternal age (IMA - 30-39 years old) and advanced maternal age women (AMA - at least 40 years old). The molecular approach was assayed by a low-input next generation RNA sequencing approach.
Hundreds of significantly differentially expressed transcripts were reported. Extracellular exosome-related transcripts were significantly higher in the trophectoderm cells that derived from young women. According to our analysis, several important transcripts were reported.
These molecular biomarkers may have a potential role in embryonic-endometrial communication and could be used in a diagnostic setting, that could help to improve the blastocyst implantation potential.

overall_design:
Trophectoderm cells from 32 blastocysts were biopsied (15 women). Comparisons in trophectoderm transcriptome patterns were made between blastocysts derived from YMA, IMA and AMA groups. A biological age component was determined mainly in the IMA group, with several IMA samples better clustered in the YMA or AMA groups.
This resulted in defining a new classification of reproductive biological maternal age, that includes rba-YMA, rba-IMA and rba-AMA groups.

The aim was to determine the trophectoderm transcriptome patterns associated with young women and successful implantation using an ultra low-input RNA-Seq approach tailored with the appropriate bioinformatics analysis in the context of the receptive endometrium. All samples were collected under full ethical approval.

first: Georgia

last: Kokkali

first: David

last: Iles

first: John

last: Huntriss

first: Maria

last: Tzetis

first: Stephen

last: Krawetz

first: Helen

last: Picton

first: Konstantinos

last: Pantos

first: Grace

last: Swanson

last: Miller


title: Beauveria bassiana Mbp1 (BbMbp1) regulating genes involved in asexual development

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

summary: Gene BbMbp1 playes an essential role in asexual differentiation, a determinant to the biocontrol  potential of entomopathogenic fungi.  The genome-wide exprssion analysis involved in fungal development was analyzed by using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly involved in asexual deveopment of  B. bassiana.

overall_design: Total RNA obtained from ∆BbMbp1 disruption mutant were compared to that of wild type strain (WT) grown under the indicated conditions.

first: Sheng-Hua

first: Ming-Guang

last: Feng


title: Profiling of N6-methyladenosine dynamics indicates regulation of oyster development by m6A-RNA epitranscriptomes.

city: Caen

first: Lorane

last: Le Franc

address: Université de Caen Normandie Esplanade de la Paix

country: France

institute: UMR BOREA

type: Methylation profiling by high throughput sequencing

summary: The N6-methyladenosine (m6A) has recently emerged as an important layer of the gene expression regulatory network with critical implications in vertebrate and insect development. However, despite an m6A-RNA pathway is present in the pacific oyster Crassostrea gigas, the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown.   We performed RNA sequencing (RNA-seq) and m6A-RNA immunoprecipitation sequencing (MeRIP-seq) on 10 developmental stages, on two distinct developments, to covering the whole oyster developement. The m6A-RNA methylomes show the conservation of m6A consensus motif RRACH, a m6A peak around the stop codon and highlight specific m6A signatures according to RNA species between mRNAs, lncRNAs and transposable elements. The differentially methylated RNAs constitute developmental clusters that correspond to chronological steps of oyster development (cleavage, gastrulation, tissues differentiation and metamorphosis). They are marked with an overall drop of mRNA and lncRNA methylation at the morula stage followed by a global increase up to pre-metamorphosis. Messenger RNA m6A levels are correlated to transcript content and shifts in methyladenine profiles correspond to expression kinetics. The m6A of TE transcripts is also regulated and peaks during the gastrulation.   Altogether our results indicate that m6A epitranscriptomes are an important regulator of oyster development. This first epitranscriptome profiling across the development of a lophotrochozoan model brings new insights into the epigenetic control of developmental processes and their evolution.

overall_design: Examination of m6A and gene expression levels in 10 embryo-larval to post-metamorphosis stages in the oyster

first: Bruno

last: Petton

first: Pascal

last: Favrel

first: Guillaume

last: Rivière


title: The enzyme paraoxonase-2 modulates hematopoiesis through redox signaling

city: Mainz

first: Piyush

last: More

address: Langenbeckstrasse 1

department: Department of Pharmacology

country: Germany

institute: University Medical Center, Johannes Gutenberg University of Mainz

summary: Long-term hematopoietic stem cells (LT-HSCs) reside in bone marrow (BM) niches with low levels of oxygen and reactive oxygen species (ROS). ROS enhancement results in differentiation of LT-HSCs. Redox disturbances are involved in BM failure and leukemia. Paraoxonase-2 (PON2) has been shown to be important for ROS control. However, the role of PON2 in the hematopoietic system has not been addressed. Analysis of young mice with inactivated Pon2 gene (Pon2-/- mice; 3 months) revealed changes in quantity of hematopoietic stem and progenitor cells (HSPCs), which indicate changes in cell differentiation. Experiments with aged PON2-/- mice (>9 months) showed alterations of the HSPC compartment indicating changed self-renewal ability of HSCs and myeloid skewing. Reciprocal BM transplantation reveals cell intrinsic as well as extrinsic phenotypes. We observed markedly enhanced superoxide levels in BM as well as slightly enhanced total ROS level in short term (ST)-HSCs and multipotent progenitor cells (MPPs) of young mice. In aged mice, total ROS level was slightly increased in all 3 fractions of the Lin-, Sca1+, ckit+ (LSK) population. No changes in the amount of DNA double-strand breaks in LSK cells and decreased apoptosis rates in LT-HSCs of young as well as LT- and ST-HSCs of aged PON2-/- mice were seen, indicating a strong compensation mechanism. Changes of gene expression in PON2-/- LT-HSCs identified by RNA sequencing strengthened our conclusions. Additionally, competitive and serial bone marrow transplantation experiments exposed advantages of PON2-/- BMCs in multi-lineage reconstitution. Collectively, these analyses propose PON2 as crucial redox control enzyme in HSCs.

overall_design: LT-HSCs from BM of 6 young WT- and 6 young Pon2-/- mice were stained using fluorescent-conjugated markers Lin, Sca1, ckit, CD135 and CD150. 10 LT-HSCs per well to a total of 8 wells per mouse were FACs sorted into a 96 well plate (8 RNA-Seq per mouse and 48 RNA-Seq per genotype). Transcriptome of WT LT-HSCs works as a reference for transcriptome of Pon2-/- LT-HSCs.

first: Lisa

last: Spiecker

first: Hartmut

last: Kleinert


title: Ventral mesencephalic dopaminergic (vmDA) precursors derived from human embryonic stem cells

status: Public on Jul 19 2021

city: Seoul

first: Dong-Wook

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Physiol.

country: South Korea

institute: Yonsei University College of Medicine

summary: Identify gene expression patterns between LMX1A+ and LMX1A- vmDA precurosrs derived from human embryonic stem cells (hESCs).

overall_design: The total of 6 samples were analyzed wich could be grouped into 2 groups.

first: Jeong-Eun

last: Yoo

first: Dongjin

last: Lee

first: Sanghyun

last: Park

first: Dong-Youn

last: Hwang


title: Germinal Center T follicular helper (GC-Tfh) cell impairment in chronic HIV infection involves c-Maf signaling [microarray]

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: We have recently demonstrated that the function of T follicular helper (Tfh) cells obtained from lymph nodes (LN) of HIV-infected individuals is impaired. We found that these cells were unable to provide proper help to germinal center (GC)-B cells, as observed by altered and inefficient anti-HIV antibody response and premature death of memory B cells. The underlying molecular mechanisms of this dysfunction remain poorly defined. Herein, we have used a unique transcriptional approach to identify these molecular defects. We consequently determined the transcriptional profiles of LN GC-Tfh cells following their interactions with LN GC-B cells from HIV-infected and HIV-uninfected individuals, rather than analyzing resting ex-vivo GC-Tfh cells. We observed that proliferating HIV-infected GC-Tfh cells were transcriptionally different than those from HIV-uninfected individuals, displaying a significant downregulation of immune- and GC-Tfh-associated pathways and genes compared to cells from uninfected individuals. Our results strongly demonstrated that MAF (coding for the transcription factor c-Maf) and its upstream signaling pathway mediators (IL6R and STAT3) were significantly downregulated in HIV-infected subjects, which could contribute to the impaired GC-Tfh and GC-B cell functions reported during infection. We further showed that c-Maf function was associated with the adenosine pathway and that the signaling upstream c-Maf could be partially restored by adenosine deaminase -1 (ADA-1) supplementation. Overall, we identified a novel mechanism that contributes to GC-Tfh impairment during HIV infection. Understanding how GC-Tfh function is altered in HIV is crucial and could provide critical information about the mechanisms leading to the development and maintenance of effective anti-HIV antibodies.

overall_design:
A total of 5 HIVneg and 7 HIVpos. LNs were collected (6 HIVpos LNs were used in the microarray assay and 3 HIVpos LNs were used in the RNA-seq assay, where 2 of the specimens were common to the 2 assays). Related RNA-seq study is GSE173500.

There were two donors in common between the two assays: LNJB(LN2) and LNNY (LN1). RNA was extracted from different sample aliquots from those two donors with several years passing in between extraction.  As such, the matching microarray and RNA-Seq datasets are not considered as technical/inter-assay duplicates.

first: Marita

last: Chakhtoura

first: Mike

last: Fang

first: Rafael

last: Cubas

first: Margaret

last: O'Connor

first: Brian

last: Richardson

first: Carmen

middle: N

last: Nichols

first: Artthi

last: Talla

first: Susan

last: Moir

middle: J

first: Virginie

last: Tardif

first: Elias

middle: K

last: Haddad


title: Germinal Center T follicular helper (GC-Tfh) cell impairment in chronic HIV infection involves c-Maf signaling [RNA-seq]

overall_design:
A total of 5 HIVneg and 7 HIVpos. LNs were collected (6 HIVpos LNs were used in the microarray assay and 3 HIVpos LNs were used in the RNA-seq assay, where 2 of the specimens were common to the 2 assays). Microarrays have not yet been submitted to a public database.

SEB coculture: Sorted CFSE-labeled GC-Tfh cells from HIVpos and HIVneg LNs were co-cultured with autologous GC-B cells in the presence of Staphylococcal Enterotoxin B (SEB).


title: Characterization of the oxyR mutant in the intracellular pathogen Legionella pneumophila

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

summary:
The intracellular pathogen Legionella pneumophila (Lp) is a strict aerobe, surviving and replicating in environments where it frequently encounters reactive oxygen species, such as the nutrient-poor water environment and inside host cells. In many proteobacteria, the oxidative stress response is regulated by the LysR-type regulator OxyR; however, the role played by the OxyR homologue in Lp is still unclear. Therefore, we undertook the characterisation of the phenotypes associated with the deletion of OxyR in Lp. OxyR is dispensable for growth in rich broth, in amoeba and in human cultured macrophages, and for the survival of Lp in water. Nevertheless, the mutant was found to be more sensitive to hydrogen peroxide than the wild-type when grown to post-exponential phase, but not when grown to exponential phase.
Moreover, the mutant is defective in forming isolated colonies on charcoal yeast extract (CYE) agar plates, but supplementation with anti-ROS molecules, such as pyruvate, α-ketoglutarate and catalase, rescued this defect. Further characterisation of this phenotype using a transcriptional reporter fusion and microarray analysis revealed that the deletion mutant is not defective for the expression of known anti-ROS genes which suggests that the growth defect on agar plates and the higher susceptibility to hydrogen peroxide are due to a broad change in the transcriptional response. Furthermore, the growth defect is suppressed when the mutant is grown on CYE plates made with agarose, suggesting that a compound present in typical agar is toxic for the oxyR mutant.

sample_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: Legionella pneumophila Philadelphia-1 strains KS79 and isogenic mutant ΔoxyR were grown in AYE broth at 37°C to post-exponential phase (PE) and exposed to 10 mM H2O2.

first: Nilmini

last: Mendis

first: Hana

last: Trigui

first: Mariam

last: Saad

first: Adrianna

last: Tsang


title: Single cell transcriptome sequencing reveals key molecules and pathways underlying the development of in vitro fertilized and pathenogenetically activated early embryos in pigs

city: Jingzhou

first: Liang

last: Hao

state: Hubei

address: JingMi road

institute: Yangtze University

summary: Successful early embryo development requires the correct reprogramming and configuration of gene networks by the timely and faithful execution of zygotic genome activation (ZGA). However, the regulatory principle of molecular elements and circuits fundamental to embryo development remains largely obscure. Here, we profiled the transcriptomes of single oocytes and blastomeres, obtained from in vitro fertilized (IVF) or parthenogenetically activated (PA) porcine early embryos (1- to 8-cell), focusing on the gene expression dynamics and regulatory networks associated with maternal-to-zygote transition (MZT) (e.g. maternal RNA clearance and ZGA). We found that minor and major ZGAs occur at 1-cell and 4-cell stages for both IVF and PA embryos, respectively. Maternal RNAs gradually decay from 1- to 8-cell embryos. Top abundantly expressed genes (CDV3, PCNA, CDR1, YWHAE, DNMT1, IGF2BP3, ARMC1, BTG4, UHRF2 and gametocyte-specific factor 1-like) in both IVF and PA early embryos identified are of vital roles for embryo development. Differently expressed genes within IVF groups are different from that within PA groups, indicating bi-parental and maternal-only embryos have specific sets of mRNAs distinctly decayed and activated. Pathways enriched from DEGs showed that RNA associated pathways (RNA biding, processing, transport and degradation) could be important. Moreover, mitochondrial RNAs were found to be actively transcribed and dynamically changed. DNA/H3K4 methylation and transcription factors also showed dynamic expression patterns. Taken together, our findings provide an important resource to investigate further the epigenetic and genome regulation of MZT events in early embryos of pigs.

overall_design: We profiled the transcriptomes of single oocytes and blastomeres, obtained from in vitro fertilized (IVF) or parthenogenetically activated (PA) porcine early embryos (1- to 8-cell), focusing on the gene expression dynamics and regulatory networks associated with maternal-to-zygote transition (MZT).

first: Cai-Xia

last: Yang

first: Zhi-Qiang

last: Du


title: Systematic feedomics provide solutions to improve human inedible crop by-products for global food production

first: Huizeng

last: Sun

address: 866 Yuhangtang Road

department: College of Animal Sciences

summary: The transcriptome of 24 samples across liver and mammary gland from 12 dairy cows with 2 different diets were generated using Illumina HiSeq2000

overall_design: The dairy cows were fed with corn stover based diet (CS) and alfalfa hay based diet (AH) for 12 weeks and were collected liver and mammary gland tissues after slaughter. Totally RNA were extracted from liver and mammary gland and sequenced using Hiseq 2000

first: Leluo

last: Guan


title: Germinal Center T follicular helper (GC-Tfh) cell impairment in chronic HIV infection involves c-Maf signaling

first: Mark

last: Cameron


title: Transcriptional signature of hypoxic preconditioning in a mouse model of ischemic acute kidney injury

city: Chicago

first: Pinelopi

last: Kapitsinou

state: Il

address: 303 East Superior Street

department: Medicine/Nephrology

institute: Northwestern University, Feinberg School of Medicine

summary:
We have performed NGS-derived transcriptome profiling (RNA-seq) to examine the impact of hypoxic preconditioning in post-ischemic kidney injury.
Experimental set up: 4 C57BL/6J (male, 8 wks of age) mice were subjected to hypoxia (8%O2) for 48hrs and then subjected to unilateral renal ischemic reperfusion mice (IRI). 4 normoxic littermates subjected to renal IRI served as controls. Injured kidneys were harvested at day 3 following renal IRI and were subjected to NGS. Methods: Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

overall_design: Kidney mRNA profiles at day 3 post ischemic AKI in mice subjected to hypoxic preconditioning compared to normoxia


title: A study on the origin of the mouse placental trophoblast lineage

first: Xiangxiang

last: Jiang

address: 1 Beichen West Road, Chaoyang District

summary: The mouse placenta forms primarily from cells in the trophectoderm (TE) of the blastocyst. Complicated lineage specification in placental trophoblast cells finally forms the functional placenta. However, at which stage the fate of mouse trophoblast lineages is determined key open questions. Lineage tracing is the most reliable approach to study cell fate determination. Herein, we took advantage of a fluorescent Cre recombinase reporter mouse for our lineage tracing experiments. Cell labeling experiments were performed by microinjection of Cre mRNA into single blastomere respectively at the two-, four- and eight-cell stage, and increasing bias of the labeled cell distribution was observed in the E12.5 fetus and placenta, which was also supported by the  single cell sequencing results.Together, our data provide direct evidence supporting the idea that the first cell fate choice of early blastomeres, toward the inner cell mass (ICM) or trophoblast fate, has become determined at the four-cell stage, and three different cell fates may exist among the four blastomeres.Compared with previous studies, it is the first study to trace the cell lineages from early stages over such a long developmental period.

overall_design: We administered a microinjection of Cre mRNA into a single blastomere of the mTmG mouse at 4- or 8-cell stages.  We isolated Labelled cells at the blastocyst stage  and perform  candidate based gene expression analyses to validate expression patterns of some key regulators that are implicated in TE vs. ICM lineage bias.

first: Shanshan

last: Guo

first: Xiuhong

last: Cui

first: Fei

last: Gao

first: Hongmei

last: Wang


title: Transcriptomics and relative potency assessments using Bench Mark Dose  of Bisphenol A, Bisphenol S, Bisphenol F, and 3,3',5,5'-Tetrabromobisphenol A in H9 human embryonic stem cells

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: In this study we used RNA-seq to characterize the dose-response for global transcriptomic alterations induced by BPA, BPF, BPS and TBBA  in H9 (WA09) human embryonic stem (hES) cells. To assess the relative biological activity and potency of BPA and structural analogs BPS, BPF and TBBP, we examined the stem cell transcriptome in H9 hES cells following exposure to these chemicals at concentrations that covered greater than three orders of magnitude (1 microM to >100 microM). These exposure levels are considered to be near human relevant and range from noncytotoxic to overtly toxic. Overall, this study provides basic mechanistic information about the effects of BPA and structural analogs BPS, BPF and TBBP on the transcriptome of hES cells and demonstrates how these data can be applied to derive benchmark dose modeling (BMD) information useful for comparing relative potencies of these structurally related chemicals.

overall_design: Examination of the stem cell transcriptomes in H9 hES cells following their exposure to BPA and structural analogs BPS, BPF and TBBP at several concentrations.

first: Vian

last: Peshdary

first: Ella

last: Atlas

first: Cheryl

last: Hobbs

first: Timothy

last: Maynor

first: Kim

last: Shepard

first: Remi

last: Gagné

first: Andrew

last: Williams

first: Byron

last: Kuo

first: Nikolai

last: Chepelev

first: Leslie

last: Recio

first: Carole

last: Yauk


title: Single cell RNA-seq reveals mRNAs and lncRNAs important for oocyte meiosis and maturation in pigs

first: Liang

last: Hao

summary: The faithful execution of molecular program underlying oocyte maturation and meiosis is vital to generate competent haploid gametes for effective reproduction in mammals. However, the organization and principle of gene modules and molecular circuits for oocyte meiosis remain obscure. Here, we employed the recently developed single cell RNA-seq technique to profile the transcriptomes of germinal vesicle (GV) and metaphase II (MII) oocytes, aiming to discover the dynamic changes of mRNAs and long non-coding RNAs (lncRNAs) during oocyte meiotic maturation. During the transition from GV to MII, total number of RNAs (mRNAs and lncRNAs) in oocytes decreased. Moreover, 1807 (602 up- and 1205 down-regulated) mRNAs and 313 (177 up- and 136 down-regulated) lncRNAs were significantly differentially expressed. During meiotic maturation, expression level of most mRNAs decreased, but mitochondrial RNAs, and also more lncRNAs and their target genes increased. Both DE mRNAs and lncRNAs were enriched in multiple biological and signal pathways potentially associated with oocyte meiosis. Highly abundantly expressed mRNAs (including DNMT1, UHRF2, PCNA, ARMC1, BTG4, ASNS and SEP11) and lncRNAs were also discovered. Weighted gene co-expression network analysis (WGCNA) revealed 20 hub mRNAs, and three modules of contrasting functions in oocyte maturation and meiosis. Taken together, our findings provide insights and resources for further functional investigation of mRNAs/lncRNAs in mammalian oocyte meiosis and maturation.

overall_design: The important lncRNAs and mRNAs in oocytes before and after meiosis

first: Cai-Xia

last: Yang

first: Zhi-Qiang

last: Du


title: Spatiotemporal dynamics of Bach2 orchestrates B cell responses and fate decision

status: Public on Jul 18 2021

city: shanghai

first: Qianwen

last: Hu

address: 重庆南路280号

institute: Shanghai Jiao Tong University School of Medicine

summary: The molecular circuits that direct early T-dependent B cell responses and alternative cell-fate decisions remain poorly understood. Here, we show that either B cell receptor (BCR) or CD40 signals promoted mTORC1-dependent translation of the transcription factor Bach2. Transient up-regulation of Bach2 protein restrained activated B cell expansion and differentiation into plasma cell while promoting the germinal center (GC) and memory B cell fates at the pre-GC stage. However, enforced Bach2 expression facilitated memory B cell generation versus other cell fates. Mechanistically, Bach2 limited access of AP-1 factors and formed a reciprocal repression loop with IRF4. BCR and CD40 signals also down-regulated Bach2 transcript in antigen-activated B cells, and diversified its abundance in various effector populations, predisposing Bach2 protein expression and subsequent cell-fate choices during memory recall and GC reaction. Thus signaling-induced differential dynamics of Bach2 protein and mRNA in activated B cell control their cell-fate outcomes and imprint the fate of their descendant effector cells.

overall_design: To gain insight into the suppressive functions of Bach2 on PC differentiation, Bach2-sufficient and deficient CD19+IgD-GL7+CD38+ activated NP-specific B cells were sorted at day 2 after immunization and subjected for transcriptional profile analysis

first: Tingting

last: Xu


title: Usp16 deletion-induced gene expression in MEFs

city: Shanghai

first: Guiqin

address: 800 Dongchuan Rd

institute: Shanghai cancer institute

summary: To determine the molecular signaling pathways responsible for USP16 regulation of cell growth, RNA sequencing was conducted on MEFs with or without Usp16 deletion

overall_design: SV40T-immortalized K-rasG12D/Usp16+/+ and K-rasG12D/Usp16flox/flox MEFs were infection with Ad-Cre to activate K-rasG12D expression and delete the floxed Usp16 alleles. These cells denoted by K-rasG12D;Usp16+/+/SV40T (KS) and K-rasG12D;Usp16-/-/SV40T (UKS). The gene expression profiling in the MEFs with or without Usp16 deletion were analyzed by RNA-seq.

first: Yongzhong

last: Liu


title: Transcription factors involved in drug resistance in acute lymphoblastic leukemia

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

summary: The efficacy of glucocorticoid receptor modulation is well established in Acute Lymphoblastic Leukemia(ALL) but the response remains heterogeneous and limited by emergence of drug resistance. Here we use, two clonally-derived cell lines (CEM-C1 and CEM-C7) from a 3-year-old T-cell ALL patient, as a model system to understand the mechanisms of drug resistance in these cell lines; the clone CEM-C1 is resistant to dexamethasone-induced apoptosis and CEM-C7 is sensitive. We performed ATACseq and RNAseq to query for TF binding motifs present in the open regions of the chromatin and expression levels of TFs that could recognize the identified motifs. We are experimentally validating our hypothesis that depletion of the TFs identified, either singly or in combination, in CEM-C7 cells will cause dexamethasone resistance in CEM-C7 cells.

overall_design: Map the hypersensitve regions in ALL sensitive and resistant cell lines. Identfy TF motifs that underlie the diffrentially accesible regions. Perform RNAseq to get the expression data for TF candidates. We have 7 ATAC libaries and 6 RNAseq libraries.  Libraries were sequenced paired end (2x75).

first: Ninad

last: Walavalkar

first: Nancy

last: Lee


title: p53 transcriptionally regulates SQLE to modulate cholesterol synthesis and tumor growth

city: beijing

first: wei

last: li

address: No.5 Dongdansantiao street, Dongcheng district

institute: Peking Union Medical College

summary: Cholesterol is essential for membrane biogenesis, cell proliferation and differentiation. The role of cholesterol in cancer development and the regulation of cholesterol synthesis are still under active investigation. Here we show that under normal-sterol conditions，p53 directly represses the expression of SQLE, a rate-limiting and the first oxygenation enzyme in cholesterol synthesis，in a SREBP2-independent manner. Through transcriptional downregulation of SQLE, p53 represses cholesterol production in vivo and in vitro, leading to tumor growth suppression. Inhibition of SQLE using small interfering RNA (siRNA) or terbinafine (a SQLE inhibitor) reverses the increased cell proliferation caused by p53 deficiency. Conversely, SQLE overexpression or cholesterol addition promotes cell proliferation, particularly in p53 wild-type cells. More importantly, pharmacological inhibition or shRNA-mediated silencing of SQLE restricts nonalcoholic fatty liver disease (NAFLD) -induced liver tumorigenesis in p53 knockout mice. Therefore, our findings reveal a role for p53 in regulating SQLE and cholesterol biosynthesis, and further demonstrate that downregulation of SQLE is critical for p53-mediated tumor suppression.

overall_design: p53 wt vs ko mice with or without HFD liver RNA seq

first: Huishan

last: Sun

first: Wenjing


title: Single-cell RNAseq in NMe wild type and NMe GATA site 1 and 2 homozygous thymocytes

city: New York

first: Laura

last: Belver

state: NY

address: 1130 St Nicholas Ave

institute: Columbia University

summary: The NOTCH1-driven MYC enhancer (NMe) is essential for T cell development, transformation and the development of acute lymphoblastic leukemia. Here we analyzed by single-cell RNAseq the gene expression profile of total thymus from NMe wild type and NMe GATA site 1 and 2 (GS1+2) homozygous mutant mice.

overall_design: Single-cell RNAseq analysis of total thymus in two genotypes.  Here we analyzed by single-cell RNAseq the gene expression profile of total thymus from NMe wild type and NMe GATA site 1 and 2 (GS1+2) homozygous mutant mice.

first: Adolfo

last: Ferrando

first: Francesco

middle: G

last: Brundu


title: LYAR promotes colorectal cancer progression by up-regulating FSCN1 expression and fatty acid metabolism

status: Public on Jul 17 2021

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

summary: Colorectal cancer (CRC) is a highly malignant tumor associated with poor prognosis, yet the molecular mechanisms are not fully understood. In this study, we showed that LYAR, a nucleolar protein, expresses at a higher level in CRC than adjacent normal tissue and LYAR expression is closely associated with distant CRC metastasis. LYAR not only significantly promotes the migration and invasion of CRC cells in vitro, also the knockdown (KD) of LYAR in CRC cells inhibits xenograft tumor metastasis in vivo. Microarray analysis of LYAR KD cells combined with ChIP assay, gene reporter assay and rescue experiment indicate that FSCN1 (encoding fascin actin-bundling protein 1, Fascin-1) serves as a new key regulator of the LYAR-promoted migration and invasion of CRC cells. Knockdown of FSCN1 significantly inhibits subcutaneous tumorigenesis of CRC cells, and leads to the down-regulation of FASN and SCD, genes encoding key enzymes in fatty acid synthesis. In summary, this study reveals a novel mechanism by which LYAR promotes tumor cell migration and invasion by up-regulating FSCN1 expression and affecting fatty acid metabolism in CRC.

overall_design: Microarray Analysis of Scramble-shRNA cells and LYAR-shRNA HCT15 cells

first: Wu

last: Yupeng

first: Ma

last: Sai


title: RNA-seq of primary islets in HFD_DMSO，HFD_CGP and ND mice

city: nanjing

first: feng

middle: ru

last: xu

address: jiangning

institute: nanjing medical university

summary: We investigated the underlying molecular mechanism of CGP 57380's effects in type 2 diabetes by comparing gene expression of whole primary islets isolated from HFD_DMSO,HFD_CGP and ND mice by RNA sequencing.C57BL/6 mice were fed an HFD for 4 months and then oral gavage DMSO and CGP 57380 for about 1 month separately to studied gene-expression differences resulting in HFD-induced hyperinsulinemia and metabolic abnormities.At the same time ,explore the therapeutic effect of CGP 57380 on type 2 diabetes,and the changes in the signal pathways in it.Gene set-enrichment ananlysis was performed using Kyoto Encyclopedia of Genomes algorithms and MSigDB software.The most enriched pathways were linked to pathyways associated with PI3K-Akt signaling pathway, pancreatic secretion and NF-kappa B signaling pathway.

overall_design: Islets mRNA of HFD_DMSO,HFD_CGP and ND male mice

first: Xiao

last: Han

first: Yunxia

last: Zhu

first: Rufeng

first: Kaiyuan

last: Wang


title: Metabolism regulates muscle stem cell self renewal by connecting the microenvironment and histone acetylation

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Skeletal muscle contains a resident population of somatic stem cells capable of both self-renewal and differentiation. The signals that regulate this important decision have yet to be fully elucidated. Here we use single cell RNAseq to identify the innate metabolic signature of muscle stem cells. We show that committed muscle progenitor cells exhibit an enrichment of glycolytic and TCA cycle genes and that extracellular monosaccharide availability regulates intracellular citrate levels and global histone acetylation. Muscle stem cells exposed to a reduced (or altered) monosaccharide environment demonstrate reduced global histone acetylation and transcription of myogenic determination factors (including myod1). Importantly, reduced monosaccharide availability was linked directly to increased rates of asymmetric division and muscle stem cell self-renewal. Our results reveal an important role for the extracellular metabolic environment in the decision to undergo self-renewal or myogenic commitment, suggesting local metabolite production may be a therapeutic target to improve muscle regeneration.

overall_design: Examination of single skeletal muscle stem cells that were either freshly isolated or cultured for 96hrs in growth media containing either high glucose (25mM), low glucose (5mM) or galactose (10mM)

first: C

last: Ly

first: Jennifer

last: Trieu

first: Luyi

last: Tian

first: Daniela

last: Zalcenstein

first: Shalin

last: Naik

first: Matthew

middle: E

last: Ritchie

first: Gordon

middle: S

last: Lynch

first: James

last: Ryall


title: RNA-seq Analysis of Wild Type(WT) and Dcaf11 overexpression (OE) ESCs

first: Yixin

last: Huang

address: Siping Road

institute: Tongji University

summary: Telomeres play vital roles in ensuring chromosome stability and are thus closely linked with the onset of aging and human disease. Telomeres undergo extensive lengthening during early embryogenesis. However, the detailed molecular mechanism of telomere resetting in early embryos remains unknown. Here, we show that Dcaf11 (Ddb1- and Cul4-associated factor 11) participates in telomere elongation in early embryos and 2-cell-like embryonic stem cells (ESCs). The deletion of Dcaf11 in embryos and ESCs leads to reduced telomere sister-chromatid exchange (T-SCE) and impairs telomere lengthening. Importantly, Dcaf11-deficient mice exhibit gradual telomere erosion with successive generations, and hematopoietic stem cell (HSC) activity is also greatly compromised. Mechanistically, Dcaf11 targets Kap1 (KRAB-associated protein 1) for ubiquitination-mediated degradation, leading to the activation of Zscan4 downstream enhancer and the removal of heterochromatic H3K9me3 at telomere/subtelomere regions. Our study therefore demonstrates that Dcaf11 plays important roles in telomere elongation in early embryos and ESCs through activating Zscan4.

overall_design: ESCs mRNA profiles of WT and Dcaf11 OE were generated by deep sequencing.

first: Rongrong

last: Le

first: Yanping

last: Zhang


title: mRNA Expression Data from Murine Hearts of Wildtype Mice over 24 hours in normal light-dark environment (12:12)

status: Public on Jul 16 2021

city: Guelph

first: Dr. Tami

middle: A.

last: Martino

address: 50 Stone Road E

department: Centre for Cardiovascular Investigations, Department of Biomedical Science

institute: University of Guelph

summary:
Male C57Bl/6 mice were accommodated in normal 12:12 LD condition for one week. Hearts were collected every 4 hours over 24 h starting at 1 h before lights on (ZT23) (ZT23, ZT03, ZT07, ZT11, ZT15, ZT19).
The microarray approach allows the investigation of daily transcriptome-wide gene expression changes in hearts over 24 hours.

overall_design: There are a total of 24 samples, 4 per each time point.

first: Tami

middle: A


title: mRNA Expression Data from Murine Hearts of Clock delta 19/delta 19 Mice over 24 hours in normal light-dark environment (12:12)

summary:
Male Clock delta 19/delta 19 mice were accommodated in normal 12:12 LD condition for one week. Hearts were collected every 4 hours over 24 h starting at 1 h before lights on (ZT23) (ZT23, ZT03, ZT07, ZT11, ZT15, ZT19).
The microarray approach allows the investigation of daily transcriptome-wide gene expression changes in hearts over 24 hours.


title: DIS3 is essential for male germ cell meiosis and spermatogenesis in mice

city: Bethesda

first: Zhengpin

state: MD

address: National Institutes of Health, 9000 Rockville Pike

department: Laboratory of Cellular and Developmental Biology

institute: NIDDK, NIH

summary: Male germ cell meiosis is essential for generating haploid spermatozoa in mice. Here, we investigate the essential role of DIS3 in male germ cell meiosis in mice. Conditional inactivation of DIS3 in spermatocytes with Stra8-cre transgenic mice have severely impaired meiotic progression, which results in defective meiosis and spermatogenesis. RNA-seq analysis reveals that Dis3 deficiency causes significant dysregulation of the expression of transcripts in mutant testes. Meiosis-associated genes are significantly decreased in the absence of DIS3. Therefore, we show that DIS3 ribonuclease plays a critical role in germ cell meiosis during spermatogenesis in mice.

overall_design: RNA-seq was performed using postnatal day 17 (P17) testes between control and Dis3 cKO mice in order to identify the differentially expressed genes.

first: Guoyun

last: Yu

first: Jurrien

last: Dean


title: Specialized endothelial tip cells guide neuroretina vascularization and blood-retina-barrier formation

city: Montreal

first: Alexandre

last: Dubrac

state: Quebec

address: 3175 Côte-Sainte-Catherine Road

institute: University of Montreal

summary: Endothelial tip cells guiding tissue vascularization are primary targets for angiogenic therapies. Whether tip cells require differential signals to develop their complex branching patterns remained unknown. Here we show that diving tip cells invading the neuroretina (D-tip cells) are distinct from tip cells guiding the superficial retinal vascular plexus (S-tip cells). D-tip cells have a unique transcriptional signature, including high TGFβ signaling, and acquire blood-retina barrier properties. Endothelial deletion of TGFβ receptor I (Alk5) inhibits D-tip cell identity acquisition and deep vascular plexus formation. Loss of endothelial ALK5, but not of the canonical SMAD effectors, leads to aberrant contractile pericyte differentiation, and hemorrhagic vascular malformations. Our data reveal stage-specific tip cell heterogeneity as a requirement for retinal vascular development and suggest that noncanonical-TGFβ signaling could improve retinal revascularization and neural function in ischemic retinopathy.

overall_design: Retinal single-cell mRNA profiles of WT and Alk5iEKO mice from P6 and P10


title: Deep sequencing for mRNA in mouse liver around the circadian clock after partial hepatectomy (PHx) or sham orperation

city: Hangzhou

first: Saisai

last: Wei

address: 3 Qingchun East Road

institute: Sir Run Run Shaw Hospital, Zhejiang University

summary: We reported the circadian rhythms for the liver transcriptome during mouse liver regeneration

overall_design: We monitored the liver transcriptome every 4 h after PHx for 32 h. On the other hand, we did PHx in the morning or evening, and monitored the liver transcriptome at 4 and 24 h

first: Qiang

last: Zheng

first: Yu

last: Pan

first: Yunwan

last: Xu

first: Jiacheng

last: Tang

first: Xiujun

last: Cai


title: Hyperglycaemia induces trained immunity in macrophages and their precursors and promotes atherosclerosis

city: Oxford

first: Robin

last: Choudhury

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

institute: University of Oxford

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: CPP stimulation

city: Meguro-ku

first: Rina

last: Kunishige

state: Tokyo

address: 202A, Building 3, 3-8-1 Komaba

department: Department of Life Sciences  Graduate School of Arts and Sciences

country: Japan

institute: The University of Tokyo

summary: HK2 treated with CPP

overall_design: HK2 treated with CPP for up to 24 hours


title: Functional antagonism of chromatin modulators regulates EMT [ATAC-Seq]

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

institute: Max-Delbrück-Centrum für Molekulare Medizin

summary: Genome-wide chromatin analyses to validate the CRISPR interference screen for modulators of mesenchymal signaling reporter in A549 and H1944 cells. ATAC-seq in naive, GSK126- and TGFB-treated A549 cells. ChIP-seq in naive A549 cells for chromatin modulators, ChIP-seq in naive and GSk126-treated cells from RNAPII in A549 cells.

first: Michela

last: Serresi

first: Matthias

last: Schmitt


title: DNA hyper-methylation during Tuberculosis dampens host immune responsiveness

city: Houston

first: Andrew

last: DiNardo

state: Texas

address: 1102 Bates St

department: Global and Immigrant Health

institute: BCM

type: Methylation profiling by genome tiling array

summary: DNA Methylation was analyzed in tuberculosis patients without HIV at baseline and 6 months after completion of successful therapy. DNA methylation was also evaluated in TB patients with HIV and in healthy controls without Tuberculosis. 500ng of gDNA was bisulfite treated prior to running the Illumina Infinium MethylEPIC array

overall_design: The study protocol was reviewed by the Baylor College of Medicine Children’s Foundation-Swaziland, Baylor College of Medicine and Eswatini National Health Research and Review Board. All participation was voluntary and implemented in accord with the institutional and international guidelines for the Protection of Human Subjects in concordance with the Declaration of Helsinki including written informed consent from participants or their guardians. In this analysis, immune cells of TB participants were analyzed if they had pulmonary disease as defined by symptoms of TB (cough, fevers, weight loss, etc) and microbiologically confirmed disease by sputum Gene Xpert and/ or culture. All participants were screened for HIV. Healthy controls were household contacts of TB patients with a TB contact score of five or greater and excluded if they progressed to active TB and did not remain asymptomatic for 12- months. All individuals were BCG vaccinated as confirmed by BCG scar and/ or vaccine card.

first: Kimal

last: Rajapakshe

first: Tomoki

last: Nishiguchi

first: Sandra

middle: L

last: Grimm

first: Godwin

last: Mtetwa

first: Qiniso

last: Dlamini

first: Jaqueline

last: Kahari

first: Sanjana

last: Mahapatra

first: Alexander

last: Kay

first: Gugu

last: Maphalala

first: Emily

middle: M

last: Mace

first: George

last: Makedonas

first: Jeffrey

last: Cirillo

first: Mihai

last: Netea

first: Reinout

last: van Crevel

first: Cristian

last: Coarfa

first: Anna

last: Mandalakas


title: Genome-wide DNA methylation change due to H19 knockdown and TET3 knockdown in UtLM

city: New Haven

first: Ying

last: Jiang

address: 310 Cedar Street

institute: Department of Obstetrics, Gynecology & Reproductive Sciences

summary: We used Methyl-MiniSeq platform from Zymo Research company to identify genome-wide methylation changes affected by H19 knockdown and TET3 knockdown in human UtLM. Following H19 and TET3 knockdown, we observed extensive genome-wide methylation pattern changes relative to siCon cells, with some genes showing increased methylation, others showing decreased methylation, and a third group with no significant change.

overall_design: human UtLM were transfected with either control siRNA, siH19 or siTET3. 48h later, cellular genomic DNA was extracted and subjected to genome-scale DNA methylation mapping using the platform of an improved version of Reduced Representation Bisulfite Sequencing (RRBS).

first: Karolyn

last: Giang

first: Hunter

last: Chung

first: Xueguang

last: Sun


title: RNA sequencing reveals the key genes and pathways in a mouse model of heart failure with preserved ejection fraction

first: zhang

middle: yun

last: long

state: beijing

address: No.10 Xitoutiao, You An Men

department: Department of Physiology and Pathophysiology,

institute: School of Basic Medical Sciences, Capital Medical University

summary: Our study helps to understand the molecular pathogenesis of HFpEF and identifiy genes and pathways that may be potential therapeutic targets for HFpEF treatment

overall_design: In this study, we applied RNA sequencing to detect the changes of gene expression profiles in mouse HFpEF model.

first: Yuxi

first: Jiaxin

last: Li

first: Yunlong

last: Zhang

last: Liu


title: Cytoplasmic long non-coding RNAs are differentially regulated and translated during human neuronal differentiation

city: Leeds

first: Julie

last: Aspden

address: Woodhouse

department: FBS

institute: University of Leeds

summary: The expression of long non-coding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of human SH-SH5Y cells. We discovered 237 cytoplasmic lncRNAs upregulated during early neuronal differentiation, 58-70% of which are associated with polysome translation complexes. Amongst these polysome associated lncRNAs, we find 45 small ORFs to be actively translated, 17 specifically upon differentiation. 15/45 of the translated lncRNA-smORFs exhibit sequence conservation within Hominidea suggesting they are under strong selective constraint in this clade. Profiling of publicly available datasets revealed that 8/45 of the translated lncRNAs are dynamically expressed during human brain development and 22/45 are associated with cancers of the central nervous system. One translated lncRNA we discovered is LINC01116, which is induced upon differentiation and contains an 87 codon smORF exhibiting increased ribosome profiling signal upon differentiation. The resulting LINC01116 peptide localises to neurites. Knockdown of LINC01116 results in a significant reduction of neurite length in differentiated cells indicating it contributes to neuronal differentiation. Our findings indicate cytoplasmic lncRNAs interact with translation complexes, are a non-canonical source of novel peptides, and contribute to neuronal function and disease. Specifically, we demonstrate a novel functional role for LINC01116 during human neuronal differentiation.

overall_design: Poly-Ribo-Seq on human neuroblastoma cells (SH-SY5Y) in 2 conditions: undifferentiated (Control) and differentiated with RA for 3 days.

first: Katerina

last: Douka

first: Isabel

last: Birds

first: Dapeng

last: Wang

first: Andreas

last: Kosteletos

first: Sophie

last: Clayton

first: Abigail

last: Byford

first: Elton

last: Vasconcelos

first: Mary

last: O'Connell

first: Jim

last: Deuchars

first: Adrian

last: Whitehouse


title: BRD4 orchestrates genome folding to promote neural crest progenitor differentiation

city: Philadelphia

first: Ricardo

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

summary: Higher-order chromatin structure is critical for proper gene regulation, but the relationship between genome folding and cellular identity remains elusive. Here, we show that genetic deletion of the Bromodomain-containing protein 4 (BRD4) in murine neural crest cells recapitulates features of cohesinopathies. We demonstrate that BRD4 interacts with NIPBL, a positive cohesin regulator, and acute depletion of BRD4 or loss of the BRD4-NIPBL interaction reduces NIPBL-occupancy, elucidating the importance of BRD4 in stabilizing NIPBL on chromatin. Genome-wide chromatin interaction mapping and quantitative imaging studies demonstrate that BRD4-depletion results in aberrant genome folding, specifically loss of a subset of chromatin loops, weakening of TADs, and compromised loop extrusion. Finally, loss of BRD4 or the interaction with NIPBL impedes neural crest differentiation which, remarkably, is rescued by WAPL depletion, a negative cohesin regulator. Our data reveal that BRD4 choreographs genome folding, illustrating the importance of balancing cohesin activity on progenitor differentiation.

overall_design: Examination of genome-wide occupancy of BRD4, NIPBL, H3K27ac and RAD21 in control and BRD4-degradation conditions (CUT&RUN). Examination of interaction frequecy in both conditions (Hi-C). Examination of gene transcription in both conditions (RNA-seq and SLAM-seq).

last: Linares-Saldana

first: Rajan

last: Jain

first: Wonho

last: Kim

first: Nikhita

last: Bolar


title: A Novel Cre Transgenic Mouse to Label Cardiac Purkinje Fibersduring Ischemic Injury

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: Purkinje fibers form a network of specializedventricularmyocardial cells to assure a coordinatedpropagation of the electrical impulseduring normalforheartefficientcontractionof the heart.Thedevelopmental origins of Purkinje fibers and their roles during cardiac arrhythmia have been reported.However, theresponse of Purkinje fibers to ischemic injury and theirfunctionrolesduring myocardialregenerationare still illusive. Here we introduceda novel inducibleCreallelemouse linethat specificallylabelsthemousecardiac conduction system. Fate mappingshowed Cre activity in different componentsofindicatedspecific labeling ofthe cardiac conduction system, including the sinoatrial and atrioventricularnodes,as well as the Purkinje fibersdifferentknown and unknowncomponents ofthecardiac conductionsystem. RNA-Seqof laser-captured Purkinje fibers showed a uniqueinjuryresponse occurredafterischemic injuryin thisventricularpart of the conductionsystemand corresponding changes in.Ccellularcompositionchange inofPurkinje fibersafter ischemic injury waswereobserved using immunostaining

overall_design: Laser capture micro-dissection of GFP+ purkinje cells followed by RNA extraction and RNA-seq. For controls, background non-GFP+ cells were used.


title: Genome-wide expression profiling in Drosophila wing imaginal discs

status: Public on Jul 15 2021

city: Washington

first: Xiaoyan

last: Zheng

state: District of Columbia

address: SEH, Suite 8840, 800 22nd Street NW

department: Anatomy and Cell Biology

institute: George Washington University School of Medicine and Health Sciences

summary:
The imaginal discs of Drosophila melanogaster, where most known Hedgehog (Hh) signaling target genes are expressed with a restricted pattern, offers an accessible model system for identifying novel targets of the Hh signaling pathway.
In the wing discs, cells near the A/P compartment boundary (B: ptc+) receive the highest level of Hh stimulation, A cells (A: hh-) further from the border receive lower levels of stimulation, while P cells (P: hh+) do not respond to Hh.
To identify target genes whose expression is controlled by Hh signaling activity, we performed a systematic comparison of gene expression profiles among the A cells (A: hh-), the A cells adjacent to the A/P compartment boundary (B: ptc+), and P cells (P: hh+) via microarray analysis.

overall_design: For this study, 200 pairs of wing imaginal discs were dissected from third instar larvae of the genotypes w; UAS-mCD8GFP/+; hh-Gal4/+ or w; UAS-mCD8GFP/+; ptc-Gal4/+. The purpose was to separate and get the homogeneous populations of the cells have the different response to Hh stimulation in imaginal discs development. To this end, three part of cells [Anterior cells which receive low levels of Hh stimulation (A: hh-), Posterior cells which do not respond to Hh (P: hh+) , and the cells near the A/P compartment boundary which receive the highest level of Hh stimulation (B: ptc+), and ] were dissociated from tissue and sorted by FACS.


title: Single-cell RNA-seq in a model for HIV latency reversal

city: Scarborough

first: Guillaume

last: Filion

address: 1265 Military Trail

department: Biological Sciences

institute: UTSC

summary: T cells are the primary target of the virus HIV-1. Upon infection, the expression of the virus may come to a complete shutdown, a phenomenon known as latency. The molecular mechanisms responsible for the latency of HIV-1 are still poorly understood. To shed light on those mechanisms, we used the J-Lat A2 model for latency reversal, that consists of a Jurkat T cell clone containing a mini HIV construct that is transcriptionally silent. We treated J-Lat A2 and Jurkat cells with the latency-reversing drugs SAHA (suberoylanilide hydroxamic acid) and PMA (phorbol 12-myristate 13-acetate), and we performed single-cell RNA-seq to identify transcriptional signatures shared among the cells where HIV is reactivated.

overall_design: Jurkat T cells and J-Lat A2 cells were treated by SAHA or PMA, or by the control drug DMSO in two experimental batches. After 24 hours, cells were FACS-sorted down to one cell per well into five 96-well plates (two plates in the first batch, three plates in the second).

first: Daria

last: Repkina


title: single cell mRNA sequencing of B cells from human endometrial cancers

city: Groningen

first: Marco

last: de Bruyn

address: Hanzeplein 1

department: Obstetrics&Gynecology

country: Netherlands

institute: University Medical Center Groningen

summary: Emerging data indicate that B-cells play a key role in cancer suppression, particularly when aggregated in tertiary lymphoid-like structures (TLS). Here, we used single-cell and bulk RNA sequencing of endometrial cancers (ECs) and found L1-cell adhesion molecule L1CAM to be significantly associated with TLS. Immunohistochemical (IHC) expression of L1CAM was restricted to the germinal centre (GC) of mature TLS, where it co-localised with follicular dendritic cell (FDC) marker CD21. Tumours surrounded by L1CAM-positive TLS were identified across all molecular EC subgroups, but enriched in mismatch repair deficient (MMRd) and polymerase-epsilon mutant (POLEmut) EC, especially when TP53 mutations were also present. Importantly, L1CAM-positive TLS appeared an independent favourable predictor of EC recurrence and death, and significantly improved the current prognostic molecular EC classification based on clinicopathological and molecular factors. Our data suggest a pivotal role of TLS in predicting outcome of EC patients, and establishes L1CAM as a simple and widely available biomarker of TLS in clinical care.

overall_design: 1513 single B cells from 6 patients


title: Dynamic regulation of mRNA associated with the developmental stages of skin pigmentation in yellow mutant rainbow trout

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

summary: Yellow mutant rainbow trout (YR) is becoming more popular for aquaculture production in China in recent years owing to its excellent meat quality and gorgeous appearance. Although much comparative research has been undertaken on two or three different skin colors of the same species, seldom attentions were focused on the genetic regulation during the developmental process of pigmentation. In this study, the skin transcriptomes in three distinct developmental stages of YR were sequenced to search for genes related to skin pigmentation.

overall_design: In the present study, RNA-seq was used to identify the candidate genes that are responsible for color formation among three developmental stages of YR.

first: Jinqiang

last: Huang

first: Shenji

last: Wu


title: Genes differentially expressed after DNA methyltransferase 1 (DNMT1) knockdown in the presence or absence of early osteoblast (OB)  differentiation

city: Guangzhou

first: Jianwei

last: Li

address: South Shatai Road

institute: southern medical university southern hospital


title: Genes differentially methylated after DNA methyltransferase 1 (DNMT1) knockdown in the presence or absence of early osteoblast (OB)  differentiation [RRBS]

summary: reduced representation bisulfite sequencing (RRBS) sequencing was performed to analyze methylation profiles regulated by DNMT1 in C3H10T1/2 MSCs with or without OB differentiation.

overall_design: C3H10T1/2 MSCs were transfected with control siRNA or siRNA of DNMT1, the cells were then either induced for OB differentiation for 3 days, or left untreated.

first: Chen

last: Tao


title: Genes differentially expressed after DNA methyltransferase 1 (DNMT1) knockdown in the presence or absence of early osteoblast (OB)  differentiation [RNA-seq]

summary: RNA sequencing was performed to analyze potential genes regulated by DNMT1 in C3H10T1/2 MSCs with or without OB differentiation.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Differentially Expressed Genes in Radiated and Non-Radiated femurs

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

summary: Mechanisms underlying radiation induced bone loss seen following clinical radiotherapy are largely unkown. In order to identify mechanisms underlying focal radiation induced bone loss, differentially expressed genes were assessed in radiated bones as compared to the contralateral leg from the same animal.

overall_design: Four-month-old C57BL/6 mice received focal radiation as a single dose of 24Gy on day 0. Using X-Rad-SmART (Precision X-Ray (PXi), North Branford, Connecticut) an image-guided focal dose of 24Gy at 6.6Gy/minute was delivered to a 5mm region of the distal metaphyseal region of the right femur (radiated, R), while the left femur served as the contralateral control (non-radiated, NR). Bones were harvested on day 21 for RNA sequencing. This time point was selected because bone loss was observed at day 28 and we wanted to assess the events preceding bone loss.

first: Abhishek

last: Chandra

first: Robert

last: Pignolo


title: Clinical Impact of Serum Exosomal microRNA in Liver Fibrosis

city: Cheonan-si

first: Jae-A

last: Han

address: 25 Bongjeong-ro Dongnam-gu

institute: Soonchunhyang University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background/Aim: We investigated alterations in the expression of serum exosomal miRNAs with the progression of liver fibrosis and evaluated their clinical applicability as biomarkers. Methods: This study prospectively enrolled 71 patients who underwent liver biopsy at an academic hospital in Korea. Exosomes were extracted from serum samples, followed by next-generation sequencing (NGS) of miRNAs and targeted real-time quantitative polymerase chain reaction. A model was derived to discriminate advanced fibrosis based on miRNA levels and the performance of this model was evaluated. Validation of the effect of miRNA on liver fibrosis in vitro was followed.
Methods: This study prospectively enrolled 71 patients who underwent liver biopsy at an academic hospital in Korea. Exosomes were extracted from serum samples, followed by next-generation sequencing (NGS) of miRNAs and targeted real-time quantitative polymerase chain reaction. A model was derived to discriminate advanced fibrosis based on miRNA levels and the performance of this model was evaluated. Validation of the effect of miRNA on liver fibrosis in vitro was followed.
Results: NGS data revealed that exosomal miR-660-5p, miR-125a-5p, and miR-122 expression were changed significantly with the progression of liver fibrosis, of which miR-122 exhibited high read counts enough to be used as a biomarker. The level of exosomal miR-122 decreased as the pathologic fibrosis grade progressed and patients with biopsy-proven advanced fibrosis had significantly lower levels of exosomal miR-122 (P < 0.001) than those without advanced fibrosis. Exosomal miR-122 exhibited a fair performance in discriminating advanced fibrosis especially in combination with fibrosis-4 score and transient elastography. In a subgroup of patients with a non-viral etiology of liver disease, the performance of exosomal miR-122 as a biomarker was greatly improved. Inhibition of miR-122 expression increased the proliferation of the human hepatic stellate cell line, LX-2, and upregulated the expression of various fibrosis related proteins.
Conclusion: Exosomal miR-122 may serve as a useful non-invasive biomarker for liver fibrosis, especially in patients with non-viral etiologies of chronic liver disease.

overall_design: Patients in various stages (0-4) of liver fibrosis was compared by miRNA-seq

first: Seongho

last: Ryu

first: Jae

middle: Y

last: Jang

first: Young

last: Chang


title: The Probiotic L. casei Zhang Slows the Progression of Acute and Chronic Kidney Disease (scRNA-Seq)

city: 武汉

first: 汉

last: 朱

state: 湖北

address: 1095 解放大道， 武汉 430030， 中国

institute: 肾

summary: The aim of this study is to explore the effects of L. casei Zhang on renal injury

overall_design: we orally gavaged male C57BL/6 mice with or without L. casei Zhang (Lac.z) for 4 weeks (1×10^9 CFU per day) prior to being subjected to ischemia-reperfusion (I/R)-induced injury, and the mice were killed on day 5,14,28 after injury.   we performed single-cell RNA-sequencing (scRNA-seq) of kidney samples dissected from these mice.

first: Han

last: Zhu

first: Rui

last: Zeng


title: The Probiotic L. casei Zhang Slows the Progression of Acute and Chronic Kidney Disease (RNA-Seq)

address: 1095 解放大道， 武汉 430030， 中国

overall_design: we orally gavaged male C57BL/6 mice with or without L. casei Zhang (Lac.z) and L. acidophilus (Lact) for 4 weeks (1×109 CFU per day) prior to being subjected to ischemia-reperfusion (I/R)-induced injury, and the mice were killed on day 5 after injury. Kidney mRNA profiles of these mice were analyzed.


title: The Probiotic L. casei Zhang Slows the Progression of Acute and Chronic Kidney Disease

address: 1095 解放大道， 武汉 430030， 中国

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

overall_design: Refer to individual Series


title: Adenovirus prevents dsRNA formation by promoting efficient splicing of viral RNA

first: Matthew

middle: Darrell

last: Weitzman

address: 4050 CTRB, 3501 Civic Center Blvd

department: Pathology & Laboratory Medicine

institute: Children's Hospital of Philadelphia

summary: Eukaryotic cells recognize intracellular pathogens through pattern recognition receptors, including sensors of aberrant nucleic acid structures. Sensors of double-stranded RNA (dsRNA) are known to detect replication intermediates of RNA viruses. It has been suggested that annealing of mRNA from symmetrical transcription of both top and bottom strands of DNA virus genomes can produce dsRNA during infection. Supporting this hypothesis, nearly all DNA viruses encode inhibitors of dsRNA-recognition pathways. However, direct evidence that DNA viruses produce dsRNA is lacking. Contrary to dogma, we show that the nuclear-replicating DNA virus adenovirus (AdV) does not produce detectable levels of dsRNA during infection. In contrast, abundant dsRNA is detected within the nucleus of cells infected with AdV mutants that lack the virus-directed ubiquitin ligase required for efficient processing of viral RNA. In the presence of nuclear dsRNA, the cytoplasmic dsRNA sensor PKR is relocalized and activated within the nucleus. Accumulation of viral dsRNA occurs in the late phase of infection, when unspliced viral transcripts form intron/exon base pairs between top and bottom strand transcripts. We propose that DNA viruses actively promote efficient splicing and mRNA processing to  limit dsRNA formation, thus avoiding detection and restriction by host nucleic acid sensors.

overall_design: dsRNA was extracted from Ad5 infected cells using J2 antibody mediated RNA pulldown from total RNA. Input RNA from matching infections of WT Ad5 or DE4 served as the control.

first: Alexander

last: Price

middle: T

last: Steinbock

first: Chao

last: Di

first: Katharina

last: Hayer

first: Yize

first: Christin

last: Herrmann

first: Jillian

last: Whelan

first: Nicholas

last: Parenti

first: Susan

middle: R

last: Weiss

middle: D


title: Up-regulation of ACE2, the SARS-CoV-2 Receptor, in Asthmatics on Maintenance Inhaled Corticosteroids

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Background: The first step in SARS-CoV-2 infection is binding of the virus to angiotensin converting enzyme 2 (ACE2) on the airway epithelium. Asthma affects over 300 million people world-wide, many of whom may encounter SARS-CoV-2. Epidemiologic data suggests that asthmatics who get infected may be at increased risk of more severe disease. Our objective was to assess whether maintenance inhaled corticosteroids (ICS), a major treatment for asthma, is associated with airway ACE2 expression in asthmatics.
Methods: Large airway epithelium (LAE) of asthmatics treated with maintenance ICS (ICS+), asthmatics not treated with ICS (ICS-), and healthy controls (controls) was analyzed for expression of ACE2 and other coronavirus infection-related genes using microarrays.
Results: AsResults: As a group, there was no difference in LAE ACE2 expression in all asthmatics vs controls. In contrast, subgroup analysis demonstrated that LAE ACE2 expression was higher in asthmatics ICS+ compared to ICS‾ and ACE2 expression was higher in male ICS+ compared to female ICS+ and ICS‾ of either sex. ACE2 expression did not correlate with serum IgE, absolute eosinophil level, or change in FEV1 in response to bronchodilators in either ICS- or ICS+. Conclusion: Airway ACE2 expression is increased in asthmatics on long-term treatment with ICS, an observation that should be taken into consideration when assessing the use of inhaled corticosteroids during the pandemic.  a group, there was no difference in LAE ACE2 expression in all asthmatics vs controls. In contrast, subgroup analysis demonstrated that LAE ACE2 expression was higher in asthmatics ICS+ compared to ICS‾ and ACE2 expression was higher in male ICS+ compared to female ICS+ and ICS‾ of either sex. ACE2 expression did not correlate with serum IgE, absolute eosinophil level, or change in FEV1 in response to bronchodilators in either ICS- or ICS+. Conclusion: Airway ACE2 expression is increased in asthmatics on long-term treatment with ICS, an observation that should be taken into consideration when assessing the use of inhaled corticosteroids during the pandemic.

overall_design: The expression of ACE2 in the large airway epithelium was compared in asthmatics and healthy controls ("nonsmokers") and in asthmatics treated with maintenance inhaled corticosteroids ("on") compared to asthmatics with no treatment ("off").

first: Sarah

last: O’Beirne

first: Jacqueline

last: Salit

first: Robert

middle: J

last: Kaner

first: Ronald

last: Crystal


title: Th1/Th17 cell associated pathways are upregulated in murine cytomegalovirus infected murine kidneys after allogeneic transplantation

city: Columbus

first: Masako

last: Shimamura

state: OH

address: 700 Childrens Drive

department: Infectious Diseases Medicine

institute: Nationwide Children's Hospital

summary:
Purpose: To characterize  transcriptional profiles of murine cytomegalovirus infected allografts after renal transplantation.
Methods: RNA was isolated from murine allografts and native kidneys, with and without MCMV infection. Libraries were generated and paired end 150 base pair sequencing was performed on the HiSeq 4000 (Illumina) (Supplementary Methods). Each sample was aligned to the GRCm38.p4 assembly of the mouse reference from NCBI using version 2.6.0c of the RNA-Seq aligner STAR. Transcript features were identified from the GFF file provided with the assembly from NCBI and raw coverage counts were calculated using HTSeq. The raw RNA-Seq gene expression data was normalized and post-alignment statistical analyses were performed using DESeq2 and custom analysis scripts written in R. Comparisons of gene expression and associated statistical analysis were made between different conditions of interest using the normalized read counts. All fold change values are expressed as test condition/control condition, where values less than 1 are denoted as the negative of its inverse.
Results: The QIAGEN Ingenuity Pathway Analysis (IPA) software was used for canonical pathway and differential gene expression analyses. IPA showed that, compared to MCMV infected native kidneys, transplantation of MCMV-infected kidneys led to significant changes in 5502 genes (adjusted p values <0.05), involved in 391 canonical pathways. The Th17 activation pathway showed 107 differentially expressed genes.Th1 pathway was one of the most highly upregulated pathways observed in the MCMV infected allografts.
Conclusions: Transcripts for Th1/Th17 cell associated activation and signaling are differentially expressed in MCMV infected kidneys after allogeneic transplantation.

overall_design: Differential genes expression profiles in murine renal allografts and native kidneys, with and without MCMV infection.

first: James

last: Fitch


title: Deciphering the effects of PYCR1 on cell function and its associated mechanism in hepatocellular carcinoma

city: Guilin

first: Xiaoli

last: Yang

state: Guangxi

address: Zhiyuan Road

institute: Guilin Medical University

summary: Although over-expression of Pyrroline-5-carboxylate reductase 1 (PYCR1) has been reported to be associated with development of certain cancers, no studies have specifically examined the impact of PYCR1 on hepatocellular carcinoma (HCC).  From The Cancer Genome Atlas (TCGA) expression array and meta-analysis conducted using Gene Expression Omnibus（GEO）, and verified via real-time quantitative RT-PCR (qRT-PCR), western blot, and immunohistochemistry analysis, we determined that PYCR1 was up-regulated in HCC compared to normal tissues (P < 0.05). Additionally, patients with low PYCR1 expression showed a higher overall survival rate; while PYCR1 over-expression was associated with females, higher levels of alpha fetoprotein, higher clinical stages (stages III and IV) and younger (< 45 years old) patients. Silencing PYCR1 inhibited cell proliferation, invasive migration, epithelial-mesenchymal transition (EMT)and metastatic properties in vitro and in vivo. Using RNA sequencing (RNA-seq) and bioinformatics tools for data-dependent network analysis, we further found binary relationships among PYCR1 and its interactors in defined pathway modules, implicating PYCR1 in a multi-functional role of coordinating a variety of biological pathways involved incell communication, cell proliferation-growth, cell migration, MAPK cascade, ion-binging, etc. The protein structure characters of key pathway components or PYCR1 interactors evaluated by molecular docking and hot spot analysis showed that the better infinities between PYCR1 and its interactors contained “arginine” in all binding site sequences. Finally, a potential regulatory microRNA (miRNA)-miR-2355-5p of PYCR1 mRNA was discovered in HCC. Overall, our study suggests that PYCR1 plays a vital role in HCC pathogenesis and may serve as a potential molecular target for HCC treatment.

overall_design: The differetial gene expression profiles of silence of PYCR1 and control in HCC cell

first: Yanzhen

last: Xu

first: Wenpu

last: Zuo

first: Xiao

last: Wang

first: Qinle

last: Zhang


title: Three Dimensional Modeling of Biologically Relevant Fluid Shear Stress in Human Renal Proximal Tubule Cells Mimics In Vivo Transcriptional Profiles

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: We performed RNA-sequencing of human RPTEC/TERT1 cells in a microfluidic chip-based 3D model to determine transcriptomic changes. We measured transcriptional changes following the treatment of cells in this device at three different fluidic shear stress. We observed that FSS changes the expression of proximal tubule cell (PTC)-specific genes and impacted genes previously associated with renal diseases in genome-wide association studies (GWAS). At a physiological FSS level, we observed cell morphology, enhanced polarization, presence of cilia, and transport functions using albumin reabsorption via endocytosis and efflux transport. Here, we present a dynamic view of human PTCs response to FSS with increasing fluidic shear stress conditions and provide insight into hPTCs cellular function under biologically relevant conditions.

overall_design: Examination of cells placed under flow rates treatments of 0.1dyn/cm2, 0.25 dyn/cm2, and a physiological level of 0.5 dyn/cm2

first: Emily

last: Ross

last: Gordon

first: Nancy

last: Cox


title: Expression data from normal adults and fetal human thyroids

city: Brussels

first: Geneviève

middle: Marie Henriette

last: Dom

address: 808 route de Lennik

department: Faculté de médecine

country: Belgium

institute: Université libre de Bruxelles

summary: Transcriptomic signature of human embryonic thyroid is not described so far. The goal of this project was to evaluate what enables the transition from differentiation to functional maturation of the human developing thyroid, by performing transcriptomic analysis of human thyroids covering the period of gestation weeks 7-11 and comparing it to adult human thyroids. We defined a non TSH (thyroid stimulating hormone) dependent transition from differentiation to maturation of thyroid. The study also sought to shed light on possible factors that could replace TSH, which is absent in this window of gestational age, to trigger transition to the emergence of thyroid function.

overall_design: RNA from human fetal and adult thyroids were hybridized onto Affymetrix arrays, and compared to other human tissues of various organs from either fetuses or adults.

first: Genevieve

first: Carine

last: Maenhaut


title: DIS3L2 is an essential regulator of spermatogonial differentiation in mice

city: Bethesda

first: Zhengpin

address: National Institutes of Health, 9000 Rockville Pike

institute: NIDDK, NIH

summary: Using conditional knockout mice model, here we report the essential role of DIS3L2 in regulating male germline proliferation, growth and differentiation to ensure male fertility. We document that DIS3L2 is essential for spermatogonial homeostasis. DIS3L2-specific deletion in spermatogonia results in the reduction of the undifferentiated spermatogonial population and the block in transition to the differentiating stage in postnatal testes.

overall_design: RNA-seq was performed using postnatal day 4 (P4) testes between control and Dis3l2 cKO mice in order to identify the differentially expressed genes.

first: Guoyun

last: Yu

first: Jurrien

last: Dean


title: C/EBPδ drives key endocrine signals in human fetal membranes at parturition [ChIP-seq]

city: Shanghai

first: Wangsheng

state: Please Select

address: 845 Lingshan Rd.

institute: Shanghai Jiao Tong University

summary: Amnion-derived prostaglandin E2 (PGE2) and cortisol are key to labor onset. Identification of the common transcription factor driving the expression of both cyclooxygenase-2 (COX-2) and 11β-hydroxysteroid dehydrogenase 1 (11β-HSD1), the key enzymes in their production, may hold the key to the treatment of pre- and post-term labor. Here, we have found that the CCAAT enhancer binding protein δ (C/EBPδ)is such a transcription factor which underlies the feed-forward induction of COX-2 and 11β-HSD1 expression by their own products PGE2 and cortisol in human amnion fibroblasts so that their production would be ensured in the amnion for the onset of labor. Moreover, the abundance of C/EBPδin amnion increases along with COX-2 and 11β-HSD1 at term and further increases at parturition. Knockout of C/EBPδ in mice delays the onset of labor further supporting the concept. In conclusion, C/EBPδmay serve as a novel pharmaceutical target in the amnion for treatment of pre- and post-term labor.

overall_design: Examination of different C/EBPδ binding site upon cortisol stimulation in human amnion cells with ChIP-seq.

first: Wang-sheng


title: Characterization of 35S::TT2 and 35S::MYB5 overexpressors RUN2

city: Gif-sur-Yvette

first: Pierre

last: Jacob

address: Bâtiment 630, Rue Noetzlin

summary: Characterization of the impact of TT2 or MYB5 overexpression on gene expression. Col 0 plants were compared to 35S::TT2 and 35S::MYB5 overexpressors in control conditions

overall_design: Investigation of TT2 and MYB5 overexpression on gene expression


title: Chronic Rapamycin treated bone marrow dendritic cells

city: Memphis

first: Canan

last: Kuscu

address: 71 S Manassas St.

institute: University of Tennessee Health Science Center

summary: Bone marrow dendritic cells were propaged with chronic treatment with Rapamycin and compared to vehicle treated cells.

overall_design: Analysis of Rapamycin treatment

first: Amandeep

last: Bajwa

first: Manjari

last: Kiran


title: SUV39H2 CONTROLS TROPHOBLAST STEM CELL FATE

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

summary: The placenta is constructed through the orchestration of trophoblast stem (TS) cell expansion and differentiation along a multi-lineage pathway. Dynamic regulation of histone H3K9 methylation is pivotal to cell differentiation for many cell lineages, but little is known about its involvement in trophoblast development. Among the twelve-known histone H3K9 methyltransferases, only SUV39H2 exhibited robust differential expression in stem versus differentiated rat TS cells. SUV39H2 transcript and protein expression were high in the stem state and rapidly declined as TS cells differentiated. Disruption of SUV39H2 expression in TS cells led to prominent phenotypic changes. Suv39h2-specific shRNA knockdown resulted in an arrest in TS cell proliferation and activation of trophoblast cell differentiation. These observations were reinforced by flow cytometry and transcript profiling. Histone H3K9 methylation status at specific loci exhibiting differentiation-dependent gene expression were regulated by SUV39H2 and also represented sites for SUV39H2 occupancy. Analyses of SUV39H2 on ex vivo rat blastocyst development supported its role in regulating TS cell expansion and differentiation. Finally, we identified SUV39H2 as a downstream target of CDX2, a master regulator of trophoblast lineage development. In summary, our findings indicate that SUV39H2 contributes to the maintenance of    the TS cell stem state and restrains trophoblast cell differentiation and thus serves as a contributor to the epigenetic regulation of hemochorial placental development.

overall_design: Suv39h2 was knocked down in rat trophoblast stem cells using lentiviral delivery of shRNA. Following selection by puromycin, cells were differentiated. Cells treated with either control shRNA or Suv39h2-specific shRNA were collected and RNA was isolated.

first: Lei

first: Damayanti

last: Chaakraborty

first: Michael

last: Soares


title: Whole cortical tissue of 6month vs 16month C57BL/6j mice

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: differential gene expression between  whole cortical tissue of 6 months (n = 3 brains) and 16 months old (n = 3 brains) C57BL/6 mice

overall_design: 6 samples in total; 3 samples of 6 month old C57BL/6 mice and 3 samples of 16 month old C57BL/6 mice

first: Anne

last: Hahn

first: Daniel

last: Pensold

first: Thomas

last: Lingner

last: Salinas-Riester

first: Tomas

last: Pieler

first: Geraldine

last: Zimmer-Bensch


title: A premature stop codon in BrFLC2 transcript results in early flowering in oilseed-type Brassica rapa plants

status: Public on Jul 14 2021

city: Anseong

first: Dong Hwan

last: Kim

state: Gyeonggi

address: 4726 Seodong-daero, Daedeok-myeon

department: Department of Plant science and Technology

institute: Chung-Ang University

summary: We report here NGS RNA-seqencing datasets for tive different vernalization time course of two different Brassica rapa cultivars, vegetable-type "Chiifu" and oilseed-type "LP08" plants

overall_design: Five different cold treatment (NV, V1, V20, V40, V40T10) to B. rapa whole plants: NV; 3weeks old (non-cold treated), V1; 1 day cold treated, V20; 20 days cold treated, V40; 40 days cold treated; 40VT10; 40 days cold treated, then followed by 10 days warm temperature

first: Dong

middle: H


title: Histone H3K4me1 and H3K27ac play roles in nucleosome depletion and eRNA transcription, respectively, at enhancers [ChIP-seq_2]

city: Busan

first: AeRi

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

institute: Pusan national university

summary: We found that H3K4me1 contributes to nucleosome depletion at enhancers but was not enhough for eRNA synthesis.

overall_design: H3K4me1, H3K27ac and H3 ChIP-seq was performed in control, MLL3/4 SET domain deletion and p300 HAT domian deletion cells.


title: Gene expression profiles analyzed using integrating RNA sequencing and microarray reveals increased inflammatory response, proliferation, and osteoclastogenesis in pigmented villonodular synovitis

city: Beijing

first: Dai

last: Hui

address: Xue Yuan Road 28, Haidian District

institute: Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University

summary: Pigmented villonodular synovitis (PVNS) is a rare condition that involves benign proliferation of the synovial tissue and is characterized by severe joint destruction and high recurrence even after surgical resection. However, poor understanding of the pathogenesis limitsitseffective therapy.

overall_design: In this study, gene expression profiles of three patients with PVNS and three patients with osteoarthritis (OA) were analyzed using integrating RNA sequencing (RNA-seq) and microarray to investigate the PVNS transcriptome.

first: Hui

last: Dai

first: Xin

last: Zhang


title: A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma

city: La Tronche

first: Alexandre

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

summary: In this study, we report on our findings in T. gondii of an m6A-dependent 3’end polyadenylation serving as a transcriptional barrier at certain loci such as stage-specific genes. We identify the core polyadenylation complex within T. gondii and establish CPSF4 as a reader for m6A-modified mRNAs, via a YTH domain within its C-terminus, a feature which is shared with plants. We bring evidence of the specificity of this interaction both biochemically, and by determining the crystal structure at high resolution of the T. gondii CPSF4-YTH in complex with an m6A modified RNA. We show that the loss of m6A, both at the level of its deposition or its recognition was associated with an increase in aberrantly elongated chimeric mRNAs emanating from impaired transcriptional termination, a phenotype previously noticed in the plant model Arabidopsis thaliana. We bring Nanopore direct RNA sequencing-based evidence of the occurrence of transcriptional read-through breaching into downstream repressed stage-specific genes, in the absence of either CPSF4 or the m6A RNA methylase components in both T. gondii and A. thaliana. Taken together, our results shed light on an essential regulatory mechanism coupling the pathways of m6A metabolism directly to the cleavage and polyadenylation processes, one that interestingly seem to serve, in both T. gondii and A. thaliana, as a guardian against aberrant transcriptional read-throughs.

sample_organism:
Toxoplasma gondii
Homo sapiens

platform_organism:
Toxoplasma gondii
Homo sapiens

overall_design: Methods: RNA profiles were generated from HFF cells infected by RHDku80 CPSF4-mAID-HA T. gondii strain for untreated conditions, auxin induced KD at 7h, 24h, and 48h of CPSF4. Total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA-sequencing was performed by GENEWIZ (South Plainfield, NJ, USA). RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA). The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA). The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.

first: D

last: Farhat

first: M

middle: W

last: Bowler

first: G

last: Communie

last: Pontier

first: B

last: Lucid

first: C

last: Mas

last: Corrao

last: Yohann

first: A

first: T

last: Lagrange

first: M-A

last: Hakimi

last: Swale