title: ASBT inhibition alleviates cholangiopathy and hepatic fibrosis development in Cyp2c70-/- mice

city: Atlanta

last: Dawson

state: GA

address: 1760 Haygood Drive

institute: Emory University

summary: RNA-seq was used to compare the liver gene differentiation between WT and Cyp2c70-/- mice fed with chow and SC-435 containing diet. We aimed to characterize the cholestatic liver phenotype in the Cyp2c70 -/- mouse and test whether ASBT inhibition reduced injury.

overall_design: Examine liver gene expression between WT and Cyp2c70-/- mice fed with chow and SC-435 containing diet.

first: Jennifer

last: Truong

first: Ajay

last: Donepudi

first: Saul

last: Karpen


title: Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [RiboSeq]

status: Public on Aug 08 2022

city: Baltimore

first: Jeff

last: Coller

address: 725 N. Wolfe St PCTB 505

country: USA

institute: Johns Hopkins University

type: Expression profiling by high throughput sequencing

summary: Oligodendrocytes are specialized cells that confer neuronal myelination. Leukodystrophies associated with oligodendrocyte and hypomyelination are known to result when a number of tRNA metabolism genes are mutated. Thus, for unknown reasons, oligodendrocytes may be hypersensitive to perturbations in tRNA biology. In this study, we survey the tRNA transcriptome in the murine oligodendrocytes cell lineage in an effort to understanding the molecular underpinning for human disease. We find that specific tRNAs are hypomodified in oligodendrocytes within or near the anticodon. This hypomodified state may be the result of differential expression of key modification enzymes during oligodendrocyte differentiation. Moreover, we observe a concomitant relationship between tRNA hypomodification and tRNA decoding potential; observing oligodendrocyte specific alterations in codon optimality-mediated mRNA decay and ribosome transit. Our results reveal that oligodendrocytes naturally maintain a delicate, hypersensitized tRNA/mRNA axis. We suggest this axis underlies disease etiology when further insult to tRNA metabolism is introduced.

overall_design: Ribosome profiling and associated RNA-Seq data (QuantM-seq) of murine Oligodendrocyte Progenitor Cells (OPCs) (2 replicates each) and Oligodendrocytes (OLs) (2 replicates each)

first: Sophie

last: Martin

first: Kevin

middle: C

last: Allan

first: Otis

last: Pinkard

first: Thomas

last: Sweet

first: Paul

middle: J

last: Tesar


title: Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [DecaySeq]

overall_design: Metabolic labeling and decay RNA sequencing data (5-EU decay-seq) of murine Oligodendrocyte Progenitor Cells (OPCs) (3 replicates) and Oligodendrocytes (OLs) (2 replicates)

last: C’Allan


title: Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design: Refer to individual Series


title: Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [QuantMseq]

overall_design: tRNA sequencing data (QuantM-seq) of murine Oligodendrocyte Progenitor Cells (OPCs) (3 replicates). Oligodendrocytes (OLs) (2 replicates) and Astrocytes (Astros) (2 replicates)


title: SETMAR regulates gene expression and alternative splicing

city: Indianapolis

first: Evan

last: Cornett

address: 980 West Walnut Street

institute: Indiana University

summary: Transcriptomic profiling of WT and SETMAR KO HEK293T cells.

overall_design: To determine how SETMAR impacts the transcriptome, CRISPR/Cas9 was used to generate HEK293T SETMAR KO cells. RNAseq was performed on two KO clones and WT cells, four replicates for each. Differential expression analysis revealed 163 genes with altered gene expression in both clones. Alternative splicing analysis revealed 255 shared alternative splicing events. Collectively, our results support a model in which SETMAR likely impacts AS through TIR-specific DNA-binding and lysine methyltransferase activities, consistent with a role in development of simian primates.

first: Millie

middle: M

last: Georgiadis

first: Alison

last: Bates

first: Joceylne

last: Hanquier


title: A spatiotemporal regulatory network for steroidogenesis of human fetal adrenal glands and gonads

city: Nanning

first: wang

last: yifu

state: Guangxi

address: Shuangyong Road 22

department: Center for Genomic and Personalized Medicine

country: China

institute: guangxi medical univercity

summary: Human fetal adrenal glands are huge endocrine organ, produce prodigious quantities of dehydroepiandrosterone and its sulfate (DHEA/DHEAS), which is the most prominent precursor for steroid hormones, adrenal gonads dysfunction leads to states of virilization or effemination. However, for a long time the function of fetal adrenal in initial sex differentiation is unclear. Herein, we draw out a single-cell transcriptional landscape of human fetal adrenals and gonad from 6 to 14 gestational weeks (GW). We found that the adrenal glands begin to express CYP17A1 steroid-related enzyme much early than testis, subsequent testis steroid express pattern support de novo or halfway testosterone synthesis. Excepted steroidogenic cell, notably, the immune cells or neurocyte shows steroid metabolism or regulation ability, such as CD5L+ macrophage interacted with steroidogenic cell and SRD5A1+ AKR1C2+ chromaffin cells synthesis active testosterone DHT through backdoor pathway. Sex different were found at adrenal glands and gonad development: there is a small HSD3B2 peak occurs only in female adrenal glands around 10-12 GW within the time window of sex differentiation. SST expression levels or SST+ cells quantity in adrenal glands and gonads are different in two gender. Our research indicates that a sex different in spatial and temporal disparities steroidogenic regulatory networks in adrenal glands and gonads, facilitating further exploration of development and physiology of human adrenal glands.

overall_design: Adrenal and gonad samples from 6-14 GW human fetuses were used for single cell RNA sequencing by 10X Genomics

first: Yifu

last: Wang

first: Bingqian

last: Guo

first: Yajie

first: Nana

last: Qi

first: Yufang

last: Lv

first: Yu

last: Ye

first: Yan

last: Huang

first: Xinyang

last: Long

first: Hongfei

last: Chen

first: Cheng

last: Su

first: Liying

last: Zhang

first: Qingyun

first: Minxi

last: Li

first: Jingling

last: Liao

first: Yunkun

last: Yan

first: Xingning

last: Mao

first: Yanyu

last: Zeng

first: Jinghang

last: Jiang

first: Zhongyuan

first: Yi

first: Shuai

last: Gao

first: Jiwen

last: Cheng

first: Yonghua

first: Zengnan

last: Mo


title: Dual ontogeny of disease-associated microglia and disease inflammatory macrophages in aging and neurodegeneration

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Mice brain at different age were digested and cell suspension were prepared. Cells were stained using anti-CD45, F4/80, CD11b and Ly6C and sorted using an cell sorter BD ARIA. Macrophages were then prepared in order to perform single cell RNA-Seq

overall_design: Brain macrophage CD45+F4/80+CD11b+Ly6C- heterogeneity was determined by single cell RNA-Seq analysis

first: Aymeric

last: Silvin

first: Josephine

last: Lum

first: Shanshan

last: Howland

first: Florent

last: Ginhoux

first: Jinmiao


title: Diverse development potency and metabolic shape of extended pluripotency are faithfully transferred to somatic cells via cell fusion reprogramming

status: Public on Aug 07 2022

city: Seoul

first: Jae Hoon

last: Song

address: 201 Songpa-daero, Songpa-gu

country: South Korea

institute: ENCell Co., Ltd.

summary: Extended pluripotent stem cells (EPSCs) are a novel cell type derived from 8-cell stage embryo or conversion of pluripotent stem cells using a chemical cocktail that blocks the cell fate decision. Previous studies have defined various aspects of EPSCs including dual differentiational potency to both extraembryonic and embryonic lineages, their ability to directly transfer extended pluripotency to differentiated somatic cells by cell fusion remains unelucidated. Here, we sought to determine whether somatic cells could be reprogrammed and obtain extended pluripotency. In this study, newly derived EPSCs are fused with neural stem cells, which is somatic stem cells, by polyethylene glycol (PEG)-mediated method. The resulting hybrid cells exhibited pluripotential properties with upregulated EPSC-specific genes. Also, hybrid cells contributed to the embryonic and extraembryonic lineages in vivo and in vitro. RNA-sequencing analysis confirmed that the global gene expression pattern of hybrid cells are similar to EPSC while there is no expression of NSC markers, indicating complete erasure of somatic memory after fusion reprogramming. Lastly, EPSCs and hybrids exhibited a bivalent energy metabolism phenotype or more active oxidative phosphorylation (OXPHOS) and glycolysis than NSCs. In conclusion, the extended pluripotency of EPSCs could be transferred to somatic cells through fusion-induced reprogramming.

overall_design: Global gene expression pattern reprogramming to the state of EPSCs after cell fusion has been verified by RNA-seq in EPSC, ESC, NSC, and hybrid cell.

first: Jae

middle: H

first: Joonhyuk

last: Choi

first: Yean

last: Hong

first: Hyeonwoo

last: La

first: Tae

middle: K

first: Kwonho

first: Jeong

middle: T

last: Do


title: ER, mitochondria and ISR regulation by mt-HSP70 and ATF5 upon procollagen misfolding (P5 parietal bone)

city: Bethesda

first: Sergey

last: Leikin

state: Maryland

department: NICHD

institute: National Institutes of Health

summary: We used single cell RNA sequencing (scRNA-seq) to identify parietal osteoblast cell stress response pathway to misfolding of type I procollagen with Gly610->Cys substitution in the triple helical region of alpha2(I) chain.

overall_design: Parietal bone cells were isolated as described in Gorrell et al, Adv Sci, 2022

first: Laura

last: Gorrell


title: Gene expression profile of E15.5 Pantr2 knockout dorsal telencephalon

first: Jonathan

middle: Joseph

last: Augustin

state: MD

address: 733 N. Broadway Rm#332

institute: Johns Hopkins Medical Institute

summary: We used single nuclei RNA sequencing to discover changes in the developmental trajectory of differentiating neural precusors in the developing murine cortex

overall_design: The dorsal telencephalon of wildtype and Pantr2 knockout mice were dissected and nuclei were isolated and used for snRNA-seq.

first: Thanh

last: Hoang

first: Loyal

middle: A

last: Goff


title: Gene expression profiling of CD244+CXCR6+ C2 iNKT cell subet and CD244-CXCR6+ C1 iNKT cell subset

city: Suita

first: TAISAKU

last: OGAWA

state: Osaka

address: 6-2-3 Furuedai

country: Japan

institute: RIKEN

summary: We identified a novel subset of iNKT cells, C2 iNKT cells, that circulate in the periphery. Correspondingly, we characterized the tissue-resident iNKT cell subset, C1 iNKT cells. The development and terminal maturation of C2 iNKT cells completely depended on the thymic epithelial IL-15 niche, whereas C1 iNKT cells were regulated also by local IL-15 niches in peripheral tissues. C2 iNKT cells expressed high levels of genes related to cytotoxicity and exhibited more NK cell-like features. Functionally, C2 iNKT cells regulated self-antigen expression for immune tolerance in the thymus and mediated cancer immunosurveillance in the periphery.

overall_design: Examination one hundred of each subset of iNKT cells freshly sorted from thymus and lung of mice at 6 weeks

first: Guangwei

last: Cui

first: Koichi

last: Ikuta

first: Taisaku

last: Ogawa

first: Katsuyuki

last: Shiroguchi


title: Transcriptome response to anti-hormonals in Esr1 and CYP19A1 genetically engineered mouse models of breast cancer risk during reproductive senescence

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

institute: Dankook University

summary: Reproductive senescence is an age-associated process in which reproductive capacity is reduced. In female mice this is associated with loss of oocytes and a corresponding reduction in ovarian estrogen production. Normal mammary gland development and function is linked to estrogen stimulation. In this study we utilize two genetically engineered mouse models of breast cancer risk, one with mammary-targeted conditional expression of  Esr1, the RNA that encodes Estrogen Receptor alpha, and one with mammary-targeted conditional expression of  CYP19A1, the RNA that encodes Aromatase, the enzyme that is responsible for estrogen synthesis from androgens to determine how reproductive senescence impacts the transcriptional response to commonly used anti-hormonals employed  for breast cancer prevention, tamoxifen and letrozole. The goals of the study are, first, to test the extent to which each of these anti-hormonals alter the mammary gland transcriptome in mice undergoing reproductive senescence and, second, determine if the response is the same or different in the presence of Esr1 as compared to CYP19A1 transgene expression targeted to mammary epithelial cells. The objectives are to identify specific genes that are significantly differentially expressed genes within each model between treatment conditions control, tamoxifen and letrozole as well as between models under each of these conditions. Transcriptome comparisons between 18- and 20-month-old mice are used to identify differences between the two models as ovarian function diminishes during reproductive senescence. Transcriptome comparisons between cohorts of 20-month-old mice that received no anti-hormonal or a two-month-exposure to tamoxifen or letrozole beginning at age 18 months are used to identify similarities and differences between the two anti-hormonal treatments as well as similarities and differences between models.

overall_design:
To investigate how the mouse mammary gland transcriptome is differentially impacted by  Esr1 as compared to  CYP19A1 over-expression during reproductive senescence and to determine if there is a differential impact of tamoxifen or letrozole exposure on the transcriptome with these two different breast cancer risk factors.
Comparative gene expression profiling analysis of RNA-seq data from mouse mammary gland tissue from 18 and 20 month old Esr1 and  CYP19A1 mice. Twenty month old mice were studied in the absence and presence of a 2-month exposure to tamoxifen or letrozole.

first: Priscilla

last: Furth


title: LAMP-5 is an essential inflammatory-signaling regulator and novel immunotherapy target for MLL-rearranged acute leukemia

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: In this study, we demonstrate that LAMP5 is essential for proliferation of MLL-rearranged leukemias. Through gene expression changes occurring upon LAMP5 knockdown, we show that LAMP5 maintains an important balance between Type I interferon and NFkB signaling, and that knockdown biases MLL leukemia cells towards activation of the interferon pathway

overall_design: Differentially expressed genes in MLL-fusion leukemia by RNAseq upon LAMP5 knockdown

first: Gabriel

last: Gracia-Maldonado

first: Jason

last: Clark

first: Matthew

last: Burwinkel

first: Mark

last: Wunderlich

first: Brenay

last: Greenslade

first: Dario

last: Leone

first: Phillippe

last: Pierre

first: Evelina

last: Gatti

first: Lynn

last: Lee

first: Ashish

middle: R

last: Kumar


title: ER, mitochondria and ISR regulation by mt-HSP70 and ATF5 upon procollagen misfolding (E18.5 femur and tibia)

first: Sergey

last: Leikin

summary: We used single cell RNA sequencing (scRNA-seq) to identify femur and tibia osteoblast cell stress response pathway to misfolding of type I procollagen with Gly610->Cys substitution in the triple helical region of alpha2(I) chain.

overall_design: Femur and tibia cells were isolated from E18.5 embryos as described in Gorrell et al, Adv Sci, 2022

first: Laura

last: Gorrell


title: BRCAness and Merkel cell carcinoma: Comprehensive molecular study of 35 cases and meta-analysis of the literature

status: Public on Aug 06 2022

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Merkel cell carcinoma (MCC) is a rare and aggressive cutaneous neuroendocrine cancer. Management of advanced MCC is mainly based on immune-checkpoint inhibitors (ICI). The high failure rate (up to 75%) warrants investigation of new therapeutic targets. The recent identification of BRCA1 or BRCA2 (BRCA1/2) mutations in some MCC raises the issue of the use of poly-(ADP-Ribose)-polymerase inhibitors (PARPi) in selected advanced cases.  The main objective of our study is to determine the accurate frequency of BRCA1/2 pathogenic variants. We studied a novel series of 35 MCC and performed a meta-analysis of BRCA1/2 variants of published cases in the literature.   In our series, we detected only one BRCA2 pathogenic variant (nonsense mutation; ENIGMA class 5) and one BRCA2 variant of unknown significance (VUS). The low frequency of BRCA1/2 pathogenic variants in our series of MCC (3%) was confirmed by the meta-analysis of BRCA1/2 variants of the literature. Among the 204 MCC studied for molecular alterations of BRCA1/2, only two BRCA1 pathogenic nonsense mutations were identified (1%), while the vast majority of BRCA1/2 variants were missense mutations classified as VUS.   BRCA1/2 pathogenic variants are uncommon in MCC. However, in BRCA-mutated-MCC, PARPi might be a valuable therapeutic option requiring validation by clinical trials.

overall_design: Merkel cell carcinoma

first: Bérengère

last: Dadone-Montaudié

first: Florence

last: Pedeutour

first: Valérie

last: Kubiniek

last: Fabas

first: Alexandre

last: Gaubert

last: Kervarrec

first: Henri

last: Montaudié

first: Fanny

last: Burel-Vandenbos

first: Nathalie

last: Cardot-Leccia

first: Ilaria

last: Di Mauro

first: Anne

last: Tallet


title: The network Regulation of Yiqi Jiedu Formulae against Cerebral Ischemia Based on Central-periphery Inflammation System

city: Beijing

first: Liming

last: Liu

address: 16 Dongzhimen nei south street, Dongcheng District, Beijing, China

institute: Institute of Chinese Materia Medica，China Academy of Chinese Medical Sciences

summary:
Connections between inflammation and gene-network regulation are suggested important in understanding the therapeutic target of stroke and in illuminating underlying mechanism. However, studies on the establishment of network relating with inflammation during stroke process are still in their early stages.
We selected the inflammation genes from the whole mRNA expression results.   And after a series of analysis, we found the promising target genes of Yiqi Jiedu formulae used in clinic for stroke, which might give an explanation to the common characteristic about TCM treatment called PK-PD inconsistent.

overall_design: In this study, we chosen 6 h after MCAO operation. The rats were divided into 3 groups: 6h sham group, 6h vehicle control group, 6h YJ groups (25mg•kg−1). After MCAO operation, the animals were sacrificed to obtain brain, spleen and blood respectively. RNAs of the three parts of each rat were extracted with Qiagen RNA kit. Total RNA was reverse transcribed, amplified, labelled and hybridized to Rat Genome 1.0 arrays (Affymetrix).

first: Sihuai

last: Xiong

first: Yuhao

last: Dai

first: Wenjie

last: Wu

first: Chen

first: Bingjie

last: Cai

first: Shaojing

last: Li


title: Sonic hedgehog Activation Restores Interneurons and Cognitive Function in Newborns with Intraventricular Hemorrhage

city: Bronx

first: XUSHENG

last: ZHANG

state: NY

address: 1300 Morris Park Ave

department: GENETICS

institute: ALBERT EINSTEIN COLLEGE OF MEDICINE

summary: We hypothesized that the occurrence of IVH would reduce interneuron neurogenesis in the medial ganglionic eminence and diminish the population of parvalbumin+ and somatostatin+ cortical interneurons. Since Sonic Hedgehog promotes the production of cortical interneurons, we also postulated that the activation of Sonic Hedgehog signaling might restore neurogenesis, cortical interneuron population, and neurobehavioral function in premature newborns with IVH.

overall_design: We compared premature newborns with and without IVH for intraneuronal progenitors, cortical interneurons, transcription factors regulating neurogenesis, single-cell transcriptome of medial ganglionic eminence,  and neurobehavioral functions. We next compared Ad-GFP and Ad-Shh treated kits with IVH for these paramters.

first: Bokun

last: Cheng

first: Deep

last: Sharma

first: Ajeet

last: Kumar

first: Hardik

last: Sheth

first: Alex

last: Agyemang

first: Michael

last: Aschner

first: Xusheng

last: Zhang

first: Praveen

last: Ballabh


title: Tracking gene expression changes following aging of C. elegans

first: An Na

last: Kang

institute: Seoul National University

summary:
Track down the differential gene expressions between young and aged C. elegans to build a aging metabolism map
Track down the differential gene expressions between young and aged C. elegans to build a aging metabolism map

overall_design: C. elegans exposed to E. coli OP50 were harvested at 6d and 12d to compare the changed gene expressions

first: An

middle: N

first: Younghoon

last: Kim


title: Dendritic cells from mice with an uromodulin mutation demonstrate changes in gene expression resulting in increased migration and efferocytosis capability

city: Little Rock

first: Annjanette

last: Stone

email: annjanettemc@yahoo.com, astone@uams.edu

state: AR

address: 4300 West 7th Street

department: Research

institute: CAVHS

summary:
Introduction: The effects of Uromodulin on the innate immune system remain uncertain. Mice with a cysteine to phenylalanine mutation (C105F) in the UMOD gene homologous to a pathogenic human mutation demonstrate high levels of circulating uromodulin following ischemia reperfusion kidney injury, increased markers of immune tolerance and improved kidney repair. We hypothesized that this may occur through interaction of circulating uromodulin with dendritic cells.
Materials and Methods: Dendritic cells were isolated from WT and C105F mutant mice and used to compare gene expression using RNA sequencing. In vitro motility and efferocytosis assays were used to verify phenotypic changes predicted from affected pathways.
Results: RNA sequencing demonstrated increased expression of scavenger receptor and motility associated genes. In vitro assays demonstrated that mutant uromodulin increased activation of the NF-kB pathway compared with WT protein and that mutant dendritic cells had increased migration and efferocytosis compared with WT cells.
Discussion/Conclusion: Dendritic cells from mutant C105F mice display gene expression and phenotypic changes associated with increased scavenger receptor expression, motility and efferocytosis. These results suggest a possible mechanism of DC regulation by circulating uromodulin that may affect tissue repair following injury.

overall_design: To understand the interaction between dendritic cells and elevated levels of circulating uromodulin following ischemia reperfusion kidney injury from mice with a cysteine to phenylalanine mutation (C105F) in the UMOD gene, and their role in increased immune tolerance and improved kidney repair.

first: Matthew

middle: D

last: Plotkin

first: Joshua

last: Williams

first: Weleetka

last: Carter


title: Single Cell RNAseq analysis of mouse NASH liver cells

city: Palo Alto

first: Laetitia

last: Coassolo

state: CA

address: 300 Pasteur Drive

department: Pathology

institute: Stanford University

summary: The liver is undergoing major rearrangements during the development of non-alcoholic steatohepatitis (NASH), from steatosis to severe lipid accumulation, inflammation and fibrosis. The mechanisms for this transition and the molecular changes preceding NASH are not fully understood. Here, we perform a single-cell RNA sequencing survey of 13,240 mouse liver cells during the development of non-alcoholic fatty liver disease. By measuring the entire transcriptome on a single-cell level from mice in the early stages of NASH development, we recognize known hepatocyte cell populations, Kupffer cells and stellate cells, as well as distinct gene expression changes in hepatocytes. We also reveal high hepatocyte heterogeneity in steatosis markers which projects a lipogenic trajectory of known and novel steatosis-associated genes. Importantly, we uncover distinct clusters of hepatocytes characterized by high or low Srebp1c expression with unique molecular signatures of lipogenesis. These results identify a novel regulatory pathway for lipogenesis in the liver that contributes to NASH progression.

overall_design: we compared the gene expression profile at single-cell level of diet-induced NASH mouse liver against chow mouse liver.

first: Yunshin

last: Jung

first: Wenyu

last: Zhou

first: Meng

last: Zhao

first: Katrin

last: Svensson


title: Establishment of radioresistant MCF-7 breast cancer cell line

last: Huo

address: 27 Taiping Rd

institute: Beijing Institute of biotechnology

summary: To explore elements contributing to radioresistance in breast cancer, we established radioresistant  human breast cancer cell line MCF-7.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF-7 IR-sensitive cell lines and MCF-7 IR-resistance cell lines.

first: Xiaojie

last: Xu


title: Progressive heterogeneity of cancer-initiating cells revealed by quantitative clonal analysis

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

summary: Different cellular compartments within a tissue present distinct cancer-initiating capacity. Current approach to dissect cellular heterogeneity in cancer-initiating capacity requires a well-understood tissue lineage hierarchy and highly-specific promoters, which are lacking for most tissues. Here, utilizing a genetic tool called Mosaic Analysis with Double Markers (MADM), we induced scattered GFP-labeled single mutant cells in a broad category of cell types and quantitatively traced their expansion at clonal level, to pinpoint cells susceptible for cancer initiation within under-defined tissues. We dissected the heterogeneous cancer-initiating capacity of fallopian tube Pax8+ cells, which are thought to be the origin for high-grade serous ovarian cancer. We revealed that only a rare primitive subset enriched in the fimbriae can fuel ovarian cancer initiation, and oncogenic mutations exaggerate their intrinsic potential and bias their differentiation for further progression. Collectively, we demonstrated a scheme to dissect cellular heterogeneity in cancer-initiating capacity in tissues lacking established lineage hierarchy.

overall_design: To compare the expression profile of small clones and large clones, from each MADM-wildtype mouse at 4 weeks old (n=6), 200 cells from small clones were collected and pooled, and another 200 cells from large clones were collected and pooled. The samples were then subjected to cDNA library construction, followed by amplifications and sequencing.

first: Jianhao

last: Zeng

first: Astrid

last: Alvarez-Yela

first: Hui

last: Zong


title: BMAL1-TTK-H2Bub1 loop deficiency contributes to impaired BM-MSC-mediated bone formation in senile osteoporosis

city: Shenzhen

first: Peitao

address: No.3025, Shennan Middle Street

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

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed multiomic high-throughput sequencing to recapitulated the BMAL1-H2Bub1 loop in mesenchymal stem cells osteogenesis. We used lentiviruses to diminish RNF40 and WAC, which are parts of the obligate complex and monoubiquitinated histone H2B, in MSCs, and analysed the H2Bub1 and PolII CUT&Tag-seq.

overall_design: Examination of the H2Bub and PolII binding to genome in MSCs

first: Huiyong

last: Shen

first: Jinteng

last: Li


title: Transcriptomics of mouse hepatocyte maturation and human hepatic reprogramming

city: Wuhan

first: Shaofeng

last: Lin

address: Luoyu Road 1037

institute: Huazhong University of Science and Technology

summary:
Here, we chemically induced liver progenitor cells (CLiPs) from mouse hepatocytes using a previously established protocol. To identify central protein kinases (PKs) that potentially promote the maturation of lpc-Hep cells, we profiled the transcriptomes and phosphoproteomes of freshly isolated primary mouse hepatocytes (MHs) and ALBUMIN+ hepatocytes (CLiP-Heps) cells. Based on the algorithm developed by us and experiment verification, we validated three PKs that promote mouse hepatocyte maturation.
Then, we use RNA sequencing technology to identify potential regulators during hepatic reprogramming with samples from HDFs 2.25 days (FHH-2.25d) and 5 days (FHH-5d) after FOXA3, HNF1A, and HNF4A (FHH) transduction, as well as HDFs transduced with GFP for 2.25 days (GFP) as the control group. After combined analysis with phosphoproteomic data with the algorithm and experiment verification, we identified 2 PKs that may be involved in hepatic reprogramming regulation. One of the five potential regulator candidates is PIM1, which can promote the progress remarkably with overexpression. Therefore, we next perform another RNA-seq to drive the molecular mechanisms under undergoing the regulation by PIM1. Finally, we revealed that cell cycle and ferroptosis pathways are involved in the regulation via PIM1.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
For human hepatic reprogramming, mRNA profiles of HDFs 2.25 days (FHH-2.25d) and 5 days (FHH-5d) after FHH transduction and GFP cells, as well as HDFs undergoing hepatic conversion with PIM1 (PIM1-FHH) or GFP (GFP-FHH) overexpression.
For mouse hepatocyte maturation, mRNA profiles of freshly isolated mouse primary hepatocytes (MH) and CLiP-Hep cells.

first: Pengyu

last: Huang

first: Yu

last: Xue

first: Yangyang

last: Yuan

first: Xuran

last: Zhuang


title: RNA-seq in SNRPD3 G96V mutation knock-in cell clones.

first: Atsushi

last: Kumanogoh

address: 2-2 Yamadaoka

institute: Osaka University

summary: Aberrant RNA splicing may contribute to carcinogenesis. Here, we focused on the G96V mutation in SNRPD3, one of the splicing factors. We found that RNA splicing is altered under hypoxia in cell lines in which the gene mutation is knocked-in.

overall_design: SNRPD3 G96V mutation knock-in cell clones were established from HEK293T cell line. RNA-seq analysis was performed on poly(A)-purified mRNA.

first: Shingo

last: Satoh

first: Kotaro

last: Miyake


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: Compare the changes in related signaling pathways before and after lncRNA-BTX knockout.

first: Xiaoqing

first: Xuetao


title: Endoribonuclease activity in hepatitis C virus-infected Huh7.5.1 cells

city: Aurora

first: Daphne

last: Cooper

state: CO

department: Department of Microbiology

institute: University of Colorado

summary: We used 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing to identify and endoribonuclease cleavage sites in host and viral RNAs during HCV infection of Huh7.5.1 cells

overall_design: To make cDNA libraries, we exploited the 2’, 3’-cyclic phosphate at the end of RNA fragments produced by RNase L and other metal-ion-independent endoribonucleases. Using Arabidopsis thaliana tRNA ligase, RNA fragments with 2’, 3’-cyclic phosphates were covalently attached to defined RNA linkers containing an 8-base long unique molecular identifier (UMI) sequence. Libraries prepared in this manner contain cDNA derived from RNA fragments with 2', 3'-cyclic phosphates. The UMI sequence allows for detailed quantitation. We applied these methods to total RNA from Huh7.5.1 cells infected by hepatitis C virus 2a (JFH1).

first: Hugo

last: Rosen

first: Robert

last: Silverman

first: Jay

last: Hesselberth

first: David

last: Barton


title: Multi-omic analysis of cell-of-origin and epigenomic state in pediatric H3K27M gliomas (multiome)

status: Public on Aug 05 2022

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

summary: Canonical (H3.1/H3.2) and noncanonical (H3.3) histone 3 K27M-mutant gliomas have unique spatiotemporal distributions, partner alterations, and molecular profiles. The contribution of the cell-of-origin to these differences has been challenging to uncouple from the oncogenic reprogramming induced by the mutation. Here, we perform an integrated analysis of 116 tumors, including single-cell transcriptome and chromatin accessibility, 3D chromatin architecture and epigenomic profiles, and show that K27M-mutant gliomas faithfully maintain chromatin configuration at developmental genes consistent with anatomically distinct oligodendrocyte-precursor-like cells (OPC). H3.3K27M thalamic gliomas map to prosomere 2-derived lineages. In turn, H3.1K27M ACVR1-mutant pontine gliomas uniformly mirror early ventral NKX6-1+/SHH-dependent brainstem OPCs, while H3.3K27M gliomas frequently resemble dorsal PAX3+/BMP-dependent progenitors. Our data suggest a context-specific vulnerability in H3.1K27M-mutant SHH-dependent ventral OPCs, which rely on acquisition of ACVR1 mutations to drive aberrant BMP signaling required for oncogenesis. The unifying action of K27M mutations is to restrict H3K27me3 at PRC2 landing sites, while other epigenetic changes are mainly contingent on the cell-of-origin chromatin state and cycling rate.

overall_design:
10 patient tumors analysed by scMultiome (ATAC and gene expression)
-------------------------------------------
Authors state "patient privacy concerns and have been deposited to EGA  instead"

first: Selin

last: Jessa

first: Abdulshakour

last: Mohammadnia

first: Ashot

middle: S

last: Harutyunyan

first: Maud

last: Hulswit

first: Srinidhi

last: Varadharajan

first: Hussein

last: Lakkis

first: Nisha

last: Kabir

first: Zahedeh

last: Bashardanesh

first: Steven

last: Hébert

first: Damien

last: Faury

first: Maria

last: Vladoiu

first: Samantha

last: Worme

first: Marie

last: Coutelier

first: Brian

last: Krug

first: Augusto

middle: F

last: Andrade

first: Manav

last: Pathania

first: Andrea

last: Bajic

first: Alexander

middle: G

last: Weil

first: Benjamin

last: Ellezam

first: Jeffrey

last: Atkinson

first: Roy

last: Dudley

first: Jean-Pierre

last: Farmer

first: Sebastien

last: Perreault

last: Garcia

first: Valerie

last: Larouche

first: Mathieu

last: Blanchette

first: Livia

last: Garzia

first: Aparna

last: Bhaduri

first: Keith

last: Ligon

first: Pratiti

last: Bandopadhayay

first: Michael

last: Taylor

first: Stephen

last: Mack

first: Nada

last: Jabado


title: Angiogenic stem cell delivery platform to augment post-infarction neovasculature and reverse ventricular remodeling

city: Stanford

first: Albert

middle: James

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

summary: This study investigates the influence of a bi-level (endothelial progenitor cell + smooth muscle cell) , human cell sheet on ischemic myocardium.

overall_design: Eight-week-old Female athymic rats were subjected to either sham operation or complete proximal left anterior descending artery ligation (myocardial infarction). Animals subjected to infarction received either no treatment or application of a bi-level cell sheet over the infarct region. One week after surgery, hearts were explanted and separate tissue samples were collected from the infarct (I), border zone (BZ) and remote (R) regions of the left ventricle and snap frozen for RNA extraction and sequencing.

first: Yasuhiro

last: Shudo


title: Multi-omic analysis of cell-of-origin and epigenomic state in pediatric H3K27M gliomas (scATAC-Seq)

first: Claudia

last: Kleinman

overall_design:
4 patient tumors analysed by scATAC-seq.
-------------------------------------------
Authors state "patient privacy concerns and have been deposited to EGA  instead"

first: Selin

last: Jessa

first: Abdulshakour

last: Mohammadnia

first: Ashot

last: Harutyunyan

first: Maud

last: Hulswit

first: Srinidhi

last: Varadharajan

first: Hussein

last: Lakkis

first: Nisha

last: Kabir

first: Zahedeh

last: Bashardanesh

first: Steven

last: Hébert

first: Damien

last: Faury

first: Maria

middle: C

last: Vladoiu

first: Samantha

last: Worme

first: Marie

last: Coutelier

first: Brian

last: Krug

first: Augusto

last: Andrade

first: Manav

last: Pathania

first: Andrea

last: Bajic

first: Alexander

last: Weil

last: Ellezam


title: CDK9 inhibition with AZD4573 in DLBCL

city: Duarte

first: Alexey

last: Danilov

state: California

address: 1500 East Duarte Road

department: Toni Stephenson Lymphoma Center

institute: City of Hope

summary: We report the effects of CDK9 inhibition (AZD4573) on the epigenetic landscape in Diffuse Large B-cell Lymphoma (DLBCL). This study utilized chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-seq) to assess genome-wide post-translational histone modifications (H3K27ac and H3K4me3) and DNA occupancy of transcriptional proteins (RNAPII and BRD4) in two DLBCL cell lines, OCI-LY3 and VAL, treated with the CDK9 inhibitor AZD4573 (30 nM). Cells were treated for 0, 3 and 8 hours prior to harvest. After 8-hour exposure, drug was washed out and cells were harvested after 24 hours. We found that CDK9 inhibition led to an increase in RNAPII promoter proximal pausing, and increase in BRD4 enrichment on the promoter, and a decrease in promoter H3K4me3. Treatment induced reprograming of the super-enhancer landscape including loss of super-enhancers next to genes in oncogenic pathways.

overall_design: Two DLBCL cell lines, OCI-LY3 (GC-DLBCL) and VAL (ABC-DLBCL), were treated with AZD4573 (30 nM) for 0, 3 and 8 hours prior to harvest. After 8-hour exposure, drug was washed out and cells were harvested after 24 hours. Samples were subjected to ChIP-sequencing. OCI-LY3 and VAL cells were immunoprecipitated for H3K4me3 and H3K27ac, and OCI-LY3 cells were additionally immunoprecipitated for RBP1 and BRD4. As controls, OCI-LY3 and VAL cells were immunoprecipitated for IgG, and samples of input DNA (no immunoprecipitation) were additionally included.

first: Nur

last: Bruss

first: Elana

last: Thieme

first: Zheng

last: Xia


title: Chromobox homolog 4 overexpression inhibits TNF-α-induced matrix catabolism and senescence by suppressing activation of the NF-κB signaling pathway in nucleus pulposus cells

city: Guangzhou

first: Yang

middle: yang

last: Zhang

state: Guangdong

address: 107 Yanjiang West Road

institute: Sun Yat Sen Memorial Hospital

summary: Chromobox homolog protein 4 (CBX4) exhibits anti-inflammatory effects and shows promising therapeutic potential. Thus, in the present study, we explore the role of CBX4 in IDD.

overall_design: For RNA sequencing, total RNA was extracted using Trizol from 4 groups of rat NP cells, i.e., control cells, CBX4-overexpressing cells, TNF-α-stimulated cells, and CBX4-overexpressing cells stimulated with TNF-α.

first: Yangyang

first: Wei

last: Ye


title: mRNA transcriptome analysis reveals key mRNAs and pathways on adipocytes

first: yanru

last: duan

state: Beijing

address: Beijing, Chaoyang

institute: Capital Medical University

summary: Our research is helpful to understand the physiological and pathological level changes caused by Chronic intermittent hypoxia

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of adipocytes at twoconditions.
In this study, the control group and the model group subjected to mRNA sequencing.

first: Duan

last: Yanru


title: Effect of Mycobacterial EST12 on gene expression  of RAW264.7 cells

city: wuhan

first: Jian

last: Wu

address: donghu road

institute: wuhan university

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Mouse RAW264.7 cells were stimulated with 2 uM purfied recombinant Mycobacterial EST12 protein for 0 h or 3 h


title: Target genes of transcription factor Myc regulated by Mycobacterium tuberculosis EST12

overall_design: RAW264.7 cells (1×107) were stimulated with 2 μM EST12 for 1 h, then treated or untreated RAW264.7 cells were collected and sent to DIATRE Biotechnology (Shanghai, China) in dry ice for CUT&Tag sequencing. Briefly, in this method, a highly active Tn5 transposase is fused to Protein A, and a library-building linker primer is loaded to form a pA-Tn5 transposition complex. Under the guidance of Myc antibody (10828-1-AP, Proteintech, China), the pA-Tn5 transposition complex can target and cut the DNA sequence near Myc-bound region.

first: Xiaolian


title: Anti-inflammatory effects of differential molecular weight hyaluronic acids on UVB-induced calprotectin-mediated keratinocyte inflammation

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

summary:
Background: The biological functions of HA are related to its molecular weight and binding to its receptor TLR4 or CD44. Recent studies have shown that LMW-HA exhibits proinflammatory effects, while HMW-HA functions as an anti-inflammatory factor. UVB-induced epidermal inflammation is mainly mediated by endogenous molecules, such as DAMPs, that cause severe skin damage by activating TLR signaling pathways.  Objective: Since both LMW- and HMW-HA have inhibitory functions on TLR-mediated macrophage inflammation, HA is assumed to suppress UVB-induced DAMP-mediated inflammation in the skin. In this study, both uLMW-HA and HMW-HA were found to inhibit UVB-induced keratinocyte inflammation.
Methods: To elucidate whether HAs have anti-inflammatory effects on inflammation induced by UVB exposure, we performed whole transcriptome analysis in  HaCaT cells treated with or without HAs after UVB exposure.
Results: UV radiation induced upregulation or downregulation of genes (FC>1.2 or FC<0.8, q<0.05) were obtained. We analyzed network of these genes with Ingenuity Pathway analysis using information collected from databases on protein interactions. IL-6 was detected as an upstream factor of HA suppressing UV-radiation effects on HaCaT cells. Canonical pathway analysis also shows uLMW-HA downregulated NF-κB, which is located downstream of TLR4 signaling pathway, although HMW-HA did not show downregulation of NF-κB signaling pathway.
Conclusions:  Both uLMW-HA and HMW-HA were found to inhibit UVB-induced keratinocyte inflammation.

overall_design: RNAseq analysis of HaCaT cells treated with or without HAs after UVB exposure.

first: Liuying

last: Hu

first: Satoshi

last: Nomura

first: Yasunari

last: Sato

first: Kyoko

last: Takagi

first: Tsuyoshi

last: Ishii

last: Honma

first: Kenji

last: Watanabe

first: Jun

last: Muto


title: The effect of 5-aminolevulinic acid on canine peripheral blood mononuclear cells

summary: 5-aminolevulinic acid (ALA) is one of the natural amino acids and a product of the first heme synthesis pathway in mitochondria. Recently, a supplement containing ALA is available in Japan and used for the purpose of the enhancement of ATP synthesis via mitochondrial activity. In humans, the immunomodulatory effect of ALA has attracted attention as a new function of ALA, and its application to cancer, inflammatory disease, and autoimmune diseases are being investigated. In the present study, to evaluate the effects of ALA on canine immunity, we performed in vitro studies using peripheral blood mononuclear cells (PBMC) from healthy dogs. Heme oxygenase-1 protein was expressed in Madin-Darby Canine Kidney cells and PBMCs treated with 5-ALA and ferrous sodium citrate (SFC), which showed that ALA works in dogs as well as humans. When PBMCs were stimulated with concanavalin A (ConA), the addition of ALA resulted in a significant increase in interferon-gamma (IFN-γ) produced by ConA-stimulated PBMCs. A comprehensive genetic alteration using next-generation RNA sequences (RNA-seq) was performed. From the result of RNA-seq, ALA enhanced the gene expression of T cell immunity including Th1, Th2, and Th17 subsets. In particular, the IL-17 signaling pathway was significantly upregulated. Then, we confirmed that ALA promoted the production of interleukin (IL)-17A in ConA-stimulated PBMCs. Together, these findings reveal that ALA promotes heme synthesis in mitochondria and enhances ConA-induced T cell immune responses in canine PBMCs.

overall_design: RNAseq analysis of PBMCs treated with or without ConA and ALA.

first: Masaya

last: Igase

first: Nao

last: Iwatani

first: Aki

last: Sakai

first: Takuya

last: Mizuno


title: Transcription activated by AP2-Z in early zygote plays an essential role in Plasmodium ookinete development [RNA-seq]

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

summary: Plasmodium berghei transcriptomes of wild-type and ap2-z knockout parasites [ap2-z(-)] were analyzed at 6 hours post starting ookinete culture (hpoc).

overall_design: Wild-type and ap2-z(-) were harvested at 6 hpoc, and total RNA was extracted. Libraries were constructed from the RNA and then sequenced by the Next Generation Sequencing.

first: Tsubasa

last: Nishi

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Masao

last: Yuda


title: HIV-1 Induction of Tolerogenic DCs is Mediated by Cellular Interaction with Suppressive T Cells

city: Linkoping

first: Cecilia

last: Svanberg

address: Molecular Virology, lab1, plan 13, Medical Faculty, Linkoping University

department: Molecular virology

country: Sweden

institute: BKV

summary: Transcriptomic analyses was performed to elucidate effects of HIV exposure on the dendritic cell phenotype after crosstalk with T cells

overall_design:
RNAseq on DCs enriched from cocultures with T cells with and without exposure to HIV
>>> Submitter declares that raw data are not available due to donor privacy concerns. <<<

first: Rada

last: Ellegard

first: Marie

last: Larsson


title: Transcription activated by AP2-Z in early zygote plays an essential role in Plasmodium ookinete development

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

overall_design: Refer to individual Series


title: Transcription activated by AP2-Z in early zygote plays an essential role in Plasmodium ookinete development [ChIP-seq]

summary: To investigate the genome-wide binding sites of early zygote AP2-family transcription factor, AP2-Z in Plasmodium berghei, the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) analyses were performed. Parasites expressing GFP-fused AP2-Z (AP2-Z::GFP) were harvested at 6 hours post starting ookinete culture (hpoc) and subjected to ChIP-seq experiments using anti-GFP antibody. Binding sites of AP2-Z were determined from the sequence data.

overall_design: AP2-Z::GFP was subjected to ookinete cultures and harvested at 6 hpoc. Chromatins associated with GFP-tagged AP2-Z was IPed with anti-GFP antibody, and DNA fragments purified from the IPed chromoatins were sequenced by the Next Generation Sequencing. Using non-IPed samples as a control, binding sites of AP2-Z were determined from the sequence data.


title: Role of the Aac11/Api5 protein in RNA expression in the Drosophila larvae

status: Public on Aug 04 2022

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

summary: Aac11/Api5 is a conserved anti-apoptotic protein that functions through a poorly understood mechanism that appears to involve splicing and transcription. Here we used a HTS approach to identify RNAs that respond to Aac11/Api5 loss in whole 3rd instar larvae.

overall_design: An Aac11/Api5 UAS-RNAi transgene was used to deplete the mRNA and its encoded protein from third instar larvae using the Actin5c-Gal4 driver.

first: Ken

last: Moberg

first: Can

last: Zhang

first: Yangping

last: Li


title: Microarrays of THP-1 derived macrophages in silencing experiments of AC136475.5 lncRNA vs. scrambled control gapmers

city: Barcelona

first: Luis

last: Hernandez

address: Rossello 153, CEK building

department: Molecular Pathology

country: Spain

institute: IDIBAPS

summary: Microarrays were performed on several THP-1 derived macrophages obtained in silencing experiments of AC136475.5 lncRNA vs. scrambled control gapmers in the context of M2 polarization (IL4/IL13).

overall_design:
Microarrays were performed on several THP-1 derived macrophages obtained in silencing experiments of AC136475.5 lncRNA vs. scrambled control gapmers.
Microarrays of two additional THP-1 polarization controls (M1/M2) were included as a comparison for further pathway enrichment studies.

first: Elena

middle: M

last: Fernandez

first: Giancarlo

last: Castellano

first: Miriam

last: Verdu

first: Christian

last: Martin


title: tRF/tiRNA expression profile of RPE-choroid-sclera complex in the laser-induced choroidal neovascularization mouse model

city: Shanghai

first: Yu

last: Liang

address: 83 Fenyang Road

institute: Eye & ENT Hospital, Fudan University

summary: To investigate the tRF/tiRNA expression pattern in the development of choroidal neovascularization, we built a laser-induced choroidal neovascularization mouse model and performed the tRF/tiRNA sequencing on RPE-choroid-sclera complexes at different time points after model establishment, while the tissues from mice without treatment were used as control group.

overall_design: Three RPE-choroid-sclera complexes were obtained from the eyes of C57BL/6 mice at day 3 and day 7 after the laser-iduced choroidal neovascularization model establishment. Three complexes from mice without treatment were used as control samples. All nine samples were used for tRF/tiRNA sequencing and data analysis.

first: Liang

last: Yu

first: Lingjie

last: Kong

first: Biao

last: Yan

first: Chen

last: Zhao


title: Protein import motor complex reacts to mitochondrial misfolding by reducing protein import and activating mitophagy

city: Frankfurt am Main

first: Martin

last: Wegner

state: Hessen

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry II

country: Germany

institute: University Hospital Frankfurt am Main, Germany

summary: Mitophagy is essential to maintain mitochondrial function and prevent diseases. It activates upon mitochondria depolarization, which causes PINK1 stabilization on the mitochondrial outer membrane. Strikingly, a number of conditions, including mitochondrial protein misfolding, can induce mitophagy without a loss in membrane potential. The underlying molecular details remain unclear. Here, we report that a loss of mitochondrial protein import, mediated by the pre-sequence translocase-associated motor complex PAM, is sufficient to induce mitophagy in polarized mitochondria. A genome-wide CRISPR/Cas9 screen for mitophagy inducers identifies components of the PAM complex. Protein import defects are able to induce mitophagy without a need for depolarization. Upon mitochondrial protein misfolding, PAM dissociates from the import machinery resulting in decreased protein import and mitophagy induction. Our findings extend the current mitophagy model to explain mitophagy induction upon conditions that do not affect membrane polarization, such as mitochondrial protein misfolding.

overall_design: Recombinant mt-mKEIMA expressing human HeLa FlpIn Trex cells with Parkin expression were transfected with viral Brunello Cas9 library and an expression cassette for Cas9 enzyme. Starting two days after transduction, cells were selected by maintaining 2 µg/ml Puromycin. After seven days cells were treated with 0.1% DMSO for 16h, collected by 0.25% trypsin/EDTA-assisted detachment and sorted as mitophagy-positive cells (DMSO1_plus) by increased 561 nm excited mt-mKEIMA fluorescence compared to untransduced cells. As a reference the same amount of Brunello Cas9 library transducd cells were collected and pooled without sorting (DMSO1_complete). The collected cells were lysed and genomic DNA extracted by GeneJet DNA purification kit (Thermo Scientific, K0721).

first: Jonas

middle: B

last: Michaelis

first: Melinda

middle: E

last: Brunstein

first: Süleyman

last: Bozkurt

first: Ludovico

last: Alves

first: Manuel

last: Kaulich

last: Pohl

last: Münch


title: Rates of LDL entry and retention in mouse aorta are dissociated and predict the course of atherogenesis

city: Aarhus

first: Jacob

middle: Fog

last: Bentzon

state: Midtjylland

address: Palle Juul-Jensens Blvd. 99

department: Clinical Medicine

country: Denmark

institute: Aarhus University

summary: To investigate capacity of LDL entry and retention changes during the pre-atherosclerotic phase, we measured gene expression at the inner curvature region of the aortic arch in the presence of normal and short-term high LDL plasma levels through RNA-seq

overall_design: To set different LDL plasma levels but with the same hepatic LDL clearance rate, two groups of mice were treated with rAAV-PCSK9 and high-cholesterol diet (4% fat, 0.3% cholesterol), but in one of the groups the plasma LDL was kept at normal levels by treating with antisense oligonucleotides targeting Apob mRNA (Apob ASO) (normal aortas). The other group was treated with control antisense oligonucleotides (Ctrl ASO) (pre-atherosclerotic aortas). After 3.5 weeks with high or normal plasma LDL, gene expression changes were evaluated at the inner curvature region of the aortic arch.

first: Esmeralda

last: Lewis

first: Rocio

last: Muñiz-Anquela

first: Ibon

last: Redondo-Angulo

first: Leticia

last: Gonzalez-Cintado

first: Verónica

last: Labrador Cantarero


title: A single cell analysis of porcine thymopoiesis and thymic iNKT cells

city: Gainesville

first: John

middle: P.

last: Driver

state: FL

address: 2250 Shealy Dr

institute: University of Florida

summary: Many aspects of the porcine immune system remain poorly characterized which poses a barrier to improving swine health and utilizing pigs as preclinical models. Here, we employed single-cell RNA sequencing (scRNA-seq) to create a cell atlas of the postnatal pig thymus. Our data found conserved features as well as species-specific differences in cell states and cell types compared to human thymocytes. We also describe several unconventional T cell types with gene expression profiles associated with innate effector functions. This includes a cell census of  >11,000 differentiating invariant natural killer T (iNKT) cells, which revealed that the functional diversity of pig iNKT cells differs substantially from the paradigm of iNKT0/1/2/17 subset differentiation established in mice. Collectively, our data characterizes key differentiation events in porcine thymopoiesis and iNKT cell maturation, which provide new insights into pig T cell development.

overall_design: We performed single-cell RNA-seq on the pig total thymocytes and iNKT thymocytes purified from the same thymi.

first: Weihong

last: Gu

middle: P


title: Engagement of Foxh1 in chromatin regulation revealed by protein interactome analyses

city: Irvine

first: Ken

last: Cho

address: University of California, Irvine

institute: University of California, Irvine

summary: Precise gene expression patterns, both in time and space, is required for developmental processes to properly progress. Early embryonic cell fates are specified through the coordinated integration of transcription factor activities and epigenetic states of the genome. Foxh1 is a key maternal transcription factor controlling the mesendodermal gene regulatory program. Proteomic interactome analyses using FOXH1 as a bait in mouse embryonic stem cells revealed that FOXH1 interacts with PRC2 subunits and Hdac1. Foxh1 physically interacts with Hdac1, and confers transcriptional repression of mesendodermal genes in the ectoderm. Our findings reveal a central role of Foxh1 in coordinating the chromatin states of the Xenopus embryonic genome.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for dissected Xenopus gastrula animal cap (ectoderm) explants of control and Foxh1 morphant embryos

first: Jeff

middle: J

last: Zhou

middle: W


title: Gene expression profile from sorted mural cells from P12 retinas of Srf-PdfgrbCre and non Cre animals

city: Uppsala

first: Michael

middle: Martin

last: Orlich

address: Dag Hammarskjölds Väg 20  Floor C11

department: Department of Immunology, Genetic and Pathology

institute: Uppsala University

summary: The aim of this work was to study the function of the transcription factor Serum Response Factor (SRF) in mural cells of the mouse retina. We used bulk RNA-sequencing to find major differences.

overall_design: Retinal mural cells (MCs) were isolated from SRF-KO and Control animals and sorted by FACS (exclusion of CD140a, CD31, CD45 and DAPI positive cells, inclusion of CD140b positive cells only)

first: Rodrigo

last: Diéguez-Hurtado


title: Dual inhibition of MAPK and PI3K/AKT pathways enhances maturation of human iPSC-derived cardiomyocytes

city: Minneapolis

first: Bayardo

middle: Isidore

last: Garay

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

summary: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide great opportunities for mechanistic dissection of human cardiac pathophysiology; however, hiPSC-CMs remain immature relative to the adult heart. To identify novel signaling pathways driving the maturation process during heart development, we analyzed published transcriptional and epigenetic datasets from hiPSC-CMs, prenatal and postnatal human hearts. These analyses revealed that several components of the MAPK and PI3K-AKT pathways are downregulated in the postnatal heart. Here, we show that dual inhibition of these pathways for only 5 days significantly enhances the maturation of day-30 hiPSC-CMs in many domains: hypertrophy, multinucleation, metabolism, t-tubule density, calcium handling, and electrophysiology, many equivalent to day-60 hiPSC-CMs. These data indicate that the MAPK/PI3K/AKT pathways are involved in cardiomyocyte maturation and provide proof-of-concept for the manipulation of key signaling pathways for optimal hiPSC-CM maturation, a critical aspect of faithful in vitro modeling of cardiac pathologies and subsequent drug discovery.

overall_design: On day 25 of the cardiac differentiation protocol, hiPSC-CMs were incubated with 10μM of mirdametinib (PD0325901, Cayman Chemical), a selective and non ATP-competitive dual MEK1 and MEK2 inhibitor, and 5μM of SB203580 (Cayman Chemical), a p38 and PDK1 inhibitor, in RPMI1640 supplemented with B27 (plus insulin). The media with cocktail of inhibitors (SP) or DMSO vehicle control (0.01%) was changed on day 28 of the differentiation protocol. On day 30, the hiPSC-CMs were harvested for further analyses. Untreated day ~90 hiPSC-CMs were used as a reference for cardiac maturation. Total RNA was isolated using TRIzol reagent (Invitrogen) and the PureLink RNA mini kit (Invitrogen, #12183025) with on-column DNase treatment following the manufacturer’s recommendations. Reverse transcription was performed using SuperScript™ VILO™ cDNA synthesis kit (Invitrogen, #11754250). Two-μg of cDNA were used for further QC and RNA-seq experiments.

middle: I

first: Sophie

last: Givens

first: Phablo

last: Abreu

first: Man

last: Liu

first: Doğacan

last: Yücel

first: June

last: Baik

first: Noah

last: Stanis

first: Taylor

last: Rothermel

first: Alessandro

last: Magli

first: Juan

last: Abrahante

first: Natalya

middle: A

last: Goloviznina

first: Hossam

last: Soliman

first: Neha

middle: R

last: Dhoke

last: Kyba

first: Patrick

last: Alford

first: Samuel

last: Dudley

first: Jop

middle: H

last: van Berlo

first: Brenda

last: Ogle

first: Rita

last: Perlingeiro


title: The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence [RNA-seq]

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

summary: Total and polysomal RNA profiling of control and DKC1-silenced MCF7 cells

overall_design: 3 biological samples per condition are used. A total of 12 samples were used: 3 total scramble, 3 polysomal scramble, 3 total shDKC1, 3 polysomal shDKC1

first: Federico

last: Zacchini

first: Alberto

last: Inga

first: Lorenzo

last: Montanaro


title: The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence


title: The pseudouridine synthase DKC1 binds to cytoplasmic transcripts containing H/ACA-box SnoRNA sequences affecting nuclear hormone receptor dependence [RIP-seq]

summary: RIP-seq of DKC1 in MCF7 cells

overall_design: 5 biological samples per condition are used. A total of 15 samples were used: 5 cytosol input, 5 cytosol IgG RIP, 5 cytosol DKC1 RIP


title: The continuum of Drosophila embryonic development at single cell resolution

city: Seattle

first: Diego

last: Calderon

address: 3720 15th Ave NE

institute: University of Washington


title: sci-RNA-seq data

summary: Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost one million, and gene expression in half a million, nuclei from eleven tightly staged, overlapping windows of its embryogenesis. Leveraging the asynchronicity of embryos within each collection, we developed a statistical model to more precisely estimate the age of each nucleus, resulting in continuous views of molecular and cellular transitions throughout the majority of embryonic development. From these data, we identify cell types, infer their developmental relationships, and link cell type-specific changes to dynamic changes in enhancer usage, transcription factor (TF) expression and the accessibility of TFs’ cognate motifs. Looking forward, this strategy may facilitate future investigations of gene regulation in vivo at arbitrarily high temporal resolution.

overall_design: Staged Drosophila embryos were collected in 11 overlapping time windows, collectively spanning 0-20 hrs of development at 25°C. Overlapping two-hour collections were used to capture the rapid transitions during early embryogenesis, followed by overlapping four-hour collections from 4-6 hrs onwards (Fig. 1A). From each such collection, embryo collections were halved and separately processed for single cell ATAC-seq or single cell RNA-seq.

first: Ronnie

last: Blecher-Gonen

first: Xingfan

last: Huang


title: Starved HEK293 cells

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

institute: Julius-Maximilians-Universität Würzburg


title: sci-ATAC-seq data


title: High-throughput small RNA sequencing of the human placenta at first and third trimester with fetal sex differences analysis

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: Human placenta bulk small RNA-seq from healthy pregnancies without infertility, from n=113 first trimester (58 female, 55 male) and n=47 third trimester (19 female, 28 male) tissue samples. Tissue was collected at Cedars-Sinai Medical Center in Los Angeles, California, USA. First trimester placenta was collected at 70-102 days of gestation from leftover chorionic villus sampling for prenatal genetic diagnosis. Third trimester placenta was collected after delivery at 254-290 days gestation from the fetal side near the umbilical cord insertion site beneath the amnion. Mothers with pre-existing diabetes or hypertension were excluded. All pregnancies were conceived without fertility treatments, were normal karyotype, and resulted in live singleton births. The average parental age was advanced (over 35 years old) but PCA analysis did not show clustering by either maternal or paternal age. Gonzalez et al 2021 [PMID: 34030457] analyzes similarities and differences between first and third trimester miRNA expression overall. Flowers et al 2021 focuses on the effect of fetal sex on miRNA expression across gestation.

overall_design: Small RNAs from human placenta were sequenced. Differential expression analysis was performed on miRNAs with the R package DESeq2 and two sample variables (trimester and fetal sex).

first: Tania

middle: L

last: Gonzalez

first: Amy

last: Flowers

first: Nikhil

middle: V

last: Joshi

first: Laura

last: Eisman

first: Di

last: Wu

first: Yizhou

last: Wang

first: Chintda

last: Santiskulvong

first: Jie

last: Tang

first: Rae

last: Buttle

first: Erica

last: Sauro

first: Ekaterina

last: Clark

first: Rosemarie

last: DiPentino

first: Caroline

last: Jefferies

first: Jessica

last: Chan

middle: T

first: Yayu

last: Lin

first: Bora

last: Lee

first: Tianyanxin

last: Sun

first: Kate

last: Lawrenson

first: Yazhen

last: Zhu

first: Yalda

last: Afshar

first: Hsian-Rong

last: Tseng

first: Kent

last: Taylor

first: John

last: Williams III

first: Margareta

middle: D

last: Pisarska


title: Monosome profiling in starved HEK293 cells

first: Florian

last: Erhard

summary: Ribosome profiling from monosome and polysome fractions of serum or amino acid starved HEK293 cells

overall_design: Human embryonic kindney cells were subjected to 2h of serum or 1h of amino acid starvation. Ribonucleoprotein complexes were separated on polysome gradients. Ribosome protected fragments were purified from pooled monosome and polysome fractions.

first: Cornelius

last: Schneider

first: Jörg

last: Vogel

first: Utz

last: Fischer


title: Bone formation in senile osteoporosisbone formation in senile osteoporosis

status: Public on Aug 03 2022

city: Shenzhen

first: Peitao

last: Xu

address: No.3025, Shennan Middle Street

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


title: TGF-β regulates the stem-like state of PD-1+ TCF-1+ virus-specific CD8 T cells during chronic infection

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

summary: In this study the effect of TGF-beta on CD8 T-cell differentiation in chronic LCMV infection was investigated

overall_design: Mice were infected with LCMV Cl13 and 30 days later CD8 P14 cells were isolated by FACS

first: Yinghong

last: Hu

first: Rafi

last: Ahmed


title: Circulating tumor DNA sequencing provides comprehensive mutation profiling for pediatric central nervous system tumors

city: Washington

first: Erin

last: Bonner

state: DC

address: 7144 13th Place NW

department: Center for Genetic Medicine Research

institute: Children's National Hospital

summary: Molecular profiling of childhood CNS tumors is critical for diagnosis and clinical management, yet tissue access is restricted due to the sensitive tumor location. We developed a targeted deep sequencing platform to detect tumor driver mutations, copy number variations, and heterogeneity in the liquid biome. Here, we present the sensitivity, specificity, and clinical relevance of our minimally invasive platform for tumor mutation profiling in children diagnosed with CNS cancer.

overall_design: Tumor tissue genomic DNA samples (n=2) were analyzed, both from the same patient diagnosed with diffuse midline glioma. One sample was obtained at initial diagnosis and the second sample was obtained at postmortem autopsy.

first: Robin

last: Harrington

first: Augustine

last: Eze

first: Miriam

last: Bornhorst

first: Cassie

middle: N

last: Kline

first: Heather

last: Gordish-Dressman

first: Adam

last: Dawood

first: Biswajit

last: Das

first: Li

last: Chen

first: Rini

last: Pauly

first: P

middle: M

last: Williams

first: Chris

last: Karlovich

first: Amanda

last: Peach

first: D'Andra

last: Howell

first: James

last: Doroshow

first: Lindsay

last: Kilburn

first: Roger

last: Packer

first: Sabine

last: Mueller

first: Javad

last: Nazarian


title: Chromatin state for BS and M cells

city: Nanjing

first: tao

middle: shen

last: tong

address: Weigang street 1st

institute: Nanjing Agricultural University

summary: We report the ChIP-seq of several histone modification markers for BS cells and H3K36me3 ChIP-seq for M cells, we found that BS-specific gene module trend to be regulated by histone acetylation.

overall_design: ChIP-seq of H3K36me3 for BS and M cells, and acetylation ChIP-seq for BS cells.

first: Wenli

last: Zhang

first: Lifen

first: Shentong

last: Tao


title: Regulatory mechanism of diurnal fluctuated laminarin in diatom Phaeodactylum tricornutum

city: shantou

first: jichen

last: chen

address: university road

institute: shantou university

summary: Diatoms played an essential role in marine primary productivity. Polysaccharide chrysolaminarin and neutral lipid, mainly TAG, were necessary carbon fixation in diatom Phaeodactylum tricornutum. Our study speculated on the metabolism pathway of chrysolaminarin, fatty acid, fatty acid β-oxidation and TAG. Transcriptional levels coordinated with carbon fixation metabolism pathway were conjoint analysis in this study.

overall_design: comparative gene expression profiling analysis of RNA-seq data for Phaeodactylum tricornutum cells in a light/dark cycle

first: xiaojuan

last: liu

first: hong

last: du

first: weizhou


title: Phloridzin reveals new treatment strategies for liver fibrosis

city: Beijing

first: Yahong

last: Shi

address: 11 Beisanhuan Dong Lu, Chaoyang District

institute: Beijing University of Chinese Medicine

summary: Liver fibrosis, is an urgent public health problem and is difficult to resolve. However, various drugs for the treatment of liver fibrosis in clinical practice have their own problems during use. In this study, we used phloridzin to treat hepatic fibrosis in the CCl4-induced C57/BL6N mouse model, which was extracted from lychee core, a traditional Chinese medicine. The therapeutic effect was evaluated by biochemical index detections and ultrasound detection. Furthermore, in order to determine the mechanism of phloridzin in the treatment of liver fibrosis, we performed high-throughput sequencing of messenger RNA (mRNA) and long non-coding RNA (lncRNA) in different groups of liver tissues, and screened for differentially expressed genes, as well as performed gene co-expression analysis of the differential lncRNAs and mRNAs. The results showed that compared with the model group, the phloridzin treated groups showed a significant decrease in collagen deposition, and decreased levels of serum alanine aminotransferase, aspartate aminotransferase, laminin and hyaluronic acid. GO and KEGG pathway enrichment analysis of the differential mRNAs was performed and revealed that phloridzin mainly affects cell ferroptosis. Gene co-expression analysis showed that the target genes of lncRNA were obvious in cell components such as focal adhesions, intercellular adhesion, and cell-substrate junctions, and in metabolic pathways such as carbon metabolism. These results showed that phloridizin can effectively treat liver fibrosis, and the mechanism may involve ferroptosis, carbon metabolism and related changes in biomechanics.

overall_design: The mice were randomly divided into 6 groups: the control group, model group, silibinin group, phloridzin low dose group, phloridzin middle dose group, and phloridzin high group.Liver fibrosis in the mouse model was induced by intraperitoneal injection of carbon tetrachloride (CCl4) dissolved in olive oil (1:9, v/v) at a dosage was 5 mL/kg body weight twice a week for 8 weeks. Drug therapy was started on the fifth week. After 8 weeks, the mice were sacrificed and the livers excised.

first: Tun

last: Yan

first: Xi

last: Lu

first: Kai

last: Li

first: Yifeng

last: Nie

first: Huizhen

last: Sun

first: Tingting

first: Chuqiao

last: Jiao

first: Xiang

first: Dong

last: Han


title: HAND1 knockdown disrupts trophoblast gene expression in vitro- human vascular endothelial cell

first: Helen

last: Jones

state: Florida

address: 1345 Center Dr

department: Physiology and FUnctional Genomics

summary: Congenital heart disease (CHD) affects nearly 1% of births annually, and neonatal and perinatal outcomes in cases of CHD are strongly impacted by pregnancy outcomes. CHD pregnancies carry increased risk of developing pathologies of abnormal placentation including fetal growth restriction, preeclampsia, preterm birth, and stillbirth. HAND1 is a gene associated with CHD.  In this study, we aimed characterize the mechanistic impacts of disrupting HAND1 on human  vascular endothelial cell gene expression.

overall_design: To silence HAND1 gene expression,  isolated human placental microvascular endothelial cells (HPMVEC; n = 3 passages), were treated for 96 h with HAND1/2 siRNA. Cells were harvested and mRNA isolated. RNA sequencing was performed using the Illumina NextSeq 550 platform (single end reads 85-101bp, read depth 25M). The Galaxy Bioinformatic Platform was used for quality control, alignment and generation of read counts. Normalization and differential gene expression analyses were conducted using general linear modeling in edgeR packages. Statistical significance was determined using a log2 fold change cut off >1.0 or <-1.0 and unadjusted ≤0.05. Overrepresentation analysis was performed using Panther DB for Reactome pathways and GO Biological Processes, and String DB for protein association network analysis.


title: The complete cell atlas of an aging multicellular organism

city: South San Francisco

first: Han

last: Yuan

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Sciences

summary: Here we describe a single-cell atlas of aging for virtually every cell type of the nematode Caenorhabditis elegans. Our findings suggest that C. elegans aging is not random in nature, but rather characterized by coordinated changes in functionally related metabolic and stress-response genes in a highly cell-type specific fashion. Aging signatures of different cell types are largely different from one another, with downregulation of energy metabolism being the only nearly universal change. Similarly, the rates at which cells aged, measured as genome-wide expression changes, differed significantly between cell types. In some, but not all, cell types, aging was characterized by an increase in cell-to-cell variance. Finally, we identified a signature for longevity transcription factors (TFs) whose activities changed coordinately across many cell types with age. We discovered new candidates, such as GEI-3, among these TFs that likely also regulate the aging rate. Our dataset can be accessed and queried at c.elegans.aging.atlas.research.calicolabs.com/.

overall_design: We performed a time series single cell RNA-seq on a C. elegans population over the course of their adult lifespan and for that purpose selected six time points (days 1, 3, 5, 8, 11 and 15 of adulthood). To reduce germ cell number, we used a temperature-sensitive gon-2(q388ts) mutant, grown at 25C, which fail to develop gonads at this non-permissive temperature. The dataset shared here was obtained with the strain CF4596: gon-2(q388) I; muIs274 [eft-3p:del:unc-54 3'UTR + Cbr-unc-119(+)] II; daf-2(mu465[daf-2::AID] III. This strain is AID-tagged in the daf-2 C-ter locus but is equivalent to a daf-2+/+ according to our test and to Venz et al Elife 2021 (https://doi.org/10.7554/eLife.71335). The same population was used for every timepoints. For each timepoint, around 10 000 cells were loaded in two independent 10x genomics chip channels. They are called technical replicates here after. For a detail protocol please refer to Roux et al Biorxiv 2022 (https://doi.org/10.1101/2022.06.15.496201).

first: Antoine

middle: E

last: Roux

first: Katie

last: Podshivalova

first: David

middle: G

last: Hendrickson

first: Rex

last: Kerr

first: Cynthia

last: Kenyon

last: Kelley


title: Long-term treatment with bortezomib induces specific methylation changes in differentiated neuronal cells

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

summary: Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylationEPIC BeadChip in DNA samples extracted from LUHMES cell line cells repeatedly treated with bortezomib (BTZ).

overall_design:
This dataset includes 6 samples of DNA extracted from LUHMES cell line cells treated with BTZ (at two timepoints) and 6 samples of DNA extracted from non-treated LUHMES cell line cells (controls at two timepoints).
The BTZ treatment was conducted in two cycles. In one treatment cycle, dLUHMES cells were incubated four times (on the day 1st, 4th, 8th, and 11th) with medium containing 0.15nM of BTZ (Cell Signalling Technology, Danvers, MA, USA) for 24h. The medium was replaced to
BTZ-free medium between each treatment. After the first treatment cycle, cells were cultured for another 10 days in BTZ-free medium, and then the BTZ treatment cycle was repeated. After each cycle, referred to as time-point 1 and time-point 2, the cells treated with BTZ, as well as non-treated controls, were harvested for DNA extraction.

first: Olga

last: Taryma-Lesniak

first: Karolina

last: Łuczkowska

first: Jan

last: Bińkowski

first: Katarzyna

last: Sokolowska

first: Dominik

last: Strapagiel

first: Justyna

last: Jarczak

first: Bogusław

last: Machaliński


title: Extracellular vesicle microRNA biomarkers of late post-sepsis survivors

city: São Paulo

first: Talita

middle: Souza

last: Siqueira

state: São Paulo

address: Galvão Bueno, 868 - Liberdade

department: Interdisciplinary Post-Graduate Program in Health Sciences

country: Brazil

institute: Cruzeiro do Sul University

summary: Sepsis is a life-threatening condition with high hospital mortality. Elevated mortality has also been observed in patients after hospital discharge, associated with post sepsis syndrome (PSS), causing systemic impairments and reduced life quality. The etiology of PSS is still not completely known but certainly involves inflammation. Extracellular vesicles (EV) are recognized as a notable mechanism of intercellular communication in inflammatory processes. It has been reported that EV microRNA (miRNA) production patterns during the acute phase of the disease may persist until after sepsis resolution and are associated with PSS.  Methods: We employed mass spectrometry and qPCR to characterize the protein and miRNA composition of plasma-derived EVs of 35 patients during sepsis-related hospitalization and after discharge (post-sepsis) for up to three years.  Findings: Fifteen differentially expressed EVs miRNAs (DEMiRs) were identified in septic patients compared to the control group. Predictive analyses revealed that these DEMiRs could influence inflammation by modulating pathways mediated by the activation of NF-κB, STAT3, and TLR4. Thirteen miRNAs (-15b-5p, -16-5p, -20a-5p, -25-3p, -27a-3p, -29a-3p, -30d-5p, -93-5p, -146a-5p, -148a -3p, -191-5p, -195-5p, -223-3p) were downregulated in the death group compared to the survivor group and are candidates for serving as prognostic markers of survival in the Intensive Care Unit. The expression of 11 miRNAs (-15b-5p, -16-5p, -21-5p, -25-3p, -27a-3p, -29a-3p, -30d-5p, -93-5p, -146a-5p -195- 5p and -223-3p) was lower one year after ICU discharge than the control group.   Interpretation: The miRNAs identified in the present study represent potential biomarkers for the survival prognosis of post-sepsis patients.

overall_design: Six samples were analyzed, which were divided into 2 groups, septic patients who survived (n=3) and septic patients who died (n=3)

last: Souza-Siqueira

first: Raquel

middle: B

last: Gritte

first: Juliana

middle: C

last: Vieira

first: Laureane

last: Mais

first: Fernanda

last: Borges

first: Eleine

last: Weimann

first: Rodrigo

first: Gilson

last: Murata

first: Laiane

middle: S

last: Oliveira

first: Silvana

last: Bordin

first: Eliane

last: Silva

first: Renata

last: Gorjão

first: Adriana

last: Levada-Pires

first: Antônio

last: Nogueira

first: Tânia

last: Pithon-Curi

first: Ricardo

last: Azevedo

first: Rui

last: Curi

first: Marcel

last: Machado

first: Francisco

last: Soriano


title: Transcriptomic effects of corticosterone on male and female skeletal muscle

city: Leiden

first: Jacobus

middle: Cornelis

last: Buurstede

state: Zuid-Holland

address: Albinusdreef 2

department: Endocrinology

country: Netherlands

institute: Leiden University Medical Center

summary:
Aim: To investigate the sexual dimorphic effects of corticosterone on skeletal muscle
Methods: Male and female mice were exposed to high levels of corticosterone by implantation of 50 mg slow-release pellets. After two weeks, quadriceps muscle was isolated and snap-frozen. Total RNA was isolated and send for 100 bp paired-end sequencing by BGI.

overall_design: Direct comparison between the transcriptomic response to corticosterone in skeletal muscle of male and female mice.

first: Jan

last: Kroon

first: Onno

last: Meijer


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Control and BRD9/7 Inhibitor-treated  Uterine Leiomyosarcoma Cell Transcriptome

city: Chicago

first: Qiwei

last: Yang

address: 5841 S. Maryland Avenue

department: Obstetrics and Gynecology

institute: University of Chicago

summary: We report that BRD9/7 inhibition alters multiple biological pathways in uterine leiomyosarcoma cells

overall_design: Examine the transcriptome alteration in uterine leiomyosarcoma cells with or without BRD9/7 inhibitors

first: Ayman

last: Al-Hendy


title: Gradient Sequencing (Grad-Seq) of starved HEK293 cells

first: Florian

last: Erhard

summary: Grad-Seq of serum or amino acid starved HEK293 cells

overall_design: Human embryonic kindney cells were subjected to 2h of serum or 1h of amino acid starvation. Ribonucleoprotein complexes were separated on polysome gradients. Poly(A)+ RNA from each gradient fraction was purified and sequenced.

first: Cornelius

last: Schneider

first: Jörg

last: Vogel

first: Utz

last: Fischer


title: A novel class of early responder T cells are indispensable for neuroprotection and functional recovery after ischemic stroke

city: Pittsburgh

first: Xiaoming

last: Hu

state: PA

address: 200 lothrop street

department: Neurology

institute: University of Pittsburgh

summary: We report that CD8+CD122+CD49dlow regulatory-like T cells (CD8+TRLs) are among the earliest lymphocytes to infiltrate mouse brain after ischemic stroke, temper inflammation, and confer neuroprotection.

overall_design: CD8+CD122+CD49dlow TRLs were FACS-isolated directly into a plate with lysis buffer from the brain and blood of young male mice 3 days after transient (60 min) middle cerebral artery occlusion (tMCAO) or blood of sham operation and subjected to RNA-sequencing analysis.

first: Jun

last: Chen


title: Dynamic changes in peripheral blood monocytes early after anti-PD-1 therapy predict clinical outcomes in hepatocellular carcinoma

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

summary: We aimed to identify peripheral blood biomarkers that predict the response of advanced HCC to anti-PD-1 therapy.

overall_design: Classical monocytes (CD11b+CD3−CD19−CD14+CD16− cells) were sorted from PBMCs collected at day0 and day7 from four patients with DCB and four patients with NDB.

first: Seung

first: Yong

middle: J

last: Lee

first: Hyung-Don

last: Kim

first: Heejin

last: Nam

first: Baek-Yeol

last: Ryoo

first: Su-Hyung

last: Park

first: Changhoon

last: Yoo

first: Eui-Cheol

last: Shin


title: Effect of Leishmania infantum infection on the gene expression of murine bone marrow-derived dendritic cells

city: Athens

first: Evdokia

last: Karagouni

state: Attica

address: 127 Vas. Sofias Avenue

department: Department of Microbiology

country: Greece

institute: Hellenic Pasteur Institute

summary: To investigate dendritic cells-Leishmania interaction, the transcriptional profile of bone marrow-derived dendritic cells (BMDCs) infected with Leishmania infantum or of cells exposed to chemically inactivated parasites was assessed

overall_design: Transcription profile analysis of murine BMDCs exposed to live or chemically inactivated Leishmania infantum parasites for 24h compared to untreated cells

first: Maritsa

last: Margaroni

first: Maria

last: Agallou

first: Giorgos

last: Skoufos

first: Dimitra

last: Karagkouni

first: Artemis

last: Hatzigeorgiou


title: NSD1 mutations in Sotos Syndrome induce differential expression of long non-coding RNAs, miR646 and genes controlling the G2/M checkpoint

city: Genova

first: Giuseppina

last: Conteduca

state: GE

address: Largo Rosanna Benzi 10

institute: IRCCS Ospedale San Martino

summary: An increasing amount of evidence indicates the critical role of NSD1 gene in the Sotos syndrome (SoS) and tumor. Molecular mechanisms affected by NSD1 mutations are largely uncharacterized. In order to assess the impact of NSD1 haploinsufficiency in the pathogenesis of SoS, we analyzed the gene expression profile of fibroblasts isolated from the skin sample of 15 SoS patients and from 5 healthy parents. We identified 7 differentially expressed genes and 5 differentially expressed non-coding RNAs. The most up-regulated mRNA was stratifin (SFN) (fold change, 3.9, p<0.05) and the most down-regulated mRNA was goosecoid homeobox (GSC) (fold change, 3.9, p<0.05).

overall_design: Fifteen individuals with classical clinical features of SoS and with the molecular diagnoses of NSD1 pathogenic variants (point mutation or deletion) were enrolled in the study. Were also enrolled five parents, of the same sex of the correspective  SoS patient, as controls selected on the basis of skin biopsy availability.

first: Davide

last: Cangelosi

first: Simona

last: Coco

first: Michela

last: Malacarne

first: Chiara

last: Baldo

first: Alessia

last: Arado

first: Rute

last: Pinto

first: Barbara

last: Testa

first: Domenico

middle: A

last: Coviello


title: Differential gene expression in DEVH1 knock-in Leishmania infantum promastigotes

city: MADRID

first: PEDRO

middle: JOSÉ

last: ALCOLEA ALCOLEA

address: Ramiro de Maeztu, 9

department: CENTRO DE INVESTIGACIONES BIOLÓGICAS

institute: CONSEJO SUPERIOR DE INVESTIGACIONES CIENTÍFICAS

summary: The DEAD/H RNA helicase LINF_220021200 (DEVH1) gene from Leishmania infantum (Kinetoplastida:Trypanosomatidae) was cloned in the pTEX expression plasmid vector for trypanosomatids. Leishmania infantunm promastigotes were transfected and a knock-in  L. infantum promastigote cell line was selected with geneticin (G418). A pTEX control promastigote line was also generated. Then, three independent biological replicate cultures of each pTEX-DEVH1 and pTEX promastigote lines were performed in the presence of the selective agent. The parasites were harvested on day 7 (stationary phase). Total mRNA samples were obtained. Cyanine dye-labelled samples were obtained from the knock-in and the control line (Cy5 and Cy3, respectively) and they were hybridized with custom whole-genome L. infantum DNA microarrays. This platform is included in GEO (GPL6781) and has also been repeatedly used in different experiments from 2009. Hybridization analysis allowed for finding differentially expressed genes due to the effect of induced over-expression of the DEVH1-encoding gene in the knock-in promastigote line compared to the control line. Genes involved in parasite infectivity and survival such as the HASP/SHERP gene cluster and an amastin gene or redox homeostasis genes are significantly down-regulated in the pTEX-DEVH1 knock-in promastigote line, whereas genes related to growth are up-regulated. This is in agreement with previous experimental data supporting that L. infantum DEVH1 knock-in promastigotes are able to recover the growth rate when stress conditions are removed.

overall_design: Six samples were analyzed. Three were biological replicates of stationary phase promastigotes of the pTEX-DEVH1 L. infantum line. All other three samples were biological replicates of stationary phase promastigotes of the pTEX L. infantum control line. The samples were cDNA labelled with Cy5 and Cy3, respectively. Normalization of fluorescence intensity values was performed by the LOWESS per pin algorithm. Student`s t-test was conducted for statistical inference, including FDR adjustment.    Please note that the 'pTEX-DEVH1 vs. pTEX' sample represents three replicates (3 raw data files; Analyzed_dataset_pTEX_DEVH1_vs_pTEX_Li.txt) and averaged data across arrays (i.e. mean of normalized fold change data).

first: Pedro

last: Alcolea


title: ATAC-seq analysis of aged-associated B cells (ABC) across three TLR9 genotypes (TLR9WT, TLR9-/- and non-signaling TLR9P915H/P915H) isolated from a mixed chimeric setting in the MRL/lpr murine model of systemic lupus erythematosus.

first: Mark

last: Shlomchik

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

summary:
Purpose: The goal of this study was to assess if TLR9 deficiency (TLR9-/-) or TLR9 incapacity to signal through MyD88 would differentially influence the epigenetic states of ABC, in a B cell intrinsic manner.
Methods : Mixed bone marrow chimeras of one-third each TLR9+/+ CD45.1/2, TLR9-/- CD45.1/1 and TLR9P915H/P915H CD45.2/2 were generated on the MRL/lpr background.  From each recipient, ABC were sorted with respect to the CD45 congenic markers at [20 weeks] post chimerism. DNA was isolated using a protocol adapted from Corces et al. Samples were sequenced to obtain 20M 2x75 bp paired-end reads using an Illumina NextSeq 550 sequencer (Illumina, Inc, California, USA).
Results: The majority of differences in open chromatin regions were observed between TLR9-/- and TLR9P915H ABCs. This must reflect the MyD88-independent regulatory function of TLR9 (lost in TLR9-/- and present in TLR9P915H).

overall_design: DAR profiles of TLR9 deficient (TLR9-/-), mutant TLR9 (P915H/P915H) and intact TLR9 (WT)  ABC of 20-week-old (3-way-mixed) BM chimera MRL/lpr mice were generated in three replicates by sequencing, using an Illumina NextSeq 550 sequencer.

first: Claire

last: Leibler

first: Shuchi

last: Smita


title: Next-generation sequencing to define the impact of metastatic prostate cancer on neutrophils

city: Frederick

first: Leah

last: Cook

state: MD

address: 1050 Boyles St, Room 21-89

institute: National Cancer Institute-Frederick

summary: Purpose: Prostate cancer most frequently metastasizes to bone and is incurable. Metastatic prostate cancer cells thrive in bone through molecular regulation of surrounding bone stroma; however, it is unclear how non-metastatic vs. metastatic cancer differentially alter the bone cells. Since neutrophils are the most abundant stromal cell in bone, the goal of this study was to identify prostate cancer-induced transcriptomic changes in bone marrow neutrophils for comparison to non-metastatic prostate cancer cells.

overall_design: For comparison of non-metastatic and metastatic prostate cancer, we utilized LNCaP (originally derived from prostate cancer patient lymph node; non-metastatic) and C42B (bone metastatic cells derived from LNCaP) cells. For cancer conditioned media, LNCaP and C42B cancer cells were cultured overnight in serum-free media to collect soluble factors. The supernatant was collected and overall protein content measured.  Human neutrophils were isolated from bone marrow using ficoll density centrifugation and were incubated in cancer conditioned media for 3 hours total.  After incubation, media was washed off of the neutrophils and RNA was collected using Trizol reagent, for downstream bulk RNA-seq analyses.


title: RNA-seq analysis of follicular (FO) and marginal zone (MZ) B cells, isolated from TLR9WT or TLR9-/- BALB/c mice, stimulated with TLR7 agonists (CL097, Invivogen) or left unstimulated .

summary:
Purpose: The goal of this study was to assess if increased TLR7 signaling could be seen in TLR9-/- compared to TLR9WT FO and MZ B cells.
Methods : FO and MZ B cells from TLR9WT or TLR9-/- BALB/c mice were sorted using FACSaria. A minimum of 100,000 cells per B cell subsets were sorted. Sorted B cell subsets were stimulated for 4 hours at 0.25M/ml  with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated. RNA was isolated using the RNeasy Plus Micro Kit (QIAGEN). Samples were sequenced on an Illumina Next-seq 2000 using a P3 200 cycle flowcell (Illumina, Inc) with 2 x 101 bp paired-end reads (20 million reads per sample).
Results: There were no significant DEG (FDR > 0.05) following TLR7 stimulation between TLR9WT and TLR9-/- FO or MZ B cells.

overall_design: mRNA profiles of TLR9 deficient (TLR9-/-) and intact TLR9 (WT) FO and MZ B cells of BALB/c mice, stimulated with TLR7 agonists (CL097) or unstimulated, were generated in three replicates by sequencing, on an Illumina Next-seq 2000 using a P3 200 cycle flowcell.


title: PLAUR-TLR2 Axis Promotes Chronic Itch

city: Kaifeng, Henan Province

first: Yanqing

last: Li

address: Jinming Avenue

institute: Henan University

summary: In the  present study, RNA-seq were performed To identify clinical relevance of PLAUR, a putative Serpin E1 receptor, in cutaneous itch signaling and crosstalk pathways with other critical itch modulators.mRNA profiles were generated by deep sequencing, in triplicate, using MGISEQ-2000. Our experiment showed Serpin E1-treatment further led to a marked  upregulation of TLR2 transcript in mDRG neurons, along with enhanced transcription of cosignaling  proteins belonging to pro-inflammatory signaling pathways including NF-κB  signaling proteins. We next investigated the consequence of TLR2 activation in mTGNs using the TLR agonists,  Pam3CSK4 (TLR1/2 agonist), FSL-1 (TLR2/6 agonist), or vehicle. Among these  transcripts, TLR2 was found upregulated strongest by both TLR2 agonists suggesting a selfenhancing  feedback loop of TLR2 activation.The PLAUR-TLR2 axis promotes cutaneous inflammation and itch, both feeding into  an aggravation of AD. This finding might help us to better understand the skin-nerve  communication in itch circuits.

overall_design: primary mouse dorsal root ganglion neurons were stimulated with serpinE1(20μg/ml) or control for 6h; primary mouse trigeminal ganglion neurons were stimulated with Pam3CSK4 (TLR1/2 agonist, 1 μg/ml), FSL-1 (TLR2/6 agonist, 1 μg/ml) or the appropriate vehicle control for 6h,  gene expression of these cells were investigated utilizing MGISEQ-2000.

first: Weiwei

last: Chen

first: Jianghui

last: Meng


title: RNA-seq analysis of bead-purified B cells of 5-week-old TLR9-/- MRL/lpr mice stimulated in vitro with TLR7 agonists (CL097, invivogen) or left unstimulated.

summary:
Purpose: The goal of this study was to develop a B-cell specific gene signature to catalog induced genes after short term in vitro TLR7 stimulation of TLR9-/- MRL/lpr B cells.
Methods : Bead purified B cells (5M) from three 5-week-old TLR9-/- MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated. RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN). Samples were sequenced on an NextSeq500 (Illumina, Inc) with 2 x 75 bp paired-end reads (20 million reads per sample).
Results: a B-cell specific gene signature of induced genes after short term in vitro TLR7 stimulation was cataloged.

overall_design: mRNA profiles of TLR9 deficient (TLR9-/-) B cells stimulated in vitro with TLR7 agonists (CL097, Invivogen) or unstimulated, were generated in three replicates, by sequencing on an Illumina NextSeq500 using PE 150 Cycles High Output flowcell.


title: RNA-seq of  High Grade Serous Ovarian cell line (OVCAR3) treated with ALDH1A1 inhibitor vs Control

city: BLOOMINGTON

first: Kenneth

middle: P.

last: Nephew

state: IN

department: Medical Sciences

institute: Indiana University

summary: Ovarian cancer (OC) is the leading cause of death from gynecologic malignancies in the US. Ovarian cancer stem cells (OCSCs) have been shown to drive chemoresistance and tumor progression but the mechanism remains incompletely understood. Aldehyde Dehydrogenase 1A1 (ALDH1A1) is a robust marker for cancer stem cells in ovarian and other cancers. We demonstrate that ALDH1A1 inhibition suppresses stemness, chemoresistance and senescence in ovarian cancer.

overall_design: In triplicate, OVCAR3 cells were treated with compound 974 (5µM for 48h) or DMSO. RNA was harvested from the cells using the RNAEasy kit (Qiagen,Catalog No; 74106). RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina #RS-122-2101) according to manufacter's protocol.

first: V

last: Muralikrishnan

first: F

last: Fang

first: R

last: Podicheti

first: T

last: Hurley

first: K


title: tendon mRNA seq after particulate matter inhalation

first: Minhyeok

last: Lee

address: 158, Gwanjeodong-ro, Seo-gu

department: Department of Internal Medicine

institute: Konyang university hospital

summary: Open tenotomy of the Achilles tendon of 6 rats was performed. The animals were divided into two groups according to exposure of PM2.5 (particulate matter less than 2.5 µm): control group (Non-PM group) or PM exposure group (PM group). After 6 weeks of PM exposure, the tendon RNA was extracted and anlyzed.

overall_design: 3 PM exposure group group/3 control group

first: Jae-Hwang

last: Song

first: Ji

middle: W

last: Son