title: expression data from colon cancer in a mouse model

first: Elena

last: Tosti

address: 1301 Morris park avenue

summary:
expression analysis in colon cancer from  Msh2 and Tgfbr2 intestinal epithelium inactivated mouse model
detailed gene expression analysis in colon cacer developed in mouse model with  Msh2 and Tgfbr2  inactivated eary n  from Villin Cre recombnase exclusively in the intestine

overall_design: Gene expression analysis of RNA isolated from  sorted epithelial cells was performed using the Mouse Gene ST 2.0 Array System (Affymetrix). Sorted epithelial cells from colon cancer tissue amd matched tumor free muosa were used for RNA extraction

first: Winfried

last: Edelmann

first: Pilib

middle: O

last: Broin

first: Mariel

last: Silva


title: mRNA profiling after knockdown of Circular RNA-INSR

status: Public on Oct 01 2022

city: hannover

first: Dongchao

last: LU

state: Deutschland

address: Carl-Neuberg-Str. 1,

country: Germany

institute: Hannover medical school

type: Expression profiling by high throughput sequencing

summary: The recent advances in anti-cancer treatments have led to a steady increase in the number of cancer survivors, paradoxically also enhancing the number of HF patients who suffer from the undesired cardiotoxic side effects of these anti-tumor treatments. Therapeutic options to reduce or reverse chemotherapy-induced HF are not available. Circular RNAs exhibit high druggability due to the high stability of their special closed loop structure. Circ-INSR overexpression prevents doxorubicin-induced cardiac dysfunction in preclinical murine and human models. Circ-INSR mimics produced in vitro also reduced cardiomyocyte death under doxorubicin stress, highlighting the potential of Circ-INSR-based RNA therapy for future clinical applications.

overall_design: HL-1 cells were treated with100 nM Circ-INSR siRNA and Scramble siRNA.  Total RNA was harvested, sequencing was performed in triplicates.

first: Christian

last: Bär

last: Lu

first: Thomas

last: Thum


title: Hepatic Transcriptomic Responses to Ethinylestradiol in Two Life Stages of Japanese Quail

city: Sainte-Anne-de-bellevue

first: Yeon-Seon

last: Jeon

state: Quebec

address: 21111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

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

overall_design: Refer to individual Series


title: Allergen-induced vital DNA release by the airway epithelium amplifies type-2 immunity

city: St. Paul

first: Scott

middle: M.

last: O'Grady

state: Minnesota

address: 480 Haecker Hall, 1364 Eckles Avenue

department: Animal Science

country: USA

institute: University of Minnesota

summary: This study has several novel aspects that address molecular mechanisms underlying type 2 immunity and allergic inflammation. We have identified a previously unknown response of human airway epithelial cells to allergens that involves rapid mobilization and release of nuclear DNA (nDNA) from epithelial cells that remain viable throughout the duration of exposure. We show that nDNA release occurs across the apical membrane, but not the basolateral membrane and that sequence analysis of the secreted DNA reveals proportionally higher amounts of promotor and exon sequences and lower intron and intergenic sequences compared to the normal distributions of these regions in the intact genome. Furthermore, unlike DNA release during NETosis, the extracellular DNA is highly fragmented, ranging in size from 1000-5000 bp. We discovered that allergen exposure stimulates caspase 3 by a non-canonical mechanism involving calcium-dependent activation of furin and that caspase 3 activity leads to DNA fragmentation as shown in comet assays. Using a mouse model of allergic inflammation, we demonstrate that allergen-induced type 2 immune responses are markedly reduced by pretreatment with a DNA scavenger and that nDNA release was significantly reduced in mice that were caspase 3 deficient. Moreover, we show that intranasal treatment with mouse genomic DNA combined with submaximal exposure to allergens amplified secretion of Th2 cytokines into bronchoalveolar lavage fluid while DNA alone had no effect. These results highlight a novel, allergen-dependent mechanism of regulated and rapid nDNA mobilization and release that amplifies type 2 immunity in airways and suggests that pharmacotherapies targeting this mechanism may be beneficial in reducing allergic inflammation and exacerbation of asthma.

overall_design: Human bronchial epithelial cells were exposed to Alternaria allergens for 4 hours. Extracellular DNA samples obtained from 3 biological replicates were harvested for DNA sequencing

first: Yotesawee

last: Srisomboon

first: Marissa

last: Macchietto

first: Hirohito

last: Kita


title: New xylose transporters support the simultaneous consumption of glucose and xylose in Escherichia coli

city: Tianjin

first: Xinna

last: Zhu

state: Tianjin

address: 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China

country: China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academic Sciences

summary: RNA-seq libraries were constructed for six samples, including AE1.0, AE2.0, PS1.0, PS2.0, REV1.0, REV2.0 . For preparation of RNA samples, Co-utilization were assessed using AM1 mineral salt media supplemented with glucose and xylose at each concentration of 50 g·L-1. Seed culture were grown overnight (16 h) in AM1 medium supplemented with 2% sugar. For each experiment, E. coli was grown at 37 ℃ in a pH-controlled fermentation vessel with the initial cell density at OD550nm of 0.1.Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The 150-nt paired-end RNA-seq libraries were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s Hiseq X Ten platform (Illumina, San Diego, USA).

overall_design: mRNA profiles of six samples were generated by deep sequencing, using Illumina’s Hiseq X Ten platform

first: Feiyu

last: Fan

first: Huanna

last: Qiu

first: Mengyao

last: Shao

first: Di

last: Li

first: Yong

last: Yu

first: Changhao

last: Bi

first: Xueli

last: Zhang


title: Characterization and function of transcriptional elongation during zygotic genome activation in mouse embryos

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

type: Genome binding/occupancy profiling by high throughput sequencing


title: 3D ECM-rich environment sustains the identity of naïve human iPSCs II

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

summary: The establishment of in vitro naïve human pluripotent stem cell cultures opened new perspectives for the study of early events in human development. The role of several transcription factors and signaling pathways during maintenance of human naïve pluripotency has been characterized. However, little is known about the role exerted by the extracellular matrix and its three-dimensional organization. Here, using an unbiased and integrated approach combining transcriptional, proteomic and secretome analyses, we found that naïve, but not primed, hiPSC colonies are characterized by a self-organized extracellular matrix (ECM)-rich microenvironment. Based on this, we developed a 3D culture system that supports robust long-term feeder-free self-renewal of naïve hiPSCs, and also allows direct and timely developmental morphogenesis simply by modulating the signalling environment. Our study opens new perspectives for future applications of naïve hiPSCs to study critical stages of human development in 3D starting from a single cell

overall_design: Comparison of the transcriptomic profile of human naïve iPSCs cultured on feeders or in 3D matrigel (feeder-free). At passage number 10, cells were harvested and a cell sorting was performed to obtain both the bulk population and SUSD2+-only cells. 4 replicates per each sample (bulk or SUSD2+) were collected and total RNA extracted with Qiagen RNeasy Mini Kit.

first: Elisa

last: Cesare

first: Anna

last: Urciuolo

first: Hannah

last: Stuart

first: Erika

last: Torchio

first: Cecilia

last: Laterza

first: Onelia

last: Gagliano

first: Sebastian

last: Martewicz

first: Meihua

last: Cui

last: Manfredi

first: Patrizia

last: Sabatelli

first: Stefano

last: Squarzoni

first: Irene

last: Zorzan

first: Riccardo

middle: M

last: Betto

first: Graziano

last: Martello

first: Davide

last: Cacchiarelli

first: Camilla

last: Luni

first: Nicola

last: Elvassore


title: RNA-Seq of circSLC38A1 knockdown (KD) samples in T24 cells

city: Jinan

first: chuanxin

last: wang

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

institute: The Second Hospital of Shandong University

summary: We profile gene expression upon circSLC38A1 KD in bladder cancer cell lines T24

overall_design: Cells were treated with a control scramble (scr) siRNA or a siRNA that specifically knock down the expression of circSLC38A1. mRNA profiling upon treatment were generated using QuantSeq

first: Peilong

last: Li

first: Qi

last: Mi

first: Juan

first: Chuanxin

last: Wang

first: Lutao

last: Du


title: CUT-tag analysis of T24 cells treated with a control scramble (scr) siRNA or a si-circSLC38A1

summary: This study aims to investigate whether circSLC38A1 could affect the enrichment of downstream genes by the transcription factor ILF3.T24 cells were treated with a control scramble (scr) siRNA or a siRNA that specifically knock down the expression of circSLC38A1, 48h after ttansfection, cells were collected and treated for CUT-tag.CUT-tag-Seq analysis provided evidence of ILF3 enrichment of downstream genes changes between si-NC and si-circSLC38A1 T24 cells.

overall_design: Cells were treated with a control scramble (scr) siRNA or a siRNA that specifically knock down the expression of circSLC38A1.Peaks bound by ILF3 were obtained using CUT-tag-Seq.


title: RNA sequencing of slow-and fast-cycling epidermal stem cells vs hair follicle stem cells in young vs old mice

city: Tsukuba

first: Hiromi

last: Yanagisawa

address: 1-1-1 Tennodai

department: TARA center

country: Japan

institute: University of Tsukuba

summary: This study was performed to compare transcriptomic changes in the heterogeneous mouse skin epidermal stem cells and hair follicle stem cells (HFSC) populations during chronological aging. Slow-cycling stem cells (label retaining cells, LRCs), fast-cycling stem cells (non-label retaining cells, nLRCs) and hair follicle stem cells express unique gene signatures in young age (2 months old) and have independent stem cell identities. The changes in aging stem cells lineage identities have been a topic of discussion and here we examined if distinct stem cells cycling speed affects their aging process by comparing the transcriptomes of slow-and fast-cycling epidermal stem cells. Our data indicates the loss of unique stem cell identities in aging slow or fast-cycling epidermal stem cells or HFSC at 2 years of age with intermediary effects seen at 1.5 year old.

overall_design: mRNA expression analysis from slow-and fast-cycling epidermal stem cells and hair follicle stem cells at 2 months old, 1.5 year old and 2 years old.

first: Gopakumar

last: Changarathil

first: Erna

last: Raja

first: Aiko

last: Sada


title: RNA sequencing of epidermal stem cells in Fbln7 WT vs Fbln7 KO mice

summary: This study was performed to compare the transcriptome of epidermal stem cells in young (2 months old) and middle aged (1 year old) fibulin 7 wild type (WT) compared to fibulin 7 knockout (KO) mice. Fbln7 gene was an ECM gene significantly upregulated in aging fast-cycling stem cells and this RNA-sequencing was done to investigate the role of Fbln7 in aging epidermal stem cells. Data indicates differences in gene expressions occuring between WT and KO at 1 year old but not at 2 months old, suggesting an age dependent role of fibulin 7. At 1 year old, other matrix-related and remodelling genes were affected, together with inflammatory responses of stem cells and lineage fate abberations, as in the case of 2 years old fast-cycling epidermal stem cells.

overall_design: mRNA expression analysis from epidermal stem cells of Fbln7 WT or KO mice at 2 months old compared to 1 year old

first: Lalhaba

last: Oinam


title: STAT5 is insufficient to drive steroid resistance in T-cell acute lymphoblastic leukemia despite activation of BCL2 and BCLXL upon glucocorticoid treatment

city: Utrecht

first: Rico

last: Hagelaar

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

summary: Overexpression of STAT5B_N642H mutant results in the ligand-independent activation of STAT5 signaling and STAT5 transcriptional activity, without affecting MAPK-ERK or PI3K-AKT signalling pathways. Overexpression of wild type (WT) STAT5B did not activate STAT5 signaling . Treatment with prednisolone boosts the expression of STAT5_N642H regulated genes, whereas NR3C1 can bind at gene loci of STAT5 regulated genes. Despite the steroid-enhanced upregulation of anti-apoptotic targets, the mutant cell line remaind sensitive to steroid treatment. We studied potential co-regulation and co-binding of NR3C1 and STAT5B in STAT5B_N642H and STAT5B_WT overexpressing cells, treated and untreated with prednisolone.

overall_design: NR3C1 and STAT5B binding for SUPT-1 cells overexpressing STAT5 wild type (WT) or STAT5 mutant (N642H), in the absence or presence of prednisolone treatment

first: Jules

middle: P

last: Meijerink

first: Jordy

middle: G

last: Zwet van der


title: TENT5 cytoplasmic non-canonical poly(A) polymerases regulate the innate immune response in animals

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

summary: Innate immunity, the first line of host defense against pathogens, is tightly regulated both transcriptionally and post-transcriptionally. Through global transcriptome and proteome analyses in Caenorhabditis elegans, we uncover a modulation of the expression of secreted innate immunity effector proteins by TENT5, one of a recently described family of cytoplasmic poly(A) polymerases. Direct RNA sequencing revealed that TENT-5 polyadenylates mRNAs with signal peptide-encoding sequences, that are translated at the endoplasmic reticulum. Loss of tent-5 function makes worms more susceptible to bacterial infection. Importantly, we demonstrate that the function of TENT-5 in innate immunity is evolutionarily conserved, as its orthologs, TENT5A and TENT5C are induced during macrophage activation and polyadenylate mRNAs, some of which are of genes orthologous to C. elegans TENT-5 targets. In summary, our study reveals cytoplasmic polyadenylation to be a previously unknown component of the post-transcriptional regulation of innate immunity in animals.

sample_organism:
Caenorhabditis elegans
Mus musculus

platform_organism:
Caenorhabditis elegans
Mus musculus

overall_design: Global transcriptomic analysis of L4-stage tent-5-deficient (TENT-5) and wild-type (WT) worms grown on non-pathogenic Escherichia coli strain HB101 (HB) or infected with Staphylococcus aureus NCTC 8325 (SA) for 8 hours. Other tent-5 IDs: F55A12.9, pqn-44. Transcriptomic analysis of bone marrow-derived macrophages (BMDM) treated with LPS for 8h compared to untreated samples.

first: Vladyslava

last: Liudkovska

first: Pawel

middle: S

last: Krawczyk

first: Seweryn

last: Mroczek


title: RNA-seq data of Phytophthora infestans 88069 infected tomato leaves

city: Nanjing

first: jie

last: Huang

address: NO.1 Weigang

institute: NJAU

summary: In both plants and animals, alternative splicing (AS) increases transcriptome and proteome diversity, and play roles in developmental and immune responses. However, the extent of host genome-wide AS changes and how these changes are modulated by adaptive pathogens during disease remain largely unknown. Here we examined AS changes in Phytophthora infestans infected Solanum lycopersicum leaves using paired-end illumina RNA-seq. Quite a number of AS events are independent of gene differential expression, indicating that AS changes may be an additional layer of plant immunity against pathogens. we also demonstrated that P. infestans regulates plant immunity by repressing the AS of positive regulator of plant immunity or activating the AS of susceptibility factor. Furthermore, we established a splicing reporter system and screened some P. infestans splicing regulatory effectors (SREs) that are involved in plant mRNA alternative splicing process. In addition, we demonstrated that the WY motif of SRE3 is required for AS activity and virulence function. Overall, our current data reveal that P. infestans delivers SREs to disrupts host AS regulation machinery and subsequently suppress host immunity.

overall_design: 16 RNA samples from the mock-inoculated control leaves and leaves that had been infected with P. infestans for 1d, 2d and 3 d, using four replicates for each treatment.

first: Suomeng

last: Dong

first: Jie


title: Hepatic Transcriptomic Responses to Ethinylestradiol in Two Life Stages of Japanese Quail [12-week old RNA-seq]

first: Yeon-Seon

last: Jeon

summary: Chemical risk assessment for avian species typically depends on information from toxicity tests performed in adult birds. Early-life stage (ELS) toxicity tests have been proposed as an attractive alternative, but incorporation of these data into existing frameworks will require knowledge about the similarities/differences between ELS and adult responses. The present study uses transcriptomics to assess hepatic gene expression in ELS and adult Japanese quail following exposure to ethinylestradiol (EE2). ELS quail were dosed with 0, 3.33, and 33.3 µg EE2/g egg via air cell injection prior to incubation. Adult quail were fed a single dose of EE2 at 0, 0.5, and 5 mg/kg body weight by gavage. Liver tissue was collected from 5-6 individuals per dose group at mid-incubation for ELS quail, and 4 days after dosing for adult birds. A total of 283 and 111 differentially expressed genes (DEGs) were detected in ELS and adult quail, respectively, 16 of which were shared across life stages. Shared DEGs included estrogenic biomarkers such as vitellogenin genes and Apovitellenin-1. For the dose groups that resulted in the highest number of DEGs (ELS [3.3 µg/g]; adult [5 mg/kg]), 21 and 35 KEGG pathways were enriched, respectively. Ten of these pathways were shared between life stages, including pathways involved with signaling molecules and interaction, and endocrine system. Taken together, our results suggest conserved mechanisms of action following estrogenic exposure across two life stages, with evidence from differentially expressed genes and enriched pathways. This study contributes to the development and evaluation of toxicogenomic and ELS approaches as alternative toxicity testing methods and supports the use of the ELS test for screening estrogenic chemicals.

overall_design: Liver mRNA profile of 12-week old Japanese quail following single exposure to either solvent or ethinylestradiol

first: Doug

last: Crump

first: Emily

last: Boulanger

first: Othman

last: Soufan

first: Bradley

last: Park

first: Niladri

last: Basu

first: Markus

last: Hecker

first: Jeff

last: Xia

first: Jessica

last: Head


title: Transcriptome profile of biopsies of melanoma patients responder or resistant to MAPKi (MAP-kinases inhibitors)

status: Public on Sep 30 2022

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: To analyse gene expression differences between melanoma patients responder or resistant to MAPKi (MAP-kinases inhibitors).

overall_design: Total RNA was extracted from biopsies of melanoma patients responder or resistant to MAPKi (MAP-kinases inhibitors).

first: R

first: P

last: Carotenuto


title: Effect of global Caspase-1 (Casp1) knockout (KO) on kidney gene expression in an orthologous mouse model of polycystic kidney disease (PKD)

city: Kansas City

first: Timothy

middle: Allen

last: Fields

state: KS

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

summary: We examined the effects of global Caspase-1 KO on kidney gene expression in an orthologous mouse model of PKD, which carries a homozygous knockin missense mutation, Pkd1RC/RC , that matches a human disease allele, PKD1 p.R3277C ("RC").

overall_design: Comparative gene expression profiling analysis of RNA-seq data from kidneys of 6 month-old wild-type (C57BL/6J), RC, and RC-Casp1KO mice (4 animals in each group).

first: Katherine

middle: A

first: Michael

last: Vitek


title: Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [R9_DAY7.5_10X_genomics]

city: Guangzhou, China

first: yunqing

last: Lin

address: Building 3, No.188 Kaiyuan Avenue, Huangpu District, Guangzhou

department: Center for Cell Lineage and Atlas (CCLA)

institute: Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)

summary: We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells gave rise to engraftable iHPC capable of developing into mature ILCs in the Rag2-/-Il2rg-/- recipients. The regenerative ILCs were detected in multiple tissues including intestine, lung, liver, spleen and thymus. We performed single cell RNA-seq on the sorted GFP+CD45.2+Lin- cells from the bone marrow of recipients at day 7.5 after iHPC transplantation. Single-cell transcriptome illustrated the existence of regenerative ILC-related progenitors including iLP, iILCP, iILC1/3P and iILC2P, and the cellular trajectory of regenerative ILCs development in vivo was closely resembles the natural ILCs development.

overall_design: At day 7.5 after iHPC transplantation, we sorted the GFP+CD45.2+ Lin- cells from the bone marrow of recipients for Droplet-based scRNA-seq.  Droplet-based scRNA-seq datasets were produced using a Chromium system (10x Genomics) following manufacture’s instruction.

first: Jiapin

last: Xiong

first: Yalan

last: Zhao

first: Yunqing

first: Lebei

last: Chen

first: Qitong

last: Weng

first: Chuanping

last: Shi

first: Xiaofei

last: Liu

first: Yang

last: Geng

first: Jinyong

last: Wang

first: Mengyun

last: Zhang


title: Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [WT_ILC/R9_iILC_SmartSeq2]

summary: We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells gave rise to engraftable iHPC capable of developing into mature ILCs in the Rag2-/-Il2rg-/- recipients. We performed single-cell RNA-seq on the entire regenerative CD45.2+GFP+Lin-CD127+ R9-ILC population from the intestine of Rag2-/-Il2rg-/- recipient mice and the CD45.2+Lin-CD127+ WT-ILC population from the intestine of wild type mice (C57BL/6, CD45.2). Single-cell transcriptome illustrated the transcriptome landscape of the R9-ILCs and wild type ILCs including ILC1, ILC2 and ILC3.

overall_design: mRNA profiles of 67 single CD45.2+GFP+Lin-CD127+ R9-ILCs and 31 single CD45.2+Lin-CD127+ WT-ILCs. Single regenerative R9-ILCs were sorted from the intestine of Rag2-/-Il2rg-/- recipient mice 3 weeks after transplantation. Single WT-ILCs were sorted from the intestine of wild type mouse (C57BL/6, CD45.2 strain). R9-ILCs and WT-ILCs were treated according to kit instructions of Discover-sc WTA Kit V2 (Vazyme) and TruePrepTM DNA Library Prep Kit V2 (Vazyme)


title: Single-cell transcriptomics in bone marrow delineates CD56dimGranzymeK+ subset as intermediate stage in NK cell differentiation

city: Leiden

first: Janine

last: Melsen

address: Albinusdreef 2

department: Pediatrics

institute: LUMC

summary: In this study we performed single-cell RNA sequencing on 7000 negatively enriched fresh NK and progenitor cells from one healthy bone marrow donor, that were pre-labeled with oligonucleotide-conjugated antibodies against CD34, CD117, CD56 and CXCR6. A new CD56dimGzmK+ subset was identified that shared features with CD56bright and CD56dimGzmK- NK cells based on transcriptome, phenotype (NKG2AhighCD16lowKLRG1highTIGIThigh) and functional analysis in bone marrow and blood, supportive for an intermediate subset. Pseudotime analysis positioned  CD56bright, CD56dimGzmK+ and CD56dimGzmK- cells in one differentiation trajectory, while ltNK cells were separated in a distinct lineage. Integrative analysis with bone marrow cells from the human cell atlas did not demonstrate a developmental connection between CD34+ progenitor and NK cells, implicating that bone marrow is not a site of active NK cell development.

overall_design: Single-cell RNA sequencing on negatively enriched NK and progenitor cells from one healthy bone marrow donor, combined with oligonucleotide-conjugated antibodies against CD34, CD117, CD56 and CXCR6.

middle: E

first: Monique

last: van Ostaijen-ten Dam

first: Dorenda

middle: J

last: Schoorl

first: Pieter

last: Schol

first: Daphne

last: van den Homberg

first: Arjan

middle: C

last: Lankester

first: Gertjan

last: Lugthart

first: Marco

middle: W

last: Schilham


title: Soluble CD83 improves and accelerates wound healing by the induction of pro-resolving macrophages

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hanover Medical School

summary: To facilitate the recovery process of chronic and hard-to-heal wounds novel  pro-resolving treatment options are urgently needed. We investigated the pro regenerative properties of soluble CD83 (sCD83) on cutaneous wound healing,  where sCD83 accelerated wound healing not only after systemic but also after  topical application, which is of high therapeutic interest. Cytokine profile  analyses revealed an initial upregulation of inflammatory mediators such as  TNFa and IL-1b, followed by a switch towards pro-resolving factors, including  YM-1 and IL-10, both expressed by tissue repair macrophages. These cells are  known to mediate resolution of inflammation and stimulate wound healing  processes by secretion of growth factors such as epidermal growth factor (EGF)  and vascular endothelial growth factor (VEGF), which promote vascularization  as well as fibroblast and keratinocyte differentiation. In conclusion, we have  found strong wound healing capacities of sCD83 beyond the previously  described role in transplantation and autoimmunity. This makes sCD83 a  promising candidate for the treatment of chronic- and hard-to-heal wounds

overall_design: RNA-seq analysis of  biopsies derived from sCD83 (100µg)- or mock-treated C57BL/6 mice 3 days after wound infliction via 6mm biopsy skin punches

first: Dmytro

last: Royzman


title: RNA sequencing of PDX-ALL samples using prime-seq

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

summary: We developed a model for acquired resistance to chemotherapy by treating mice carrying patient derived xenografts (PDX) of acute lymphoblastic leukemia with widely-used cytotoxic drugs for 18 consecutive weeks. Transcriptome and proteome showed shared dysregulations between replicate tumors providing putative targets to overcome resistance.

overall_design:
PDX-ALL were treated with standard combination chemotherapy in vivo. Untreated, sensitive, persisting and resistant cells of PDX-ALL cells were isolated of murine bone marrow at different disease stages and mRNA expression pattern was analyzed.
----------------------------
Authors state "Due to German law, we are not allowed to publish raw sequencing data."

first: Jeremias

last: Irmela

first: Wirth

last: Anna-Katharina

first: Herold

last: Tobias

first: Wange

last: Lucas


title: 3D ECM-rich environment sustains the identity of naïve human iPSCs [Naive_3Dvs2D_p6]

first: Lucio

last: Di Filippo

overall_design: Comparison of the transcriptomic profile of human naïve iPSCs cultured on feeders or in 3D matrigel (feeder-free). At passage number 6, cells were harvested and a cell sorting was performed to obtain both the bulk population and SUSD2+-only cells. 4 replicates per each sample (bulk or SUSD2+) were collected and total RNA extracted with Qiagen RNeasy Mini Kit.

first: Elisa

last: Cesare

first: Anna

last: Urciuolo

first: Hannah

last: Stuart

first: Erika

last: Torchio

first: Cecilia

last: Laterza

first: Onelia

last: Gagliano

first: Sebastian

last: Martewicz

first: Meihua

last: Cui

last: Manfredi

first: Patrizia

last: Sabatelli

first: Stefano

last: Squarzoni

first: Irene

last: Zorzan

first: Riccardo

last: Massimiliano Betto

first: Graziano

last: Martello

first: Davide

last: Cacchiarelli

first: Camilla

last: Luni

first: Nicola

last: Elvassore


title: Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [WT-CHILP/iR9-CHILP_SmartSeq2]

first: yunqing

last: Lin

summary: We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells (PSCs) gave rise to engraftable iHPC capable of developing into common helper innate lymphoid progenitors (CHILPs) in the Rag2-/-Il2rg-/- recipients. To assess the gene-expression pattern of the PSC-derived R9-iCHILPs, we performed single-cell RNA-seq on the regenerative CD45.2+GFP+Lin-CD127+CD135-α4β7+Sca1mid/-CD25- R9-iCHILPs from the bone marrow of Rag2-/-Il2rg-/- recipient mice and the CD45.2+Lin-CD127+CD135-α4β7+Sca1mid/-CD25- WT-CHILPs from the bone marrow of wild type mice (C57BL/6, CD45.2).

overall_design: mRNA profiles of 34 single CD45.2+GFP+Lin-CD127+CD135-α4β7+Sca1mid/-CD25- R9-iCHILPs and 29 single CD45.2+Lin-CD127+CD135-α4β7+Sca1mid/-CD25- WT-CHILPs. Single R9-iCHILP were sorted from the bone marrow of Rag2-/-Il2rg-/- recipient mice four weeks after transplantation and were treated according to kit instructions of Discover-sc WTA Kit V2 (Vazyme) and TruePrepTM DNA Library Prep Kit V2 (Vazyme).

first: Jiapin

last: Xiong

first: Yalan

last: Zhao

first: Yunqing

first: Lebei

last: Chen

first: Qitong

last: Weng

first: Chuanping

last: Shi

first: Xiaofei

last: Liu

first: Yang

last: Geng

first: Jinyong

last: Wang

first: Mengyun

last: Zhang


title: Basal transcriptomic profiling of immortalized cholangiocyte and breast cancer cell lines.

city: Bangkoknoi

first: Somponnat

last: Sampattavanich

state: Bangkok

address: 2 Wanglang Road

department: Department of Pharmacology

country: Thailand

institute: Faculty of Medicine Siriraj Hospital, Mahidol University

summary: RNA sequencing profiles of immortalized cholangiocyte and breast cancer cell lines.

overall_design: Basal, unstimulated mRNA profiles of cell lines were generated by RNA-sequencing, using Illumina Hiseq2000.

first: Supawan

last: Jamnongsong

first: Patipark

last: Kueanjinda

first: Pongsakorn

last: Buraphat

first: Phuwanat

last: Sakornsakolpat

first: Kulthida

last: Vaeteewoottacharn

first: Seiji

last: Okada

first: Siwanon

last: Jirawatnotai


title: Basal transcriptomic profiling of cholangiocarcinoma cell lines

summary: RNA sequencing profiles of cholangiocarcioma cell lines from Thai and Japanese sources.

overall_design: Basal, unstimulated mRNA profiles of cholangiocarcinoma cell lines were generated by RNA-sequencing, using Illumina Hiseq 2000.


title: Transcriptomic profiling of immortalized cholangiocyte and cholangiocarcinoma cell lines in basal and drug-treated states.

summary: RNA sequencing profiles of immortalized cholangiocyte and cholangiocarcinoma cell lines in untreated (basal), dasatinib-treated, and PD-0325901-treated states.

overall_design: Transcriptomic (mRNA) profiles of cell lines were generated by RNA-sequencing, using Illumina Hiseq2000.


title: Targeting an alternate Wilms Tumor Antigen-1 peptide bypasses immunoproteasome dependency

city: Seattle

first: Miranda

last: Lahman

state: WA

address: 1100 Fairview Ave N

department: CRD

institute: Fred Hutchinson Cancer Research Center

summary: scRNAseq reveals immune evasion from engineered T cell receptor gene therapy by acquisition of immunoproteasome deficiency in acute myeloid leukemia

overall_design: examine two timepoints for two patients as part of the second arm of a clinical trial (NCT1640301)

first: Aude

last: Chapuis

first: Valentin

last: Voillet

first: Kelly

last: Paulson

first: Philip

middle: D

last: Greenberg

first: Daniel

last: Hunter


title: Early-life exposure to tobacco smoke alters airway signaling pathways in D. melanogaster and later mortality in D. melanogaster

city: Borstel

first: Susanne

last: Krauss-Etschmann

address: Parkallee 1-44

department: Early Life Origins of Chronic Lung Diseases

institute: Resarch Center Borstel, Leibniz Lung Center

summary:
To investigate the effect of cigarette smoke exposure on gene expression in airway epithelial cells of Canton S Drosophila melanogaster larvae, we isolated the airways of cigarette smoke exposed larvae and air controls.
We then performed gene expression profiling analysis using data obtained from RNA-seq of smoke-exposed males, smoke-exposed females, air-control males and air-control females.
For each group 4 biological replicates were prepared, representing 40-50 larval airways.

overall_design: Comparative gene expression analysis of RNA-seq data for isolated trachea of smoke exposed and air controls of Canton S Drosophila melanogaster larvae, separated into males and females

first: Karolina-Theresa

last: Sirocko

first: Hanna

last: Angstmann

first: Stephanie

last: Papenmeier

first: Christina

last: Wagner

first: Michael

last: Spohn

first: Daniela

last: Indenbirken

first: Draginja

last: Kovacevic

first: Birte

last: Ehrhardt

first: Barbara

last: Hammer

first: Cecilie

last: Svanes

first: Klaus

middle: F

last: Rabe

first: Thomas

last: Roeder

first: Karin

last: Uliczka


title: Elucidating the Role of the Desmosome Protein p53 Apoptosis Effector Related to PMP-22 in Growth Hormone Tumors

status: Public on Sep 29 2022

city: AURORA

first: Katja

last: Kiseljak-Vassiliades

state: Colorado

address: 12801  E 17TH AVE, RC1SOUTH, ENDOCRINOLOGY MS8106

institute: UNIVERSITY OF COLORADO

overall_design: Our cohort consisted of 21 GH tumors (11 DG and 10 SG) and 20 samples of normal human pituitary. Total RNA was isolated using TRIzol method (Invitrogen, Carlsbad, CA), followed by clean-up with a QIAGEN Bioinformatics RNeasy mini kit (Redwood City, CA). RNA was quantified by spectrophotometry, and RNA integrity was verified using the Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA). Microarray targets were prepared and labeled from 150 ng of total RNA using the Ambion WT (Thermo Fisher Scientific, Waltham, MA) expression kit following the manufacturer’s instructions. An Affymetrix Human Gene 1.1 ST array plate (Thermo Fisher Scientific) was hybridized with 2.3 µg of fragmented and labeled single-stranded complementary DNA (cDNA). Hybridization and scanning were done on the Affymetrix GeneTitan instrument. Hybridization intensities were quantified and normalized across all arrays using the robust multichip average algorithm available as an array processing tool on Partek Genomics Suite software (Partek, St. Louis, MO).


title: Integrated stress response couples mitochondria protein translation with oxidative stress control

city: Dallas

first: GUANGYU

last: ZHANG

state: TX

address: 5323 Harry Hines Blvd

department: Cardiology

institute: UTsouthwestern Medical Center

summary: Under stress conditions, cells elicit integrated stress response (ISR) to cope with intracellular and extracellular disturbances. However, its role in ischemic heart disease remains to be elucidated. Here, we show that oxygen deprivation in cardiomyocytes triggers significant changes in protein translation. Importantly, ischemia and ischemia/reoxygenation leads to suppression of protein synthesis, which is caused by activation of the PERK/eIF2α axis of ISR. At the functional level, cardiac specific elimination of PERK exacerbates cardiac response to ischemia/reperfusion whereas selective activation of PERK in the heart confers cardioprotection against reperfusion injury. Mechanistically, PERK-mediated improvement in cardiomyocyte survival depends on suppression of protein synthesis and consequently relieves energetic demand on mitochondria. We went further to show that mitochondrial complex components are targeted by protein translation suppression, which significantly diminishes mitochondria-associated production of reactive oxygen species. Indeed, pharmacological activation of ISR protects the heart from ischemia/reperfusion damage, even after the release of occluded coronary artery, highlighting clinical significance for myocardial infarction. Taken together, these findings suggest that ISR improves cell survival through selectively suppressing mitochondrial protein synthesis and reducing oxidative stress in ischemic heart disease.

overall_design: There is 6 sample in this RNA-seq data. The first three sample are replicated sample which belong to control group. Another three sample are also replicated sanples which belong to the PERK overexpression group.All of the samples were treat with stimulated ischemia reperfusion.

first: Guangyu

last: Zhang

first: Yu

last: An

first: Zhao

middle: V

last: Wang

first: Xiaoding

first: Chao

last: Li

first: Qinfeng

first: Xiang

last: Luo

first: Yingfeng

last: Deng

last: Gillette

first: Philipp

last: Scherer


title: The Small RNA Teg41 Is a Pleiotropic Regulator of Virulence in Staphylococcus aureus [wt teg41]

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

summary: Staphylococcus aureus is Gram-positive commensal bacteria that can also cause human disease ranging from mild, self-resolving skin infections to life-threatening conditions like endocarditis, osteomyelitis, and septicemia. Previously we demonstrated a role for the S. aureus sRNA, Teg41 in regulating production of the alpha Phenol Soluble Modulin toxins (αPSMs). In this study, we further characterize the regulatory role of Teg41. RNAseq analysis shows Teg41 influences the abundance of not just the αPSM transcript, but a variety of other transcripts as well compared to wild type S. aureus. Proteomic analysis confirms that eliminating Teg41 from the cell influences both the cytoplasmic and secreted protein profile of S. aureus. Finally, we observe that the Teg41Δ3′ strain is more severely attenuated in two murine infection models than a ∆αPSM strain, indicating that Teg41 regulation reaches beyond the αPSMs. Overall, we show that Teg41 is a unique pleiotropic sRNA in S. aureus that influences several key cellular processes.

overall_design: 18 datasets in total. Two strains (wild type and Teg41D3' strain) grown to three timepoints (3, 6, 9 h), with three replicates for each strain at each timepoint.

first: Paul

last: Briaud

first: Rachel

middle: L

last: Zapf

first: Ariana

last: Mayher

first: Andrew

last: Frey

first: Lindsey

middle: N

last: Shaw

first: Jeffrey

last: Bose

middle: K


title: The Small RNA Teg41 Is a Pleiotropic Regulator of Virulence in Staphylococcus aureus [teg41 psm]

overall_design: 6 datasets in total. Two strains (Teg41D3' strain and Dpsm mutant) with three replicates for each strain.


title: Gene expression data from JUNB depleted exponentially growing U2OS-derived UTA6 cells

city: Valencia

first: Rosa

last: Farràs

state: Valencia

address: Eduardo Primo Yúfera, 12

institute: Centro de Investigación Príncipe Felipe

summary:
To address the role of JUNB in cell proliferation, we investigated the consequences of JUNB depletion using U2OS human bone osteosarcoma cells.
We used microarrays to detail the  programme of JUNB dependent gene expression underlying cell proliferation and identified distinct classes of up and down-regulated genes during this process.

overall_design: Exponentially growing U2OS-derived UTA6 cells were transfected with siJUNB or siControl for 72 hours before RNA preparation and probing of Affymetrix GeneChip Human Transcriptome 2.0 Arrays.

first: Beatriz

last: Pérez-Benavente


title: Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells

first: yunqing

last: Lin

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

overall_design: Refer to individual Series


title: The Small RNA Teg41 Is a Pleiotropic Regulator of Virulence in Staphylococcus aureus

status: Public on Sep 28 2022


title: Microarray analysis reveals changes in tRNA-derived small RNAs (tsRNAs) expression in mice with septic cardiomyopathy

city: Changsha

first: Ludong

last: Yuan

address: Department of Pathophysiology, Xiangya School of Medicine, Central South University,

institute: Central south university

summary: Our previous work has focused on the relationship between non-coding RNAs and sepsis, so we chose to use microarray analysis to investigate the relationship between septic cardiomyopathy and a novel class of small non-coding RNA - tRNA-derived small RNAs(tsRNAs). Meanwhile, tRNA-derived small RNA has been studied in many cardiovascular diseases, but the relationship between tsRNAs and septic cardiomyopathy has not been investigated. We sought to analyze changes of tsRNAs expression profile in septic cardiomyopathy and reveal an important role for tsRNAs.

overall_design: C57BL6 male wild type (WT) mice (each 9 weeks old and weighing 20-25g) were purchased from the Department of Central South University Laboratory Zoology (Changsha, China). The mice were reared with strict specific-pathogen-free (SPF) conditions (room temperature at 25℃ and 12 h light-dark cycle), and had free access to standard rodent water and food. After one week of acclimatization, the mice were randomly separated into two groups: Control and LPS24h groups. Intraperitoneal injection of LPS (10mg/kg) was used to establish the model of septic cardiomyopathy. After 24 hours, the heart and serum were collected after sacrificed by cervical dislocation. Three mice in LPS24h Group and sham-operation group were used in the follow-up microarray experiment.

first: Bimei

last: Jiang


title: JUNB ChIP-seq

summary: Genome-wide mapping of JUNB binding sites in U2OS cell line by ChIP-seq.

overall_design: Examination of JUNB binding sites in U2OS cells.


title: JUNB transcriptional regulation in cell cycle control and tumorigenic cell invasion


title: IMP1/IGF2BP1 enters extracellular vesicles in colorectal cancer

city: PORTLAND

first: Sarah

last: Andres

state: OR

address: 3181 SW Sam Jackson Pk Rd

institute: OHSU

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Gene expression was examined in n=2 HT-29 cell lines of each genotype. HT-29 null in which IMP1 was deleted using CRISPR and HT-29 IMP1OE in which IMP1 was re-expressed on the null background using a Piggybac vector system.

first: Madeline

last: Kuhn

first: Yang

last: Zhang

first: John

last: Favate

first: Mayu

last: Morita

first: Aurora

last: Blucher

first: Sukanya

last: Das

first: Shun

last: Liang

first: Ranjan

last: Preet

first: Louis

middle: R

last: Parham

first: Kathy

last: Willams

first: Sudheer

last: Molugu

first: Randall

last: Armstrong

first: Wei

first: Jeigang

last: Yang

first: Kathryn

last: Hamilton

first: Dan

last: Dixon

first: Gordon

last: Mills

first: Terry

last: Morgan

first: Premal

last: Shah


title: CXCR2 intrinsically drives the maturation and function of neutrophils in mice

city: Montpellier

first: Gwendal

last: LAZENNEC

address: 1682 rue de la Valsiere

country: France

institute: CNRS

summary: We report the comparison of gene expression of neutrophils  in the spleen of WT and -Cxcr2-/- animals

overall_design: mRNA profile was generated by deep sequencing using Novaseq 6000 SP Illumina.

last: Lazennec


title: CpxAR of Actinobacillus pleuropneumoniae Contributes to Heat Stress Response by Repressing Expression of Type IV Pilus Gene apfA

city: Wuhan

first: Feng

last: Liu

state: Hubei

address: No.1, Shizishan Street, Hongshan District, Wuhan City, Hubei Province, PRC

department: State Key Laboratory of Agricultural Microbiology

institute: Huazhong Agricultural University

summary: Acute pleuropneumonia in swine, caused by Actinobacillus pleuropneumoniae (APP), is characterized by a high and sustained fever. Fever creates an adverse environment for many bacteria leading to reduced bacterial proliferation; however, most pathogenic bacteria can tolerate higher temperatures. CpxAR is a two-component regulation system, ubiquitous among Gram-negative bacteria, which senses and responds to envelope alterations that are mostly associated with protein misfolding in the periplasm. Our previous study showed that CpxAR is necessary for the optimal growth of Actinobacillus pleuropneumoniae (APP) under heat stress. Here, we showed that mutation of the type IV pilin gene apfA rescued the growth defect of the cpxAR deletion strain under heat stress. RNA-seq analyses revealed that 265 genes were differentially expressed in the ∆cpxAR strains grown at 42°C, including genes involved in type IV pilus biosynthesis. We also demonstrated direct binding of the CpxR protein to the promoter of the apf operon by an electrophoretic mobility shift assay, and identified the binding site by a DNase I footprinting assay. In conclusion, our results revealed the important role of CpxAR in APP resistance to heat stress by directly suppressing the expression of ApfA.

overall_design: To investigate the role of CpxAR in the fever-like temperature-resistance of APP, we performed RNA-seq analysis to compare the transcriptome of the cpxAR mutant with that of the wild-type (WT) strain grown under heat stress.

last: Peng

first: Kang

last: Yan


title: THAP1 is cell type dependent regulator of SP1 family crucial for dystonic syndromes in human and rat [Striatum_RNA-seq]

city: Tuebingen

first: Fubo

last: Cheng

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

institute: University of Tuebingen

summary: THAP1 is a transcription factor and its mutations are responsible for DYT6 dystonia. However, how THAP1 mutations lead to these gene expression alterations and whether the gene expression changes are also reflected in the brain of THAP1 patients are still unclear. In this study we used epigenetic and transcriptomic approaches combined with multiple model systems to uncover the function of THAP1 and the potential pathogenesis of DYT6 dystonia. THAP1 mutations lead to dysregulation of genes mainly through regulation of SP1 family members, SP1 and SP4, in a cell type dependent manner.

overall_design: RNA-seq analysis of wild-type and THAP1 heterozygous knock-out rat striatum tissues

first: Olaf

last: Riess


title: THAP1 is cell type dependent regulator of SP1 family crucial for dystonic syndromes in human and rat

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: PROX1 Orchestrates Tumor Metabolic Plasticity by Integrating LKB1-AMPK Signaling with BCAA Catabolism (RNA-Seq)

status: Public on Sep 27 2022

city: Shanghai

first: Yan

middle: Feng

state: State...

address: No.160 Pu Jian Road, Pudong New Area

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Tumor cell metabolic plasticity is essential for tumor progression and therapeutic response, but the mechanism for regulation of metabolic plasticity remain poorly explored. Here, we identify PROX1 as an essential determinant for tumor metabolic plasticity. Notably, PROX1 is significantly reduced in response to metabolic stress or AMPK activation and is elevated in LKB1-deficient tumors in mice and human. Furthermore, the Ser79 phosphorylation of PROX1 by AMPK significantly alters its protein activity and allows a rapid recruitment of CUL4-DDB1 E3 ubiquitin ligase to promote PROX1 degradation under glucose starvation, a critical event that drives BCAA metabolism rewiring to suppress mTOR signaling. Importantly, PROX1 loss or Ser79 phosphorylation in HCC shows therapeutic resistance to metformin. Consistently, genetic ablation of PROX1 renders LKB1‐deficient KRAS-driven lung cancer resistant to phenformin treatment. Conversely, mice harboring non-phosphorylated PROX1 mutant or LKB1 mutant exhibit high PROX1 stabilization, promoting liver and lung cancer progression. Clinically, AMPK-PROX1 axis in human cancers is important for patient clinical outcomes. Collectively, our results demonstrate that the deficiency in the LKB1-AMPK axis in cancers reactivates PROX1 to sustain intracellular BCAA pools, resulting in enhanced mTOR signaling, and facilitating tumorigenesis and aggressiveness.

overall_design: we analyzed the RNA-sequencing (RNA-seq) data of liver sections from wild-type (Prox1f/f) and Prox1 liver specific knockout (Alb-Cre; Prox1f/f) mice

first: Yanfeng

first: WeiQiang

last: Gao

first: Yonglong

last: Zhang

first: Fan

last: Wang


title: THAP1 is cell type dependent regulator of SP1 family crucial for dystonic syndromes in human and rat [SHSY5Y_RNA-seq]

overall_design: RNA-seq analysis of wild-type and THAP1 heterozygous knock-out SHSY5Y cells


title: MYO10-filopodia support basement membranes at pre-invasive tumor boundaries

city: Turku

first: Emilia

last: Peuhu

address: Medisiina D5, Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of turku

summary: Myosin-X -silenced and control-silenced subcutaneous breast tumor xenografts in female NOD.scid mice

overall_design: mRNA sequencing data from subcetaneous breast tumor xenografts of MCF10DCIS.com cell lines expressing non-targeting control shRNA (4 tumors) or Myosin-X targeting shRNA  (4 tumors).

first: Johanna

last: Ivaska

first: Guillaume

last: Jacquemet


title: mesendoderm differentiation with Hif-1a overexpression and knockdown under normoxia or hypoxia

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

institute: Anhui Normal University

summary: To study the gene expression profile in the mesendoderm differerntiation of control and Hif-1a overexpression, we performed RNA-seq on the total RNA samples collected from the differentiation of control and Hif-1a overexpression AB2.2 mESCs at differentiation day 4.In addition, to study the gene expression profile in the mesendoderm differerntiation of Hif-1a knockdown under normoxia and hypoxia, we performed RNA-seq on the total RNA samples collected from the differentiation of Hif-1a knockdown AB2.2 mESCs under normoxia or hypoxia at differentiation day 4. Cell lines were  built by  infecting AB2.2 cells with lentiviruses. Each group contained three biological replicates. The expression matrix was obtained by Hisat2 followed by Stringtie.

overall_design: RNA-seq of control, Hif-1a overexpression,  shHif-1a under normoxia, and  shHif-1a under hypoxia AB2.2 cells at differentiation day 4

first: Meng

last: Li


title: PROX1 Orchestrates Tumor Metabolic Plasticity by Integrating LKB1-AMPK Signaling with BCAA Catabolism


title: THAP1 is cell type dependent regulator of SP1 family crucial for dystonic syndromes in human and rat [SHSY5Y_ChIP-seq]

overall_design: ChIP-seq analysis of wild-type and THAP1 heterozygous knock-out SHSY5Y cells


title: meRIP_seq m6A mapping

status: Public on Sep 26 2022

city: Merced

first: Michael

last: Cleary

state: CA

address: 5200 N. Lake Rd.

department: School of Natural Sciences

institute: University of California, Merced

type: Methylation profiling by high throughput sequencing

summary: meRIP_seq and Input total RNA_seq in neuroblast-biases brains, neuron-biased brains, and Mettl3 null brains

overall_design: MeRIP = anti_m6A RNA immunoprecipitation followed by RNA_seq, Input = RNA_seq (mock immunoprecip)

first: Mike


title: The NMD endonuclease SMG6 co-operates with the piRNA pathway in germ granules to shape the male germ cell transcriptome

first: Matthieu

last: Bourgery

address: Kiinamyllynkatu 10

institute: University of Turku

summary: Nonsense-mediated RNA decay (NMD) is a conserved RNA turnover pathway. Here we report that the sole endonuclease in the NMD pathway, SMG6, is essential for the male germline. Germ-cell conditional knockout (cKO) of Smg6 causes complete arrest of spermatogenesis at the early haploid cell stage. Smg6-cKO round spermatids accumulate NMD target mRNAs with long 3’ untranslated regions (UTRs) and fail to eliminate transcripts normally expressed during meiosis, the previous step in spermatogenesis. SMG6 and PIWI-interacting (pi) RNA pathway components are highly enriched in the chromatoid body (CB), a specialized cytoplasmic granule in male germ cells. This led to the intriguing possibility that the CB is a site where SMG6 and the piRNA pathway co-operate to regulate RNA metabolism. Several findings supported this hypothesis: (i) SMG6 and the piRNA-binding protein PIWIL1 have almost identical temporal expression and localization patterns, (ii) SMG6 and PIWIL1 physically interact, (iii) scores of genes upregulated in Smg6-cKO round spermatids overlap with those upregulated in Piwil1-KO round spermatids, and (iv) the phenotypic defects caused by SMG6 loss phenocopies the defects caused by PIWIL1 loss. Together, our results demonstrate that SMG6 is an essential regulator of the male germline transcriptome and highlight the CB as a molecular platform coordinating RNA regulatory pathways to control sperm production and fertility.

overall_design: A germ cell-specific Smg6 conditional knockout mouse line (Smg6-cKO) was generated by crossing a mouse line harboring loxP sites on either side of Smg6 exon 9 with a transgenic mouse line expressing the Cre recombinase under the control of the Neurogenin 3 (Ngn3)-promoter. Wild type-like littermates were used as controls. RNA sequencing was performed to analyze differential expression of long poly(A)-containing RNAs and small RNAs in pachytene spermatocytes (Spc) and round spermatids (RS), as well as differential levels of long RNAs in chromatoid bodies (CB). 1) RNA-seq of CBs: CBs were isolated from Smg6-cKO and control testes using anti-DDX4 immunoaffinity protocol. Four control samples and three Smg6-cKO samples were analyzed. For each sample, material from 2-4 individual mice were pooled. 2) RNA-seq and 3) smallRNA-seq of testicular cells: Both testes from either one adult Smg6-cKO or one adult control mouse were used to isolate RS and Spc using BSA-gradient velocity sedimentation. For RNA-seq, three biological replicates were analyzed per genotype. For smallRNA-seq, three RS and five Spc biological replicates were analyzed per genotype.

first: Tiina

last: Lehtiniemi

first: Lin

last: Ma

first: Noora

last: Kotaja


title: Magnesium Hexacyanoferrate Nanocatalyst Attenuates Chemodrug-Induced Cardiotoxicity through Ferromodulation-Driven Anti-Apoptosis

first: Minfeng

last: Huo

state: Shanghai

address: 500 Zhennan Road

institute: School of Medicine, Tongji University

summary: For investigation of the pathology associated to Doxorubicin-induced cardiotoxicity and the therapeutic mechanism enabled by Dexrazoxane and synthetic Magnesium Hexacyanoferrate Nanocatalyst.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H9c2 cells subjected with different treatments (Untreated; Doxorubicin; Doxorubicin + Dexrazoxane; Doxorubicin + MgHCF NCs).

first: Zhimin

last: Tang

first: Liying

first: Linlin

first: Haiyan

last: Guo

first: Yu

last: Chen

first: Ping

last: Gu

first: Jianlin

last: Shi


title: PROX1 Orchestrates Tumor Metabolic Plasticity by Integrating LKB1-AMPK Signaling with BCAA Catabolism (ATAC-Seq)

first: Yan

last: Liu

overall_design: Examination of chromatin accessibility of liver tissues from wild-type (Prox1f/f) and Prox1 liver specific knockout (Alb-Cre; Prox1f/f) mice.

first: Yanfeng

first: WeiQiang

last: Gao

first: Yonglong

last: Zhang

first: Fan

last: Wang


title: INO80 is required for the cell cycle control, survival, and differentiation of mouse ESCs by transcriptional regulation

city: Seoul

first: Kwonho

last: Hong

address: 120 Neungdong

country: South Korea

institute: Konkuk university

overall_design: RNA-seq of WT differentiating ESCs and Ino80 knockout differentiating ESCs

first: Seonho

last: Yoo

first: Eun

last: Lee

first: Nguyen

middle: X

last: Thang

first: Hyeonwoo

last: La

first: Hyeonji

first: Chanhyeok

last: Park

first: Dong

last: Han

first: Hyuk

last: Song

first: Jeong-Tae

last: Do

first: Youngsok

last: Choi


title: Germline ERCC6L2 mutations lead to impaired erythropoiesis and reshaping of the bone marrow niche

city: London

first: Findlay

last: Bewicke-Copley

address: John Vane Science Centre, Barts Cancer Institute

country: United Kingdom

institute: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London

summary: Despite the inclusion of inherited myeloid malignancies as a separate entity in the WHO Classification, our understanding of the etiology of familial leukemia remains limited. ERCC6L2-deficiency is a rare, life-threatening inherited condition that gives rise to bone marrow failure (BMF), myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) resulting from germline mutations in DNA repair factor ERCC6L2. Here we employ a lentiviral shRNA approach to functionally characterize the impact of ERCC6L2 loss on hematopoietic stem/progenitor cells (HSPCs) and mesenchymal stromal cells (MSCs). By combining cell culture assays and transcriptomic analysis of knockdown and ERCC6L2-mutated patient cells, we find that ERCC6L2-deficiency reduces HSPC clonogenic potential and delays erythropoiesis, while in MSCs it induces a significant lineage skewing, with increased osteogenesis and suppressed adipogenesis. Altogether, we demonstrate that ERCC6L2-deficiency impacts both hematopoietic and stromal compartments, and that our ex vivo model recapitulates patient phenotypes, providing a robust system to study germline mutations in hematological malignancies.

overall_design: 30 Samples. 6 patient bone marrow and 24 Primary cells. 2 knockdown and corresponding scramble samples per media condition, except for Erythroid media where there are 4 samples each across two batches.

first: Hannah

last: Armes

first: Ana

last: Rio-Machin

first: Anna

last: Wozniak

first: Doriana

last: Di Bella

first: Céline

last: Philippe

first: Hemanth

last: Tummala

first: Jun

first: Teresa

last: Ezponda

first: Felipe

last: Prosper

first: Inderjeet

last: Dokal

first: Tom

last: Vulliamy

first: Outi

last: Kilpivaara

first: Ulla

last: Wartiovaara-Kautto

first: Jude

last: Fitzgibbon

first: Kevin

last: Rouault-Pierre


title: Ubiquitinated PCNA drives USP1 synthetic lethality in cancer

city: Boston

first: Tianshu

last: Feng

state: MA

address: 201 Brookline Ave Suite 901

institute: Tango Therapeutics

summary: CRISPR Cas9-based functional genomics screening is a powerful approach for identifying and characterizing novel oncology drug targets. Here, we elucidate the synthetic lethal mechanism of deubiquitinating enzyme USP1 in cancers with underlying DNA damage vulnerabilities, specifically BRCA1/2 mutant tumors and a subset of BRCA1/2 wild-type (WT) tumors. In sensitive cells, pharmacological inhibition of USP1 leads to decreased DNA synthesis concomitant with the induction of S-phase-specific DNA damage. Genome-wide CRISPR-Cas9 screens identified RAD18 and UBE2K, which promote PCNA mono- and polyubiquitination respectively, as downstream mediators of USP1 dependency. The accumulation of mono- and polyubiquitinated PCNA following USP1 inhibition was associated with a reduction in total PCNA protein levels. Ectopic expression of WT and ubiquitin-dead K164R PCNA reversed USP1 inhibitor sensitivity. Our results demonstrate, for the first time, that USP1 dependency hinges on the aberrant processing of mono- and polyubiquitinated PCNA. Moreover, this mechanism of USP1 dependency extends beyond BRCA1/2 mutant tumors to a novel subset of BRCA1/2 WT cancer enriched in ovarian and lung lineages. We further show PARP and USP1 inhibition are strongly synergistic in BRCA1/2 mutant cell lines and xenograft models. We postulate USP1 dependency unveils a previously uncharacterized vulnerability linked to post-translational modifications of PCNA. Taken together, USP1 inhibition may represent a unique therapeutic strategy for BRCA1/2 mutant tumors and a subset of BRCA1/2 WT tumors.

overall_design: MDA-MB-436 and NCI-H1693  cells were divided into DMSO control, 50 nM I-138 (continuous treatment), and 200 nM I-138 (5 days on, 5 days off) arms at 72 hours post infection.

first: Antoine

last: Simoneau

first: Justin

last: Engel

first: Madhavi

last: Bandi

first: Katherine

last: Lazarides

first: Shangtao

last: Liu

first: Samuel

last: Meier

first: Ashley

middle: H

first: Hongxiang

last: Zhang

first: Binzhang

last: Shen

first: Lauren

last: Martires

first: Deepali

last: Gotur

first: Truc

last: Pham

first: Fang

last: Li

first: Lina

last: Gu

first: Shanzhong

last: Gong

first: Minjie

first: Erik

last: Wilker

first: Xuewen

last: Pan

first: Douglas

last: Whittington

first: Scott

last: Throner

first: John

middle: P

last: Maxwell

first: Yingnan

last: Chen

first: Yi

last: Yu

first: Alan

last: Huang

first: Jannik

last: Andersen


title: Systems analysis of de novo mutations in congenital heart diseases identified a protein network in the hypoplastic left heart syndrome

city: San Francisco

first: Jingjing

address: 35 Medical Center Way

institute: UCSF

summary: Congenital heart diseases (CHD) are a class of birth defects affecting ~1% of live births. These conditions are hallmarked by extreme genetic heterogeneity, and therefore, despite a strong genetic component, only a very handful of at-risk loci in CHD have been identified. We herein introduced systems analyses to uncover the hidden organization on biological networks of genomic mutations in CHD, and leveraged network analysis techniques to integrate the human interactome, large-scale patient exomes, the fetal heart spatial transcriptomes, and single-cell transcriptomes of clinical samples. We identified a highly connected network in CHD where most of the member proteins had previously uncharacterized functions in regulating fetal heart development. While genes on the network displayed strong enrichment for heart-specific functions, a sub-group, active specifically at early developmental stages, also regulates fetal brain development, thereby providing mechanistic insights into the clinical comorbidities between CHD and neurodevelopmental conditions. At a small scale, we experimentally verified previously uncharacterized cardiac functions of several novel proteins employing cellular assays and gene editing techniques. At a global scale, our study revealed developmental dynamics of the identified CHD network and observed the strongest enrichment for pathogenic mutations in the network specific to hypoplastic left heart syndrome (HLHS). Our single-cell transcriptome analysis further identified pervasive dysregulation of the network in cardiac endothelial cells and the conduction system in the HLHS left ventricle. Taken together, our systems analyses identified novel factors in CHD, revealed key molecular mechanisms in HLHS, and provides a generalizable framework readily applicable to studying many other complex diseases.

overall_design: iPSC-CMs mRNA profiles of wild type (WT) and four knockout genes (ASH2L, RBBP5, TEAD2, TLK1)

first: Yuejun

last: Wang

first: Xicheng

last: Zhang

first: Chi

last: Lam

first: Hongchao

last: Guo

first: Cheng

first: Sai

first: Joseph

last: Wu

first: Michael

last: Snyder


title: Mesoderm specification under hypoxia

first: Xiaopeng

last: Shen

summary: AB2.2 cells were subjected to hanging-drop differentiation under normoxia and hypoxia, respectively. RNA-seq were performed at differentiation day 4, when mesoderm markers peaked. Three biological replicates were set for both groups.The expression matrix was obtained by Hisat2 followed by Stringtie.

overall_design: RNA-seq of AB2.2 Cells hanging-drop differentiated for 4 days under normoxia vs hypoxia


title: EC_tagging pulse-chase to measure mRNA decay in Drosophila larval neuroblasts and neurons

last: Cleary

summary: Nascent RNA was tagged with EU, via EC feeding, in targeted cells (neuroblasts or neurons) then purified after the initial pulse labeling or after a chase using media containing excess unmodified uridine

overall_design: Neuroblasts were targeted using insc-GAL4 to drive UAS-CD:UPRT.  Neurons were targeted using nSyb-GAL4 to drive UAS-CD:UPRT.  Tagged RNA was purified following a 12 hour pulse feeding of 5-ethynylcytosine or at subsequent chase timepoints in which larvae were fed an excess of unmodified uridine: 3 hour chase, 6 hour chase, 12 hour chase.

first: Mike


title: Adaptive single-KIR+NKG2C+ NK cells expanded from superdonors show potent missing-self reactivity and efficiently control HLA-mismatched acute myeloid leukemia

city: Oslo

first: Karl-Johan

last: Malmberg

address: Ullernchausseen 70

country: Norway

institute: Oslo University Hospital

summary: Adoptive natural killer (NK) cell therapy in combination with hematopoietic stem cell transplantation (HSCT) can provide cure for acute myeloid leukemia (AML) but is in part dependent on variable NK cell reactivity. Adaptive NK cells are a highly potent NK cell subsets that can be utilized to maximize ‘missing-self’ reactivity against tumor cells. What this study adds: It describes a novel GMP-compliant protocol to expand clinically relevant numbers of adaptive NK cells from third-party ‘superdonors’. These NK cells provide strong reactivity in a mouse model of AML as well as against primary AML blasts ex vivo. How this study might affect research, practice or policy:  These pre-clinical data demonstrate the feasibility of an NK cell-based cell therapy with a non-engineered and yet highly specific NK cell population, representing the first route to clinical testing of missing-self recognition.

overall_design:
CITEseq was performed as outlined in Biolegend ‘TotalSeqTM-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol’ with minor modifications, using Biolegend oligo-conjugated antibodies and streptavidin TotalSeq reagents. Briefly, ADAPT-NK cells were stained with CD56-biotin mAb (Miltenyi, clone REA196), followed by TotalSeq antibodies and streptavidin-PE and Live/Dead Aqua (Invitrogen). Cells were subsequently sorted for viable CD56+ cells by flow cytometry.

Submitter states: Raw data uploaded to EGA with accession EGAS00001006614<<<

first: A

last: Haroun-Izquierdo

first: M

last: Vincenti

first: H

last: Netskar

first: K

first: E

last: Sohlberg


title: scRNA-seq analysis of murine periodontal ligament

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

summary: Periodontal tissue supports teeth in the alveolar bone socket via fibrous attachment of the periodontal ligament (PDL).   The PDL contains many stromal cell types, including osteoblasts, cementoblasts, periodontal fibroblasts, and stem/progenitor cells.   However, the characteristics and lineage hierarchy of each cell type remain poorly defined. Here we present a single-cell atlas of PDL, highlighting diverse cell populations in PDL.

overall_design: scRNA-seq experiment was performed using freshly isolated cells from the murine periodontal ligament

first: Tomoaki

last: Iwayama


title: Links to disease and the social environment in the aging brain transcriptome

city: Tempe

first: Kenneth

last: Chiou

state: AZ

address: 427 E Tyler Mall

department: Center for Evolution and Medicine

institute: Arizona State University

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

overall_design: Refer to individual Series


title: Transcriptomic signatures of the aging brain at bulk-tissue resolution

summary: Aging is a major risk factor for neurodegenerative diseases that impose tremendous burdens on people and societies today. To understand trajectories of neurological aging in a primate, we generated one of the most comprehensive brain transcriptional datasets to date in a unique population of naturalistic, behaviorally phenotyped rhesus macaques. We demonstrate that age-related changes in the level and variance of gene expression are associated with neural functions and neurological diseases, including Alzheimer's disease. Further, we demonstrate that higher social status in females is associated with younger relative transcriptional ages, providing a compelling link between the social environment and aging in the brain. Our findings lend insight into biological mechanisms underlying brain aging and indicate promising directions for improving social gradients in neurological health.

overall_design: 527 bulk tissue transcriptomes derived from a free-ranging population of rhesus macaques. The datataset includes 15 distinct brain regions sampled from 36 males and females spanning the natural adult rhesus macaque age distribution.

first: Alex

last: DeCasien

last: Montague

last: Platt

first: Noah

last: Snyder-Mackler


title: A sputum bioassay for airway eosinophilia using an eosinophil peroxidase aptamer

status: Public on Sep 25 2022

city: Hamilton

first: Monsur

last: Ali

state: ON

address: ETB 303, Biointerface Institute, 1280 Main St West

department: Biointerfaces Institute

institute: McMaster University

summary:
We genearted a DNA aptamer against EPX via SELEX protocol using a random DNA library and developed an assay to monitor EPX in patients spitum samples
After 15 rounds of selection, the aptamer sequences were obtained by high throughput sequencing

overall_design: A random DNA library was obtained by chemical synthesis, the target EPX was covalently immobilized on magnetic beads, then in vitro selection was caried out.  After selection, we did deep sequencing with the Illumina MiSEQ instrument which gave us the fastq files. These files were analyzed and processed by Oracle software to sort out our top scored sequences. Top 5 sequences were used in our project to evaluate binding and developing assay.

middle: M

middle: G

last: Wolfe

last: Mukharjee

last: Radford

first: Z

last: Patel

first: D

last: White

first: J

last: Milojevic

last: Capretta

first: P

last: Nair

last: Brennan


title: Systematic analysis of brain and skull ischemic injury expression profile reveals associations of tumor immune microenvironment and cell death with ischemic stroke

city: Zhanjiang

first: Wei

last: Feng

address: 236 Yuanzhu Road

institute: Central People's Hospital of Zhanjiang

summary: Background: Previous study showed that stroke may be a potential first sign of neoplasia. But the relationship between them remains unclear. Besides, ischemic stroke is a complex brain disease, which involves cell death or complex immune regulation. Thus, it is necessary to reveal the association of tumor immune microenvironment and cell death with ischemic stroke.   Methods:   Here, a photothrombosis-induced ischemic injury models of brain and skull was established. We compared and analyzed the pattern of gene expression profile between brain and skull after ischemic injury by transcriptome analysis. Further, we investigated the enrichment of relevant differential genes in cancer pathways and cell death pathways, and analyzed changes in the immune microenvironment after ischemic injury. Moreover, the pan-cancer genomic and prognosis analysis of ischemic injury related gene set were performed.   Results:   The results showed that the gene expression patterns were different in temporal and spatial locations after ischemic injury. We found that the effect on the transcriptome of the brain after skull ischemic injury was particularly large, but it could be recovered in a short period, while the effect on the skull after brain ischemic injury was long-lasting. The expression of genes related to ischemic injury is also associated with cell death and cancer hallmark pathways. In addition, changes in the abundance of immune cells indicate that brain ischemic injury may disrupt its immune microenvironment for a longer time, while skull can better balance the stability of immune microenvironment. Moreover, the brain ischemic injury-related gene sets are highly correlated with a variety of tumors, especially GBM, KIRC, LGG and UVM after stroke have a greater risk of death.   Conclusion:   This study gives us a new understanding of the role of the skull in brain ischemic injury, and reveals the association of tumor immune microenvironment and cell death with ischemic stroke.

overall_design: Transcriptome changes in brain and skull at representative time points after ischemic injury were analyzed. The mouse brain and skull tissue contains ischemic and peri-ischemic regions were harvested for RNA sequencing.

first: Chao

last: Zhang


status: Public on Sep 24 2022

city: Chicago

first: David

middle: A

last: Reed

state: IL

address: 801 South Paulina Street

department: Department of Oral Biology

institute: University of Illinois at Chicago

summary: Changes in the mechanical homeostasis of the temporomandibular joint (TMJ) can lead to the initiation and progression of degenerative arthropathies such as osteoarthritis (OA). Cells sense and engage with their mechanical microenvironment through interactions with the extracellular matrix. In the mandibular condylar cartilage, the pericellular microenvironment is composed of type VI collagen. NG2/CSPG4 is a transmembrane proteoglycan that binds with type VI collagen, and has been implicated in the cell stress response through mechanical loading-sensitive signaling networks including ERK 1/2. The objective of this study is to define the role of NG2/CSPG4 in the initiation and progression of TMJ OA and to determine if NG2/CSPG4 engages ERK 1/2 in a mechanical loading dependent manner. In vivo, we induced TMJ OA in control and NG2/CSPG4 knockout mice using a surgical destabilization approach. In control mice, NG2/CSPG4 is depleted during the early stages of TMJ OA and NG2/CSPG4 knockout mice have more severe cartilage degeneration, elevated expression of key OA proteases, and suppression of OA matrix synthesis genes. In vitro, we characterized the transcriptome and protein from control and NG2/CSPG4 knockout cells and found significant dysregulation of the ERK 1/2 signaling axis. To characterize the mechanobiological response of NG2/CSPG4, we applied mechanical loads on cell-agarose-collagen scaffolds using a compression bioreactor and illustrate that NG2/CSPG4 knockout cells fail to mechanically activate ERK 1/2 and are associated with changes in the expression of the same key OA biomarkers measured in vivo. Together, these findings implicate NG2/CSPG4 in the mechanical homeostasis of TMJ cartilage and in the progression of degenerative arthropathies including OA.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data comparing c57/BL6J and NG2/CSPG4 knockout primary mandibular fibrochondrocytes collected from 10-14 day old pups
Data analysis published in Reed et al, "NG2/CSPG4 regulates cartilage degeneration during TMJ osteoarthritis". Frontiers in Dental Medicine
Sequencing and bioinformatic analysis done by LC Sciences


title: A novel mammalian gene controls mammal-specific neuronal functioning

status: Public on Sep 23 2022

city: Berlin

first: Amit

last: Pande

address: Robert-Rössle-Straße 10

institute: Max Delbruck Center for Medicine


title: Real-time quantitative PCR analysis of  30 apple cyclophilin genes under abiotic stress

city: taian

first: Zhiwen

last: Qiao

state: China

address: shandongtaian

institute: Shandong Agricultural University

summary: Plant cyclophilins are widely involved in a variety of abiotic stress regulation processes. Thirty cyclophilin members were identified from apple and their patterns of response to abiotic stress were examined. Apple seedlings with consistent growth were selected, cultivated under drought stress conditions simulated by PEG6000, sampled according to different time periods, and quickly frozen in liquid nitrogen.Total RNAs of apple plantlets were isolated using an RNA extraction kit (Tiangen, Beijing, China).

overall_design: qPCR gene expression profiling.Six samples were obtained from apple seedlings in different time periods (0h, 1h, 3h, 6h, 12h and 24h) after drought treatment.


title: Small molecule screening identifies Syk kinase inhibition and Rutaecarpine as modulators of macrophage training and SARS CoV-2 infection

city: Bethesda

first: Iain

last: Fraser

state: MD

address: 9000 Rockville Pike, Bldg. 4, Rm. 109A, MSC-0421

department: NIAID

institute: NIH

summary: Biologically active small molecules can impart modulatory effects in immune cells, in some cases, providing extended long-term memory. In a screen of biologically active small molecules for regulators of TNF induction, we identified several compounds with the ability to induce training effects on human macrophages. Rutaecarpine was identified both as an acute and long-term modulator, enhancing LPS-induced pro-inflammatory cytokine secretion and relieving LPS tolerance in human macrophages. Rutaecarpine inhibited β-glucan-induced H3K4Me3 marks at the promoters of several proinflammatory cytokines, highlighting the potential of this molecule to modulate 47 epigenetic topology. In further work, a Syk kinase inhibitor (SYKi IV) screen hit promoted an enhanced response to LPS similar to that previously reported for β-glucan-induced training. Macrophages trained with SYKi IV showed a high degree of resistance to influenza A, multiple variants of SARS CoV-2 and OC43 coronavirus infection, highlighting a potential application of this molecule and other Syk kinase inhibitors as a prophylactic treatment for viral susceptibility.

overall_design: Primary macrophage cells treated with Syk inhibitor IV, rutaecarpine, or DMSO for 0, 4, or 2h followed by LPS unless otherwise indicated. mRNA-seq on all samples was completed in triplicate.

first: Sinu

last: John

first: Tovah

middle: E

last: Markowitz


title: Podocalyxin-Like Protein 1 Regulates Pluripotency through the Cholesterol Biosynthesis Pathway

status: Public on Sep 22 2022

city: Nankang

first: Jean

last: Lu

state: Taipei

address: 128 Academia Road, Section 2, IBMS, N401F

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: Deciphering signaling mechanisms critical for the extended pluripotent stem cell (EPSC) state and primed pluripotency is necessary for understanding embryonic development. Here, we identify a membrane protein, Podocalyxin-like protein 1 (PODXL) as being essential for extended and primed pluripotency. Alteration of PODXL expression levels affects self-renewal, protein expression of c-MYC and telomerase, and induced pluripotent stems cell (iPSC) and EPSC colony formation. PODXL is the first membrane protein reported to regulate de novo cholesterol biosynthesis, and human pluripotent stem cells (hPSCs) are more sensitive to cholesterol depletion than fibroblasts. The addition of exogenous cholesterol fully restores PODXL knockdown-mediated loss of pluripotency. PODXL affects lipid raft dynamics via the regulation of cholesterol. PODXL recruits the RAC1/CDC42/actin network to regulate SREBP1 and SREBP2 maturation and lipid raft dynamics. Single-cell RNA sequencing reveals PODXL overexpression enhanced chimerism between human cells in mouse host embryos (hEPSCs 57%). Interestingly, in the human-mouse chimeras, laminin and collagen signaling-related pathways are dominant in PODXL overexpressing cells. We conclude that cholesterol regulation via PODXL signaling is critical for ESC/EPSC.

overall_design: We performed transcriptomic analysis by using data obtained from RNA-sequencing of shRFP, shPODXL#1, shPODXL#2 and each is prepared with two biological repeats. And shRFP was served as the control cells.

first: Wei-Ju

last: Chen


title: Transcriptomic signatures of the aging brain at single-cell resolution

first: Kenneth

last: Chiou

summary: Aging is a major risk factor for neurodegenerative diseases that impose tremendous burdens on people and societies today. To understand trajectories of neurological aging in a primate, we generated one of the most comprehensive brain transcriptional datasets to date in a unique population of naturalistic, behaviorally phenotyped rhesus macaques. In this experiment, we generated 71,863 single-nucleus RNA-seq transcriptomes from the dorsolateral prefrontal cortex of 24 adult females spanning all ages. We find that, of all tested cell classes, oligodendrocytes were the only cell type to significantly increase in proportion with age. We also identify hundreds of genes that change significantly with age in one or more cell types, providing a valuable window into cell-type-specific aging in the prefrontal cortex.  Our findings lend insight into biological mechanisms underlying brain aging and indicate promising directions for improving neurological health.

overall_design: 71,863 single-nucleus transcriptomes derived from the dorsolateral prefrontal cortex of 24 female rhesus macaques spanning the natural age distribution.

first: Michael

middle: J

last: Montague

last: Platt

first: Jay

last: Shendure

last: Snyder-Mackler


title: ChIP-seq data for Glioma

city: Rochester

first: ARIJIT

last: PANDA

state: MINNESOTA

address: 200 1st street SW

institute: MAYO CLINIC

summary: We profiled glioma samples to determine the histone modifications relative to different molecular markers, as well as different germline alterations.

overall_design:
Examination of 4 histone marks in human glioma samples, H3K27ac, H3K4me1, H3K4me3, H3K36me3

>>>Submitter states that raw data files are not available due to patient privacy concerns<<<

first: Robert

middle: B

last: Jenkins

first: Kristen

last: Drucker


title: A novel mammalian gene controls mammal-specific neuronal functioning [ChIP-Exo]

summary:
In mammals brain evolution, specifically that of the cerebellum, is a focus of evolutionary change.  Here we functionally characterize the phylogenetically-restricted novel gene, piggyBac transposable element.
The ChiP-exonuclease assay protocol was performed as in Serandour's method. The libraries were quantified by using the KAPA library quantification kit for Illumina sequencing platforms (KAPA Biosystems, KK4824) and sequenced on HiSeq following the manufacturer’s protocol.

overall_design: DNA binding of PGBD1 domesticated transposase

first: Tamás

last: Raskó


title: Single-cell RNA sequencing of meningiomas

status: Public on Sep 19 2022

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Gene expression profiling via RNA-sequencing has become standard for measuring and analyzing the gene activity in bulk and at single cell level. Increasing sample sizes and cell counts provides substantial information about transcriptional architecture of samples. In addition to quantification of expression at cellular level, RNA-seq can be used for detecting of variants, including single nucleotide variants and small insertions/deletions and also large variants such as copy number variants. The joint analysis of variants with transcriptional state of cells or samples can provide insight about impact of mutations. To provide a comprehensive method to jointly analyze the genetic variants and cellular states, we introduce XCVATR, a method that can identify variants, detect local enrichment of expressed variants, within embedding of samples and cells. The embeddings provide information about cellular states among cells by defining a cell-cell distance metric. Unlike clustering algorithms, which depend on a cell-cell distance and use it to define clusters that explain cell clusters globally, XCVATR detects the local enrichment of expressed variants in the embedding space such that embedding can be computed using any type of measurement or method, for example by PCA or tSNE of the expression levels. XCVATR searches local patterns of association of each variant with the positions of cells in an embedding of the cells. XCVATR also visualizes the local clumps of small and large-scale variant calls in single cell and bulk RNA-sequencing datasets. We perform simulations and demonstrate that XCVATR can identify the enrichments of expressed variants. We also apply XCVATR on single cell and bulk RNA-seq datasets and demonstrate its utility.

overall_design: We report single-cell RNA sequencing from one meningioma patient. This one patient had two meningioma tissues from postal and frontal regions.

first: Arif

last: Harmanci

first: Akash

last: Patel

first: Tiemo

last: Klisch


title: A novel mammalian gene controls mammal-specific neuronal functioning [RNA-Seq]

first: Amit

last: Pande

summary: n mammals brain evolution, specifically that of the cerebellum, is a focus of evolutionary change.  Here we functionally characterize the phylogenetically-restricted novel gene, piggyBac transposable

overall_design: RNA sequencing of PGBD1 depleted and overexpressed neuroprogenitor cells


title: Integration of whole transcriptome spatial profiling with protein markers

status: Public on Sep 20 2022

city: New York

first: Xiang

last: Niu

state: NY

address: 413 E 69th Street

department: Medicine

institute: Weill Cornell Medical College

summary: Spatial transcriptomics and proteomics provide complementary information that independently transformed our understanding of complex biological processes. However, experimental integrations of these modalities are limited. To overcome this, we developed Spatial PrOtein and Transcriptome Sequencing (SPOTS) for high-throughput simultaneous integration of spatial transcriptomics and protein profiling. Compared to unimodal measurements, SPOTS substantially improves signal resolution and cell clustering and enhances the discovery power in differential gene expression analysis across tissue regions.

overall_design: Multimodal spatial profiling of whole transcriptomes and extracellular proteins in mouse spleen and breast cancer.

first: Nir

last: Ben-Chetrit

first: Ariel

last: Swett

first: Marlon

last: Stoeckius

first: Dan

last: Landau


title: Primary cilia contribute to the aggressiveness of atypical teratoid/rhabdoid tumors

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

summary: Atypical teratoid/rhabdoid tumor (AT/RT) is the most common malignant brain tumor in infants and is characterized by loss of nuclear SMARCB1 protein expression. Recent studies show that AT/RTs comprise three molecular subgroups with epigenetic differences, including distinct expression patterns of genes involved in ciliogenesis, but little is known on the functional role of primary cilia in the biology of AT/RT. Here, we show that primary cilia are present across all AT/RT subgroups with specific enrichment in AT/RT-TYR patient samples. Furthermore, we demonstrate that primary ciliogenesis contributes to AT/RT biology in vitro and in vivo. Specifically, we observed a significant decrease in proliferation and clonogenicity following disruption of primary ciliogenesis in AT/RT cell line models. Apoptosis was significantly increased via the induction of STAT1 and DR5 signaling, as detected by proteogenomic profiling. In a Drosophila model of SMARCB1 deficiency, concomitant knockdown of several cilia-associated genes resulted in a substantial shift of the lethal phenotype with more than 20% of flies reaching adulthood. Finally, we demonstrated significantly extended survival in an orthotopic xenograft mouse model of AT/RT upon disruption of primary ciliogenesis, confirming a survival benefit across different species with SMARCB1 deficiency. Altogether, our findings indicate that targeting primary ciliogenesis or its downstream signaling may constitute a novel therapeutic approach for AT/RT.

overall_design: siRNA-mediated knockdown of KIF3A (siKIF3A) in comparison to the control (siCTRL) in two AT/RT cell line models (BT-12 and CHLA-266)

first: Daniel

last: Picard

first: Lena

last: Bluemel


title: Anti-cancer activity of ST101, a novel antagonist of CCAAT/enhancer binding protein β

city: Harrison

first: Lila

last: Ghamsari

address: 500 Mamaroneck Ave, Suite 320

institute: Sapience Therapeutics

summary: To investigate the impact of ST101 on transcriptional activity of C/EBPβ protein, U251, A549 and MCF7 tumor cell lines were exposed to 10µM ST101 for 24 hours. Gene expression profiling analysis demonstrates attenuation of C/EBPβ target gene transcriptions, including a significant decrease in expression of survival, transcription factors and cell cycle-related proteins.

overall_design: Comparative gene expression profiling analysis of RNA-Seq data for U251, A549 and MCF7 cells. Triplicate samples of cells were either treated with ST101 or vehicle.

first: Siok

middle: F

last: Leong

first: Jim

last: Rotolo

first: Barry

last: Kappel


title: BRD8 maintains glioblastoma by epigenetic reprogramming of the P53 network [ATAC-seq]

status: Public on Sep 16 2022

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Chromatin accessibility profiling by high throughput sequencing

overall_design: Chromatin accessibility in response to BRD8 and H2AZ knockout

first: Xueqin

last: Sun

first: Alea

last: Mills


title: Single-cell transcriptome profiling of the human endometrium from patients with recurrent implantation failure

city: shanghai

first: li

last: mingqing

address: NO.419 fangxie Road, Shanghai

institute: Affiliated obstetrics and Gynecology Hospital of Fudan University

summary: Despite great advances in assisted reproductive technology (ART), unexplained recurrent implantation failure (RIF) due to disorder of endometrial receptivity still cannot be effectively avoided. More importantly, cell characteristics and cell communication that regulate endometrial receptivity and differentiation, and its disorders in RIF at the window of implantation (WOI) remain rudimentary. Here we characterized the transcriptomes of four major cells in human endometrium from healthy control and RIF patients at single-cell resolution. We discovered the dynamic change characteristics of four major endometrial fibroblast-like cells with different endometrial receptivity, reported a novel pluripotent endometrial glandular epithelial cell with high levels of progesterone receptor and exosomes, and defined a unique ITGA1+CXCR4+ NK cell for connecting endometrial nonimmune cells and immune cell infiltration at the WOI. Additionally, we developed a systematic repository of cell-cell communication for endometrial differentiation and the opening of endometrial receptivity via the ligand-receptor complexes interactions. Our study provides deeper insights into aberrant molecular and cellular characterizations, and the endometrial microenvironmental disorders of RIF patients that are potentially applicable to improve the etiological diagnosis and therapeutics of unexplained RIF.

overall_design: Endometrium mRNA profiles of the Ctrl and RIF patients were generated by deep sequencing,using 10X Genomics.

first: Mingqing

last: Li

first: Zhenzhen

last: Lai


title: RNA-seq data for Glioma

first: ARIJIT

last: PANDA

summary: We profiled glioma samples to determine the RNA expression patterns relative to different molecular markers, as well as different germline alterations.

overall_design:
Examination of expression of Total RNA following Ribodepletion in glioma tissues

>>>Submitter states that raw data files are not available due to patient privacy concerns<<<

first: Robert

last: Jenkins

first: Kristen

last: Drucker


title: RNA sequencing of AGO2 -/- Mouse embryonic fibroblast under ER stress conditions

city: Koln

first: Jorge

last: Boucas

address: Joseph-Stelzmann-Str. 9b

department: Bioinformatics

institute: Max Planck Institute for Biology of Ageing

summary: The goal of this experiment was to identify RNAs regulated by AGO2 under ER stress conditions.

overall_design: biological replicates of AGO2 -/- Mouse embryonic fibroblasts under ER stress conditons in comparison with wt Mouse embryonic fibroblasts under ER stress conditions

first: Lena-Sophie

last: Schuetter

first: Thorsten

last: Hoppe


title: Screen1 VOA6406gain-of-function meki-resistance data

status: Public on Sep 21 2022

city: Amsterdam

first: Katrien

last: Berns

state: Noord Holland

address: Plesmanlaan 121

department: Molecular Carcinogenesis

institute: The Netherlands Cancer Institute

summary: Gain and loss of function genome wide CRISPR/Cas9 screens in LGSOC cell lines to identify genes that modulate response to MEK inhibitor trametinib

overall_design: LGSOC cells were transduced with genome-wide CRISPR knockout or overexpression libraries. After selection  and recovery, a T0 sample was taken and transduced cells were plated in the absence (UT) and presence (TR) of trametinib. For resistance screens, cells were harvested after 3-4 weeks, for the enhancer screen after 10 days. Screen was performed in triplicate (I, II, III).


title: Long-term engraftment of engineered human plasma cells

status: Public on Sep 15 2022

city: Seattle

first: Rene

last: Cheng

state: WA

address: 1900 9th AVE

institute: Seattle children research institute

summary: Due to their unique longevity and capacity to secrete high levels of protein, plasma B cells play have the potential to be used as a cell therapy for protein replacement. Here, we show that ex vivo engineered human plasma cells exhibited transcriptional features of long-lived plasma cells.

overall_design: Ex vivo culture human B cell with proliferation and differentiation stimulants. Followed by CD138 isolation and CD38 isolation at day13 (D11), collecting isolated cell and keep culture this two groups (CD138+ vs CD38+) of cells. After 6 days, harvest these two groups of cells at day19(D17). All the collected cells are put in trizol and store in -20.

middle: Y

first: Richard

last: James


title: Enrichment of type I interferon signaling in colonic group 2 innate lymphoid cells in experimental colitis

city: Shinjuku-ku

first: Yohei

last: Mikami

state: Tokyo

address: Shinanomachi 35

institute: Keio University School of Medicine

summary: Group 2 innate lymphoid cells (ILC2) are enriched in colonic tissues, but their precise role under intestinal inflammation, including inflammatory bowel disease (IBD) other than helminth infection, is poorly understood. Here, we analysed global gene expression of colonic ILC2 in healthy and colitis mice and found that type I interferon (T1IFN)-stimulated genes (ISGs) are enriched in ILC2 under DSS-induced colitis. Enhancement of T1IFN signaling in ILC2 under DSS-induced colitis were correlated to downregulation in cytokine production of ILC2, such as IL-5. Blocking T1IFN signaling during colitis resulted in exaggeration of colitis both in wild-type and Rag2-deficient mice. Collectively, these findings show the potential roles of T1IFN in ILC2 contributing to the development of colitis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of colonic ILC2s  in healthy and colitis mice. Colonic ILC2s were enriched by using EasySep Mouse ILC2 Enrichment Kit (STEMCELL) and colonic ILC2s (CD127+ NK1.1−CD3−CD5-CD19-B220−KLRG1+ cells) cells  were sorted by BD FACSAria II (BD Bioscience).

first: Emi

last: Irie

first: Rino

last: Ishihara

first: Yuya

last: Hagihara

first: Ichiro

last: Mizushima

first: Takanori

last: Kanai


title: Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution

city: New York City

first: Tim

last: Stuart

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility, and other factors. However, most current single-cell-resolution methods are unable to measure more than one aspect of chromatin state in a single experiment, limiting our ability to accurately measure chromatin states. Here, we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), a new assay capable of measuring the genome-wide presence of multiple histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq utilizes recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk- and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and cells of the human immune system, demonstrating the high accuracy and sensitivity of the method. We further extend NTT-seq to enable simultaneous profiling of cell-surface protein expression alongside multimodal chromatin states to study cells of the immune system.

overall_design: NTT-seq applied to human cell culture (K562 and HEK), peripheral blood mononuclear cells (PBMCs), and bone marrow mononuclear cells (BMMCs)

first: Stephanie

last: Hao

first: Bingjie

last: Zhang

first: Levan

last: Mekerishvili

first: Dan

last: Landau

first: Silas

last: Maniatis

first: Rahul

last: Satija

first: Ivan

last: Raimondi


title: RNA sequencing of exogenous RNAi mutants under CPL-1* expression

first: Jorge

last: Boucas

summary: The goal of this experiment was to identify RNAs that are regulated by the exogenous RNAi pathway under ER stress conditions.

overall_design: biological replicates of rde-1(ne219); cpl-1*::yfp and drh-1(ok3495); cpl-1*yfp and cpl-1*yfp

first: Lena-Sophie

last: Schuetter

first: Thorsten

last: Hoppe