title: SRT1720 Inhibits the Growth of Bladder Cancer in Organoids and Murine Models through the SIRT1-HIF axis

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

country: China

institute: Sichuan University

summary: Methods: Mouse bladder tumor organoids with Trp53, Pten, Rb1 mutation and Myc, KrasG12D amplification were treated with 10μM SRT1720 and Vehicle for 12 hours respectively. RNA libraries of SRT1720 and vehicle treated mouse bladder organoids were constructed according to standard Illumina protocols, and bulk RNA-seq were performed using Illumina NovaSeq 6000 sequencing platform.

overall_design: Bulk RNA sequencing in SRT1720 and Vehicle treated mouse bladder tumor organoids.

first: Ping

last: Tan

first: Manli

last: Wang

first: Yiyun


title: Male-specific lymphomagenesis by serial inverse dysregulation of the RNA helicases DDX3X and DDX3Y [Cell Line Clones]

status: Public on Sep 01 2021

city: Cambridge

first: Daniel

middle: J

last: Hodson

address: The Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus

department: Department of Haematology

country: United Kingdom

institute: Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge

type: Expression profiling by high throughput sequencing

summary: DDX3X is a ubiquitously expressed RNA helicase involved in multiple stages of RNA biogenesis. DDX3X is frequently mutated in Burkitt lymphoma but the functional basis for this is unknown. Here, we show that loss-of-function DDX3X mutations are also commonly found in MYC-translocated diffuse large B cell lymphoma and reveal functional co-operation between mutant DDX3X and MYC. We show that DDX3X promotes translation of mRNAs encoding components of the core translational machinery, thereby driving global protein synthesis. Loss-of-function DDX3X mutations moderate MYC-driven global protein synthesis, thereby buffering MYC-induced proteotoxic stress during early lymphomagenesis. Established lymphoma cells subsequently restore full protein synthetic capacity by ectopic expression of DDX3Y, a Y-chromosome homologue that is normally expressed exclusively in testis. These findings highlight the vulnerability of MYC-driven lymphoma to proteotoxic stress and identify an unexpected male-specific mechanism of carcinogenesis, namely the commandeering of a testis-specific Y-chromosome gene to drive full malignant transformation.

overall_design: RNA-Seq sequencing data comparing DDX3X R475C knockin versus control edited cell line clones

first: Chun

last: Gong

first: Joanna

last: Krupka

first: Jie

last: Gao


title: Male-specific lymphomagenesis by serial inverse dysregulation of the RNA helicases DDX3X and DDX3Y.

overall_design: Ribo-Seq and RNA-Seq sequencing data in 2 lymphoma cell lines Mutu and U2392 following DDX3X shRNA knockdown at 2 time points: 24h and 48h; RNA-Seq sequencing data comparing DDX3X R475C knockin versus control edited cell line clones


title: Deficiency of histone methyltransferase SETD2 in liver leads to abnormal lipid metabolism and hepatocarcinoma

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Deficiency of histone methyltransferase SETD2 in liver leads to abnormal lipid metabolism and hepatocarcinoma [ChIP-Seq]

summary: H3K36me3 catalyzed by histone methyltransferase SETD2 is one of the most conserved epigenetic marks from yeast to mammals. SETD2 is frequently mutated in multiple cancers and acts as a tumor suppressor. Here, utilizing a liver-specific deletion of Setd2 mice model, we found that Setd2 depletion is sufficient to trigger hepatocarcinoma (HCC) spontaneously. Meanwhile, in a DEN-induced HCC model, Setd2 depletion significantly promoted tumor number and size. The mechanistic study showed that Setd2 suppresses HCC not only through modulating DNA damage response, but also regulating lipid metabolism in liver. Setd2 deficiency down-regulated the expression of cholesterol efflux genes and caused lipid accumulation. ChIP-Seq analysis further revealed that Setd2 deletion induced AP-1 activation in liver, which was probably trigged by accumulated cholesterol. AP-1 is a well-known oncogene in HCC and inhibits p53 in Setd2-deficient cells. Taken together, we found the role of an important epigenetic gene in regulating cholesterol homeostasis and HCC, and revealed the underlying mechanisms.

overall_design: Examination of H3K36me3 and H3K27ac in  liver tissues and tumor from Setd2 WT/KO mice.

first: Xue-jing

first: Qing-lan

first: Lin-gao

last: Ju

first: Lan-shen

last: Zhao

first: Jia-wen

last: Du

first: Lian-yun

first: Li

first: Min

last: Wu


title: ROR1-targeted delivery of miR-29b results in epigenetic reprogramming with p21-dependent cell cycle arrest

city: Columbus

first: Pearlly

last: Yan

state: Ohio

department: Comprehensive Cancer Center

country: USA

institute: The Ohio State University

summary: RNAseq analysis of purified splenic CD19+ B lymphocytes from the hRORxTCL1 mouse model treated with 2A2-miR-29b-ILP or 2A2-scramble-ILP. Moreover, 128 of the 233 differentially expressed genes are related to cell growth and proliferation.

overall_design: Gene expression profiling of engrafted murine leukemia identified reprogramming of cell cycle regulators with decreased SP1 and increased p21 expression following miR-29b treatment. The experiment was further confirmed by protein modulation leading to cell cycle arrest.

first: Natarajan

last: Muthusamy

first: Nick

last: Chiang

middle: S


title: Suppression of biofilm formation by Candida albicans and multispecies by nepodin of Rumex root via hyphal inhibition

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

summary: Biofilms are sessile microbial communities that are often resistant to conventional antimicrobial therapeutics and the host immune system. Candida albicans is an opportunistic pathogenic yeast and responsible for candidiasis. It readily colonizes host tissues and implant devices, and forms biofilms, which play an important role in pathogenesis and drug resistance. Its morphological transition from budding yeast to hyphal form and subsequent biofilm formation is regarded as the crucial factor for drug tolerance and virulence of Candida infections. In this study, nepodin (also called musizin) from Rumex japonicus root was investigated for antibiofilm, antihyphae, and antivirulence activities against fluconazole-resistant C. albicans strain. Nepodin at 2 µg/ml from Rumex plant effectively inhibited C. albicans biofilm formation by more than 90% but had no effect on planktonic cell growth. Also, Rumex root extract and nepodin inhibited hyphal growth and cell aggregation of C. albicans. Interestingly, nepodin also showed antibiofilm activity against Staphylococcus aureus or A. baumannii strains and two systems of dual biofilms of C. albicans and S. aureus or A. baumannii, respectively. Transcriptomic analysis using RNA-seq and qRT-PCR showed nepodin repressed the expressions of several hypha/biofilm related genes (ECE1, HWP1, and UME6) and overexpressed several transport genes (CDR4, CDR11, IFD6, and TPO2), which supported observed phenotypic changes.

overall_design: Gene expression changes by Nepodin in Candida albicans

first: Jin-Hyung


title: Transcriptome analysis of two near-isogenic lines with different NUE under normal nitrogen conditions in wheat

status: Public on Aug 31 2021

city: Yangzhou

first: Xinbo

last: Zhang

state: jiangsu

address: 88 University South Road

department: Agricultural College

institute: yangzhou university

summary: Nitrogen (N) is an essential nutrient element for crop productivity. Unfortunately, the nitrogen use efficiency (NUE) of crop plants gradually decreases with the increase of the nitrogen application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. The use of near-isogenic lines (NILs) in transcriptome analysis can reduce genetic background noise. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling in NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions. The results showed that 7,023 DEGs (4,738 up-regulated and 2,285 down-regulated) were identified in the 1Y vs 1W comparison. The responses of 1Y and 1W to normal nitrogen differed significantly in the transcriptional regulation mechanisms. Several genes belonging to the GS and GOGAT gene families were up-regulated in 1Y compared with 1W, and the enhanced carbon metabolism might lead 1Y to produce more C skeletons, metabolic energy, and reductants for nitrogen metabolism. A subset of transcription factors (TFs) family members such as ERF, WRKY, NAC, and MYB were also identified. Collectively, these identified candidate genes provided new information for a further understanding of the genotypic difference in NUE

overall_design: A total of twelve samples, including two treatments (N1 and N0). Each treatment was detected  at a time point with 3 replicates. Two forms of Nitrogen fertilizers treatments: normal nitrogen (1.6g pot–1),  which is referred to as N1, and a control (no nitrogen application), which is referred to as N0.


title: Cancer-associated mutations in VAV1 trigger variegated signaling outputs and drive T cell lymphomagenesis

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

summary:
Mutations in VAV1, a multifunctional signaling protein essential for T lymphocytes, have been recently found in peripheral T cell lymphoma (PTCL) and other tumors. However, their pathobiological significance remains unsettled.
Here, we show that these mutations belong to several subclasses according to the spectra of VAV1 signaling branches deregulated by them. These mutations target both known and new regulatory hotspots as well as transitional activation states of the protein. The most frequent VAV1 mutant subclass drives PTCL formation in mice by exacerbating normal VAV1- dependent signaling responses in follicular helper T cells.

overall_design: CD4+ T cells expressing either GFP or oncogenic Vav1 were introduced in immunocompromised mice and analyzed 6 months later.

first: Javier

last: Robles-Valero

first: Lucía

last: Fernández-Nevado

first: L

middle: F

first: Myriam

last: Cuadrado

first: Isabel

last: Fernández-Pisonero

first: Sonia

last: Rodríguez-Fdez

first: Elsa

middle: N

last: Astorga-Simón

first: Antonio

last: Abad

first: Rubén

last: Caloto

first: Dionisio

last: Martín-Zanca

first: Moisés

last: Mallo

first: Xosé

middle: R

last: Bustelo


title: Human Wharton's jelly-derived mesenchymal  stem cells alleviate Concanavalin A-induced fulminant hepatitis by repressing NF-κB signaling and glycolysis

city: Guangzhou

first: Yan

last: Xu

state: Guangdong

address: No. 600 Tianhe Road

institute: The Third Affiliated Hospital of Sun Yat-Sen University

summary: RNA sequencing of mouse liver tissues 24 hours after Concanavalin A (Con A) administration.

overall_design: Mouse liver tissues from Control (Ctrl), Con A, and Con A plus human Wharton's jelly-derived mesenchymal stem cells (Con A + MSCs) (4 replicates for each group) were collected and sequenced to identify the differently expressed genes and related pathways. Con A was administrated at 15mg/kg body weight and MSCs were infused 30 mins after Con A administration.

first: Qiuli

last: Liu

first: Yanli

last: Li

first: Qi


title: Inherited human c-Rel deficiency disrupts myeloid and lymphoid immunity to a variety of infectious agents

city: Doha

first: Nico

last: Marr

address: Education City

country: Qatar

institute: Hamad Bin Khalifa University

overall_design: Refer to individual Series.


title: Inherited human c-Rel deficiency disrupts myeloid and lymphoid immunity to a variety of infectious agents [primary T and B cells]

summary: We investigated transcriptional responses following in vitro stimulation of peripheral blood naive CD4+ T cells and naive B cells obtained from a patient with inherited c-Rel deficiency. Samples from unrelated healthy donors and a patient with CD40 deficiency were analyzed for comparison.

overall_design: RNA seq was performed on (i) isolated naive CD4+ T cells from 4 healthy donors and a patient with AR c-Rel deficiency, 2 hours after activation with PMA, or with different combinations of coated beads with anti-CD3, anti-CD2 or anti-CD28 Mabs; (ii) isolated naive B cells from 4 healthy donors, a patient with AR CD40 deficiency and a patient with AR c-Rel deficiency, 2 hours after activation with PMA, CD40L, or F(ab')2 goat anti-IgM.

first: Romain

last: Levy

first: Taushif

last: Khan

first: Tanwir

last: Habib

first: Andrea

last: Guennoun

first: Vivien

last: Béziat

first: David

last: Langlais

last: Lévy

first: Franck

last: Rapaport

first: Jean-Laurent

last: Casanova


title: Inherited human c-Rel deficiency disrupts myeloid and lymphoid immunity to a variety of infectious agents [EBV B-cells]

summary: We investigated transcriptional responses following in vitro stimulation of EBV-B cells derived from a patient with inherited c-Rel deficiency.

overall_design: RNA sequencing was performed on EBV-B cells from a patient with AR c-Rel deficiency, either non-transduced (NT), or transduced with an empty retrovirus (EV), or encoding the wild type c-Rel (WT), 2 hours after activation with PDBu.


title: Combination of Sulindac and Bexarotene for Prevention of Intestinal Carcinogenesis in Familial Adenomatous Polyposis

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: Texas

address: 1515 Holcombe Blvd, Unit 1360

institute: UT MD Anderson Cancer Center

summary: In this study, we performed whole transcriptomics analysis (RNA-seq) in a cohort of colorectal polyps and the matched normal tissue in FAP patients, which reveals a significant activation of inflammatory and cell proliferation pathways.

overall_design: RNA-seq data to identify potential FAP preventive targets by comparing paired colorectal adenomas (TA) to adjacent normal colonic mucosa (UM) from FAP patients.

last: Vilar


title: Effects of RDD2 overexpression in leaf blades and leaf sheaths

city: Tsukuba

first: Masao

last: Iwamoto

state: Ibaraki

address: 3-1-3 Kannondai

department: Division of Crop Genome Editing

country: Japan

institute: Institute of Agrobiological Sciences, NARO

summary: Transcriptional profiling of wild-type (WT) and RDD2 overexpressing plants (RDD2-OX) to examine function of RDD2 in rice

overall_design: WT (leaf blade), WT (leaf sheath), RDD2-OX (leaf blade), RDD2-OX (leaf sheath). Three biological replicates (Three independent lines of RDD2-OX plants).

first: M


title: Histone H3K27 demethylase negatively controls the memory formation of Ag-stimulated CD8+ T cells

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

institute: Ehime University

summary: Although the methylation status of histone H3K27 plays a critical role in CD4+ T cell differentiation and its function, the role of Utx, histone H3K27 demethylase, in the CD8+ T cell-dependent immune response remains unclear. We therefore generated T cell-specific Utx knockout (Utx KO) mice to determine the role of Utx in CD8+ T cells. Wild-type (WT) and Utx KO mice were infected with Listeria monocytogenes expressing OVA to analyze the immune response of Ag-specific CD8+ T cells upon primary and secondary infections. There was no significant differences in the primary expansion of Ag-specific CD8+ T cells between WT and Utx KO mice. However, Utx deficiency resulted in an increased secondary expansion of Ag-specific CD8+ T cells. Adoptive transferred Utx KO CD8+ T cells resulted in increased numbers of CD127hi KLRG1lo memory precursors in the primary expansion and larger numbers of memory cells. We observed a decreased gene expression of effector-associated transcription factors, including Prdm1 encoding Blimp1, in Utx KO CD8+ T cells upon primary infection. We confirmed that the tri-methylation level of histone H3K27 in the Prdm1 gene loci in the Utx KO cells was higher than in the WT cells. The treatment of CD8+ T cells with Utx-cofactor α-ketoglutarate hampered the memory formation, while Utx-inhibitor GSK-J4 enhanced the memory formation and increased the secondary expansion in WT CD8+ T cells. These data suggest that Utx negatively controls the memory formation of Ag-stimulated CD8+ T cells by epigenetically regulating the expression of genes, including Prdm1. Based on these findings, we identified a critical link between Utx and the differentiation of Ag-stimulated CD8+ T cells upon infection

overall_design: Profile of histone H3K27me3 in WT and Utx KO CD8 T cells

first: Takeshi

last: Yamada


title: These data describe bulk RNAsequencing in wild-type cerbreal organoids sampled across a time series

status: Public on Aug 30 2021

city: Munich

first: Elisabeth B

last: Binder

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

summary: Organoid transcriptomes were mapped onto brain development trajectories using bulk RNA sequencing (RNAseq) at seven successive developmental times from day-17 (2 weeks) today-158 (11 weeks)

overall_design: Bulk RNA sequencing was performed in wild-type cerebral organoids grown in vitro or 17-158 days. Three biological replicates were employes at ea ch timepoint, and randomization was performed in advance of library preparations.

first: Cristiana

last: Cruceanu

first: Elisabeth

last: Bider

first: Simone

last: Roeh


title: microRNA profile of control vehicle- and coagulation protease factor VIIa-released endothelial extracellular vesicles

status: Public on Aug 29 2021

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Coagulation protease factor VIIa (FVIIa) is shown to induce anti-inflammatory and barrier protective effects via endothelial cell protein C receptor (EPCR)-dependent, protease-activated receptor-1 (PAR1)-mediated cell signaling. FVII-EPCR-PAR1 signaling also induces the release of extracellular vesicles from endothelial cells. To obtain clues on whether microRNA (miR) carried out by FVIIa-released EEVs contribute to anti-inflammatory and barrier protective effects, we analyzed miR expression in control- and FVIIa-released EEVs by deep sequencing. These data revealed that several anti-inflammatory miR expression was higher (more than 2-fold) in FVIIa-released EEVs compared to control EEVs, the most predominant being miR10a-5p. The differential expression of miR10a-5p and several other abundant miRs were validated by qRT-PCR.  Subsequent in vitro and in vivo experiments showed that miR10a in FVIIa-released EEVs contribute to anti-inflammatory and barrier protective effects.

overall_design: EEVs were isolated from control vehicle- and FVIIa-treated human umbilical vein endothelial cells (24 h treatment). Equal number of EEVs (1x109) were subjected to microRNA analysis by deep-sequencing (UT Southwestern Core Facility)

first: Kaushik

last: Das

first: L

middle: V

last: Mohan Rao

first: Usha

last: Pendurthi


title: Rhinovirus-induced human lung tissue responses mimic respiratory disease signatures allowing evaluation of therapeutics

city: Stevenage

first: Ken

middle: A

last: Saunders

state: Hertfordshire

address: Gunnels Wood Road

institute: GSK

summary:
Human rhinovirus (RV) is a major risk factor for COPD and asthma exacerbations, but exploration of RV pathogenesis has been hampered by a lack of disease relevant model systems. We performed a detailed characterization of host mRNA responses to RV infection in human precision cut lung tissue ex vivo (comparing to previously published asthma and COPD studies) and explored the impact of antiviral treatment.
Genomic analyses revealed that RV not only induced anti-viral immune responses but also triggered changes in epithelial cell-associated pathways. Strikingly, the RV response in PCLS was reflective of gene expression changes described previously in COPD and asthma patients. While RV-induced host immune responses were abrogated by rupintrivir, RV-triggered epithelial processes were largely refractory to antiviral treatment.

overall_design: Precision cut lung slices were prepared in duplicate from 5 human donors before challenging with rhinovirus 1B or control for 24 or 72 hours, with or without addition of 100nM  pleconaril or rupintrivir to culture

first: Mark

last: Lennon

first: Edith

middle: M

last: Hessel

first: Katherina

last: Sewald

first: Armin

last: Braun


title: Deficiency of histone methyltransferase SETD2 in liver leads to abnormal lipid metabolism and hepatocarcinoma [RNA-Seq]

first: Qinglan

last: Li

overall_design: Liver tissue or tumor mRNA profiles of 8-month old wild type (WT) and Setd2 knockout  mice were generated by deep sequencing, in triplicate.

first: Xue-jing

first: Qing-lan

first: Lin-gao

last: Ju

first: Lan-shen

last: Zhao

first: Jia-wen

last: Du

first: Lian-yun

first: Li

first: Min

last: Wu


title: Thyroid hormone receptor sumoylation modulates preadipocyte proliferation and white adipose tissure stores

status: Public on Aug 27 2021

city: Los Angeles

first: Kailtyn

middle: Yan-Yun

last: Liu

state: CA

address: 10833 Le Conte Ave

department: Medicine

institute: UCLA/VA

summary: We generated sumoylation -defective mouse model carrying double mutation at mouse Thra gene, resulting in amino acids change at TRHA K283Q and K288R. We found that THRA K283/K288R (mutant) mouse has significant reducution in white adipose stores and 50% less serum leptin, compared to WT mice. The mechanims reduction in fat store is in part due to the mutant disrupts the adipocytes proliferation through delaying G1/S transition, which is the consequences of THRA mutant interfers with CREB-mediated gene expression of the cell cycle regulators, CCNA1, CCND2, Cdk2 and Cuin3.

overall_design: Global knockin generates mutation in mouse Thra gene, which produced THRA K283Q/K288R mutation. Comparing WT and mutant mice fat content ad  fat stem cells proliferation.

first: Kaitlyn

first: Gregory

last: Brent


title: RNA sequencing of siPI4KIIIβ-transfected lung cancer cells

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We speculated that Golgi fragmentation in PI4KIIIβ-deficient cells resulted from apoptosis, which initiates caspase-mediated cleavage of the Golgi ribbon at an early stage of the execution phase. Indeed, siPI4KIIIβ-transfected H23 and H2122 lung cancer cell lines demonstrated evidence of apoptosis on the basis of western blotting, flow cytometry, and RNA sequencing, which identified 717 genes up-regulated in shPI4KIIIβ-transfected H23 cells (fold-change > 1.4, P-value < 0.01 by t-test, false discovery rate<10%) that were enriched in, among other Gene Ontology terms, “positive regulation of apoptotic process” (20 genes, P=0.005), “extracellular matrix” (18 genes, P=1.3E-05), and “extracellular matrix organization” (29 genes, P=1.8E-06) (one-sided Fisher’s exact test using Gene Ontology terms). To determine whether apoptosis resulted from impairment of PI4KIIIβ-dependent secretion, we performed conditioned media transfer experiments and found that the proliferative activity of shPI4KIIIβ-transfected cells was rescued by conditioned media from PI4KIIIβ-replete, but not -deficient, cells.

overall_design: Cells from H23 lung cancer cell line were transfected with either shRNAs against human PI4KIIIβ or control shRNAs and subjected to RNA seqeuncing.

first: Fengju

last: Chen

first: Jonathan

last: Kurie


title: Single-cell sequencing reveals differential cell types in skin tissues of Liaoning Cashmere Goats and key genes related potentially to the fineness of cashmere fiber

status: Public on Aug 25 2021

city: Shenyang

first: Ying

middle: Ze

last: Wang

state: Liaoning

address: 120 Dongling Road, Shenhe District, Shenyang

institute: 沈阳农业大学

summary: we used single-cell RNA sequencing (scRNA-seq) and computational models to identify 13 skin cell types in Liaoning Cashmere Goats. We also analyzed the molecular changes by Cell Trajectory Analysis in the development process and revealed the maturation process in gene expression profile in Liaoning Cashmere Goats. Weighted gene co-expression network analysis (WGCNA) explored hub genes in cell clusters related to cashmere formation. Secondary hair follicle dermal papilla cells (SDPCs) play an important role in the growth and density of cashmere. ACTA2, a marker gene of SDPCs, was selected for immunofluorescence (IF) and western blot (WB) verification. Our results indicate that ACTA2 is mainly expressed in SDPCs, and WB results showed different expression levels. COL1A1 is a highly expressed gene in SDPCs, which was verified by IF and WB. We then selected CXCL8 of SDPCs to verify, and prove the differential expression in the coarse type and the fine type of Liaoning Cashmere Goats. Therefore, CXCL8 gene may regulate cashmere fineness. These genes may be involved in regulating the fineness of cashmere in goat secondary hair follicle dermal papilla cells, our research will provide new insights into the mechanism of cashmere growth and cashmere fineness regulation by cells.

overall_design: We used single-cell RNA sequencing (scRNA-seq) and computational models to identify 13 skin cell types in Liaoning Cashmere Goats.

first: ZEYING

last: WANG

first: YUANYUAN

last: ZHENG

first: YANRU

first: TAIYU

last: HUI

first: RUI

last: CHEN


title: Two ISREs functioning cooperatively regulate ISG expression in West Nile virus infected IFNAR-/- MEFs

city: Atlanta

first: Emilio

middle: E.

last: Espínola

state: Georgia

address: 145 Piedmont Ave SE

department: Biology

institute: Georgia State University

summary: We previously identified a subset of interferon stimulated genes (ISGs), including Irf7, Irf1, Oas1a and Oas1b, upregulated by a West Nile virus (WNV) infection in wildtype mouse embryo fibroblasts (MEFs) after viral proteins had inhibited type 1 interferon (IFN)-mediated JAK-STAT signaling and also in WNV-infected STAT1-/-, STAT2-/-, IFNAR-/-, IRF3-/-, IRF7-/-, and IRF3/7-/- MEFs. In this study, ISG upregulation by WNV infection was inhibited in RIG-I/MDA5-/- but not in single knockout MEFs. ISGs upregulation was detected in WNV-infected IRF1-/- and IRF5-/- but was minimal in IRF3/5/7-/- MEFs, suggesting redundant IRF involvement. ISG upregulation by WNV infection in IFNAR-/- MEFs was confirmed by RNA-seq. We previously showed that a single proximal interferon stimulated response element (ISRE) in the Oas1a and Oas1b promoters bound the ISGF3 complex during IFN-dependent upregulation. In this study, we used wild-type and mutant promoter luciferase reporter constructs to identify critical regions in the Oas1b and Ifit1 promoters for IFN-independent transcriptional regulation. Two ISREs were required for both promoters. Mutation of these ISREs in an Ifit1 promoter DNA probe reduced in vitro complex formation. An NF-κB inhibitor decreased Ifit1 promoter activity in cells and in vitro complex formation. IRF3 and p50 binding was detected by ChIP for four upregulated ISGs with two proximal ISREs in their promoters. The data indicate that IFN-independent ISG expression of some ISGs is upregulated by two ISREs functioning cooperatively and the binding of a complex consisting of IRF3, 5, and/or 7 and an NF-κB component(s) as well as other as yet unknown factors.

overall_design: Analysis of differentially expressed genes in mock-infected and West Nile W956-infected IFNAR-/- MEFs at 12 and 24 hours post infection

first: Dan

last: Cui

middle: E

first: Komal

last: Arora

first: Margo

last: Brinton


title: High-throughput mediation analysis of human proteome and metabolome identifies mediators of post-bariatric surgical diabetes control

status: Public on Aug 24 2021

city: Boston

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: To improve the power of mediation in high-throughput studies, here we introduce High-throughput mediation analysis (Hitman), which accounts for direction of mediation and applies empirical Bayesian linear modeling. We apply Hitman in a retrospective, exploratory analysis of the SLIMM-T2D clinical trial in which participants with type 2 diabetes were randomized to Roux-en-Y gastric bypass (RYGB) or nonsurgical diabetes/weight management, and fasting plasma proteome and metabolome were assayed up to 3 years. RYGB caused greater improvement in HbA1c, which was mediated by growth hormone receptor (GHR). GHR’s mediation is more significant than clinical mediators, including BMI. GHR decreases at 3 months postoperatively alongside increased insulin-like growth factor binding proteins IGFBP1/BP2; plasma GH increased at 1 year. Experimental validation indicates (1) hepatic GHR expression decreases in post-bariatric rats; (2) GHR knockdown in primary hepatocytes decreases gluconeogenic gene expression and glucose production. Thus, RYGB may induce resistance to diabetogenic effects of GH signaling.

overall_design:
Randomized controlled trial with n=19 assigned to RYGB or DWM, measured over time.

Raw data were not provided by SomaLogic.

first: Mary Elizabeth

last: Patti


title: mRNA stability experiments with control or CNOT1-targeting siRNA treatment in HEK293 cells

status: Public on Aug 22 2021

city: Glasgow

first: Sarah

middle: Louise

last: Gillen

address: Beatson Institute, Garscube Estate, Switchback Road, Bearsden

institute: Beatson Institute for Cancer Research

summary: Determination of mRNA half-life in HEK293 cells with and without the depletion of CNOT1.

overall_design: HEK293 cells were treated with control or CNOT1-targeting siRNA for 48hrs. Transcription was then inhibited with 1uM triptolide and RNA samples taken at multiple time points (0, 0.5, 1, 2, 4, 8 & 16 hours after transcriptional inhibition). Poly(A) selected RNA was then subject to RNA-seq. This was conducted for three biological replicates.

middle: L


title: RNA sequencing to detect the differentially expressed genes in AngII infused mice model after QDG treatment.

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The mice (n=15) were randomly divided into 3 groups: Control, Ang Ⅱ, and Ang Ⅱ+QDG groups (n = 5 for each group). Mice in Control and Ang Ⅱ groups were infused with saline or 500 ng/kg/min of Ang Ⅱ respectively, and orally administrated with saline; while mice in Ang Ⅱ + QDG group were infused with Ang Ⅱ (500 ng/kg/min) and orally administrated with 1.145 g/kg /day of QDG for 2 weeks. Then the cardiac tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with heart tissue of  control, AngII and QDG treated (n = 5 for each group ) mice to identify the differently expressed genes and related pathway.

last: Cheng

first: Aling

last: Shen

first: Zhiqing

first: Xiangyan

last: Wu

first: Xiaoping

first: Jiapeng

last: Li


title: STK4 deficiency underlies impaired interferon signaling and T cell immunity

first: Nico

last: Marr

summary: We investigated transcriptional responses following in vitro stimulation of peripheral blood mononuclear cells (PBMCs) obtained from a patient with inherited STK4 deficiency. Samples from the heterozygous parents and unrelated healthy donors with a wild-type genotype were analyzed for comparison.

overall_design: PBMCs from the STK4-deficient patient, the parents and from three healthy unrelated donors were stimulated for 2 hours either with IFNa+IFNb, or PMA+Iononycin. Each subject and condition was assessed in duplicate and samples were subjected for mRNA sequencing.

first: Andrea

last: Guennoun

first: Salim

last: Bougarn

first: Taushif

last: Khan


title: CD73+ memory CD4 T cells are a long-lived population with elevated effector function and prone to differentiate into TRM-like cells [RNA-seq]

status: Public on Aug 28 2021

city: Palo Alto

first: Fengqin

last: Fang

address: 3801 Miranda Avenue

department: Rheumatology&Immunology

institute: Stanford University

summary: The understanding of heterogeneity of human memory T cells will help to know the function, development and maintenance of memory population, then to improve the recall response or effective immunotherapy. Ecto-5’-nucleotidase CD73 expression in four subsets of memory T cells decreases with aging. The resistance to apoptosis and high expression of IL7R entitle CD73+ memory T cells to be long-lived population. We found antigen-specific memory T cells have overwhelming CD73 expression. The transcriptional and chromatin accessibility profiles indicate the elevated effector functions in CD73+ memory CD4 T cells comparing to CD73- counterparts. Homer analysis and Transcriptional factor (TF)-regulatory element-target gene triplet network clearly show the crucial role of RUNT and NR family TFs in CD73+ cells. Furthermore, CD73+ memory CD4 T cells were prone to differentiate into TRM-like cells under in-vitro sequential TCR and TGF/IL-15 signaling. The decreased percentage of CD73+ memory T cells with age leads to the less replenishment of TRM cells from peripheral blood.

overall_design: Examine the difference of transcriptome and chromatin accessibility in two memory CD4 T cell subsets (CD73+ vs CD73-)

first: Lingjie

first: Sadhana

last: Gaddam

first: Jorg

last: Goronzy


title: CD73+ memory CD4 T cells are a long-lived population with elevated effector function and prone to differentiate into TRM-like cells

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

overall_design: Refer to individual Series


title: Epigenetic therapies in ovarian cancer alter repetitive element expression in a TP53-dependent manner

status: Public on Aug 20 2021

city: Washington

first: James

last: McDonald

state: DC

address: 800 22nd St, NW, Suite 8960

institute: The George Washington University

type: Methylation profiling by high throughput sequencing


title: Locus-specific chromatin profiling of evolutionarily young transposable elements [Hi-C]

status: Public on Aug 19 2021

city: London

first: Miguel

last: Branco

address: 4 Newark Street

institute: Blizard Institute

summary: Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of Hi-ChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we show that young TEs display locus- and tissue-specific chromatin profiles in both mice and humans. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Methylated DNA was immunoprecipitated from Hi-C libraries, and ends were mapped using a pipeline (PAtChER) that uses 3D information to map repetitive reads, producing ChIP-like profiles.

first: Darren

last: Taylor

first: Robert

last: Lowe

first: Claude

last: Philippe

first: Kevin

middle: C

first: Gael

last: Cristofari


title: CD73+ memory CD4 T cells are a long-lived population with elevated effector function and prone to differentiate into TRM-like cells [ATAC-seq]

overall_design: Examine the difference of transcriptome and chromatin accessibility in two memory CD4 T cell subsets (CD73+ vs CD73-).


title: Subclone specific microenvironmental impact and drug response in refractory multiple myeloma revealed by single cell transcriptomics

status: Public on Aug 18 2021

city: Heidelberg

first: Karsten

last: Rippe

address: Im Neuenheimer Feld 280

department: Chromatin Networks

institute: German Cancer Research Center

summary: Virtually all patients with multiple myeloma become unresponsive to treatment over time. Relapsed/refractory multiple myeloma (RRMM) is accompanied by the clonal evolution of myeloma with heterogeneous genomic aberrations and profound changes of the bone marrow microenvironment (BME). However, the molecular mechanisms that drive drug resistance remain elusive. Here, we have analyzed the heterogeneous tumor cell population of 20 RRMM patients and its complex interaction network with the BME by single cell RNA-sequencing before/after treatment. Subclones with chromosome 1q-gain expressed a specific transcriptomic signature and frequently expanded during treatment. Furthermore, RRMM cells shaped an immune suppressive BME by upregulation of inflammatory cytokines and close interaction with the myeloid compartment. It was characterized by the accumulation of PD1+ γδ T-cells and tumor-associated macrophages as well as the depletion of hematopoietic progenitors. Thus, our study resolves transcriptional features of subclones in RRMM and mechanisms of microenvironmental reprogramming with implications for clinical decision-making.

overall_design: Single cell RNA-seq of tumor cells and bone marrow microenvironment in  relapsed/refractory multiple myeloma, **The submitter declares that the raw data were deposited to EGA (EGAS00001004805) due to data protection regulations.**

first: Stephan

last: Tirier

first: Simon

last: Steiger

first: Jan-Phlipp

last: Mallm

first: Alexandra

last: Poos


title: AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states in via Akt hyperactivation

city: New York

first: Li

last: Gan

state: NY

address: 413 E 69th Street

institute: Weill Cornell Medicine

summary: The hemizygous R47H variant of TREM2, a microglia-specific gene in the brain, increases risk for late-onset Alzheimer’s disease (AD). In this study, we identified a subpopulation of microglia with disease-enhancing proinflammatory signatures associated with the R47H mutation in human AD brains and tauopathy mouse brains. Using transcriptomic analysis at the single-nuclei level from AD patients with the R47H or the common variant (CV)-TREM2 with matched sex, pathology and clinical dementia status, we found that the R47H mutation was associated with cell type- and sex-specific transcriptional changes in human AD brains. Further characterization of microglia revealed that R47H-associated microglial subpopulations had enhanced inflammatory signatures reminiscent of previously-identified disease-associated microglia (DAM) and hyperactivation of AKT, one of the signaling pathways downstream of TREM2. In a newly-generated tauopathy knock-in mouse model expressing one allele of human TREM2 (hTREM2) with either the R47H mutation or CV, R47H induced and exacerbated tau-mediated spatial memory deficits in female mice. Single-cell transcriptomic analysis of microglia from these mice also revealed transcriptomic changes induced by R47H that had significant overlaps with R47H microglia in human AD brains, including robust increases in proinflammatory cytokines, activation of Akt-signaling, and elevation of a subset of disease-associated microglial signatures. Strikingly, pharmacological Akt inhibition largely reversed the enhanced inflammatory signatures induced by R47H in primary microglia treated with tau fibrils as well as rescued the tauopathy-induced synapse loss in R47H heterozygous mice. By unraveling the disease-enhancing properties of the R47H mutation in mouse and human, our findings shed light on an immune-linked AD subtype and provide new directions for modulating microglial immune responses to treat AD.

overall_design: RNA sequencing of R47H/+ and Trem2+/+ primary microglia at baseline and after tau fibril treatment with and without MK-2206 (Akt inhibitor) treatment

first: Faten

last: Sayed

first: Lay

last: Kodama

last: Fan

first: Gillian

middle: K

last: Carling

first: Joe

last: Udeochu

first: David

last: Le

first: Qingyun

last: Li

first: Lu

last: Zhou

first: Man

middle: Y

last: Wong

first: Rose

last: Horowittz

first: Pearly

last: Ye

first: Hansruedi

last: Mathys

first: Minghui

last: Wang

first: Xiang

last: Niu

first: Linas

last: Mazutis

first: Xuueqiao

last: Jiang

first: Xueting

first: Fuying

last: Gao

first: Matthew

last: Brendel

first: Maria

last: Telpoukhovskaia

first: Tara

last: Tracy

first: Georgia

last: Frost

first: Yungui

first: Yaqiao

first: Yue

last: Qiu

first: Zuolin

last: Cheng

first: Guoqang

last: Yu

first: John

last: Harrdy

first: Giovanni

last: Coppola

first: Shiaoching

last: Gong

first: Fei

first: Michael

last: DeTure

first: Bin

last: Zhang

first: Lei

last: Xie

middle: Q

last: Trajnowsski

first: Virginia

last: Lee

first: Subhash

last: Sinha

first: Dennis

middle: W

last: Dickson

first: Wenjie

last: Luo


title: Effect of laminin-332 pemphigoid IgG on the keratinocyte transcriptome

status: Public on Aug 26 2021

city: Chicago

first: Kyle

last: Amber

state: Illinois

address: 1735 W Harrison St. Lab 741

institute: Rush University Medical Center

summary: To determine the role of laminin-332 autoantibodies in inducing a pro-inflammatory and proteolytic response by keratinocytes

overall_design: Primary human keratinocytes were treated with 3mg/mL of IgG from patients with laminin-332 pemphigoi (n=4) or normal control IgG (n=3)


title: DNA Methylation Status in Mouse Liver Affected by Maternal High-fat, High-sucrose diet

city: Fukuoka

first: Tomoyo

last: Kawakubo-Yasukochi

address: 3-1-1 Maidashi

institute: Kyushu University

summary: We report that maternal high-fat, high-sucrose diet during pregnancy affects metabolic disorders on the liver of offspring via DNA hypermethylation and hypomethylation.

overall_design: Dams were fed normal diet (ND) or high-fat, high-sucrose diet (HFS) during gestational period, and liver was extracted from their pups at postnatal day 24

first: Masato

last: Hirata


title: Neurocognitive and hypokinetic movement disorder with features of parkinsonism following BCMA-targeting CAR-T cell therapy

first: Samir

last: Parekh

address: 1470 Madison Avenue, 5-114, Box 1079

department: Tisch Cancer Institute

institute: Icahn School of Medicine at Mount Sinai

summary: B-cell maturation antigen (BCMA) is a prominent tumor-associated target for chimeric antigen receptor (CAR)-T cell therapy in multiple myeloma (MM). We describe the case of a MM patient, enrolled in the CARTITUDE-1 trial (NCT03548207), who developed a progressive movement disorder with features of parkinsonism approximately three months after BCMA-targeted ciltacabtagene autoleucel CAR-T cell infusion, associated with CAR-T cell persistence in the blood and cerebrospinal fluid, and basal ganglia lymphocytic infiltration. We demonstrate BCMA expression on neurons and astrocytes in the basal ganglia of the patient. Public transcriptomic datasets further confirm BCMA RNA expression in the caudate of normal human brains, suggesting this may be an on-target effect of anti-BCMA therapy. Given reports of three patients with grade ≥3 parkinsonism on the phase 2 cilta-cel trial and of grade 3 parkinsonism in the idecabtagene vicleucel (ide-cel) package insert, our findings support close neurological monitoring of patients on BCMA-targeted T cell therapies.

overall_design: We conducted CITE-seq on peripheral blood mononuclear cells (PBMC) of 1 healthy donor and 4 patients of the CARTITUDE-1 clinical trial. Samples of trial patients were collected at variable time after CAR-T infusion (range 14-128 days). Samples were split into two aliquots and were either "stimulated" or "unstimulated". Stimulated aliquots were incubated for 3hrs at 37ºC with PMA/Ionomycin. After these incubations the 10 aliquots were hashed and pooled. Sequencing was done using Illumina NextSeq (hashtag-oligos/HTO and antibody-derived tags/ADT) over four lanes (technical replicates) and using Illumina NovaSeq S2 (gene expression/GEX) over two lanes (technical replicates).

first: Oliver

last: Van Oekelen


title: V. cholerae transcriptome without treatment and with indole or sub-MIC tobramycin

city: Paris

first: Zeynep

last: Baharoglu

address: 28 Rue du Docteur Roux

department: Génomes et Génétique

country: France

institute: Institut Pasteur

summary: We study gene expression levels of V. cholerae N16961 hapR+ corrected strain in exponential phase without and with indole or tobramycin.

sample_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: Bacterial cells were grown to OD 0.4 and RNAseq was performed.

first: Manon

last: Lang

first: Evelyne

last: Krin

first: Hugo

last: Varet

first: Odile

last: Sismeiro

first: Didier

last: Mazel


title: 5’ half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos

city: Beijing

first: Anming

last: Meng

state: Beijing

address: Tsinghuayuan Street

department: School of Life Science

institute: Tsinghua University


title: Ezh2 is essential for the generation of functional yolk sac derived erythro-myeloid progenitors.

status: Public on Aug 16 2021

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

institute: Cancer Research UK Manchester Institute


title: Ezh2 is essential for the generation of functional yolk sac derived erythro-myeloid progenitors [RNA-seq]

summary: Yolk sac (YS) hematopoiesis is critical for the survival of the embryo and a major source of tissue-resident macrophages that persist into adulthood. Here we report that the epigenetic regulator Ezh2 is essential for YS hematopoiesis but dispensable for subsequent aorta–gonad–mesonephros (AGM) blood development. Loss of Ezh2 activity in hemogenic endothelium (HE) leads to the generation of phenotypically intact but functionally deficient erythro-myeloid progenitors (EMP). Ezh2 activity is critical at the onset of the endothelial-to-hematopoietic transition generating EMPs but rapidly dispensable after that. We identified a lack of downregulation of Wnt signaling as the primary reason in the generation of non-functional EMPs. Together, our findings demonstrate a critical and specific role of Ezh2 in modulating Wnt signaling during the generation of EMPs from YS HE.

overall_design: RNA-seq profile of E10.5 yolk sac erythro-myeloid progenitors

first: Wen

middle: H

last: Neo

first: Yiran

first: Alba

last: Rodriguez-Meira

first: Emanuele

last: Azzoni

first: Christopher

last: Booth

first: Supat

last: Thongjuea

first: Marella

middle: F

last: de Bruijn

first: Sten

last: Jacobsen

first: Adam

middle: J

last: Mead


title: 5’ half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [tRNA-seq]

summary: 5’tRFls are small tRNA fragments derived from 5’ half of mature tRNAs. However, it is unknown whether 5’tRFls could feed back to regulate tRNA biogenesis. Here we show that 5’tRFlGly/GCC and 5’tRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis, dynamics of 5’tRFlGly/GCC and 5’tRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino-mediated knockdown of 5’tRFlGly/GCC or 5’tRFlGlu/CTC down-regulates tRNAGly/GCC or tRNAGlu/CTC levels respectively, and causes embryonic lethality that is efficiently rescued by co-injection of properly refolded corresponding tRNA. In zebrafish embryos, tRNA:DNA and 5’tRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically, unstable 5’tRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA genes transcription. The uncovered mechanism may be implicated in other physiological and pathological processes.

overall_design: tRNAs from wildtype zebrafish eggs and early embryos were detected by high throughput sequencing. Total RNAs from mature egg, 1cell, 256c sphere, shield and 24hpf stage embryos were extracted by Trizol reagent. Then, 60-120 nt length RNA was enriched by separation and elution from denature gel. RNA was treated with a combination of ALKB protein to remove some modifications before library preparation.

first: Luxi

last: Chen

first: Wei

last: Xu

first: Kunpeng

last: Liu

first: Zheng

last: Jiang

first: Yang

last: Han

first: Hongbin

last: Jin

first: Lin

last: Zhang

first: Weimin

last: Shen

first: Shunji

last: Jia

first: Qianwen

last: Sun


title: A fungal transcription regulator of vacuolar functions modulates Candida albicans interactions with host epithelial cells

status: Public on Aug 15 2021

city: Würzburg

first: Philipp

last: Reuter-Weissenberger

state: Bavaria

address: Josef-Schneider-Str.

institute: Institute of Molecular Infection Biology

summary: We employed RNA-Seq to identify ZCF8-dependent and ZCF8-indepenent transcriptional changes in Candida albicans cells treated with nigericin.

overall_design: Comparison of the transcriptome of Candida albicans wild-type reference strain vs. zcf8 deletion mutant treated with nigericin or a mock control. Two growth conditions, two biological replicates per condition. RNA-seq data generated with Illumina HiSeq-PE150.

first: J

last: Pérez


title: 5’ half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [small RNA-Seq, ssDRIP-seq]

first: Anming

last: Meng

overall_design:
For small RNA sequencing,  total RNA were extracted respectively from wildtype zebrafish embryos (Tübingen Strain) of 6 chosen stages, and then subjected to small RNA library preparation individually.
To investigate the distribution and stability of R-loop on genome, we performed ssDRIP-seq with S9.6 antibody, which specifically recognize RNA:DNA hybrid.  Two replicates from wildtype embryos of 256c, sphere and shield stage were collected to perform ssDRIPseq. RNaseH pre-treated genome DNA was used as negative control, which was also performed the standard ssDRIP-seq procedure. Genomic DNA extracted from these samples were fragmentated by restriction enzymes, and then immunoprecipitated by S9.6 antibody.The ssDNA strands in RNA:DNA hybrids were purified and subjected to library preparation.


title: A fungal transcription regulator of vacuolar functions modulates Candida albicans interactions with host epithelial cells [RNA-seq]

summary: We employed RNA-Seq to identify targets of regulation of the transcription regualtor ZCF8 in nitrogen-starved Candida albicans cells.

overall_design: Comparison of the transcriptome of Candida albicans wild-type reference strain vs. zcf8 deletion or a strain overproducing ZCF8. Cells were grown for 6 hours in media lacking a nitrogen source. One growth condition, two biological replicates per sample. RNA-seq data generated with Illumina HiSeq-PE150.


title: A fungal transcription regulator of vacuolar functions modulates Candida albicans interactions with host epithelial cells [ChIP-seq]

summary: We employed ChIP-Seq to identiy direct targets of regulation of the Candida albicans transcription regulator Zcf8p.

overall_design: Full genome chromatin immunoprecipitation of Candida albicans strain encoding myc-tagged Zcf8p. One growth condition, four biological replicates of the tagged strain and two replicates of the untagged control. ChIP-seq data was generated with Illumina HiSeq 2000.


title: CRISPR-Cas9 generated SARM1 knockout and epitope tagged mice reveal no role in transcription, despite confirmation of protein expression in macrophages

status: Public on Aug 14 2021

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: The aim of this study was initially to determine the mechanism by which SARM1 regulates Ccl5 expression in murine macrophages. RNA sequencing revealed that the commonly used Sarm1tm1Aidi mouse, generated by targeted gene disruption, harbours passenger genes on chromosome 11 which confound interpretation of differential gene expression. Next-generation SARM1-deficient and epitope-tagged mice generated by CRISPR/Cas9 reveal no broad role for SARM1 in transcription in macrophages or brainstem, despite SARM1 protein expression there.

overall_design: Examination of total transcribed RNA in BMDM from WT or Sarm1tm1Aidi mice (four biological replicates of each), unstimulated or stimulated for three hours with the TLR-7 ligand CL075.

first: Ciara

middle: G

last: Doran

first: Ryoichi

last: Sugisawa

first: Michael

last: Carty

first: Fiona

last: Roche

first: Claire

last: Fergus

first: Vincent

middle: P

last: Kelly

first: Andrew

last: Bowie


title: mRRBS analysis of C1qbp sufficient and deficient CD8+ T cells sorted from mice post infection with LCMV Armstrong

status: Public on Aug 21 2021

city: Xiamen

first: liu

last: kai

address: Xiang'an Campus, Xiamen University, Xiang'an District

institute: Xiamen University

summary: This study is aimed to explore whether C1qbp deficiency affects the DNA methylation status during the differentiation stage of CD8+ T cells. Transferred WT and C1qbp KO P14 cells sorted from the spleen of donor mice on day 5 post-infection with LCMV Armstrong were collected. Genomic DNA was isolated for mRRBS. mRRBS analysis provided evidence of DNA methylation changes between WT and C1qbp KO CD8+ T cells. Our study have shown that, on day 5 post-infection with LCMV Armstrong, C1qbp KO CD8+ T cells have increased level of Global DNA methylation. Moreover, C1qbp KO CD8+ T cells show hegher DNA methylation at some effector cells-signature genes.

overall_design: mRRBS analysis of transferred WT and C1qbp KO P14 cells sorted from the spleen of donor mice on day 5 post-infection with LCMV Armstrong

first: Kai

last: Liu

first: Xingyuan

last: Zhai

first: Hongkun

last: Fang


title: Angiogenin Released from ABCB5+ Stromal Precursors Improves Healing of Diabetic Wounds by Promoting Angiogenesis

status: Public on Aug 12 2021

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm

summary: Severe angiopathy is a major driver for diabetes associated secondary complications. Knowledge on underlying mechanisms essential for advanced therapies to attenuate these pathologies is limited. Injection of ABCB5+ stromal precursors (SPs) at the edge of non-healing diabetic wounds in a murine db/db model, closely mirroring human type II diabetes, profoundly accelerates wound closure. Strikingly, enhanced angiogenesis was substantially enforced by the release of the ribonuclease angiogenin from ABCB5+ SPs. This compensates for the profoundly reduced angiogenin expression in non-treated murine and human chronic diabetic wounds. Silencing of angiogenin in ABCB5+ SPs prior to injection significantly reduced angiogenesis, reduced numbers of M2 macrophages and delayed wound closure in diabetic db/db mice implying an unprecedented key role for angiogenin in tissue regeneration in diabetes. These data hold significant promise for further refining SPs-based therapies of non-healing diabetic foot ulcers and other pathologies with impaired angiogenesis.

overall_design: Total RNA was isolated either from FACS sorted HUVEC co-culture with wildtype and db/db murine dermal fibroblasts or artery and vein tissues from wildtype and db/db mice. Total  from total skin was first rRNA depleted using either Ribominus Eukaryotic system v2 kit (ThermoFisher Scientific). rRNA depleted RNA was subjected to preparation of Illumina compatible RNA-seq libraries using NEBNext Ultra II Directional RNA Library Prep Kit (NEB). RNA-seq libraries were quality controlled through Qiaxcel advanced system (Qiagen) and finally measured by Qubit fluorimeter (ThermoFisher Scientific). Validated libraries were sequenced on Illumia Novaseq 6000 system using S1 and S2 kit (2x 100 cycles) (MLL Dx GmbH) .


title: Locus-specific chromatin profiling of evolutionarily young transposable elements [HiChIP]

first: Miguel

middle: R

last: Branco

overall_design: Methylated DNA was immunoprecipitated from Hi-C libraries, and ends were mapped using a pipeline (PAtChER) that uses 3D information to map repetitive reads, producing ChIP-like profiles.

first: Darren

last: Taylor

first: Robert

last: Lowe

first: Claude

last: Philippe

first: Kevin

last: Cheng

first: Gael

last: Cristofari


title: Locus-specific chromatin profiling of evolutionarily young transposable elements

overall_design: Refer to individual Series


title: Short duplex RNAs induce potent immunostimulation via  Hoogsteen G-G base pairing-mediated dimerization

city: Boston

first: Haiqing

last: Bai

address: 5th floor, Center for Life Science, 3 Blackfan Circle

institute: Wyss Institute

summary: Here we describe a new class of immunostimulatory short duplex RNAs that potently induce production of type I interferon (IFN-I), and particularly IFN-β, in a wide range of human cell types via end-to-end dimerization, direct binding to RIG-I, and activation of the RIG-I/IRF3  pathway. These RNAs require a minimum of 20 base pairs, lack any sequence or structural  characteristics of known immunostimulatory RNAs, and instead require a unique conserved  sequence motif (sense strand: 5’-C, antisense strand: 3’-GGG) that mediates the self-assembly  of end-to-end RNA dimers by Hoogsteen G-G base-pairing. The presence of terminal hydroxyl  or monophosphate groups, blunt or overhanging ends, or terminal RNA or DNA bases also did  not affect their ability to induce IFN-I production. Immune stimulation mediated by these duplex  RNAs results in broad spectrum inhibition of infections by many respiratory viruses with  pandemic potential, including SARS-CoV-2, SARS-CoV, MERS-CoV, and influenza A, as well  as the common cold virus HCoV-NL63 in cell lines and in human Lung Chips that mimic organlevel  lung pathophysiology. These novel immunostimulatory motifs potentially could be  harnessed to create broad-spectrum antiviral therapeutics, but they should be avoided when  designing siRNAs to minimize immunological side effects.

overall_design: A549 cells were transfected with RNA-1, RNA-2 or a scrambled dsRNA control, collected for mRNA isolation at 48 h later

first: Donald

last: Ingber


title: Distinct exosomal miRNA profiles from BALF and lung tissue from COPD and IPF patients

status: Public on Aug 13 2021

city: Rochester

first: Irfan

last: Rahman

address: 601 elmwood ave

department: Environmental Medicine

institute: University of Rochester Medical Center

summary:
Exosomal miRNAs have been studied in relation to many diseases. However, there is little to no knowledge regarding the miRNA population of BALF or the lung tissue derived exosomes in COPD and IPF. Considering this, we determined and compared the miRNA profiles of BALF and lung tissue-derived exosomes from healthy non-smokers, healthy smokers, and patients with COPD and IPF.
NGS results identified three differentially expressed miRNAs in the BALF, while one in the lung-derived exosomes from COPD patients as compared to healthy non-smokers. Of these, we found three- and five-fold downregulation of miR-122-5p amongst the lung tissue-derived exosomes from COPD patients as compared to healthy non-smokers and smokers, respectively. Interestingly, there were key 55 differentially expressed miRNAs in the lung tissue-derived exosomes of IPF patients compared to non-smoking controls.

overall_design: miRNA profiling of BALF and lung-tissue derived exosomes from healthy non-smokers, smokers, COPD patients and IPF patients

first: Gagandeep

last: Kaur

first: Krishna

last: Maremanda

first: Michael

last: Campos

first: Hitendra

middle: S

last: Chand

first: Feng

last: Li

first: Nikhil

last: Hirani

first: Haseeb

last: Siddiqi


title: An oncomicropeptide Regulates translation in leukemia

city: Guangzhou

first: Wen-Tao

last: Wang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

summary: We identified an oncomicropeptide that was enriched on ribosomes and regulated translation. We further performed the ribosome profiling and RNA-seq libraries sequenced to globally identify the mRNAs that the peptie targeted. Interestingly, the ribo-seq data has shown that a large number of mRNAs were significantly downregulated in the peptide-knockdown samples. Finally, we discovered that high expression of the peptide supported a specific translation program to facilitate cancer progression.

overall_design: Sh-NC and sh-Speptide MOLM-13 cells used

first: Yue-Qin

last: Chen

first: Lin-Yu

last: Sun

first: Cai

last: Han


title: Ezh2 is essential for the generation of functional yolk sac derived erythro-myeloid progenitor [CUT&RUN]

first: Georges

last: Lacaud

overall_design: RNA-seq, ATAC-seq and CUT&RUN profile of E10.5 yolk sac erythro-myeloid progenitors

first: Wen

last: Neo

first: Yiran

last: Meng

first: Alba

last: Rodriguez-Meira

first: Muhammad

middle: Z

last: Fadlullah

first: Christopher

middle: A

last: Booth

first: Emanuele

last: Azzoni

first: Supat

last: Thongjuea

first: Marella

last: de-Bruijn

first: Sten

last: Jacobsen

first: Adam

last: Mead


status: Public on Aug 04 2021

city: Nanjing

first: gui

middle: Hong

last: La

address: XuanWu

institute: Nanjing Agricultural University

summary: Transcriptome of Arabidopsis thaliana mem1-1 mutant and Col-0 under normal and 200ppm MMS treatment conditions, respectively

overall_design: 4 sets of data, each of them containing 2 biological replicates

first: Honggui

first: Qianqian

first: Yumei


title: Metastasis-entrained eosinophils enhance lymphocyte-1 mediated anti-tumor immunity

status: Public on Aug 06 2021

city: ROSH HAAYIN

first: Shai

last: Dulberg

address: Maayan 5, apt 47

department: Department of Pathology

country: Israel

institute: Tel Aviv University

summary: The recognition of the immune system as a key component of the tumor microenvironment (TME) led to promising therapeutics. Since such therapies benefit only subsets of patients, understanding the activities of immune cells in the TME is required. Eosinophils are an integral part of the TME especially in mucosal tumors.Nonetheless, their role in the TME and the environmental cues that direct their activities are largely unknown, especially in metastasis. We report that breast cancer-driven lung metastasis is characterized by resident and recruited eosinophils. Eosinophil recruitment to the metastatic lung was regulated by G protein coupled receptor signaling but independent of CCR3. Functionally, eosinophils promoted lymphocyte-mediated anti53 tumor immunity. Transcriptome and proteomic analyses identified the TME rather than intrinsic differences between eosinophil subsets as a key instructing factor directing anti tumorigenic eosinophil activities. Specifically, TNF-a/IFN-g-activated eosinophils facilitated CD4+ and CD8+ T cell infiltration and promoted anti-tumor immunity. Collectively, we identify a mechanism by which the TME entrains eosinophils to adopt anti-tumorigenic properties, which may lead to the development of eosinophil-targeted therapeutics.

overall_design: Cancer cell lines were injected to the tail vein of mouse and located at the lungs. The whole lung was removed and EOS cells were extracted using flow cytometry.

first: Sharon

last: Grisaru-Tal

first: Lir

last: Beck

first: Chunyan

last: Zhang

first: Michal

last: Itan

first: Soroor

last: Hediyeh-zadeh

first: Julie

last: Caldwell

first: Perri

last: Rozenberg

first: Avishay

last: Dolitzky

first: Shmuel

last: Avlas

first: Inbal

last: Hazut

first: Yaara

last: Gordon

first: Ophir

last: Shani

first: Shlomo

last: Tsuriel

first: Motti

last: Gerlic

first: Neta

last: Erez

first: Nicolas

last: Jacquelot

first: Gabrielle

middle: T

last: Belz

first: Marc

middle: E

last: Rothenberg

first: Melissa

last: Davis

first: Hua

last: Yu

first: Tamar

last: Geiger

first: Asaf

last: Madi

first: Ariel

last: Munitz


title: PKM2-TMEM33 axis regulates lipid homeostasis in cancer cells by controling SCAP stability

city: Madison

first: Wei

last: Xu

state: WI

address: 7459 WIMR II 1111 Highland Ave.

institute: UW-Madison

summary:
Purpose:  The goals of this study are to investigate the effect of PKM2 KO or TMEM33 overexpression on genes expression.
Methods: Fresh PKM2 KO MCF7, PKM2 KO MDA-MB-231 and TMEM33 OE MDA-MB-231 cell pellets, and their respective parental cells, were used for RNA extraction. RNA sequencing libraries were prepared using the Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer’s instructions. Each library was sequenced in single read mode, 1 x 50 bp, using the HiSeq4000 platform. Sequencing reads were aligned to human genome (hg38) by STAR (version 2.5.2b).  Expression levels of genes annotated in GENCODE (version 24 for PKM2 KO and their parental cells; version 27 for TMEM33 OE and their control cells) were quantified by RSEM (version 1.3.0).  Parameters of STAR and RSEM were set following ENCODE’s long RNA-seq processing pipeline.  Differentially expressed genes were identified by DESeq2 (version 1.24.0) under the requirement of at least two-fold changes and an adjusted p-value < 0.05.
Results: Differential gene expression analyses identified 269 and 504 significantly up-regulated and 204 and 289 significantly down-regulated genes in MDA-MB-231 and MCF7 PKM2 KO cells compared to their parental cells (>=2-fold, adjusted P value < 0.05); Gene set enrichment analysis (GSEA) showed that cholesterol homeostasis and fatty acid metabolism were among the top down-regulated pathways in MDA-MB-231 TMEM33 OE cells. Moreover, the differential gene expression profiles between PKM2 KO and TMEM33 OE cell lines were positively correlated. Notably, the mRNAs of genes related to cholesterol homeostasis were decreased in both PKM2 KO and TMEM33 OE cells.
Conclusions: TMEM33 acts as a downstream effector of PKM2 that regulates activation of SREBPs and lipid metabolism.

overall_design: Breast cancer cell lines mRNA profiles of parental and PKM2KO or TMEM33 overexpression cells

first: Fabao

last: Liu

first: Peng


title: Characterization of m6A in domesticated yak testis before and after sexual maturity

status: Public on Aug 03 2021

city: Lanzhou

first: Xingdong

last: Wang

address: The west lake street

institute: CAAS

summary: N6-methyladenosine (m6A) is the most common internal modification of eukaryotic mRNA, and its potential regulatory role has recently been identified in mammals, plants, and yeast. However, little is known about the role of m6A methylation in mammalian sexual maturation. In this study, the testicular tissue of yaks before and after sexual maturation was taken as the research object, and the m6A map of testicular tissue of yaks before and after sexual maturation was obtained through the preliminary experiment and MERIP-seq. The results showed that only spermatogonial cells and some primary spermatocytes could be seen in the testicular tissue of yak before sexual maturation, while spermatogenic cells at different stages could be seen in the testicular tissue after sexual maturation. It was found that the methylation level was higher after sexual maturation than before by detecting the expression of methylation related enzymes and the overall methylation level of testis. There were 1438 differential methylation peaks before and after sexual maturation, of which 1226 were significantly up-regulated and 212 were significantly down-regulated after sexual maturation. Through annotation, it was found that the differential methylation peaks were mainly concentrated in the exon region, followed by 3'UTR, and finally 5'UTR. KEGG pathway analysis showed that Homologous recombination, Notch signaling pathway, Growth hormone synthesis and other signaling pathways may be related to testicular development and maturation. m6A modification was positively correlated with mRNA abundance, suggesting that m6A plays a regulatory role in mammalian sexual maturation. In this study, we reported for the first time the m6A transcriptional map of yak testis, providing a starting point for revealing the function of m6A that may affect the development of yak testis.

overall_design: Detection of m6A in Yak testis before and after sexual maturity

first: Jie

last: Pei

first: Shaoke

last: Guo

first: Xian


title: The m6A RNA modification modulates gene expression and fibrosis-related pathways in hypertrophic scar

status: Public on Aug 08 2021

city: wuxi

first: Siyu

address: Street of River Deans, Binhu District, Wuxi City

institute: Jiangnan University Affiliated Hospital

summary: Purpose: To systematically analyze the overall m6A modification pattern in hyperplastic scars (HS).  Methods: The m6A modification patterns in HS and normal skin (NS) tissues were described by m6A sequencing and RNA sequencing, and subsequently bioinformatics analysis was performed. The m6A-related RNA was immunoprecipitated and verified by real-time quantitative PCR.  Results: The appearance of 14,791 new m6A peaks in the HS sample was accompanied by the disappearance of 7,835 peaks. The unique m6A-related genes in HS were thus associated with fibrosis-related pathways. We identified the differentially expressed mRNA transcripts in HS samples with hyper-methylated or hypo-methylated m6A peaks.  Conclusion: This study is the first to map the m6A transcriptome of human HS, which may help clarify the possible mechanism of m6A-mediated gene expression regulation.

overall_design: Hypertrophic scar (SC, n=3) and  normal skin (SK, n=3) samples

first: Fenglai

last: Yuan


title: transcriptomics during pollen development in Oryza longistaminata

status: Public on Jul 31 2021

city: Nanchang

first: Xiaosong

last: Peng

state: Jiangxi

address: No. 1101, Zhimin Avenue, Nanchang Economic Development Zone

department: College of Agronomy

institute: Jiangxi Agricultural University

summary: Oryza longistaminata is an African wild rice species that possesses special traits for breeding applications. Self-incompatibility is the main cause of sterility in O. longistaminata, but here we demonstrated that its pollen fertility and vitality are normal. Lipid and carbohydrate metabolism were active throughout pollen development. In this study, transcriptomics quantitative analysis was used to investigate the profiles of genes related to lipid and carbohydrate metabolism in 4-, 6- and 8.5-mm O. longistaminata spikelets before flowering. We documented cytological changes throughout important stages of anther development, including changes in reproductive cells as they formed mature pollen grains through meiosis and mitosis. RNA-seq and proteome association analysis indicated that fatty acids were converted to sucrose after the 6-mm spikelet stage, based on the abundance of most key enzymes of the glyoxylate cycle and gluconeogenesis. In conclusion, our study provides novel insights into the pollen viability of O. longistaminata at the transcriptome level, which can be used to improve the efficiency of male parent pollination in hybrid rice breeding applications.

overall_design: Transcriptome examination of three stages during pollen development in Oryza longistaminata

first: Yue

last: Sun


title: Epigenetic therapies in ovarian cancer alter repetitive element expression in a TP53-dependent manner: MeDIPseq and MREseq

city: Washington

first: James

last: McDonald

address: 800 22nd St, NW, Suite 8960

institute: The George Washington University

summary:
Abstract: Epithelial ovarian carcinomas (OC) are particularly deadly due to intratumoral heterogeneity, resistance to standard-of-care therapies, and poor response to alternative treatments such as immunotherapy. Targeting the OC epigenome with DNA methyltransferase inhibitors (DNMTi) or histone deacetylase inhibitors (HDACi) increases immune signaling and recruits CD8+ T cells and NK cells to fight OC in murine models. This increased immune activity is caused by increased transcription of repetitive elements (RE) that form double-stranded RNA (dsRNA) and trigger an interferon response. To understand which REs are affected by epigenetic therapies in OC, we assessed the effect of DNMTi and HDACi on OC cell lines and patient samples. Subfamily-level (TEtranscripts) and individual locus-level (Telescope) analysis of REs showed that DNMTi treatment upregulated more REs than HDACi treatment. Upregulated REs were predominantly LTR and SINE subfamilies, and SINEs exhibited the greatest loss of DNA methylation upon DNMTi treatment. Cell lines with TP53 mutations exhibited significantly fewer upregulated REs with epigenetic therapy than wild type TP53 cell lines. This observation was validated using isogenic cell lines; the TP53 mutant cell line had significantly higher baseline expression of REs but upregulated fewer upon epigenetic treatment. In addition, p53 activation increased expression of REs in wild type but not mutant cell lines. These data give a comprehensive, genome-wide picture of RE chromatin and transcription-related changes in OC after epigenetic treatment and implicate p53 in RE transcriptional regulation.
The data in this data series represent the analysis of MeDIP-seq and MRE-seq libraries generated from the A2780, Hey, Kuramochi, and TykNu ovarian carcinoma cell lines. Each cell line was treated with ITF-2357 (HDACi), 5-azacytidine (DNMTi), or a combination of both. MeDIP-seq and MRE-seq libraries were sequenced, trimmed, aligned, and analyzed with methylMnM and methylCRF software.

overall_design: Single replicates of MeDIP-seq and MRE-seq were performed in A2780, Hey, Kuramochi, and TykNu cell lines given mock, ITF-2357, 5-azacytidine, or ITF-2357/5-azacytidine combined.

middle: I

first: Noor

last: Diab

first: Elisa

last: Arthofer

last: Hadley

first: Tomas

last: Kanholm

first: Uzma

last: Rentia

first: Stephanie

last: Gomez

first: Angela

first: Erin

last: Grundy

first: Olivia

last: Cox

first: Michael

last: Topper

first: Xiaoyun

last: Xing

first: Pamela

middle: L

last: Strissel

first: Reiner

last: Strick

first: Ting

first: Stephen

middle: B

last: Baylin

first: Katherine

last: Chiappinelli


title: Continuous clonal labeling reveals uniform progenitor potential in the adult exocrine pancreas

status: Public on Aug 05 2021

city: Amsterdam

first: Leandro

last: Moreno

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

summary: The tissue dynamics that govern maintenance and regeneration of the pancreas remain largely unknown. In particular, the presence and nature of a cellular hierarchy remains a topic of debate. Previous lineage tracing strategies in the pancreas relied on specific marker genes for clonal labeling, which left other populations untested and failed to account for potential widespread phenotypical plasticity. Here we employed a tracing system that depends on replication-induced clonal marks. We found that in homeostasis, steady acinar replacement events characterize tissue dynamics, to which all acinar cells have an equal ability to contribute. Similarly, regeneration following pancreatitis was best characterized by an acinar self-replication model, as no evidence for a cellular hierarchy was detected. In particular, rapid regeneration in the pancreas was found to be driven by an accelerated rate of acinar fission-like events. Together these results provide a comprehensive and quantitative model of cell dynamics in the exocrine pancreas.

overall_design: Examination of single cell RNA expression profiles of labeled and non-labeled pancreatic cells during homeostasis and during cerulein-induced pancreatitis (9DPI)

first: Louis

last: Vermeulen

first: Maarten

last: Bijlsma

first: Sophie

last: Lodestijn

first: Tom

last: Bosch


title: MiRNA regulation of T cell exhaustion in cutaneous T cell lymphoma [cell line]

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: To study how miRNAs (miRs) regulate T cell exhaustion, we performed miRseq analysis, and RNAseq on CTCL cell lines.

overall_design: miRNA and RNA seq analysis in CTCL cell lines (H9, HH, HuT78, MyLa) and healthy control

first: Zhen

last: Han

first: Christiane

last: Querfeld


title: Convalescent COVID-19 patients without comorbidities display similar immunophenotypes over time despite divergent disease severities

status: Public on Jul 30 2021

city: Graz

first: Silvia

last: Fibi-Smetana

state: Styria

address: Stremayrgasse 16

department: Biomedical Informatics

country: Austria

institute: Graz University of Technology

summary: COVID-19, the disease caused by SARS-CoV-2 infection, can assume a highly variable disease course, ranging from asymptomatic infection, which constitutes the majority of cases, to severe respiratory failure. This implies a diverse host immune response to SARS-CoV-2. However, the immunological underpinnings underlying these divergent disease courses remain elusive. We therefore set out to longitudinally characterize immune signatures of convalescent COVID-19 patients stratified according to their disease severity. Our unique convalescent COVID-19 cohort consists of 74 patients not confounded by comorbidities. This is the first study of which we are aware that excludes immune abrogations associated with non-SARS-CoV-2 related risk factors of disease severity. Patients were followed up and analyzed longitudinally (2, 4 and 6 weeks after infection) by high-dimensional flow cytometric profiling of peripheral blood mononuclear cells (PBMCs), in-depth serum analytics, and transcriptomics. Immune phenotypes were correlated to disease severity. Convalescence was overall associated with uniform immune signatures, but distinct immune signatures for mildly versus severely affected patients were detectable within a 2-week time window after infection.

overall_design: Gene expression patterns in memory-T-cells of Covid-19 patients with mild and severe (patients were hospitalized) symptoms

first: Chang-Feng

last: Chu

first: Florian

last: Sabath

first: Shan

last: Sun

first: Rupert

last: Öllinger

first: Elfriede

last: Nößner

first: Ying-Yin

last: Chao

first: Linus

last: Rinke

first: Elena

last: Winheim

first: Roland

last: Rad

first: Anne

last: Krug

first: Leila

last: Taher

first: Christina

last: Zielinski


title: RNA Seq analysis following RNAi perturbation of Hox genes in flatworm

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: Hox genes are highly conserved transcription factors renowned for their roles in the segmental patterning of the embryonic anterior-posterior (A/P) axis1. Emerging evidence for Hox gene expression and function in postnatally derived structures has fueled interest in their additional roles beyond embryogenesis2,3. We report novel functions for Hox genes in A/P directed adult tissue segmentation and transverse fission behavior underlying asexual reproduction in the planaria, Schmidtea mediterranea. Silencing of each of the 13 planarian Hox family members revealed 5 Hox genes required for asexual reproduction. Amongst these, silencing of hox3 genes resulted in supernumerary segments, while silencing of post2b eliminated segmentation altogether. The opposing roles of hox3 and post2b in segmentation are paralleled in the regulation of fission behavior. Silencing of hox3 increases the frequency of fission behavior initiation, while silencing of post2b eliminates fission behavior entirely. Furthermore, we identified a network of downstream effector genes mediating Hox gene regulation of asexual reproduction, thereby providing insight into their respective mechanisms of action. In summation, our study identifies roles for planarian Hox genes as mediators of adult tissue segmentation and behavior, as well as providing the first lines of evidence that Hox genes function post-embryonically to regulate asexual reproduction.

overall_design: RNA profiling by RNA Seq of unc22 Control or Hox gene RNAi animals in quadruplicate.

first: Christopher

last: Arnold

first: Analí

last: Migueles-Lozano

first: Frederick

last: Mann

first: Jeffrey

last: Lange

first: Alejandro

last: Alvarado


title: Preliminary Study on the Mechanism of GmNTLs in Soybean Adaptation to Aluminum Toxicity

status: Public on Jul 27 2021

city: Guang Zhou

first: Yan

last: Lin

state: Guang Dong

address: 广州市石榴岗路10号

department: Institute of Nanfan ＆Seed Industry

institute: Guangdong Academy of Sciences

summary: More than 40% of the world’s potentially arable lands are composed of acid soils, and the area exceeds 20 million hectares in China.Aluminum (Al) toxicity have become major factors threating crop production on acid soils. NTL proteins are a group of NAC transcription factors, and play an important role in the mechanisms of plant response to various abiotic stresses, such as drought, salt and cold stress. However, the underlying adaption mechanism of whether NTL is involved in regulating Al toxicity in plants remain poorly understood. Soybean is important grain and oil crop. Therefore, this study focused onanalyzing the function of GmNTLs in soybean adaptation to Al toxicity. Bioinformatics analysis and expression pattern analysis were performed on 15 members of the GmNTL family in the soybean. At the same time, we preliminary analyzed the function of some members in the adaptation mechanism of aluminum toxicity by overexpressing the genes in Arabidopsis thaliana.

overall_design: Transcriptomic analysis was conducted in arabidopsis of WT and GmNTL4-OX lines at 48h after Al treatment.

first: Cuiyue

last: Liang

first: Jiang

last: Tian

first: Xueqiong

last: Guo

first: Yaoliang

last: Pan


title: Alternative splicing regulation of cell cycle genes by SPF45/SR140/CHERP complex controls cancer cell proliferation

city: Barcelona

first: Claudia

last: Vivori

address: Carrer Dr Aiguader 88

institute: Centre for Genomic Regulation

summary: SPF45, SR140 and CHERP were knock downed using lentiviral delivery of shRNAs in HeLa cells

overall_design: HeLa cells were transducted with shRNA lentiviral particles and selected with puromycin 48h later. After 2 days of puromycin treatment cells were grown in fresh media for one day and RNA was extracted for RNA-seq analysis

last: Martín

first: Malgorzata

last: Rogalska

first: Juan

last: Valcárcel


title: Gene regulatory networks controlling temporal patterning, neurogenesis, and cell fate specification in the mammalian retina.

city: Baltimore

first: Seth

last: Blackshaw

state: Maryland

address: 733 N. Broadway Avenue

institute: Johns Hopkins University

summary: Gene regulatory networks (GRNs), consisting of transcription factors and their target cis-regulatory sequences, control neurogenesis and cell fate specification in the developing central nervous system, but their organization is poorly characterized.  In this study, we performed integrated scRNA-seq and scATAC-seq analysis from both mouse and human retina to profile dynamic changes in gene expression, chromatin accessibility and transcription factor footprinting during retinal neurogenesis and gliogenesis.  We identified multiple interconnected, evolutionarily-conserved GRNs consisting of cell type-specific transcription factors that both activate expression of genes within their own network and often inhibit expression of genes in other networks.  These GRNs control state transitions within primary retinal progenitors that underlie temporal patterning, regulate the transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type.  We confirmed the prediction of this analysis that the NFI transcription factors Nfia, Nfib, and Nfix selectively activate expression of genes that promote late-stage temporal identity in primary retinal progenitors.  We also used GRNs to identify additional transcription factors that selectively promote (Insm1/2) and inhibit (Tbx3, Tcf7l1/2) rod photoreceptor specification in postnatal retina.  This study provides an inventory of cis- and trans-acting factors that control retinal development, identifies transcription factors that control the temporal identity of retinal progenitors and cell fate specification, and will potentially help guide cell-based therapies aimed at replacing retinal neurons lost due to disease.

overall_design:
[scATAC-seq_whole retina]  To comprehensively profile dynamic changes in chromatin accessibility across the full course of retinogenesis, we conducted scATAC-seq analysis using the 10x Genomics Chromium platform on dissociated cell nuclei from whole mouse retina at 11 timepoints: embryonic (E) day 11, 12, 14, 16, and 18, as well as postnatal (P) day 0, 2, 5, 8, 11 and 14.
[scATACseq_electroporation]  We used ex vivo electroporation to overexpress human homologues of NFIA/B/X in E14 retina, and then profiled changes in gene expression and chromatin accessibility in primary RPCs at E16 using scATAC-seq. In parallel, we performed similar analysis in P2 and P14 Nfia/b/x cKO retina
[ChIPseq]  We used ex vivo electroporation to overexpress human homologues of NFIA/B/X in E14 retina, and then profiled changes in gene expression and chromatin accessibility in primary RPCs at E16 and P0 using scRNA-seq. In parallel, we performed similar analysis in P2 and P14 Nfia/b/x cKO retina
[scRNAseq]  We used ex vivo electroporation to overexpress human homologues of NFIA/B/X in E14 retina, and then profiled changes in gene expression and chromatin accessibility in primary RPCs at E16 and P0 using scRNA-seq. In parallel, we performed similar analysis in P2 and P14 Nfia/b/x cKO retina

first: Pin

last: Lyu

first: Thanh

last: Hoang

first: Clayton

last: Santiago

first: Eric

middle: D

last: Thomas

first: Andrew

last: Timms

first: Haley

last: Appel

first: Megan

last: Gimmen

first: Nguyet

last: Le

first: Lizhi

last: Jiang

first: Dong

last: Kim

first: Siqi

last: Chen

first: David

last: Espinoza

first: Ariel

last: Telger

first: Kurt

last: Weir

first: Brian

last: Clark

first: Timothy

last: Cherry

last: Qian


title: miRNA regulation of T cell exhaustion in cutaneous T cell lymphoma [CTCL_antimir]

first: Xiwei

last: Wu

state: CA

summary: Cobomarsen (MRG‐106), an oligonucleotide inhibitor of miR‐155, has been evaluated in a clinical phase 1/2 trial for CTCL. We used lesional skin samples from 6 CTCL patients to identify the critical pathways affected by miR‐155 inhibition in CTCL.

overall_design: 6 CTCL patients (baseline and after 4 weeks of treatment with cobomarsen to identify the critical pathways affected by miR‐155 inhibition in CTCL.

first: Zhen

last: Han

first: Christiane

last: Querfeld


title: HIRA-dependent H3.3 deposition and its modification H3.3K36me3 facilitate somatic hypermutation of immunoglobulin genes by maintaining the proper chromatin state and transcription

status: Public on Jul 29 2021

city: Frederick

first: GuoJun

last: Yu

state: MD

address: 560 CHANDLER STREET

department: Cell Biology

institute: National Institutes of Health

summary: The H3.3 histone variant and its chaperone HIRA are involved in active transcription but their detailed roles in regulating somatic hypermutation (SHM) of immunoglobulin variable regions in human B cells is not yet fully understood. In this study we show that, knockout (KO) of HIRA significantly decreased SHM and changed the mutation pattern of the variable region of immunoglobulin heavy chain (IGH) in the human Ramos B cell line without changing the levels of AID and other major proteins known to be involved in SHM. Except for H3K79me2/3, many factors related to active transcription, including H3.3, were substantively decreased in HIRA KO cells and this was accompanied by decreased nascent transcription in IGH locus. The abundance of ZMYND11 that specifically binds to H3.3K36me3 on the Ig locus was also reduced in the HIRA KO. Somewhat surprisingly HIRA loss increased the chromatin accessibility of Ig V region locus. Furthermore, stable expression of ectopic H3.3G34V and H3.3G34R mutants that inhibit both the trimethylation of H3.3K36 and the recruitment of ZMYND11 significantly reduced SHM in Ramos cells, while the H3.3K79M did not. Consistent with HIRA KO, the H3.3G34V mutant also decreased the occupancy of various elongation factors and of ZMYND11 on the IGH variable and downstream switching regions. Our results reveal an unrecognized role of HIRA and the H3.3K36me3 modification in SHM and extend our knowledge of how transcription coupled chromatin structure and accessibility contribute to SHM in human B cells.

overall_design: Examination of HIRA and H3.3G34 in chromatin accessibility by ATAC-seq in human B cell line Ramos.

first: Zhi

last: Duan

first: Thomas

last: MacCarthy

first: Matthew

last: Scharff


title: STAT3 regulates osteogenesis, making it critical for skeletal development and bone homeostasis

status: Public on Jul 28 2021

city: Shanghai

first: Qian

last: Bian

state: Shanghai

address: Pudong New District, Jinzun Rd, No.115

department: Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: Skeletal deformities are typical clinical manifestations of autosomal dominant hyper-immunoglobulin E syndrome (AD-HIES), but the treatment is still limited. AD-HIES is mainly caused by dominant-negative mutations in signal transducer and activator of transcription 3 (STAT3). Clarifying the mechanisms by which STAT3 inactivation destructs bone metabolism is, therefore, important. Although, a few lines of data indicate osteoporosis induced by STAT3 inactivation may be related to increased osteoclast activity, here, we firstly report that deletion of Stat3 in osteoblasts, but not in osteoclasts, induced AD-HIES-like bone defects, including craniofacial malformation, osteoporosis, and spontaneous bone fracture in mice, and these defects were resulted from impaired osteogenesis induced by STAT3 inactivation in osteoblasts, but not increased osteoclast activity. Mechanistic analysis revealed a novel regulatory model in which STAT3 drove osteoblast differentiation via promoting distal-less homeobox 5 transcription in cooperation with MSX1. Furthermore, inducible deletion of Stat3 in osteoblasts also inhibited osteogenesis and induced bone loss in adult mice. Meaningfully, pharmacological inhibition of STAT3 induced bone loss, while activation of STAT3 partially prevent bone loss due to tail sus-pension. Taken together, STAT3 is critical for both modulating skeletal development and maintaining bone homeostasis, and inactivation of STAT3 in osteoblasts, but not in osteoclasts, induced AD-HIES-related skeletal deformities by impairing osteogenesis, providing new insights for their treatment.

overall_design: To analyze the effects of deleting Stat3 in osteoblasts on global gene expression patterns, we performed RNA-seq with total RNA extracted from the calvarias of newborn OsxCre;Stat3fl/fl and OsxCre littermates.

first: Siru

last: Zhou

first: Qinggang

last: Dai

first: Weiguo

last: Zou


title: Contrasting gene expression patterns associated with high and low rhinovirus stimulated IFN-α production

city: Woolloongabba

first: Gayathri

last: Thillaiyampalam

state: QLD

address: 37 Kent Street

department: UQDI

country: Australia

institute: University of Queensland

summary:
Introduction: Viral respiratory infections cause considerable morbidity and economic loss. While rhinoviruses (RV) typically cause little more than the common cold, they can produce severe infections and disease exacerbations in susceptible individuals, including those with chronic lung diseases. Variations in the regulation of key antiviral cytokines, particularly type I interferon (IFN-α and IFN-b), may contribute to RV susceptibility, but are not well understood.
Method: Whole genome transcription patterns were assessed in samples from 74 individuals demonstrating high or low IFN-α production following RV stimulation in vitro.
Results: In unstimulated samples (baseline) the high IFN-α producer group showed higher expression of genes associated with plasmacytoid dendritic cells, the complement system, B-cell chemokines, immune regulation, macrophages, and vitamin D activation and lower expression of genes linked to haemoglobin and haem biosynthesis, wound healing, stress response and pro-inflammatory genes than the low IFN-α producer group. After RV stimulation, the high IFN-α producer group showed more intense upregulation of diverse immune function genes including IFNs and greater downregulation of genes linked to structural and extra-cellular matrix functions than the low IFN-α producer group. Patterns of antibacterial gene expression varied between groups. Healthy people and those with asthma generally showed similar gene expression patterns. These findings highlight multiple biological pathways whose expression patterns differ substantially between high and low IFN-α producers. These differences likely contribute to variations in anti-RV immunity and immunopathology between individuals.

overall_design: Differentially expressed genes between high and low IFN-α producing PBMC

first: Liisa

middle: M

last: Murray

first: Yang

last: Xi

first: Alexandre

last: Cristino

first: Manuel

last: Ferreira

first: John

middle: W

last: Upham


title: Long-term maintenance of dystrophin expression and resistance to injury of skeletal muscle in gene-edited mice

city: Dallas

first: Jiwoong

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Duchenne Muscular Dystrophy (DMD) is a lethal muscle disease caused by mutations in the dystrophin gene. CRISPR/Cas9 genome-editing has been used to correct DMD mutations in animal models at young ages. However, the longevity and durability of CRISPR/Cas9 editing remained to be determined. To address these issues, we subjected DEx44 DMD mice to systemic delivery of AAV9 expressing CRISPR/Cas9 gene editing components to reframe exon 45 of the dystrophin gene, allowing robust dystrophin expression and maintenance of muscle structure and function. We showed that genome correction by CRISPR/Cas9 confers lifelong expression of dystrophin in mice and that corrected skeletal muscle is highly durable and resistant to myofiber necrosis and fibrosis, even in response to chronic injury. In contrast, when muscle fibers were ablated by barium chloride injection, satellite cells were unable to restore dystrophin expression due to restriction of gene editing components. Analysis of on-target and off-target gene editing in aged mice confirmed the stability of gene correction and the lack of significant off-target editing at 18 months of age. These findings demonstrate the long-term durability of CRISPR/Cas9 genome editing as a therapy for maintaining the integrity and function of DMD muscle, even under conditions of stress.

overall_design:
RNA profiles of quadriceps from WT, delEx44, and corrected-delEx44 mice prior to and after 1 month of forced downhill running.
RNA profiles of quadriceps from 18-month-old WT, delEx44, and corrected-delEx44 mice.

first: Dileep

last: Karri

first: Yu

last: Zhang

first: Rhonda

last: Bassel-Duby

first: Eric

last: Olson


title: Next Generation Sequencing Facilitates Quantitative Analysis of control, stress, and stress treated with IL-22fc Transcriptomes in NRG857c colonized mice

status: Public on Jul 22 2021

city: Hamilton

first: Ryan

last: Shaler

state: Ontario

address: 1280 Main Street West

country: Canada

institute: McMaster University

summary: Pyschological stress produces unique transcriptomic changes, many of which can be reversed by IL-22fc pre-treatment

overall_design: Ileal gene expression changes induced by restraint stress in NRG857c colonized mice, with or without IL-22fc pre-treatment

first: Christopher

first: Alexandra

last: Parco

first: Brian

last: Coombes


title: PolyA Sequencing of K562 Cells

city: Irvine

first: Whitney

last: England

address: 2403 Natural Sciences I

department: Pharmaceutical Sciences

institute: University of California Irvine

summary: RNA chemical structure analysis using icSHAPE and icLASER reveals hexameric sequences that have structure differences inside and outside of cells. One such sequence that had higher in-cell reactivity was the sites of polyadenylation or PAS sequence within the 3’-UTRs. We aimed to understand this difference as we postulated it could be utilized to predict transcriptome-wide polyadenylation.  To obtain direct positions with high polyadenylation sequence signal, we generated the first polyadenylation sequencing data (PAS-seq) for K562 cells. PAS-seq uses polyA tail priming to identify the sites of polyA tail selection directly. Inspection of PAS reads demonstrated clear buildup of read depth at the 3’-end of transcripts and we obtained sites of high PAS read depth and low PAS read depth.

overall_design: One sample

first: Dalen

last: Chan

first: Chao

last: Feng

first: Dana

last: Wyman

last: Flynn

first: Xiuye

last: Wang

first: Yongsheng

last: Shi

first: Ali

last: Mortazavi

first: Robert

middle: C

last: Spitale