title: Direct chemical reprogramming of human cord blood erythroblasts to induced megakaryocytes that produce platelets

first: Jinhua

last: Qin

address: Taiping Road

institute: Beijing Institute of Transfusion

summary: The shortage of platelets is becoming increasingly prominent owing to their short shelf life, limited supply, and increasing demand in response to public health incidents. It is an attractive idea to obtain large numbers of transfusible megakaryocytes (MKs) and platelets from somatic cells via cell lineage reprogramming. However, generating human MKs from somatic cells using a pharmacological reprogramming approach has not been widely explored. Here, we report the successful generation of human induced MKs (iMKs) from cord blood erythroblasts (EBs) using a chemical reprogramming strategy with a combination of four small molecules (4M): Bix01294, RG108, VPA, and PD0325901. The iMKs exhibited the ability to produce proplatelets and release vital functional platelets in vitro, demonstrating their similarity to natural MKs. Importantly, after injection into mice, iMKs were able to mature and give rise to functional platelets that were incorporated into newly formed thrombi. The reprogramming process was carefully examined using single-cell RNA sequencing, which revealed an efficient, rapid, and successful cell fate conversion of EBs to iMKs by 4M via the intermediate state of bipotent precursors. Assay for transposase-accessible chromatin sequencing results indicated that 4M induced genome-wide chromatin remodeling during MK reprogramming from EBs. 4M drove the transition of the transcription factor gene network by downregulating the key erythroid transcription factor genes KLF1 and MYB and subsequently upregulating MK development-associated transcription factor genes, including FLI1 and MEIS1. This process eventually led human cord blood EBs to acquire the MK fate. Thus, our chemical reprogramming of cord blood EBs to iMKs provides a simple and efficient approach to generating clinically transfusible MKs and platelets.

overall_design: We performed single cell RNA-Seq and assay for transposase-accessible chromatin sequencing to analyse the molecular mechanism of  chemical reprogramming system.

first: Jian

last: Zhang

first: Jianan

last: Jiang

first: Yanhua

first: Xuetao

last: Pei


title: miRNA-seq data of PAMs from 4 pig breeds

status: Public on Aug 28 2022

city: Wuhan

first: Xiangbin

last: You

state: Hubei

address: Huazhong agricultural university, hongshan district, wuhan

country: China

institute: Huazhong Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: miRNA-seq data of pig alveolar macrophages from 4 pig breeds.

overall_design: PRRSV-infected and uninfected PAMs were chosen to systematically investigate the effect of PRRSV infection on PAMs’ miRNAomes of different pig breeds, 24 small RNA libraries from PRRSV-infected/uninfected PAMs in vitro were analyzed using Solexa/Illumina deep-sequencing technology.

first: Dequan

last: Xu

first: Min

last: Liu


title: Post-Transcriptional Regulation of HRAS by N6-methyladenosine Drives Tumor Progression

status: Public on Aug 27 2022

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

type: Expression profiling by high throughput sequencing

summary: To functionally determine the effect of m6A-regulated HRAS, we specifically demethylated the m6A of HRAS using dm6ACRISPR system, fusing the catalytically dead Type VI-B Cas13 enzyme with the m6A demethylase FTO (dCas13b-FTO).The dCas13b-FTO combined with HRAS-gRNA or gRNA-control were transfected into bladder cancer 5637 cells, and then subjected to RNA-sequencing analysis.

overall_design: Bladder cancer 5637 cells were co-transfected with dCas13b-FTO and HRAS-gRNA or gRNA-control for 48 h, then subjected to RNA-sequencing analysis.

first: Yongbo

last: Pan

first: Yinming

last: Gu


title: Transcriptional profile of Cas9+HoxB8 neutrophil progenitors at day 0 and day 2 after withdrawal of estrogen

city: Berkeley

first: Sarah

middle: Ann

last: Stanley

state: California

address: Li Ka Shing Center 500C, mc3370

department: School of Public Health

country: USA

institute: University of California, Berkeley

summary: To identify transcriptional changes that accompany the differentiation of this cell line from the progenitor to the neutrophil state upon estradiol withdrawal

overall_design: RNAseq of cells prior to and after estradiol withdrawal. Cells are transduced with a control non-targeting sgRNA

first: Robyn

last: Jong

first: Sagar

last: Rawal


title: Inferring Epigenetic and Genetic Biomarkers of cancer in cell-free DNA

first: Shicai

state: Jiangsu

address: Sipailou 2#, Sipailou 2#

summary: Aims: Cancer is an important public health problem worldwide. In recent years, methods based on the analysis of plasma cfDNA which is as an emerging technology have been largely explored for noninvasive prenatal testing and cancer liquid biopsy. We inferred both epigenetic and genetic biomarkers of esophageal cancer (ESCA) in cfDNA with adapted SALP-seq. Materials & methods: Next Generation Sequencing libraries of cfDNA samples from ESCA patients and healthy people were constructed by using SALP-seq. We performed bioinformatics analysis on our sequencing data to find cancer-specific biomarkers. Results & conclusion: 54 important regulatory elements of ESCA, 49 epigenetic and 37 genetic ESCA-specific genes were inferred in cfDNA with SALP-seq, which may ultimately contribute to the development of effective diagnostic and therapeutic approaches for ESCA.

overall_design: The cell free DNA of 50 samples were sequenced with adapted SALP-seq.

last: Wu

first: Qiang

last: Xia

first: Jinke

last: Wang


title: Transcriptomic profile (by Real-time quantitative PCR analysis) of oak leaves from the second growth cycle after leaf herbivory over two successive growth cycles

city: Salamanca

first: Ivan

last: Fernandez Lopez

address: Cordel de Merinas 40

country: Spain

institute: IRNASA

summary: Priming of plant defenses provides increased plant protection against herbivores and reduces the allocation costs of defense. Defense priming in woody plants remains obscure, in particular due to plant development traits such as the endogenous rhythmic growth displayed by oaks (Quercus robur). By using bioassays with oak microcuttings, and by combining transcriptomic and metabolomic analyses, we investigated how leaf herbivory by Lymantria dispar and root inoculation with the ectomycorrhizal fungus Piloderma croceum prime oak defenses. We further investigated how defense priming is modulated by rhythmic growth of the oaks. A first herbivory challenge in oak leaves primed newly grown leaves for an enhanced induction of jamonic acid (JA)-related direct defenses, or enhanced emission of volatiles, depending on the specific growth stage at which the plants where challenged. Root inoculation with Piloderma abolished the enhanced induction of JA-related defenses and volatile emission. Our results indicate that a first herbivore attack primes direct and indirect defenses of newly formed oak leaves, and that the specific display of defense priming is modulated by rhythmic growth. Our results further show that the priming memory in oaks can be transmitted to the next growth cycle even to the leaves of the new shoot unit.

overall_design:
Transcriptomic profile of oak leaves from the second growth cycle after leaf herbivory over two successive growth cycles, analyzed by the 96.96 Dynamic Array™ IFC chip for Gene Expression (Fluidigm, San Francisco, CA, USA) and the BioMark™ Systems for Genetic Analysis (Fluidigm).
qPCR gene expression profiling. Oak microcuttings, during shoot flush (SF) or root flush (RT), were inoculated with the ECM fungus (Pc) and non-inoculated with the ECM fungus (Co). The oak microcuttings were exposed to different L. dispar treatments: 1) no_Ld (not exposed to L. dispar); 2) Ld_prim_Ld_trig (exposed to L. dispar in two successive growth cycles, in the first growth cycle as priming stimulus and in the following growth cycle as triggering stimulus); 3) Ld_prim (exposed to L. dispar only as priming stimulus) and 4) Ld_trig (exposed to L. dispar only as triggering stimulus). Every treatment includes three biological replicates with two technical replicates.

last: Fernandez

first: Marie-Lara

last: Bouffaud

first: Ainoa

last: Martinez-Medina

first: Martin

last: Schädler

first: Mika

last: Tarkka

first: Alexander

last: Weinhold

first: Nicole

last: van Dam

first: Sylvie

last: Herrmann

first: Francois

last: Buscot


city: Hangzhou

first: junli

last: liu

state: zhejiang

address: 866 Yuhangtang

institute: Zhejiang university

summary: Long noncoding RNAs (lncRNAs) participate in regulating many biological processes. However, their roles in PDCoV pathogenicity are largely unknown. Here, we analyzed the expression profile of lncRNAs and mRNAs in the PDCoV-infected cells by high-throughput sequencing

overall_design: Expression profiles of long noncoding RNAs and mRNAs in ST cells infected by PDCoV were generated by deep sequencing, in duplicates, using Illumina Hiseq 4000.

first: Junli

last: Liu

first: Jinyan

last: Gu

first: Jiyong

last: Zhou


title: Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish

city: WuHan

first: Guan

middle: Peng

last: Peng

state: HuBei

address: shizishan street

department: college of informatics

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [WGBS]

summary: Here, we describe environmental Cu2+ in promoting zebrafish (Danio rerio) developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system, even the Cu2+ concentration is at 10 μg/L, the National Quality Standards of fishery water (GB11607-89); 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci-specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS, retina, and digestive system development during F1 embryogenesis; 3. Loci-specific hypoDMRs in the pmpcb promoter and loci-specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance, respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding, suggesting that environmental Cu2+ might pose a dramatic and long-lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis.

overall_design: Adult zebrafish (F0 fish) at 3 months of age were divided into three groups: exposure separately to normal water environment (control), 0.078 μM (5 μg/L), and 0.156 μM (10 μg/L) Cu for over 21 days, with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment (no Cu added).The sperms of 10-12 adult zebrafish (F0) for each of the 3 groups (control males; 0.078 μM Cu stressed males; 0.156 μM Cu stressed males) and 50-60 larvae chosen biasedly based on their phenotypes (F1 offspring) at 96 hpf in each of 3 groups (control; 0.078 μM group; 0.156 μM group) were collected for genomic DNA extraction using the ammonium acetate method.

first: Zhipeng

last: Tai

first: Pengpeng

last: Guan


title: Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA-Seq]

overall_design: Adult zebrafish (F0 fish) at 3 months of age were divided into three groups: exposure separately to normal water environment (control), 0.078 μM (5 μg/L), and 0.156 μM (10 μg/L) Cu for over 21 days, with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment (no Cu added). Briefly, 50-60 embryos (F1 offspring) were collected biasedly based on their phenotypes from each of the 3 groups (control; 0.078 μM group; 0.156 μM group) at 24 hpf and 96 hpf, respectively, and lysed by Trizol reagent (Ambion, Life Technologies) for RNA extraction and RNA-sequencing (RNA-Seq).


title: Global co-function network of plant autophagy pathway

status: Public on Aug 26 2022

city: Shanghai

first: Moyang

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

summary: Autophagy is essential for plant response to a variety of developmental and environmental factors. However, unlike yeast and animals, only a few autophagy genes in plants are functionally conserved in the biological world. An important question is, how plants form autophagy related functions in evolution? Here, we developed and verified a workflow that identified 997 high-confidence autophagy related genes (ARG) in A.thaliana using multi-group data from nearly 10,000 samples and established a co-network of autophagy containing 3,419 new presumptive connections. Of note, through the genomic analysis of 76 representative plants from lower to higher levels, we found that ARGs were preferentially retained after polyploidization followed by terrestrialization, forming plant-specific autophagy-related functions. In addition, we provide the evolutionary gains and losses of ARGs function in monocotyledons and dicotyledons, and verified two novel genes ml2 and ml5 presumed to be involved in autophagy and leaf senescence. This work provides valuable resources for the study of plant autophagy and highlights that ARGs may selectively promote the success of plant autophagy through polyploidy in the process of evolution.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 7 day dark treated wt, ml2, and ml5 A. thaliana leaves .

first: Xu

last: Wang


title: Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency

city: Haining

first: Xinyu

last: Xiang

address: East Haizhou Road

department: Zhejiang University-University of Edinburgh Institute

institute: Zhejiang University

type: Genome binding/occupancy profiling by high throughput sequencing


title: Integrative analyses of transcriptome and proteome provides new insights into energy metabolism and light utilzation in cigar tobacco  during different light intensities

city: qingdao

first: ying

middle: xiao

last: wu

state: shangdong

address: China and South Korea the street

department: Cultivation and nutrition center

institute: Tobacco Research Institute, Chinese Academy of Agricultural Sciences

summary: In this study, we have used the comparative transcriptomic and proteomic approaches to decipher the changes in genes and protein abundances in cigar tobacco leaves under LL. In this study, DEGs and DEPs related to glycolysis, starch and sucrose metabolism, tyrosine metabolism, photosynthesis-antenna proteins, and photosynthesis pathways are significantly enriched. This study offers novel insights into both transcriptome and proteome levels response mechanisms under different light intensities.

overall_design: The cigar tobacco H382 variety was used as test material in this study。A total of nine RNA samples were prepared from three treatments and three biological replicates (3╳3 = 9). Total RNA was extracted from the leaves samples using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) consulting manufacturer instructions. GOseq R package was used to identify significantly enriched GO terms and KOBAS software was used to test the statistical enrichment of differential expression genes in KEGG pathways. qRT-PCR was performed using SYBR Premix Ex Taq II (Takara, Japan).

first: Xiaoying

last: Wu

first: Xinghua

last: Ma


title: Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1 (RNA-seq and Ribo-seq)

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

summary:
Purpose: To systematically investigate the molecular mechanisms resulting from Mycn loss-of-function.
Methods:  Approximately 30 mycn mutant or WT zebrafish embryos at 72 hpf (hours post fertilization) were harvested . Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000074) according to the manufacturer’s protocol for 10000 cells recovery.
Results: More than 3,000 genes showed reduced tranlation efficiency in Mycn mutant.
Conclusions: mTOR signaling was reduced in Mycn mutant.

overall_design: wild-type or mycn zebrafish embryos at 72 hpf were harvested for RNA-seq and Ribo-seq.

last: Cheng

first: Yunfei

last: Li


title: 10X genomics single cell sequencing of sheep testis (6 months-old)

city: Lanzhou

first: Yao

middle: jing

last: Yue

address: NO.335 Jiangouyan, Qilihe District Lanzhou 730050, Gansu, P. R. C

department: Lanzhou Institute of Husbandry and Pharmaceutical Sciences,

institute: Chinese Academy of Agricultural Sciences

summary: A 6-month-old healthy male Hu sheep was selected and castrated for testis collection, then single cell suspension was obtained using enzymatic digestion method for single cell sequencing. And the cell types of sheep testis and marker genes of each cell type were identified based on the RNA sequencing.

overall_design: mRNA profile of one Hu sheep testis sample was generated by single cell sequencing

first: Yaojing

first: Yi


title: Single-cell atlas of diverse immune populations in the advanced biliary tract cancer microenvironment

city: shanghai

first: xuebing

last: Shi

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Institute, Second Military Medical University

summary: Immunotherapies have been explored in treating solid tumors, albeit with disparate clinical effects in distinct cancer types. Systematic interrogation of immune cells in the tumor microenvironment (TME) is vital to the prediction of immunotherapy response and the development of innovative immunotherapeutics. To comprehensively characterize the immune microenvironment in advanced biliary tract cancer (BTC), we utilized single-cell RNA sequencing in unselected viable cells from 16 matched samples. We identified nineteen cell subsets from a total of 45,851 cells, in which exhausted CD8+ T cells, macrophages, and dendritic cells (DCs) in BTC were shown to augment and communicate within the TME. Transcriptional profiles coupled with T cell receptor (TCR) sequences revealed that exhausted CD8+ T cells retained clonal expansion and high proliferation in the TME, and some of them highly expressed the endoplasmic reticulum stress (ER) sensor XBP1, indicating its key role in remodeling TME. Functional assays demonstrated that XBP1 and common immune checkpoints (PD1, TIGIT) were significantly upregulated in CD8+ T cells cocultured within the TME of BTC cell lines (GBC-SD, HCCC-9810). When treating the coculture groups with the specific inhibitor of IRE1α-XBP1 (4μ8C), the downregulation of TIGIT was observed in the treatment group. Collectively, comprehensive transcriptome profiling provides deeper insights into the immune atlas in advanced BTC, which might be instrumental in exploring novel immunotherapy strategies.

overall_design: Five patients diagnosed with cholangiocarcinoma in the Eastern Hepatobiliary Surgery Hospital were incorporated into the current study, including two intrahepatic cholangiocarcinoma (iCCA), two gallbladder carcinoma (GBC) and one dCCA patients. Of note, none of the patients have undergone any preoperative treatments (chemotherapy, radiation or anti-tumor medicines) prior to tumor resection. Tumor primary locus and metastasis as well as lymph node were consistently harvested for each participant, if available. Meanwhile, peripheral blood samples were collected prior to surgical procedures using anticoagulant tubes.

first: X

middle: B

first: Z

middle: X

first: L

last: Chen


title: MicroRNA expression of fetal pulmonary hypertension in an ovine model

city: Cleveland

first: Devashis

last: Mukherjee

state: OH

address: 11100 Euclid Ave

department: Pediatrics

institute: Case Western Reserve University

summary: Persistent pulmonary hypertension of the newborn (PPHN) occurs when pulmonary vascular resistance (PVR) fails to decrease at birth. Decreased angiogenesis in the lung contributes to the persistence of high PVR at birth. MicroRNAs (miRNAs) regulate gene expression through transcript binding and degradation. They were implicated in dysregulated angiogenesis in cancer and cardiovascular disease. We investigated whether altered miRNA levels contribute to impaired angiogenesis in PPHN. We used a fetal lamb model of PPHN induced by prenatal ductus arteriosus constriction and sham ligation as controls. We performed RNA sequencing of pulmonary artery endothelial cells (PAECs) isolated from control and PPHN lambs. We observed a differentially expressed miRNA profile in PPHN for organ development, cell-cell signaling, and cardiovascular function. MiR-34c was upregulated in PPHN PAECs compared to controls. Exogenous miR34c mimics decreased angiogenesis by control PAEC and anti-miR34c improved angiogenesis of PPHN PAEC in vitro. Notch1, a predicted target for miR-34c by bioinformatics, was decreased in PPHN PAECs, along with Notch1 downstream targets, Hey1 and Hes1. Exogenous miR-34c decreased Notch1 expression in control PAECs and anti-miR-34c restored Notch1 and Hes1 expression in PPHN PAECs. We conclude that increased miR-34c in PPHN contributes to impaired angiogenesis by decreasing Notch1 expression in PAECs."

overall_design: Examination of differential microRNA expression between PPHN and control pulmonary arteral endothelial cells

first: Girija

middle: G

last: Konduri

first: Alison

last: Kriegel

first: Pengyuan

last: Liu


title: In vitro modeling and rescue of ciliopathy associated with mutations in IQCB1 (Nephrocystin 5) using patient-derived cells

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Mutations in IQCB1/NPHP5 gene encoding the ciliary protein Nephrocystin 5 cause early-onset blinding disease Leber congenital amaurosis (LCA), together with kidney dysfunction in Senior-Løken Syndrome. For in vitro disease modeling, we obtained dermal fibroblasts from NPHP5-LCA patients, which were reprogrammed into induced pluripotent stem cells (iPSCs) and differentiated into retinal pigment epithelium (RPE) and retinal organoids. Patient fibroblasts and RPE demonstrated aberrantly elongated ciliary axonemes. Organoids revealed impaired development of outer segment structures, which are modified primary cilia, and mislocalization of visual pigments to photoreceptor cell soma. All patient-derived cells showed reduced levels of CEP290 protein, a critical cilia transition zone component interacting with NPHP5, providing a plausible mechanism for aberrant ciliary gating and cargo transport. Disease phenotype in NPHP5-LCA retinal organoids could be rescued by AAV-mediated NPHP5 gene augmentation therapy. Our studies thus establish a human disease model and a path for treatment of NPHP5-LCA.

overall_design: RNA was extracted from 3 frozen organoids per sample. Each group of control (804), untreated patient and patient with AAV treatment contains triple samples.

first: Kamil

last: Kruczek

first: Zepeng

last: Qu

first: Emily

last: Welby

first: Swaroop

last: Anand


title: Genome-wide transcriptome profiling Brain-Chip and Conventional Cell Culture System Using RNA-seq

city: Boston

first: Lorna

last: Ewart

state: MA

address: 27 Drydock Avenue

institute: Emulate Inc.

summary: The goal of this study was A) to compare the global RNA-sequencing (RNA-seq) profiles data of the neurovascular units constructed in i) conventional cell cultures (n=4), ii) Cortical Brain-Chips cultured under constant flow (n=4), and iii) human adult brain-derived contex (n=8) retrieved from the Genotype-Tissue Expression (GTEx) Portal.

overall_design: Global RNA expression profiles of Brain-Chips day 5 and 7 (n=4, Brain Channel); Conventional cell culture systems day 5 and 7 (n=4 brain side)  were generated by deep sequencing using Illumina HiSeq 4000.

first: Iosif

last: Pediaditakis

first: Dimitris

middle: V

last: Manatakis


title: Investigation of the changes induce by inhibiting mitochondrial respiration on DNA methylation and hydroxymethylation in periosteal cells

city: Leuven

first: Bernard

last: Thienpont

state: Vlaams-Brabant

address: Herestraat 49

department: Human Genetics

country: Belgium

institute: KU Leuven Association

summary: The metabolic changes induced by blocking mitochondrial respiration result in a decrease of 5hmC levels. This experiment aims to further investigate the changes in DNA demethylation induced by Antimycin A treatment using both regular bisulfite- and oxidative bisulfite-chip sequencing.

overall_design: Periosteal cells isolated from 3 pools of mice were treated either by Antimycin A (AMA) or vehicle as control. 10 days after isolation, the effect on DNA methylation and hydroxymethylation was investigated.

first: Guillaume

last: Tournaire

first: Geert

last: Carmeliet


title: SARS-CoV-2 infection activates AhR signaling

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

institute: Institute of Medical Biology

summary: Purpose:To determine the effect of SARS-CoV-2 infection on AhR signaling, we performed single-cell RNAseq (scRNA-Seq) from macaque lung tissue infected with SARS-CoV-2.   Methods: Rhesus monkeys (3-5 kg, 3-5years old) were used for this study. One monkey is infected by intragastric administration with 1x 10^7 PFU of SARS-CoV-2 in 1mL of PBS, and another monkey was intranasally injected with 1x10^6 of SARS-CoV-2 in 200 µl of PBS. One monkey was intranasally and intragastrically treated with PBS as a control. We analyzed the tissues collected on the 4 dpi following   Intranasal and intragastrical inoculation. Single-cell sequencing of were sequenced by an Illumina Novaseq6000 sequencer, the sequencing depth of each cell was at least 100,000 reads, and the paired-end 150 bp (PE150) reading strategy was adopted.  Results and Conclusions: The scRNA-Seq results showed that the increased expression of upstream gene IDO1 and downstream transcriptional targets CYP1A1 and CYP1B1 of AhR in response to SARS-CoV-2 infection.

overall_design: We analyzed the single cell transcriptomes of  the left lung and right lung of monkey collected on the 4 dpi intranasal and intragastrical inoculation.

first: Wenhai

last: Yu


title: Distinct tau neuropathology and cellular profiles of a APOE3 Christchurch homozygote protected against Autosomal Dominant Alzheimer’s dementia

city: Santa Barbara

first: Kenneth

middle: S

last: Kosik

state: CA

address: 5165 Biology II

department: Molecular, Cellular, and Developmental Biology

institute: University of California Santa Barbara

summary: We describe in vivo follow-up PET imaging and postmortem findings from an autosomal dominant Alzheimer’s disease (ADAD) PSEN1 E280A carrier who was also homozygous for the APOE3 Christchurch (APOE3ch) variant and was protected against Alzheimer’s symptoms for almost three decades beyond the expected age of onset. We identified a distinct anatomical pattern of tau pathology with atypical accumulation in vivo and unusual postmortem regional distribution characterized by sparing in the frontal cortex and severe pathology in the occipital cortex. The frontal cortex and the hippocampus, less affected than the occipital cortex by tau pathology, contained Related Orphan Receptor B (RORB) positive neurons, homeostatic astrocytes and higher APOE expression. The occipital cortex, the only cortical region showing cerebral amyloid angiopathy (CAA), exhibited a distinctive chronic inflammatory microglial profile and lower APOE expression. Thus, the Christchurch variant impacts the distribution of tau pathology, modulates age at onset, severity, progression, and clinical presentation of ADAD, suggesting possible therapeutic strategies.

overall_design: We performed comparative gene expression profiling analysis using data obtained from three different brain regions (Frontal cortex, hippocampus and occipital cortex) of a post mortem brain of a patient carrier osf the autossomal dominant PSEN-1E280A mutation and homozygours fro the APOE3 Christchurch variant.

first: Diego

last: Sepulveda-Falla

first: Justin

last: Sanchez

first: Maria

middle: C

last: Almeida

first: Daniela

last: Boassa

first: Juliana

last: Acosta-Uribe

first: Clara

last: Vila-Castelar

first: Liliana

last: Ramirez-Gomez

first: Ana

last: Baena

first: David

last: Aguillon

first: Nelson

middle: D

last: Villalba-Moreno

first: Jessica

middle: L

last: Littau

first: Andres

last: Villegas

first: Thomas

last: Beach

first: Charles

last: White III

first: Mark

last: Ellisman

first: Susanne

last: Krasemann

first: Markus

last: Glatzel

first: Keith

last: Johnson

first: Reisa

last: Sperling

first: Eric

middle: M

last: Reiman

first: Joseph

middle: F

last: Arboleda-Velasquez

first: Francisco

last: Lopera

first: Yakeel

middle: T

last: Quiroz


title: Effect of enhanced early life nutrition on the bull calf testes transcriptome

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

summary: This study evaluated the effect of enhanced dietary intake during the early life period on testes transcriptome in bull calves. Between 2-12 weeks of age bull alves were offered either a high (HI; n=15) or moderate (MOD; n=15) plane of nutrition, with diets designed to evoke growth rates of 1.0 and 0.5 kg/day, respectively. At 12 wk of age,  testes parenchyma tissue samples were harvested from all calves and subsequently subjected to mRNAseq. Subsequent bioinformatics analyses revealed differential expression of genes invovled in cellular adhesion and immune function.

overall_design: 30 testes RNA samples were analysed for this study, comprising. 15 samples were derived from bull calves fed the High plane of nutrition (HI, n=15) and 15 samples  derived from the calves fed the Moderate plane of nutrition (MOD, n=15). Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates. The MOD plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 0.5 kg of concentrates. All tissue samples were collected at the same time-point (12 weeks of age).

first: Stephen

last: Coen

first: Pat

last: Lonergan

first: Sean

last: Fair

last: Kenny


title: The role of lncRNA-BTX in viral replication

city: Tian Jin

first: Yang

last: Cao

address: No. 94 Weijin Road

institute: Nankai University

summary: To investigate the  function of lncRNA-BTX in the regulation of viral replication , we constructed lncRNA-BTX knockout mice.We separately took the peritoneal macrophages of lncRNA-BTX-/- and lncRNA-BTX+/+ mice, extracted RNA after VSV virus stimulation, and performed RNA-seq.

overall_design: We performed RNA-seq on PM before and after virus VSV stimulation to find lncRNAs with significantly different expression changes

first: Xiaoqing

last: Xu

first: Xuetao


title: Deciphering Runx1 interacted RNAs during definitive hematopoiesis by ultra-low-input RIP-seq

city: Beijing

first: Di

last: Liu

address: No. 45 West Street, Beijing

institute: Xuanwu Hospital, Capital Medical University

summary: our work established a powerful method for physically studying TF-RNA interaction in very few cells, and provide valuable recourse for decoding more precious regulatory network of Runx1 during embryonic hematopoiesis.

overall_design: E10.0 caudal half  Cd31+ cells form C57BL/6 mice were isolated by Fluorescence-activated cell sorting (FACS)  and analyzed using RUNX1 RIP-seq

first: Haizhen

last: Wang

first: Haifeng

last: Chen

first: Jie

last: Zhou


title: Genome Wide DNA Methylation in the Neuronal Fraction of the Prefrontal Cortex from Depressed, Suicide, and Normal Control Subjects

city: Chicago

first: Dennis

middle: R

last: Grayson

state: IL

department: Psychiatry

institute: University of Illinois Chicago

type: Methylation profiling by genome tiling array

summary: We analyzed the levels of DNA methylation in DNA purified from BA9 of 21 depressed suicide completers and 21 healthy controls, using the Infinium® MethylationEPICBeadChip. The goal of the study was to determine which genes were differentially methylated in neurons between the two groups. We identified1,236 differentially methylated CpGs with a p ≤ 0.001.  Gene Ontology and Ingenuity Pathway Analysis were performed to determine classes of genes and pathways associated with the suicide completers.

overall_design: Compare CpG methylation levels in DNA isolated from neurons of the PFC (BA9) of 21 adult depressed suicide completers and 21 healthy control subjects

first: Hooriyah

last: Rizavi

first: Hui

last: Zhang

first: Jenny

last: Drnevich

first: Subhash

last: Pandey

first: Miljana

last: Petkovic

first: Ghanshyam

middle: N


title: Whole transcriptome analysis of leaves and petioles in Chinese cabbage

city: Shenyang

first: Zhiyong

state: Liaoning Province

address: Dongling Road 120

institute: Shenyang Agriculral University

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

overall_design: Refer to individual Series


title: Effect of enhanced early life nutrition on testes miRNA transcriptome in bull calves

first: Kate

last: Keogh

summary: The aim of this study was to measure the impact of contrasting feeding regimes in the first 12 wk of life, known to impact age at puberty on the molecular control of the testes in bull calves. Holstein bull calves  were designated to high (HI; n=15) or moderate (MOD; n=15) dietary groups, with diets designed to provoke growth rates of 1.0 and 0.5 kg/day, respectively. At 12 wk of age, all calves were euthanized, and testes parenchyma harvested. RNA was extracted from the testes and used for miRNAseq. Bioinformatic analysis identified 7 miRNA as differentially expressed between the HI and MOD treatment groups, with target mRNA genes invovled in pathways related to AMPK and IGF-1 signaling.

overall_design: In total 30 testes RNA samples were analyzed, 15 samples were derived from bull calves fed the High plane of nutrition (HI, n=15) and 15 samples were derived from the calves fed the Moderate plane of nutrition (MOD, n=15). From 2 weeks of age calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates, whilst  the MOD group received 0.5 kg of milk replacer (4 litres) per day and 0.5 kg of concentrates. Tissue samples were collected from all calves at 12 weeks of age.

first: Stephen

first: Pat

first: David


title: Identification of transcriptional drifts in endothelial cells associated with environmental changes

city: Tucson

first: Casey

middle: E

last: Romanoski

state: AZ

address: 1657 E. Helen St.

department: Cellular & Molecular Medicine

institute: University of Arizona

summary: Environmental cues, such as shear stress and heterotypic cell interactions play a critical role in endothelial cell function, yet their unique contributions to the endothelial cell transcriptome remain unclear. Using cell preparations from human umbilical cords (ex vivo), we performed individual sample analysis to assess transcriptional drifts associated with environmental changes but independent of sex or background. Global gene expression profiling by RNA-seq, ATACseq, and MS/MS directed proteomics distinguished freshly isolated endothelial cells from genetically matched culture (in vitro) samples. Over 43% of the transcriptome was significantly changed by the in vitro environment. Amongst several signatures, we observed that TGF-beta and BMP target genes were reduced. In contrast, cytoskeleton-based processes and proliferation-related genes were increased. Subjecting cultured cells to long-term shear stress significantly rescued the expression of approximately 17% of genes including targets of BMP and Notch signaling known to be sensitive to flow. In contrast, co-culture of endothelial cells with smooth muscle cells normalized networks related to cell growth and differentiation, clathrin-vesicle related genes, and recovered targets downstream TGF-beta, recovering approximately 9% of the original in vivo signature. Our findings highlight specific genes, pathways and functional features of endothelial cells that require contextual information and exposure to physical forces. This transcriptional modulation is important to consider in all paradigms that are focused on understanding the ability of endothelial cells to maintain homeostasis and respond to disease processes.

overall_design: To apply next-generation sequencing technologies, including ATAC-seq, to identify similarities and differences between human endothelial cells (HUVECs) assayed ex-vivo (cord) versus cultured.

first: Yalda

last: Afshar

first: Luisa

last: Iruela-Arispe


title: Whole transcriptome analysis of leaves and petioles in Chinese cabbage [miRNA]

summary: We use Chinese cabbage PHL as the material and sample during maturing repeating three times. 44796 differentially expressed mRNAs were identified by complete transcriptome sequencing of leaf and petiole, of which 10646 were significant differentially expressed. There were 10422 significant differentially expressed mRNAs annotated into molecular function, biological process and cell components. There were 723 GO terms, and the most enriched GO term was membrane component (GO: 0016021) . KEGG analysis showed that there were 31 significant pathways. Among them, the plant hormone signal transduction pathway (Ko04075) is the pathway with the most differentially enriched genes.A total of 2553 differentially expressed lncRNAs were obtained, of which 303 were significant differentially expressed lncRNAs. Target genes of significantly differentially expressed lncRNAs were predicted, and the predicted target genes were analyzed by GO and KEGG. There were 2425 GO terms and 127 pathways. The most enriched GO term was nucleus (GO: 0005634) , the most abundant pathway is starch and sucrose (Ko00500) .A total of 1070 differentially expressed miRNAs were obtained, of which 195 were significant differentially expressed. Go and KEGG analyses of the predicted target genes were performed. There were 551 GO terms and 24 pathways. The most abundant GO terms were membrane components (GO: 0016021) , the most abundant pathway is starch and sucrose (Ko00500) .A total of 886 differentially expressed circRNAs were obtained, including 7 significant differentially expressed circRNAs, which have 3 up-regulated circRNAs and 4 down-regulated circRNAs.

overall_design: Examination gene expression difference of mRNA and small RNA in Chinese cabbage leaves and petioles

first: Yang

last: Jiang


title: Whole transcriptome analysis of leaves and petioles in Chinese cabbage [circRNA]


title: Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells

first: Keji

last: Zhao

address: 10 Center Dr

department: Systems Biology Center

institute: NHLBI

summary: We describe a novel indexing protocol that employs the activities of terminal DNA transferase and T4 DNA ligase to add unique cell barcodes to DNase-digested DNA ends. This protocol allows profiling of genome-wide DHSs in over 10,000 single-cells in an individual experiment.

overall_design: Profiling genome-wide DHSs with terminal DNA transferase and T4 DNA ligase

first: Weiwu

last: Gao

first: Wai

last: Ku

first: Jonathan

last: Perrie

first: Gangqing

last: Hu

first: Jun

last: Zhu

first: Bing

last: Ni


title: Assessment of the stabilty of Treg cell subsets in the bone marrow [targeted Bisulfite-seq]

city: Regensburg

first: Philipp

last: Beckhove

address: Franz-Josef-Strauss-Allee 11

country: Germany

institute: Regensburg Center for Interventional Immunology

summary: We analyzed the methlation status of bone marrow conventional T cells, pTregs, tTregs, Tregs induced by bone marrow Aire-expressing cells, and in vitro-induced Tregs

overall_design: 6.5TCR (HA-specific CD4) T cells were transferred into Aire-HA host and bone marrow T cell subsets were sorted 14 days post transfer for comparison of their methylation status of TSDR and Treg-specific signature genes

first: Chih-Yeh

last: Chen

first: Michael

last: Delacher

first: Charles

last: Imbusch

first: Markus

last: Feuerer


title: A novel role of the RNA binding protein CPEB3 in colorectal cancer progression

city: Guangzhou

first: Qun

last: Yan

address: NO.1838 Guangzhou Avenue

institute: Nanfang Hospital

summary:
CPEB3 inhibits a cluster of signaling pathways associated with tumor progression.
Gene expression profiling analysis was performed to identify the potential pathways of CPEB3.

overall_design: SW480 cells transfected with Cytoplasmic polyadenylation element binding protein 3 (CPEB3） or negative control（NC） were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Yuxin

last: Fang


title: Molecular Control of Circuit Plasticity and the Permanence of Imprinted Odor Memory

city: Kansas City

first: Congrong

middle: Ron

last: Yu

state: Missouri

institute: Stowers Insitute for Medical Research


title: Molecular Mechanisms of Axonal Growth and Neuronal Differentiation on Surface with Adhesion Energy Nanogradients

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: Neuronal repair is promoted after a nerve injury by chemical and physical stimuli from their environment. Among them, local adhesion energy gradients generated on surfaces trigger cone formation and neurite outgrowth without any nerve growth factor (NGF) addition.  In this study,  the molecu-  lar mechanisms leading to neuronal differentiation after stimulation via energy gradients are inves- tigated. For this purpose, PC12 cells are cultured on n-[3-(trimethoxysilyl)propyl] ethylendiamine (EDA) and n-hexyl trimethoxysilane (HTMS), two functionalized surfaces possessing local energy gradients but chemically different. These surfaces similarly trigger neurite and growth cone forma- tion after 3 days in culture.  The gene expression analysis of a microarray reveals the activation of  the PI3/Akt signaling pathway  from these surfaces in the same way  than NGF does after binding    on its TrkA receptor. The biological downstream effectors of this signaling pathway are also upreg- ulated, thereby promoting cell survival, growth cone formation and neurite outgrowth. EDA and HTMS surfaces act as an ongoing stimulus of the TrkA receptor as the addition of 100 nM K252a,  its specific inhibitor, leads to the inhibition of neurite growth. Taken together, these results show that functionalized surface with energy surface gradients could be useful to promote nerve repair after an injury.

overall_design: For each surface, i.e EDA, HTMS, PLL and PLL + activation via NGF, three samples were analyzed.

first: Océane

last: Sénépart

first: Claire

last: Legay

first: Christophe

last: Helary

first: Ahmed

last: Hamraoui


title: Assessment of genome-wide chromatin accessibility of subsets of bone marrow-resident antigen presenting cells [ATAC_BMACs]

summary:
Chromatin accessibility of bone marrow-resident Aire expressing cells was compared to those of bone marrow plasma cells and B cells via ATAC-seq
Bone marrow (BM) harbors a large repertoire of regulatory T (Treg) cells, which    are essential in hematopoiesis and peripheral tolerance. Treg cell accumulation    in BM has been viewed as a consequence of preferential immigration of    thymus-derived Treg cells. Here we report a novel subset of antigen presenting    cells, which expresses the autoimmune regulator (Aire). These BM    Aire-expressing cells resemble a subset of CD138+B220-TACI+Blimp-1+MHC-II+    plasma cells (pc-BMACs) and express a diverse repertoire of tissue-restricted    self-antigens. pc-BMACs present self-antigens to na  ve CD4+ T cells and can    efficiently convert these into functionally competent CD25+Foxp3+ bona fide    peripheral Treg cells (pTregs) capable of exerting immune suppression in vitro    and in vivo. Aire expression may contribute to the tolerogenic function of    pc-BMACs as it regulates the expression of genes involved in pTreg induction    and function, including Icosl and retinoic acid synthesis-related genes,    Aldh1a2 and Aldh1b1. Our data thus demonstrate an Aire-expressing plasma cell    subset in the BM capable to promote peripheral tolerance by ectopically    expressing tissue-restricted self-antigens and generating pTregs.

overall_design: Cell subsets were sorted from bone marrow of naive Adig mice for comparison of their chromatin accessibility

first: Christian

last: Schmidl

first: Dania

last: Riegel

first: Franziska

last: Durst


title: Gene expression data from CD34+ BMMCs/PBMCs from JAK2V617F positive MPN patients vs. Healthy controls

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

summary:
Philadelphia chromosome-negative myeloproliferative neoplasms (MPN) consist of primary myelofibrosis (PMF), polycythemia vera (PV), essential thrombocythemia (ET) and seconday myelofibrosis (pPV-MF or pET-MF)
In this dataset, we compare the gene expression data of bone marrow (BM) or peripheral blood (PB) mononuclear cells of CD34+ cells from JAK2V617F mutated patients vs. healthy donors

overall_design: 19 JAK2V617F MPN patients and 6 healthy controls were analyzed

first: Julian

last: Baumeister

first: Nicolas

last: Chatain

first: Annika

last: Hubrich

first: Tiago

last: Maié

first: Ivan

last: Costa

first: Lijuan

last: Han

first: Caroline

last: Küstermann

first: Stephanie

last: Sontag

first: Kristin

last: Seré

first: Klaus

last: Strathmann

first: Martin

last: Zenke

first: Andreas

last: Schuppert

first: Tim

last: Brümmendorf

first: Kamil

last: Kranc

first: Steffen

last: Koschmieder

first: Deniz

last: Gezer


title: Induction of autoreactive regulatory T cells through promiscuous gene expression by bone marrow-resident Aire+ antigen-presenting cells

first: Philipp

last: Beckhove


title: Evaluation of Genome-wide chromatin accessibility of BM T cell subsets [ATAC_TC]

summary:
Chromatin accessibility of bone marrow conventional T cells, pTregs, tTregs, BMAC-induced Tregs and in vitro-induced Tregs were compared
Bone marrow (BM) harbors a large repertoire of regulatory T (Treg) cells, which    are essential in hematopoiesis and peripheral tolerance. Treg cell accumulation    in BM has been viewed as a consequence of preferential immigration of    thymus-derived Treg cells. Here we report a novel subset of antigen presenting    cells, which expresses the autoimmune regulator (Aire). These BM    Aire-expressing cells resemble a subset of CD138+B220-TACI+Blimp-1+MHC-II+    plasma cells (pc-BMACs) and express a diverse repertoire of tissue-restricted    self-antigens. pc-BMACs present self-antigens to na  ve CD4+ T cells and can    efficiently convert these into functionally competent CD25+Foxp3+ bona fide    peripheral Treg cells (pTregs) capable of exerting immune suppression in vitro    and in vivo. Aire expression may contribute to the tolerogenic function of    pc-BMACs as it regulates the expression of genes involved in pTreg induction    and function, including Icosl and retinoic acid synthesis-related genes,    Aldh1a2 and Aldh1b1. Our data thus demonstrate an Aire-expressing plasma cell    subset in the BM capable to promote peripheral tolerance by ectopically    expressing tissue-restricted self-antigens and generating pTregs.

overall_design: 6.5TCR (HA-specific CD4) T cells were transferred into Aire-HA host and bone marrow T cell subsets were sorted 14 days post transfer for comparison of their chromatin accessibility

first: Chih-Yeh

last: Chen

first: Christian

last: Schmidl

first: Dania

last: Riegel

first: Franziska

last: Durst


title: Genome-wide maps of gene transcription level in wild-type and mpbR-deleted Mycobacterium tuberculosis H37Ra strains

city: WuHan

first: Yugang

last: Li

address: shizishan street

institute: Huazhong Agricultural University

summary: We report the application of RNA-seq technology for high-throughput profiling of gene transcription in M. tuberculosis H37Ra strains. By obtaining over four billion bases of sequence from mRNA, we generated genome-wide gene transcription maps of wild-type and mpbR-deleted Mycobacterium tuberculosis H37Ra strains. We find that a group of genes is significantly up-regulated in the mpbR-deleted mutant strain. This finding indicates that MpbR negatively regulates gene expression.

overall_design: Examination of gene expression level in 2 strains.

first: Zhengguo

last: He


title: Transcriptome and translatome analysis of THP1 cells with doxycycline induced FXR1 Knockdown

status: Public on Aug 25 2022

first: Shobha

last: Vasudevan

address: 185 Cambridge St

department: Cancer Center

institute: Massachusetts General Hospital

type:
Expression profiling by array
Other

summary: FXR1 depletion in THP1 cells causes changes in polysome associated mRNAs. This leads to a distinct translatome in the cell.

overall_design:
The experiment is comprised of 16 HuGene 2.0 ST arrays, profiling input RNA and sucrose-gradient-purified polysomal RNA obtained from leukemic cells transfected with pTRIPZ inducible non-silencing control or cells transfected with a TRIPZ lentiviral vector containing an shRNA targeting the gene FXR1, collected either during normal mitotic growth (S+ phase) or after inducing cell cycle arrest (G0 phase).
Total RNAs and RNAs associated with polysomes were purified from THP1 cells (control shRNAs), THP1 cells (FXR1 knockdown) under proliferating and serum starvation conditions and hybridization on affymetrix microchips. Polysomes were isolated by fractionation on sucrose gradients. RNA was purified from either total cell lysate and or from only polysome fractions. Translatome change was analysed after normalizing mRNA levels on polysome to their level in total cell lysate.

first: Datta

last: Chandreyee

first: Vasudevan

last: Shobha

first: Gower

last: Adam


title: MiRNA microarray for exosome of H1299 cells after irradiation

first: Tongxin

last: Yang

address: No.374 Dianmian Road

department: The Department of Urology

institute: The Second Affiliated Hospital of Kunming Medical University

summary: Objective: to find out the exosome miRNA of H1299 cells that can be changed by ionizing radiation

overall_design: H1299 cells cultured in vitro received 0Gy (control group) and 10Gy (experimental group) ionizing radiation, and then the supernatant was taken to extract exosomes. The above exosomes were detected by miRNA microarray in groups.

first: Xian

first: Wenhui


title: Effect of LIF treatment on human macrophages

city: Toronto

first: Robin

last: Hallett

state: ON

address: 101 College Street

department: Translation

country: Canada

institute: Northern Biologics

summary: Human macrophages were treated with LIF to test if immunosuppressive gene expression programs were induced

overall_design:
Comparative gene expression profiling of LIF treated and untreated human macrophages
*** Raw data for this submission is unavailable (accidentally destroyed) ***


title: Transcriptome and translatome analysis of constitutively overexpression of FXR1 and control THP1 cells

city: Boston

summary: FXR1 overexpression in THP1 cells causes changes in polysome associated mRNAs. This leads to a distinct translatome in the cell that contributes to chemo- and immune- survival

overall_design:
The experiment is comprised of 8 HuGene 2.0 ST arrays, profiling input RNA and sucrose-gradient-purified polysomal RNA obtained from leukemic cells from Vector control and FXR1 Overexpressing THP1 cells
Total RNAs and RNAs associated with polysomes were purified from THP1 cells (control vector), THP1 cells (FXR1 overexpression) and hybridization on affymetrix microchips. Polysomes were isolated by fractionation on sucrose gradients. RNA was purified from either total cell lysate and or from only polysome fractions. Translatome change was analysed after normalizing mRNA levels on polysome to their level in total cell lysate.


title: Chemokines profiling in tumors treated with UNC1999

city: Chiba

first: Junjie

last: Ao

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology

country: Japan

institute: Graduate School of Medicine, Chiba University

summary: Increased expression of chemokines in UNC1999-treated tumor tissues were successfully checked out through chemokines profiles screening of a total 25 different mouse chemokines using control and UNC1999-treated tumor tissues.

overall_design: In this study, we used 4 control and 4 UNC1999-treated tumor tissues to screening identify 14 chemokines, respectively.

first: Tetsuhiro

last: Chiba

last: Qiang


title: CD9 contributes to exit from a stem cell-like and embryonic diapause states and transit to drug resistant states

city: Portland

first: Gordon

last: Mills

state: Oregon

address: 2730 SW Moody Ave

department: Precision Oncology

institute: Oregon Health & Science University

summary: In order to identify state changes that mediate the transition from sensitive to a resistant cell states, we applied RNA velocity analysis to an existing single-cell RNAseq (scRNAseq) dataset of BRD4 inhibitor sensitive and resistant SUM149 and SUM159 triple negative breast cancer cell lines. Both SUM149 and SUM159 cell lines treated with or without JQ1 had similar cell communities and trajectories including a stem cell-like and embryonic diapause (SCLED) cell state, a transiting cell state and a number of drug resistant states. Interestingly a transcriptional signature derived from the transiting state but not the SCLED state was associated with worsened outcomes in basal-like breast cancer patients as well as with a micrometastasis signature suggesting that the ability to transit from the SCLED state to drug resistant states could contribute to patient outcomes. The shift from the SCLED state to a transiting cell state was characterized by elevated expression of the CD9 tetraspanin. CD9 knockdown sensitized SUM149 tumor cells to JQ1 in vitro and in vivo trapping cells in the SCLED state and limiting transit to resistant cell states. CD9 knockdown sensitized SUM149 to multiple additional cytotoxic drugs suggesting a generalized role in drug resistance. Thus, CD9 appears to be critical for the ability of triple negative breast cancer cells to escape from a stem cell-like/embryonic diapause state and transition into a treatment resistant state.

overall_design: scRNA-seq by 10x genomics of shCD9 or shCON SUM149 tumors growing in NSG mouse after 30 days of 10mg/kg/day JQ1 treatment and 10 days treatment withdrawal.

first: Grodon

first: Xi


title: In vitro polarization of primary human blood derived macrophages

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

summary:
Purpose: Generate a benchmark to assess extent of macrophage polarization in disease or infection models.
Method: Monocytes were isolated from blood donors who gave informed written consent (Ethics approval number: 161/17, Philipps University Marburg, Germany) by MACS CD14 positive selection. Monocytes were cultured for 7 days in the presence of 1% human off-the-clot AB serum. On day 7, macrophage morphology was assessed by microscope, and cells were left untreated (ctrl), stimulated with 100ng/ml LPS + 20 ng/ml IFNgamma (M1) or 20 ng/ml IL4 + 20 ng/ml IL-13 for 18h. Additionally, a separate set of cells was infected with Legionella Pneumophila Corby wild type and flagellin deficient at MOI1 for 18 h. Then RNA was isolated by phenol chloroform extraction, sample quality was assessed by Bioanalyzer, and samples with a RNA integrity > 8 were sequenced on an Illumina HiSeq 1500.

overall_design: 4 biological donors who gave monocytes that were for each donor differentiated into control, M1, and M2, or served as separate set for Legionella Infection.

first: Bernd

last: Schmeck


title: The mitochondrial protein OPA1 regulates the quiescent state of adult muscle stem cells

status: Public on Aug 24 2022

city: Ottawa

first: Mireille

last: Khacho

state: Ontario

address: 451 Smyth Rd

department: BMI

institute: University of Ottawa

summary: Regulation of quiescence is essential for adult stem cell maintenance, longevity and sustained regeneration potential. Our studies have uncovered that physiological and transient changes in mitochondrial shape regulate the quiescent state of adult muscle stem cells (MuSCs). We show that mitochondria in MuSCs rapidly fragment in response to an activation stimulus, via a systemic HGF/mTOR mechanism, to drive the exit from deep quiescence. Deletion of the mitochondrial fusion protein OPA1 and forced mitochondrial fragmentation is sufficient to transition MuSCs into G-alert quiescence causing premature activation and depletion upon a stimulus. Loss of OPA1 activates a glutathione (GSH) redox signaling pathway that promotes cell-cycle progression, myogenic gene expression and commitment. MuSCs with chronic OPA1 loss and mitochondrial fragmentation, leading to mitochondrial dysfunction, continue to reside in a primed state but acquire severe cell cycle defects. Additionally, we provide evidence that OPA1 decline and impaired mitochondrial dynamics may contribute to age-related MuSC dysfunction. These findings reveal a fundamental role for OPA1 and mitochondrial dynamics in establishing the quiescent state and activation potential of adult stem cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for freshly FACS sorted muscle stem cells from OPA1-WT and OPA1-KO mice at 8-10 weeks

first: M

first: N

last: Baker


title: Evaluating the gut microbiota shifts caused by two diets based on ancient grains

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Total DNA was extracted from stool specimens, amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

overall_design: Two class comparison of individuals fed with different diets

first: Monica

last: Dinu

first: Amedeo

last: Amedei

first: Simone

last: Baldi

first: Leandro

last: Di Gloria


title: Genome-wide maps of ZBTB38 in human cells

first: Benoit

last: Miotto

address: 24 Rue du Faubourg Saint Jacques

department: Development, Reproduction and Cancer

institute: INSERM U1016, Institut Cochin

summary: ZBTB38 is a transcription factor with affinity for methylated sequences in vitro. Here, we address ZBTB38 binding selectivity in vivo by mapping 3232 ZBTB38 binding sites throughout the human genome. These target sites are over-represented in Alu-repeats, and in the CpG island shores of highly expressed genes, hundreds of base pairs upstream of the transcription start site. In addition, the ZBTB38 target sites are highly similar to E2F4-binding motifs, but they are methylated, not bound by E2F4, and the corresponding genes are not cell-cycle regulated.

overall_design: ChIP-seq of ZBTB38 in HeLa-S3 cells expressing a tagged ZBTB38

first: Claire

last: Marchal

first: Pierre-Antoine

last: Defossez


title: Expression data from AZA treated megakaryocytic cells under TPO-RA stimulation

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary:
Thrombocytopenia is an independent prognostic indicator in patients with MDS (de Swart, L. et al, Br J Haematol, 2015) and we sought to evaluate the contribution of azacitidine to the worsening of this condition in patients with MDS and acute myeloid leukemia (AML). Since MDS/AML may have lower amounts of residual healthy cells, we sought to model this effect of AZA on healthy cord blood derived megakaryocytic cells.
We used microarrays to detail the global programme of gene expression in the presence of azacitidine under megakaryocytic differentiation stimulants and identified distinct classes of dysregulated genes and pathways during this process.

overall_design: To assess the effects of AZA on megakaryocytic cells at the transcriptional level, we treated cord blood mononuclear cells with or without 0.3uM AZA for 16 hours in serum and cytokine free conditions in plain stem span media in the presence of thrombopoietin receptor agonists (TPO-RA) 100ng/mL TPO or 5ug/mL eltrombopag (EP). Followed by FACS sorting of viable cMPL expressing cells for microarray analysis.

first: Ujunwa

last: Okoye-Okafor


title: Gene expresssion analysis in liver and white adipose tissues from miR-322-503-351 knock out mice.

city: Nanjing

first: Yuncai

last: Zhou

state: Jiangsu

address: No. 818 Tianyuan East Road, Jiangning District

institute: Nanjing medical university

summary: To investigate the effect of miR-503 in aging associated type 2 diabetes, target genes of miR-503 need to be investigated. The global miR-322-503-351 deletion (KO) mouse was constructed, and RNA-seq was then performed on aged mouse liver and white adipose tissue (WAT).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of liver and WAT from 52-week-old WT and KO mice.

first: Kerong

last: Liu

first: Yunxia

last: Zhu

first: Xiao

last: Han


title: Primed smooth muscle cells acting as first responder cells in disease

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: Vascular smooth muscle cell (VSMC) dysregulation is a hallmark of vascular disease, including atherosclerosis. In particular, the majority of cells within atherosclerotic lesions are generated from pre-existing VSMCs and a clonal nature has been documented for VSMC-derived cells in multiple disease models. However, the mechanisms underlying the generation of oligoclonal lesions and the phenotype of proliferating VSMCs are unknown.Here we analyse clonal dynamics in multi-color lineage-traced animals over time after vessel injury to understand the cellular mechanisms underlying clonal VSMC expansion in disease.We demonstrate that VSMC proliferation is initiated in a small fraction of VSMCs that initially expand clonally in the medial layer and then migrate to form the oligoclonal neointima. Selective activation of VSMC proliferation also occurs in vitro, suggesting that this is a cell-autonomous feature. Mapping of VSMC trajectories using single-cell RNA-sequencing reveals a continuum of cellular states after injury and suggests that VSMC proliferation initiates in cells that have downregulated the contractile phenotype and show evidence of pronounced phenotypic switching. We show that proliferation is associated with induced expression of stem cell antigen 1 (SCA1) and the expression signature previously identified in SCA1+ VSMCs in healthy arteries. A remarkably increased proliferation of SCA1+ VSMCs, directly validated in functional assays, indicates that SCA1+ VSMCs act as "first responders" in vascular injury. Early atherosclerotic lesions also had clonal VSMC contribution and we show that the proliferation-associated injury response is conserved in plaque VSMCs, extending these findings to atherosclerosis. Finally, we identify VSMCs in healthy human arteries that correspond to the SCA1+ state in mouse VSMCs and show that genes identified as differentially expressed in this human VSMC subpopulation are enriched for genes showing genetic association with cardiovascular disease. We show that cell-intrinsic, selective VSMC activation drives clonal proliferation after injury and in atherosclerosis. Our study suggests that healthy mouse and human arteries contain VSMCs characterised by expression of disease-associated genes that are predisposed for proliferation. Targeting such "first responder" cells in patients undergoing vascular surgery could effectively prevent injury-associated VSMC activation and neoatherosclerosis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: This entry contains data from the following analyses: (1) 10X single-cell RNA-seq analysis of VSMC-lineage labeled cells isolated by flow-assisted cell sorting (FACS) from ligated left carotid arteries of Myh11-EYFP-Ki67/RFP animals 5 days after surgery. (2) 10X single-cell RNA-seq analysis of human medial cells isolated from a healthy aorta (65-year-old male). (3) 10X single-cell RNA-seq analysis of VSMC-lineage labeled cells isolated by flow-assisted cell sorting (FACS) from ligated left carotid arteries of Myh11-EYFP-Ki67/RFP animals 7 days after surgery. (4) Single-cell RNA-seq of index-sorted cells from Myh11-EYFP-Ki67/RFP animals 7 days after surgery and control unligated animals. (5) 10X single-cell RNA-seq analysis of VSMC-lineage labeled cells and other arterial cells generated 5 days after surgery.

first: Helle

last: Jørgensen

first: Matt

last: Worssam

first: Jordi

last: Lambert

first: Sebnem

last: Oc

first: Annabel

last: Taylor

first: Lina

last: Dobnikar

first: Mikhail

last: Spivakov


title: Detergent exposure induces epithelial barrier dysfunction and eosinophilic inflammation in the esophagus

city: Scottsdale

first: Alfred

last: Doyle

state: Arizona

address: 13400 E Shea Blvd

institute: Mayo Clinic

summary: To investigate the effects of the common household detergent Sodium Dodecyl Sulfate (SDS) on the esophagus we provided mice with 0.5% SDS in their drinking water for 14 days and assessed the effects by various methods including RNA-Seq of whole esophagus homogenates.

overall_design: Comparative gene expression profiling analysis using data obtained from RNA-seq of whole mouse esophagus samples comparing mice  provided 0.5% SDS in drinking water for 2 weeks(n=3) vs. untreated water controls (n=5)

first: Benjamin

last: Wright


title: Stat1 activation, through systemic interferon signaling, and upregulation of innate immune system receptors drives inflammaging, that is ameliorated by dietary restriction intervention [ATAC-seq]

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

summary: Aging is the result of an accumulation of molecular damages, driven by multiple factors like metabolic and oxidative stress, (epi)genetic alterations, and microbiome dysbiosis. In addition, aging is characterized by a chronic, low-grade inflammation known as inflammaging that represents a high significant risk factor for most, if not all, age-related diseases. Dietary restriction (DR) is the best-known non-invasive method to ameliorate the aging phenotype in many organisms. While it has been shown that DR reduces the inflammation in some tissues, the molecular mechanisms in old individuals are still largely unknown. Here we identify a multi-tissue gene network which regulates the inflammaging and that is ameliorated by DR. Using transcriptional profiling (RNA-seq), we found that aging upregulates the innate immune system receptor together with the activation of a systemic interferon (IFN) signaling through the Interferon Regulatory Factors (Irf), inflammatory cytokines and finally Stat1 transcription factor. Our results suggest that DR is able to ameliorate inflammaging by downregulating the expression and the activity of almost all the components of this gene network. In addition, chromatin accessibility genome-wide analysis showed that the binding site of Irf and Stat1 in the promoter of their target genes are more open in aging and become closer upon DR treatment indicating a transcriptional control of the inflammaging phenotype involving epigenetic modifications. Our results provide a comprehensive understanding of the molecular network regulating the inflammation in aging and DR and present novel anti-inflammaging therapeutic targets.

overall_design: ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) of kidney and liver in young, old, and long-term dietary restriction.

first: Seyed

first: Francesco

last: Annunziata

first: Anna

last: Krepelova

first: Suneetha

last: Nunna

first: Nadja

last: Gebert

first: Lisa

last: Adam

first: Sandra

last: Käppel

first: Alessandro

last: Ori

last: Neri


title: Stat1 activation, through systemic interferon signaling, and upregulation of innate immune system receptors drives inflammaging, that is ameliorated by dietary restriction intervention [RNA-seq]

overall_design: Transcriptional profile of kidney, liver, lung, muscle, skin, brain, blood and heart in aging, short-term and long-term dietary restriction.


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Monocyte-Depleted Brain Transcriptomes

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived brain transcriptome profiling (RNA-seq) to reveal the difference of cellular pathways in adult brains of wild type (WT) and monocyte-depleted (CCR2-DTR) mice 8 days post infection of Trichinella spiralis.
Methods: Illumina compatible RNAseq library was prepared using NEB next ultra RNAseq library preparation kit. The sequencing of the cDNA libraries was performed on the Illumina NextSeq platform (Illumina, San Diego, CA) using the high output 1X75 cycles configuration. CLC Genomics Workbench 11.0.1 version (http://www.clcbio.com/products/clc-genomics-workbench/ ; Qiagen) was used for RNA-seq analysis. De-multiplexed fastq files from RNA-Seq libraries are imported into the CLC software. Bases with low quality were trimmed and reads are mapped to reference genome Mus musculus genome GRCm38. The reference genome sequence and annotation files were downloaded from ENSEMBLE, release.92 (Mus_musculus.GRCm38.92.fa, and Mus_musculus.GRCm38.92.gtf). The aligned reads were obtained using the RNA-Seq Analysis Tool of CLC Genomics Workbench. Statistical analysis of differentially expressed genes is carried out based on a negative binomial model using a tool in CLC Genomic Workbench. The reference genome sequence and annotation files were downloaded from ENSEMBL, release.92 (Mus_musculus.GRCm38.92.fa, and Mus_musculus.GRCm38.92.gtf). The aligned reads were obtained using the RNA-Seq Analysis Tool of CLC Genomics Workbench.
Results: Using an optimized data analysis workflow, we mapped over 50 million sequence reads per sample to the mouse genome (GRCm38) and found that Trichinella-infected mice depleted of monocytes presented with significantly increased expression of proinflammatory genes compared to controls.

overall_design: Brain mRNA profiles of adult wild type (WT) and monocyte-depleted (CCR2-DTR) mice 8 days post infection of Trichinella spiralis.

first: Chandler

last: Sy

first: Mark

last: Siracusa


title: Gene expression data from human prostate cancer cell line PC3 and PAR1 and PAR-2-knockout PC3 cells generated using CRISPR/Cas9 targeting

city: London

first: Rithwik

last: Ramachandran

address: 1151 Richmond Street

institute: University of Western Ontario

summary:
We found that PC3 cells secrete proteases that cleavae and activate PAR1 and PAR2. In order to understand gene regulation by this autocrine signaling loop, PAR1 and PAR2 knockout cell gene expression was compared to WT PC3 cell gene expression.
Proteinase activated receptors (PARs) are G protein-coupled receptors (GPCRs) activated by limited N-terminal proteolysis. A variety of proteolytic enzymes derived from the coagulation cascade and inflammatory milieu activate PARs, however specific activators in different physiological and pathophysiological contexts remain poorly defined. PARs are highly expressed in many cancer cells and regulate various aspects of tumor growth and metastasis. Endogenous proteinases that regulate PARs in the setting of various tumors however remains unresolved. Prostate cancer (PCa) remains a major cause of mortality in men despite advances in early detection and clinical intervention. PAR expression has been reported in PCa, however, their role here remains poorly defined. In androgen independent PC3 cells, we find functional expression of PAR1 and PAR2 but not PAR4. Using genetically encoded PAR cleavage biosensors, we find that PCa cells secrete proteolytic enzymes that cleave PARs and trigger autocrine signaling. Deletion of PAR1 and PAR2 using CRISPR/Cas9 combined with microarray analysis revealed genes that are differentially regulated by this autocrine signalling mechanism. Interestingly, several genes that are known PCa prognostic factors or biomarker were differentially expressed in PAR1-KO and PAR2-KO PC3 cells. We also examined PAR1 and PAR2 regulation of PCa cell proliferation and migration using PAR1 and PAR2-KO PC3 cells, as well as PAR1 and PAR2 specific agonists and antagonists. We find that PAR1 and PAR2 have opposite effects on PC3 cell proliferation and migration. In summary, we have identified an autocrine signaling mechanism through PARs as a regulator of PCa cell function.

overall_design: Gene expression in WT PC3 cells, PAR1-KO PC3 cells and PAR-2-knockout PC3 cells was compared

first: Arundhasa

last: Chandrabalan


title: Engineering bone-forming callus-organoid implants in a xenogeneic free differentiation medium

city: Leuven

first: Tim

last: Herpelinck

address: Herestraat 49

department: Development and Regeneration

institute: KU Leuven

summary: The field of tissue engineering aspires to provide clinically relevant solutions for patients through the integration of developmental engineering principles with a bottom up manufacturing approach. However, manufacturing of cell based advanced therapy medicinal products is hampered by protocol complexity, lack of non-invasive critical quality controls, and dependency on animal-derived components for tissue differentiation. We investigate a serum-free, chemically defined, xeno- and lipid-free chondrogenic differentiation medium to generate bone-forming callus organoids. Our results show an increase in microtissue homogeneity during prolonged differentiation and a high quality of in vivo bone forming organoids. The low protein content of the culture media potentially allows for monitoring of relevant secreted biomarkers as (critical) quality attributes . Together, we envisage that this xeno- and lipid-free chondrogenic medium is compatible with industrial scale-up and automation, while facilitating the implementation of non-invasive imaging and use of quality control parameters based on secreted biomarkers.

overall_design: Human periosteum-derived cells (hPDCs) were isolated from periosteal biopsies of 6 different donors of which one cell pool was created (ages of 20-32). The hPDCs were expanded until passage 7 at 37 °C, 5 % CO2 and 95 % humidity in Dulbecco’s modified Eagle medium (DMEM, Gibco, UK) with 10 % fetal bovine serum (South Afrika FBS, BioWest, France) and 1 % antibioticantimycotic solution (Invitrogen, USA). Medium was changed every 3-4 days. At a confluence of 80 %, cells were harvested with TrypLE Express (Life Technologies, UK). A microwell platform (AggreWell™800, STEMCELL Technologies Inc, Canada) was coated with Anti-Adherence Rinsing Solution (STEMCELL Technologies Inc, Canada) to avoid cell attachment. Homogenous microwell coating was ensured by centrifugation, followed by a washing step with basal medium before cell seeding. hPDCs were harvested with TrypLE Express (Life Technologies, UK) and seeded at 300 000 cells per well to contain 1000 cells per microwell upon sedimentation. The cells selfaggregated and were differentiated for 21 days. Two serum-free, chemically defined chondrogenic media were compared. Both contain LG-DMEM (Gibco) supplemented with 1% antibiotic– antimycotic (Invitrogen), 1 × 10-3 M scorbate-2 phosphate, 1 × 10-7 M dexamethasone, 40 µg mL-1 L-proline, 20 × 10-7 M of Rho- kinase inhibitor Y27632 (Axon Medchem), 100 ng mL-1 BMP2 (INDUCTOS), 100 ng mL-1 GDF5 (PeproTech), 10 ng mL-1 TGF-β1 (PeproTech), 1 ng mL-1 BMP-6 (PeproTech), and 0.2 ng mL-1 basic FGF-2 (R&D systems). Xenofree chondrogenic medium (xfCM) was then supplemented with ITS Premix Universal Culture Supplement (containing 6.25 µg mL-1 insulin, 6.25 µg mL-1 transferrin and 6.25 ng mL-1 selenious acid, Corning), while chondrogenic medium (CM) was supplemented with ITS+ Premix Universal Culture Supplement (containing 6.25 µg mL-1 insulin, 6.25 µg mL-1 transferrin and 6.25 ng mL-1 selenious acid, 5.35 µg mL-1 linoleic acid and 1250 µg mL-1 bovine serum albumin to solubilize the linoleic acid, Corning). Half of the medium was changed on days 3, 7, 10, 14, and 17.

first: Isaak

last: Decoene

first: Ioannis

last: Papantoniou


title: Next Generation Sequencing Facilitates Single Cell Analysis of Wild Type and Monocyte-Depleted Brain Transcriptomes

summary:
Methods: Cells isolated from the whole brains of naive wild type, infected wild type, and infected CCR2-DTR mice were sort-purified on live CD45hi cells from five biological replicates and pooled. Sort-purified cells were then processed using the 10X Genomics Chromium Controller. Cell suspensions were loaded onto the Chromium Single Cell A Chip for cell lysis and barcoding. RNA from individual cells was reverse transcribed and sequencing libraries prepared using the Chromium Single Cell 3’ Library Kit v2 following the manufacturers protocol. Samples were sequenced using an Illumina NextSeq 550 with standard 10X Genomics Configuration (26 bp x 98 bp). After sequencing, raw bcl files were processed using the cellranger mkfastq command for sample demultiplexing and conversion to .fastq files, followed by cellranger count for cell barcode and UMI deconvolution as well as mapping to the respective reference genome. Processed digital gene expression matrices were imported into R studio for analysis using the Seurat package. Samples were aligned along common sources of variation and compared using canonical correlation analysis to identify unique clusters of cells within the samples. Marker genes for each sample and cluster were identified and used for generation of downstream plots within the Seurat package. All packages are maintained to be best in class and are regularly updated to their most recent release.
Results: 10 distinct cell clusters were identified and we found that two populations were found at increased proportions post-infection but were substantially reduced in the monocyte-depleted animals (CCR2-DTR). We confirmed that these populations to be monocytes and monocyte-derived cells, and valicated their immunoregulatory molecules by RT-qPCR analysis.

overall_design: Brain CD45hi cells mRNA profiles of adult wild type (WT) and monocyte-depleted (CCR2-DTR) mice 8 days post infection of Trichinella Spiralis


title: Differentially Expressed Genes of Pseudomonas aeruginosa Isolates from Eyes with Keratitis and Healthy Conjunctival Sacs

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

summary: P. aeruginosa isolates from keratitis and healthy conjunctival sacs were obtained. The transcriptome profile of P. aeruginosa was characterized by a high throughput RNA-seq strategy using the Illumina HiSeq 2500 platform. The DEGs were analyzed with DESeq and validated through quantitative real-time polymerase chain reaction (PCR) and with experimental mice.

overall_design: RNA-seq analysis of P. aeruginosa from keratitis and healthy conjunctival sacs

first: Xiubin

last: Ma

first: Yusen

last: Huang


title: The novel role of hnRNP UL1 in human cell nucleoli

city: Poznan

first: Kishor

last: Gawade

address: Uniwersytetu Poznańskiego 10

department: Faculty of Biology

country: Poland

institute: Adam Mickiewicz University

summary: hnRNPUL1 plays an important role in the cell nuclei, where it is recruited to DNA damage sites and is involved in the repair of DNA double-strand breaks. Furthermore, this protein is known as a transcriptional repressor of RNA polymerase II genes. In the present study, we have shown that hnRNP UL1 is also localized in the nucleoli. Revealing its function, we figured out that hnRNP UL1 stimulates ribosomal DNA (rDNA) gene transcription. We have performed high-throughput sequencing of libraries prepared from nucleolar and cytoplasmic-nuclear RNA fractions to identify differentially expressed ribosomal RNAs in wild-type and HNRNPUL1 knockout HEK293T cells.

overall_design: We performed Nucleolar (NO) and Nuclear-Cytoplasmic (CN) fractionation of HEK293T wild-type and hnRNPUL1 knockout cells. The fractionated RNA was used to prepare libraries with biological triplicates from NO and CN RNA fractions from wild-type and HNRNPUL1KO cells.

first: Marlena

last: Cichocka

first: Katarzyna

last: Raczyńska


title: Retrograde Control of Cytosolic Translation Targets Synthesis of Plastid Proteins and Nuclear Responses for High-Light Acclimation.

city: ACTON

first: Marten

last: Moore

state: ACT

address: 134 Linnaeus Way

department: Research School of Biology

country: Australia

institute: The Australian National University

summary: Canonical retrograde signalling comprises information transmission from organelles to the nucleus and in particular controls gene expression for organellar proteins. The need to re-assess this paradigm was suggested by discrepancies between de novo protein synthesis and transcript abundance in response to excess light. Here we uncover major components of a translation-dependent retrograde signalling pathway that first impacts translation and then transcription. The response realization depends on the kinases Mitogen-activated protein kinase 6 (MPK6) and Sucrose non-fermenting 1-related kinase (SnRK1) subunit, AKIN10. Global ribosome foot-printing revealed differential ribosome association of 951 transcripts within 10 min after transfer from low to high light. Despite predominant translational repression, 15 % of transcripts were increased in translation and enriched for chloroplast-localized photosynthetic proteins. About one third of these transcripts, including Stress associated proteins (SAP) 2 and 3, share regulatory motifs in their 5`-UTR that act as binding sites for glyceraldehyde-3-phosphate dehydrogenase (GAPC) and light responsive RNA binding proteins (RBPs). SAP2 and 3 are both translationally regulated and interact with the calcium sensor Calmodulin-like 49 (CML49), which promotes relocation to the nucleus inducing a translation-dependent nuclear stress response. Thus, translation-dependent retrograde signalling bifurcates to directly regulate a translational circuit of chloroplast proteins and simultaneously initiate a nuclear circuit synchronizing retrograde and anterograde response pathways, serving as a rapid mechanism for functional acclimation of the chloroplast.

overall_design: Ribosome protected fragment (RPF)-sequencing and total RNA sequencing was performed on whole Arabidopsis rosettes from plants plants grown under low-light (LL) (8µE) or 10 min of LL to high light (HL) (800µE) treated. 3 g of pulverized plant material was used with 6 mL polysomal extraction buffer (PEB; 0.2 M Tris, pH 9.0, 0.2 M KCl, 25 mM EGTA, 35 mM MgCl, 1 % Brij, 1 % Triton X-100, 1 % Tween 20, 1 % Igepal CA630, 1% sodium deoxycholate (DOC), 1 % polyethylene-10-tridecylether (PTE), 5 mM DTT, 1 mM PMSF, 100 µg/mL cycloheximide, 100 µg/mL chloramphenicol, 100 µg/mL lincomycin). The suspension was passed twice through MiraclothTM and subsequently cleared by centrifugation. Extracts were loaded on a sucrose cushion (0.2 M Tris, pH 9.0, 0.2 M KCl, 0.025 M EGTA, 0.035 M MgCl, 1.75 M sucrose, 5 mM DTT, 50 µg/mL cycloheximide, 50 µg/mL chloramphenicol, 50 µg/mL lincomycin) and centrifuged for 18 h at 100,000 xg in a Beckmann SW71Ti rotor. The sediment was suspended in 100 µL RNase digestion buffer (20 mM Tris-HCl, pH 8.0, 140 mM KCl, 35 mM MgCl2, 50 µg/µL cycloheximide, 50 µg/µL chloramphenicol, 50 µg/µL lincomycin) and used immediately for RNase If digestion.  RNase If digest was performed with 2,000 relative absorbance units OD260 of the in RNase digestion buffer suspended polysomes by adding 50 U of RNase If (New England Biolabs) in 250 µL total volume by incubation at room temperature with constant rotation for 1 h. In parallel same amounts of polysomes were treated with 5 µL SUPERase RNase inhibitor (Thermo) and kept on ice as control sample. The digestion was stopped by adding 5 µL SUPERase RNase inhibitor and the RNA precipitated by adding 1 volume of isopropanol, 300 mM NaOAc pH 5.2 and 20 µg glycogen at -80 over-night. The supernatant was discarded after centrifugation at 16,000 xg at 4 °C for 30 min and the sediment was washed twice with 75 % ethanol and resuspended in RNA loading buffer for size exclusion electrophoresis.  Total RNA was isolated using Tri Reagent (Sigma-Aldrich) from extracts suspended in polysomal extraction buffer (see sucrose cushion for polysome isolation, above). Briefly, 500 µL of extract was combined with 1 mL of TriReagent, followed twice by extraction of the organic phase with 200 µL chloroform. RNA was precipitated with equal volume 100% isopropanol and incubated overnight at -20°C. The RNA was recovered by centrifugation and washed with 75% ethanol before resuspension in water. RNA quality was assessed using a LabChip GXII (Perkin-Elmer). Total RNA was DNase-treated using TURBO DNase (Invitrogen) following the manufacturer’s protocol. Preparation of total RNAseq libraries was carried out using Illumina TruSeq Stranded Total RNA with Ribo-Zero plant, scaled at half reaction volumes.  Libraries of ribosome-protected fragments (RPFs) were prepared from three biological replicates per time-point and sample following RNase If digestion (above) according to Juntawong et al. (2014)

first: Aaron

last: Smith

first: Barry

middle: J

last: Pogson

first: Karl-Josef

last: Dietz


title: The regulators of peroxisomal acyl-carnitine shuttle CROT and CRAT promote metastasis in melanoma

city: Logroño

first: Ignacio

last: Larrayoz

state: Please Select

address: C\ Piqueras 98, Ed CIBIR

department: Oncology Area

institute: CIBIR

summary: For cancer cells to use the haematogenous route of metastasis overcoming anoikis is a prerequisite. By performing RNAseq in melanoma cells, we discovered that after detachment melanoma cells display increased expression of regulators of fatty acid transport and fatty acid beta-oxidation

overall_design: Comparative gene expression profiling analysis of RNA-seq data for adherent and in supension,  501mel and WM266-4 melanoma cell lines, grown with different glucose concentrations.

first: Imanol

last: Arozarena

first: Irene

last: Lasheras-Otero


title: Expression data from  SQ, TRI-SQ and Tetra-SQ-treated HFDPCs

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

summary: Gene expression profiling reveals a potential role of SQ, Tri-SQ, and Tetra-SQ in stimulating hair growth in dermal papilla cells. Squalene (SQ) was found to exhibit a strong antioxidant and anti-inflammatory activity; however, its biological effects is underestimated because of its insolubility. To overcome this problem, new amphiphilic SQ derivatives were synthesized and were used in this study to check their potential effect in vitro and in vivo on inducing hair growth while exhibiting an anti-aging property.

overall_design:
HFDPCs were human primary cells line, treated with 2.5 µM with all samples for 48 h. Microarray gene expression profiling was conducted for two biological replicates
RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Retrograde Control of Cytosolic Translation Targets Synthesis of Plastid Proteins and Nuclear Responses for High-Light Acclimation

summary:
Canonical retrograde signalling comprises information transmission from organelles to the nucleus and in particular controls gene expression for organellar proteins. The need to re-assess this paradigm was suggested by discrepancies between de novo protein synthesis and transcript abundance in response to excess light. Here we uncover major components of a translation-dependent retrograde signalling pathway that first impacts translation and then transcription. The response realization depends on the kinases Mitogen-activated protein kinase 6 (MPK6) and Sucrose non-fermenting 1-related kinase (SnRK1) subunit, AKIN10. Global ribosome foot-printing revealed differential ribosome association of 951 transcripts within 10 min after transfer from low to high light. Despite predominant translational repression, 15 % of transcripts were increased in translation and enriched for chloroplast-localized photosynthetic proteins. About one third of these transcripts, including Stress associated proteins (SAP) 2 and 3, share regulatory motifs in their 5`-UTR that act as binding sites for glyceraldehyde-3-phosphate dehydrogenase (GAPC) and light responsive RNA binding proteins (RBPs). SAP2 and 3 are both translationally regulated and interact with the calcium sensor Calmodulin-like 49 (CML49), which promotes relocation to the nucleus inducing a translation-dependent nuclear stress response. Thus, translation-dependent retrograde signalling bifurcates to directly regulate a translational circuit of chloroplast proteins and simultaneously initiate a nuclear circuit synchronizing retrograde and anterograde response pathways, serving as a rapid mechanism for functional acclimation of the chloroplast
CML49 KO and SAP3 KO 0' and 60' of low light (8µE) to high light (800µE) transfer in comparison to Col-0

overall_design: As in Oelze et al 2012: sap3, cml49 KO and Col-0 WT plants were grown for 3 weeks under normal light (80µE) before shifting to low light (8µE) for 10 days. Plants were then shifted to high light (800µE) for 60 min and harvested at mid photo period (3 pm) together with low light control (8µE).


title: Single-cell transcriptomic analysis of aged mouse subcutaneous adipose tissue

city: Beijing

first: XIN

last: FU

address: 33 Ba-Da-Chu Road

department: Research Center

institute: Plastic Surgery Hospital (Institute), Peking Union Medical College & Chinese Academy of Medical Sciences

summary: Adipose tissue (AT) is an essential endocrine organ which undergoes significant changes during aging. Functions of vascular endothelial cells are altered in aged AT, and markedly affect the metabolic homeostasis of AT. However, little is known about the aged alterations of EC in AT, and whether and how their metabolic changes contribute to AT aging.

overall_design: Stromal vascular fraction (SVF) cells in inguinal subcutaneous adipose tissues (SAT) were isolated from young (3-months-old, n=4) and old (18-months-old, n=3) mice and subjected to single-cell RNA sequencing (scRNA-seq) using 10× Genomics platform.

first: Xin

last: Fu

first: Yu

last: Zhao

first: Siyuan

last: Yang

first: Zhigang

first: Fuxing

last: Gong

first: Ran

last: Xiao


title: Stat1 activation, through systemic interferon signaling, and upregulation of innate immune system receptors drives inflammaging, that is ameliorated by dietary restriction intervention

first: Seyed Mohammd Mahdi

last: Rasa

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

overall_design: Refer to individual Series


title: MARCH1 controls an exhaustion-like program of effector CD4+ T cells promoting allergic airway inflammation

city: Stanford

first: Kamir

last: Hiam-Galvez

address: 240 Pasteur Drive

institute: Stanford University

summary: Persistent antigenic signalling leads to T cell exhaustion, a dysfunctional state arising in many chronic infections and cancers. Little is known concerning mechanisms limiting exhaustion in immune stimulatory diseases such as asthma. We report that membrane-associated RING-CH1 (MARCH1), the ubiquitin ligase that mediates surface turnover of MHCII and CD86 in professional APCs, plays an essential role in restraining exhaustion of effector CD4+ T cells in a mouse model of asthma. Mice lacking MARCH1 or the ubiquitin acceptor sites of MHCII and CD86 exhibited increased MHCII and CD86 surface expression on lung APCs, and this increase promoted enhanced expression of immune inhibitory receptors by effector CD4+ T cells and inhibited their proliferation. Remarkably, ablation of MARCH1 in mice with established asthma reduced airway infiltration of eosinophils and Th2 cells. Thus, MARCH1 controls exhaustion of effector CD4+ T cells during allergic airway inflammation and may serve as a therapeutic target for asthma.

overall_design: WT mice were sensitized to house dust mite (HDM) by repeated oropharyngeal aspiration of HDM extract (days 0, 7-11). On day 14, donor CD4 T cells were enriched from the lung, labeled with Cell Trace Violet (CTV) and adoptively transferred into WT or KO mice. Recipient mice were then challenged with HDM extract and  at day 4 post challenge, CTV low (proliferating) donor cells were sorted from the lung for scRNA-seq.

first: Carlos

last: Castellanos

first: Satoshi

last: Ishido

first: Ansuman

last: Satpathy

first: Jeoung-Sook

last: Shin


title: A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its role in familial AML/MDS

city: Edinburgh

first: Javier

last: Caceres

address: Crewe Road

department: MRC HGU

institute: University of Edinburgh


title: CRISPR base editing of cis-regulatory elements enables target gene perturbations

city: Urbana

first: Thomas

last: Gaj

state: IL

address: 1406 W. Green St.

department: Bioengineering

institute: University of Illinois Urbana-Champaign

summary: CRISPR technology has demonstrated broad utility for controlling target gene expression. However, there remains a need for strategies capable of modulating expression via the precise editing of non-coding regulatory elements. Here we demonstrate that CRISPR base editors, a class of gene-modifying proteins capable of inducing single-base substitutions in DNA, can be harnessed to perturb target gene expression via the targeted mutagenesis of cis-acting sequences. Using the promoter region of the human huntingtin (HTT) gene as an initial target, we show that editing of the binding site for the transcription factor NF-κB led to a marked reduction in HTT gene expression. We find that these gene perturbations were persistent and specific, as a transcriptome-wide RNA-seq analysis revealed virtually no off-target effects. We further show that this base-editing platform could lower HTT in vivo, as its delivery to a mouse model of Huntington’s disease decreased HTT expression in striatal neurons, an outcome that we show also increased survival. Finally, we use this approach to target the amyloid-beta precursor protein, demonstrating that multiplexed editing of its promoter region could significantly perturb its expression, supporting the applicability of this method. These findings thus demonstrate the potential for base editors to regulate target gene expression.

overall_design: Differentially expressed gene analysis of RNA-seq data of RNA extracted from HEK293T cells transfected with a third generation base editor targeting the HTT promoter vs a non-targeting third generation base editor.

first: Colin

middle: K

last: Lim

first: Tristan

last: McCallister

first: Christian

last: Saporito-Magriña

first: Garret

last: McPheron

first: Ramya

last: Krishnan

first: M

last: Zeballos

first: Jackson

last: Powell

first: Lindsay

last: Clark

first: Pablo

last: Perez-Pinera


title: A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its role in familial AML/MDS (RNA-Seq I)

summary: To investigate the effect of DHX34 depletion on transcription and splicing, DHX34 was knocked down in HeLa cells.

overall_design: DHX34 was knocked down in HeLa cells

first: Nele

last: Hug

first: Dasa

last: Longman

first: Stuart

last: Aitken

first: Michela

last: Raab

first: Hannah

last: Armes

first: Abigail

last: Mann

first: Ana

last: Rio-Machin

first: Jude

last: Fitzgibbon

first: Kevin

last: Rouault-Pierre


title: A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its role in familial AML/MDS (RNA-Seq II)

first: Javier

last: Caceres

summary: To investigate the effect of DHX34 and UPF1 depletion on transcription and splicing, DHX34 and UPF1 were knocked down in K562 cells.


title: A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its role in familial AML/MDS (CLIP-Seq)

summary: To investigate binding of DHX34 protein to RNA, RNA IP was performed in HEK293T cells using the seCLIP protocol.

overall_design: RNA IP was performed in HEK293T