title: Gene expression comparison between glioblastoma and non-neoplastic brain tissue samples using NanoString nCounter Pan-Cancer Pathways Panel

city: Tucson

first: Christopher

middle: Michael

last: Morrison

state: AZ

address: 3838 N Campbell Ave, Bldg #2

department: Radiation Oncology

institute: University of Arizona Cancer Center

summary: Most treatment failures of glioblastoma (GBM) occur within high-dose radiation fields, in part due to increased capacity for DNA damage repair. We retrospectively quantified the expression levels of key repair genes GBM tissue samples and correlated those expression levels with overall survival (OS).  Differential expression analysis identified 7 repair genes that were significantly upregulated in GBM tissues relative to the controls (> 4-fold difference and all adjusted p values < 0.001).  Of these 7 genes, Cox proportional hazards models identified RAD51 as being associated with an increased risk of death (HR = 3.49; p = 0.03).  Kaplan-Meier (KM) analysis also demonstrated that patients with high levels of RAD51 had significantly shorter OS compared to patients with low levels (median OS of 10.6 months vs 20.1 months, log-rank p = 0.03).  These findings were then validated in a larger external dataset of 162 patients using publicly available gene expression data quantified by the same NanoString technology (median OS of 13.8 months vs. 17.4 months; log-rank p = 0.006)

overall_design: We identified 24 adult GBM patients homogenously treated with maximal safe resection followed by conventionally fractionated radiation to at least 60 Gy with concurrent and adjuvant temozolomide.  mRNA from these samples was quantified using NanoString Technologies’ nCounter platform and differential expression analyses were performed with 12 non-neoplastic temporal lobe tissue samples used as a control.

first: Eric

last: Weterings

first: Daruka

last: Mahadevan

first: Abhay

last: Sanan

first: Martin

last: Weinand

first: Baldassarre

last: Stea


title: Genome-wide maps of chromatin state in nucleus pulposus cells from ChIP-seq experiments using the H3K27ac antibody

status: Public on Feb 08 2022

city: Shenzhen

first: Yulin

last: Huang

state: Guangdong

address: 628 Zhenyuan Road, Xinhu Street, Guangming District

department: Department of Orthopedics Surgery

country: China

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

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We analysed the presence of H3K27ac histone marks bound to DNA of nucleus pulposus cells cultured in DMEM-F12 medium with 10% FBS.

overall_design: Examination of histone modification H3K27ac in nucleus pulposus cells.

first: Fuxin

last: Wei


title: RNA-seq of neutrophils  from mouse heart treated with AngII or saline

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

country: USA

institute: Case Western Reserve University

type: Expression profiling by high throughput sequencing

summary: AngII infusion in mouse is a classic model of cardiac hypertrophy. Here we aimed to understand the role of neutrophils in the myocardium.

overall_design: Lyz2-Cre and Lyz2-KLF2-KO mice were subjected to AngII infusion at the dose of 1.0 ug/kg/min for one week. Neutrophils were isolated from heart and analyzed by the RNA-seq approach.

first: Xudong

last: Liao

first: Mukesh

middle: K

last: Jain


title: RNAseq analyses of nucleus pulposus cells treated with control siRNA and LINC02569 siRNA

summary: Nucleus pulposus cells (NPCs) were used to examine the effect of LINC02569, a novel lncRNA. In particular, its effect in intervertebral disc degeneration was determined. Treatment of LINC02569 siRNA (si-02569)  was to be compared with negative control siRNA (si-NC).

overall_design: Different samples of NPCs under 2 different condtions are prepared: si-02569 treatment & si-NC treatment.


title: gp130/STAT3 signaling is required for homeostatic proliferation and anabolism in postnatal growth plate and articular chondrocytes [scRNA-seq]

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

summary: Growth of long bones and vertebrae is maintained postnatally by a long-lasting pool of progenitor cells. Little is known about the molecular mechanisms that regulate the output and maintenance of the cells that give rise to mature cartilage. Here we demonstrate that postnatal chondrocyte-specific deletion of a transcription factor Stat3 results in severely reduced proliferation coupled with increased hypertrophy, growth plate fusion, stunting and signs of progressive dysfunction of the articular cartilage. This effect is dimorphic, with females more strongly affected than males. Chondrocyte-specific deletion of the IL-6 family cytokine receptor gp130, which activates Stat3, phenocopied Stat3-deletion; deletion of Lifr, one of many co-receptors that signals through gp130, resulted in a milder phenotype. These data define a new molecular circuit that regulates chondrogenic cell maintenance and output and reveals a novel, hitherto unrecognized function of IL-6 cytokines in the skeletal system with direct implications for skeletal development and regeneration.

overall_design: Single-cell mRNA sequencing for Stat3fl/fl (control) and Acan-Cre+/Cre;Stat3fl/fl (Stat3KO) female mice using 10x Genomics.

first: Ben

last: Van Handel


title: HDAC6-LINC00461 pathway as a potential target for glioblastoma therapy

city: Taipei

first: Wen-Bin

last: Yang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei Medical University

summary:
Background: Glioblastoma (GBM) is the most aggressive and lethal brain tumor. Although the histone deacetylase (HDAC)/Sp1 axis promotes growth and temozolomide (TMZ) resistance in glioblastoma, whether HDACs including HDAC6 are involved in modulating long non-coding RNAs (lncRNAs) to affect glioblastoma malignancy remains obscure.
Methods: Integrative analysis of microarray and RNA-seq was performed to identify lncRNAs governed by HDAC6. Half-life measurement and RNA-protein pull-down assay combined with iTRAQ-based proteomic analysis were conducted to identify RNA modulators. The effect of LINC00461 on glioblastoma malignancy was evaluated using animal models and cell proliferation-related assays. Functional analysis of the LINC00461 downstream network was performed comprehensively using ingenuity pathway analysis and public databases.
Results: We identified a lncRNA, LINC00461, which was substantially increased in TMZ-resistant glioblastoma cells. It was inversely correlated with the survival of mice bearing glioblastoma and was stabilized by interaction between HDAC6 and RNA-binding proteins (RBPs) such as CNOT6 and FUS. Targeting LINC00461 using MPT0B291, an HDAC6 inhibitor, decreased cell division-related proteins via the lncRNA-microRNA (miRNA)-mRNA network and caused cell cycle arrest, thereby suppressing proliferation in parental and TMZ-resistant glioblastoma cells and prolonging the survival of mice bearing glioblastoma.
Conclusions: This study sheds light on the role of LINC00461 in glioblastoma malignancy and provides a novel therapeutic strategy for targeting the HDAC6/RBP/LINC00461 axis and its downstream effectors in patients with GBM.

overall_design: Whole transcriptome profiles of temozolomide (TMZ) -resistant U87MG cells treated with non-targeting control siRNA or siHADC6, and U87MG cells treated with non-targeting control siRNA or siLINC00461.

first: An-Chih

last: Wu

first: Jian-Ying

last: Chuang


title: PRDM proteins control Wnt/β-catenin activity to regulate craniofacial chondrocyte differentiation

city: Easton

first: Ezra

last: Lencer

state: PA

address: 746 High Street

department: Department of Biology

institute: Lafayette College

summary: Cranial neural crest (NCC)-derived chondrocyte precursors undergo a dynamic differentiation and maturation process to establish a scaffold for subsequent bone formation, alterations in which contribute to congenital birth defects. Here, we demonstrate that transcription factor and histone methyltransferase proteins Prdm3 and Prdm16 control the differentiation switch of cranial NCCs to craniofacial cartilage. Loss of either results in hypoplastic and unorganized chondrocytes due to impaired cellular orientation and polarity. We show that PRDMs regulate cartilage differentiation by controlling the timing of Wnt/β-catenin activity in strikingly different ways: prdm3 represses while prdm16 activates global gene expression, though both by regulating Wnt enhanceosome activity and chromatin accessibility. Finally, we show that manipulating Wnt/β-catenin signaling pharmacologically or generating prdm3-/-;prdm16-/- double mutants rescues craniofacial cartilage defects. Our findings reveal upstream regulatory roles for Prdm3 and Prdm16 in cranial NCCs to control Wnt/β-catenin transcriptional activity during chondrocyte differentiation to ensure proper development of the craniofacial skeleton.

overall_design: Cranial neural crest mRNA and chromatin accessibility (ATAC) profiles from isolated sox10:GFP positive cells from 48 hours post fertilization wildtype (wt), prdm3-/- and prdm16-/- zebrafish

first: Lomeli

middle: C

last: Shull

first: Hyun

middle: M

last: Kim

middle: S

first: James

last: Costello

first: Kenneth

last: Jones

first: Kristin

middle: B

last: Artinger


title: PRMT5 inhibition increases PD-L1 expression and immunoresistance in lung cancer

city: shanghai

first: bingqian

last: zhou

state: 上海

address: 上海市杨浦区控江路新华医院

institute: 上海交大医学院附属新华医院

summary:
Purpose: We sequenced mRNA from 3 biological replicates each of NCI-H460 lung adenocarcinoma cell lines expressing shRNA against GFP (control) or PRMT5.We then determined differential gene expression to identify the relationship between PRMT5 expression and tumorigenesis.
Methods: PRMT5 shRNA and control shRNA NCI-H460 cells were generated by lentivirus targeting PRMT5 or GFP(control), in triplicate,using illumina Novaseq™ 6000.
Results:PRMT5 specific knockdown cells were enriched in the negative regulation of T cells and type I IFN response,we found that negative regulation of T cell molecules like Arg2, CD274 and IDO1 were increased in the PRMT5 shRNA group compared with the control group.

overall_design: Transcriptome analysis of mRNA testing the role of PRMT5  by knockdown in NCI-H460 human lung adenocarcinoma cells

first: Bingqian

last: Zhou

first: Yingxia

last: Zheng


title: Intratumoral anti-CTLA-4 delivery by an oncolytic Vaccinia virotherapy virus elicits CD8+ T cell immunity and synergizes with anti-PD-1 to reject “cold” tumors

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

country: France

institute: Transgene SA

summary: CTLA-4 is a clinically validated antibody target for cancer immunotherapy. Toxicity, which is linked to efficacy in available anti-CTLA-4 regimens has, however, restricted their use and precluded full therapeutic dosing. Here we describe and preclinically characterize a potentially safe and highly efficacious strategy to target CTLA-4. Intratumoral administration of an oncolytic Vaccinia virus, engineered to encode a novel Treg depleting, checkpoint-blocking, anti-CTLA-4 antibody and GM-CSF (VVGM-aCTLA4) achieved tumor-restricted CTLA-4 receptor saturation and Treg-depletion, and regressed diverse tumors spanning inflamed to immunologically ignorant microenvironments. Critically, intratumorally “ignited” antitumor immunity translated into stronger systemic expansion of tumor-specific CD8+ T cells compared with systemic anti-CTLA-4. In a clinically relevant mouse model resistant to systemic immune checkpoint blockade, i.t. VVGM-aCTLA4 synergized with anti-PD-1 to reject “cold” tumors. Based on our established proof-of-concept, a clinical trial evaluating i.t. VVGM-aCTLA4 (BT-001) alone and in combination with anti-PD-1 in metastatic or advanced solid tumors has commenced.

overall_design: CT26 tumours treated with the vaccinia virus mBT-001 expressing anti-CTLA-4 and GM-CSF, the empty vaccinia virus, or untreated.


title: Single-cell RNA sequencing of CD45+ cells resided in the small intestine of wild-type and Dusp6 knockout mice

city: Zhunan

first: Cheng-Yuan

last: Kao

address: 35 Keyan Road

department: Immunology Research Center

institute: National Health Research Institutes

summary: To assess whether Dusp6 deficiency exerts alteration to intestinal immune cells specifically, we further applied the single-cell RNA sequencing with 10X Genomics platform in Dusp6-knockout (D6KO) mice and littermate wild-type (WT) control mice under chow diet. The intestines of wild-type and Dusp6-knockout mice (11 weeks old) were harvested and the live intestinal immune cells from the intraepithelial compartment and the laminar propria were collected with CD45+ marker by magnetic-activated cell sorting (MACS) MicroBeads and fluorescence-activated cell sorting (FACS) for downstream 10X Genomics Chromium Single Cell 3' Solution.

overall_design: Comparison of intestinal CD45+ cells between wild-type and Dusp6 knockout mice

first: Cherng-Shyang

last: Chang


title: Inhibition of Jumonji demethylases transcriptionally reprograms severe cardiac hypertrophy and prolongs survival.

city: Dallas

first: Elisabeth

last: Martinez

state: Texas

address: 6000 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

summary: Cardiac hypertrophy is a potentially fatal disease characterized by increased cardiomyocyte size, and maladaptive transcriptional remodeling that leads to arrythmias and contractile failure. Transgenic mice constitutively expressing high levels of calcineurin develop extreme heart hypertrophy and generally die within a few weeks of birth. Here, we characterize the transcriptional and epigenetic pathways that are aberrant in this mouse model and establish a pharmacological approach to treating cardiac hypertrophy based on our observation that a subset of histone demethylases of the Jumonji KDM family that act on H3K4me3 or H3K9me3 are markedly increased at the protein level and show enhanced enzymatic activity in diseased hearts. Inhibition of Jumonji demethylases in vivo results in lower histone demethylase enzymatic activity in the heart without toxicity, and leads to partial reduction of heart size, to the reversal of maladaptive transcriptional programs, to improved heart function, and to prolongation of survival. Mechanistically, MEF2, KDM4A and KDM3A target genes are specifically regulated in response to pharmacological or genetic inhibition of Jumonji demethylases and NFAT remains largely cytoplasmic.  Similar transcriptional reversal of disease genes is seen in a second disease model based on cardiac mechanical overload, suggesting the generality of this approach. Our findings establish the use of pharmacological inhibitors of Jumonji enzymes as potential therapeutics for the treatment of cardiac hypertrophy across disease models and provides evidence of the reversal of maladaptive transcriptional reprogramming in the heart leading to partial restoration of cardiac function.

overall_design: MHC-CnAtg mice were treated with vehicle or JIB-04 starting at 4 week old and hearts vere collected when mice are 45 days old.  Wild type mice were treated the same way, but only with vehicle.  Alternatively, MHC-CnAtg mice were treated with vehicle or JIB-04 starting at 5 week old and hearts vere collected when mice are 77 days old.

first: Tram

middle: A

last: Tran


title: Inhibition of Jumonji demethylases transcriptionally reprograms severe cardiac hypertrophy and prolongs survival: part 2.

overall_design: MHC-CnATg mice treated with vehicle or JIB-04 starting from 4 weeks of age at 50 mg/kg, 3 times/weeks until mice reach 158day old.  Hearts were collected and transcriptomes were examined by RNAseq.

first: Tram-Anh

middle: T

middle: D


title: Temporal Analyses of Postnatal Liver Development   and Maturation by Single Cell Transcriptomics

city: La Jolla

first: Yan

last: Liang

address: 9500 Gilman Drive, BRFII Room 1220 Bay B

institute: UC San Diego

summary: The liver is the largest metabolic organ in mammals to process most nutrients and cellular wastes, although its development and maturation in postnatal life is unclear. We performed single cell RNA-sequencing (scRNA-seq) analysis focusing on postnatal development and maturation of murine liver. A total of 52,834 single cell transcriptomes, collected from the newborn to adult livers, were analyzed. We observed dramatic changes in cellular compositions during liver postnatal development. We characterized the process of hepatocytes and sinusoidal endothelial cell zonation establishment at single cell resolution. Furthermore, trajectory and gene regulatory analyses showed development of circadian clock in early liver as well as response of several critical metabolic pathways in order to adapt to the abrupt environmental changes at birth and in the postnatal life. Finally, we identified a special type of macrophages, enriched at postnatal day 7, with hybrid phenotype of both macrophage and endothelial cells. Cell-cell interaction analysis indicated this group of cells involved in regulation of liver sinusoidal vascularization and Treg cell activity. This study provides a comprehensive blueprint for further dissection of liver functions and diseases.

overall_design: Hepatic cells were isolated from wildtype C57BL/6 livers, at postnatal day 1, 3, 7, 21 and 56 (indicated by D1, D3, D7, D21, and D56, respectively).

first: Kota

last: Kaneko

first: Bing

last: Xin

first: Jin

last: Lee

first: Xin

last: Sun

first: Kun

last: Zhang

first: Gen-Sheng

last: Feng


title: Inhibition of Jumonji demethylases transcriptionally reprograms severe cardiac hypertrophy and prolongs survival


title: Splicing modulation increases BCL2 dependence and sensitizes Multiple Myeloma cells to Venetoclax

city: Milan

first: Antonino

last: Neri

state: Milan

address: Via Francesco Sforza, 35

country: Italy

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

summary:
Identification of novel vulnerabilities in the context of therapeutic resistance is emerging as key challenge for cancer treatment. Recent studies have detected pervasive aberrant splicing in cancer cells, supporting its targeting for treatment of hematological malignancies.We here evaluated the expression of several spliceosome machinery components in primary multiple myeloma (MM) cells and the impact of splicing modulations on MM cell growth and viability.Our comprehensive gene expression analysis confirmed deregulation of spliceosome machinery components in MM cells compared to normal plasma cells (PCs) from healthy donors, while pharmacological and genetic modulation of splicing confirmed significant impact on growth and survival of MM cell lines and patient-derived malignant PCs.
Transcriptomic analysis revealed deregulation of BCL2 family membersincluding decrease of proapoptotic long form of myeloid cell leukemia-1 (MCL1) expression in cells treated with splicing inhibitors. This caused a shift in the apoptotic priming resulting in improved BCL2-dependenceand increased sensitivity to Venetoclax, a BCL2 small molecule inhibitor, in vitro and in vivo. Overall, our data provide a rationale for supporting clinical use of splicing modulators as strategy to reprogram apoptotic dependencies, making MM patients more vulnerable to BCL2 inhibitors.

overall_design: Human Myeloma Cell Line (HMCLs) were purchased from ATCC or DSMZ. Cell lines were Mycoplasma-free and routinely tested for it. Cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS; GIBCO), 4mM glutamine, 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin (GIBCO). H929 cells were treated with 3 nM Meayamicin B for 8 hours. Control and treatment conditions were each considered in duplicates (rep_1, rep_2). Meayamicin B kindly gifts from Prof. Kazunori Koide (University of Pittsburgh),

first: Debora

last: Soncini

first: Claudia

last: Martinuzzi

first: Pamela

last: Becherini

first: Elisa

last: Gelli

first: Samantha

last: Ruberti

first: Katia

last: Todoerti

first: Luca

last: Mastracci

first: Paola

last: Contini

first: Antonia

last: Cagnetta

first: Antonella

last: Laudisi

first: Fabio

last: Guolo

last: Minetto

first: Maurizio

last: Miglino

first: Sara

last: Aquino

first: Riccardo

last: Varaldo

first: Daniele

last: Reverberi

first: Matteo

last: Formica

first: Mario

last: Passalacqua

first: Alessio

last: Nencioni

first: Nikhil

last: Munshi

first: Mehmet

last: Samur

first: Mariateresa

last: Fulciniti

first: Roberto

last: Lemoli

first: Michele

last: Cea


title: mRNA Expression Data from Murine Hearts of Pcyt2+/- Male and Female Mice at 8 Months of Age

city: guelph

first: Chelsea

last: Furtado

state: Ontario

address: 50 stone road E

department: Human Health and Nutritional Sciences

country: Canada

institute: University of Guelph

summary:
Hearts were collected from Pcyt2+/- male and female mice at 8 months of age
The microarray approach allows the investigation of gene expression changes of all genes in Pcyt2+/- male and female hearts.

overall_design: There are a total of 8 samples, 4 from Pcyt2+/- males 8 months old and 4 from  Pcyt2+/- females 8 months old.

first: Marica

last: Bakovic


title: Differentially-expressed mRNAs, microRNAs and long noncoding RNAs in intervertebral disc degeneration identified by RNA-sequencing

city: Nanning

first: Zhimin

last: Li

address: Shuangyong Road

institute: School

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aimed to identify the crucial molecules and explore the function of noncoding RNAs and related pathways in IDD. We randomly selected 3 samples each from an IDD and a spinal cord injury group (control) for RNA-sequencing. We identified 463 differentially-expressed long noncoding RNAs (lncRNAs), 47 differentially-expressed microRNAs (miRNAs), and 1,334 differentially-expressed mRNAs in IDD. Three hundred fifty-eight lncRNAs as cis-regulators could potentially target 865 genes. Protein–protein interaction (PPI) network analysis confirmed that IL-6, VEGFA, IGF1, MMP9, CXCL8, FGF2, IL1B, CCND1, ITGAM, PTPRC, FOS and PTGS2 were hub genes. We built a competing endogenous RNA (ceRNA) network and identified lncRNA XIST–hsa-miR-4775–PLA2G7 and lncRNA XIST–hsa-miR-424-5p–AMOT/TGFBR3 ceRNA axes.

overall_design: The miRNA, lncRNA and mRNA profiles of  in intervertebral disc degeneration

first: Yu

last: Sun

first: Maolin

last: He

first: Jianwei

last: Liu


title: Transcriptome reprogramming of key transcription factor deletion strains of Saccharomyces cerevisiae compared with the wild type strain  grown at normal temperature by RNA-Seq

city: Tianjin

first: Qinhong

last: Wang

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: Saccharomyces cerevisiae cells have evolved remarkably sophisticated and flexible transcriptional regulatory networks (TRNs) that allow them to survive and thrive in stress conditions, such as high temperature, osmotic and oxidative conditions, etc. Furthermore, transcription factor plays a central role in transcriptional regulatory networks of stress response. To achieve a thorough understanding of master transcription factors and transcriptional regulatory networks in specific response to prolonged thermal stress, we previously sequenced mRNA from the cultures of the wild type strain ScY01a as well as three key transcription factor deletion strains including ScY01a (srb2∆), ScY01a (sin3∆) and ScY01a (mig1∆) grown at 40ºC in biological duplicates. Here, we further sequenced the corresponding samples cultured at 30ºC as a control. Differences in gene expression comparing the transcription factor deletion strains with the wild type strain by RNA deep sequencing revealed a hierarchical transcriptional regulatory network centered on these three transcription factors in S. cerevisiae.

overall_design: mRNA levels in the wild type strain of Saccharomyces cerevisiae ScY01a as well as three key transcription factor deletion strains including ScY01a (srb2∆), ScY01a (sin3∆) and ScY01a (mig1∆) were examined by RNA Sequencing, in duplicate, using on Illumina platform using 150-bp paired-end sequencing. We sequenced 2 samples from ScY01a, 2 samples from ScY01a (srb2∆), 2 samples from ScY01a (sin3∆) and 2 samples from ScY01a (mig1∆),  and identified differential expressions in the transcription factor deletion strain versus the wild type strain by using mRNA levels the wild type strain as a reference.

first: Yuping

last: Lin

first: Yufeng

last: Guo

first: Xianni

last: Qi

first: Yuman

last: Gan


title: Gene expression analysis of murine splenic IL-10+ and IL-10- B cells

city: Udine

first: Silvia

last: Tonon

state: IT

address: Piazzale Kolbe 4

department: Dep of Medical Area

institute: University of Udine

summary: B cells belong to the adaptive immune system and have multiple functions. Besides their well characterized role in the promotion of the immune response, specific B cell subsets were shown to have an anti-inflammatory function. These cells are termed regulatory B cells and they exert their function mainly through the production of interleukin 10 (IL-10). This study focuses on B cells capable of producing IL-10 after 5 hours of stimulation with LPS, PMA and ionomycin, without any distinction based on surface markers.

overall_design: total B cells were stimulated for 5h with LPS, PMA and ionomycin and separated through an IL-10 secretion assay coupled to FACS-sorting.

first: Francesca

last: Mion

first: Matteo

last: Dugo

first: Mario

middle: P

last: Colombo

first: Carlo

last: Pucillo


title: The mechanistic studies of GATA1 regulation of SREBP2 in G1-ER4 cells

city: Jinan

first: Zhiyuan

last: Lu

state: Shandong

address: 6699 Qingdao road

department: School of Pharmaceutical Sciences & Institute of Materia Medica

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

summary: In our work, we uncovered a critical role for cholesterol homeostasis in terminal erythropoiesis. The master transcriptional factor GATA1 binds to Sterol-regulatory element binding protein 2 (SREBP2) to downregulate cholesterol biosynthesis, leading to a gradual reduction in intracellular cholesterol levels. To reveal genetic interactions and epistatic relations between GATA1 and SREBP2 on depth at the whole genome level, we performed RNA sequencing to analyze the gene expression profiles change between treated with Vehicle or β-estradiol in overexpressing active SREBP2 G1E-ER4 cells.

overall_design: G1E-ER4 cells were transduced with retrovirus to express active SREBP2 (1-468aa), cells were then treated with Vehicle or β-estradiol (200nM) for 6 h, and total RNA was extracted using the TRIzol reagent. RNA sequencing was conducted using the BGIseq500 platform (Shenzhen, China) in triplicate.

first: Baobing

last: Zhao


title: RNA-seq Analysis of Prmt1f/f and Lrat-Cre; Prmt1f/f Mouse Fibrotic Liver Transcriptomes

status: Public on Feb 07 2022

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

summary:
Purpose: To identify the alterations of genes transcriptional profile of livers obtained from Prmt1f/f mice and Lrat-Cre; Prmt1f/f mice treated with thioacetamide (TAA).
Methods: Lrat-Cre mice were crossed with and Prmt1f/f mice to generate Lrat-Cre; Prmt1f/f mice. Prmt1f/f mice and Lrat-Cre; Prmt1f/f mice were treated with TAA (400mg/L, drinking water for 16 weeks) to induce liver fibrosis. Liver mRNA profiles of 10-week-old Prmt1f/f  and  Lrat-Cre; Prmt1f/f mice treated with TAA were generated by deep sequencing, using Illumina Novaseq 6000. We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05. RT–PCR validation was performed using SYBR Green PCR Kit.
Results: We identified 16916 transcripts in the livers of Prmt1f/f and Lrat-Cre; Prmt1f/f mice. 726 transcripts showed differential expression between Prmt1f/f and Lrat-Cre; Prmt1f/f livers, with a  |log2FC| > 1 and P value < 0.05. Altered expression of 4 genes was confirmed by qRT–PCR.
Conclusion:  Our study represents the first detailed analysis of liver transcriptomes of Lrat-Cre; Prmt1f/f mice during liver fibrogenesis. RNA-seq based transcriptome analysis would provide us better understanding of complex biologic functions of Prmt1 in the hepatic stellate cell during the pricess of hepatic fibrogenesis in mice.

overall_design: Examine the liver mRNA profiles of 10-week old Lrat-Cre; Prmt1f/f mice and Prmt1f/f mice treated with TAA by RNA-seq technolodgy

first: Fang-Zhi

last: Yan

first: Fang

first: Hui

last: Qian

first: Chen-Hong

last: Ding


title: Transcriptome profiling in advanced colorectal cancer

city: Tokyo

first: Fuyuki

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

country: Japan

institute: Keio University

summary: In total, 89 samples were collected from 89 patients with colorectal cancer (CRC), of which 66 patients had stage IV CRC. We sequenced the mRNAs purified from the formalin-fixed paraffin embedded (FFPE) blocks.

overall_design:
Transcriptome profiles obtained from 89 individuals with colorectal cancer using Illumina HiSeq 4000.

**RAW data not provided due to patient privacy concerns**

first: Toshitaka

last: Sugawara

first: Toshiaki

last: Ishikawa

first: Artem

last: Lysenko

first: Jo

last: Nishino

first: Takashi

last: Kamatani

first: Akira

last: Takemoto

first: Keith

last: Boroevich

first: Kazuhiro

last: Kakimi

first: Yusuke

last: Kinugasa

first: Minoru

last: Tanabe

first: Tatsuhiko

last: Tsunoda


title: Transcriptome reprogramming of key transcription factor deletion strains of Saccharomyces cerevisiae compared with the wild type strain by RNA-Seq

first: Qinhong

last: Wang

summary: Saccharomyces cerevisiae cells have evolved remarkably sophisticated and flexible transcriptional regulatory networks (TRNs) that allow them to survive and thrive in stress conditions, such as high temperature, osmotic and oxidative conditions, etc. Furthermore, transcription factor plays a central role in transcriptional regulatory networks of stress response. To achieve a thorough understanding of master transcription factors and transcriptional regulatory networks in specific response to prolonged thermal stress, we sequenced mRNA from the cultures of the wild type strain ScY01a as well as four key transcription factor deletion strains including ScY01a (ric1∆), ScY01a (srb2∆), ScY01a (sin3∆) and ScY01a (mig1∆) grown at 40ºC in biological duplicates. Differences in gene expression comparing the transcription factor deletion strains with the wild type strain by RNA deep sequencing revealed a hierarchical transcriptional regulatory network required for long-term thermal stress tolerance of S. cerevisiae, which is centered on these four transcription factors.

overall_design: mRNA levels in the wild type strain of Saccharomyces cerevisiae ScY01a as well as four key transcription factor deletion strains including ScY01a (ric1∆), ScY01a (srb2∆), ScY01a (sin3∆) and ScY01a (mig1∆) were examined by RNA Sequencing, in duplicate, using on Illumina HiSeq 4000 using 150-bp paired-end sequencing. We sequenced 2 samples from ScY01a, 2 samples from ScY01a (ric1∆), 2 samples from ScY01a (srb2∆), 2 samples from ScY01a (sin3∆) and 2 samples from ScY01a (mig1∆),  and identified differential expressions in the transcription factor deleiton strain versus the wild type strain by using mRNA levels the wild type strain as a reference.

first: Yuman

last: Gan

first: Yufeng

last: Guo

first: Xianni

last: Qi

first: Yuping

last: Lin


title: Genetic analysis of cancer drivers reveals cohesin and CTCF as suppressors of PD-L1

city: Boston

first: Stephen

middle: J

last: Elledge

state: MA

address: 77 Avenue Louis Pasteur NRB160

institute: Brigham and Women's Hospital | HHMI

summary: PD-1/PD-L1 Immunoinhibitory axis has recently been demonstrated to play a key role in immune evasion of cancer cells and therapies targeting PD-1/PD-L1 axis have demonstrated high efficacy in certain cancer types. Understanding how cancer drivers regulate immune surveillance can allow for development of novel therapeutic strategies which interfere with cancer-mediated immune evasion as well as identification of new biomarkers for application of these therapies. Here we utilized genetic screening with curated library of top 500 tumor suppressor genes to identify cohesin ring, one of the most mutated complex in cancer, as the most significant suppressor of PD-L1. Additionally, we comprehensively describe the consequences of loss of STAG2 subunit of cohesin and identify induction of IFN and NFκB response. Our findings thus elucidate transcriptional changes in immune related pathways as well as upregulation of key immune regulatory molecules including PD-L1, PD-L2 and MHC in cohesin deficient cells which could have significant implications on cancer microenvironment of cohesin deficient tumors.

overall_design: RNA-Seq for wild-type and STAG2-KO U937 cells, and HMEC cells treated with siRNA targeting STAG2 and control siRNAs.

first: Ena

last: Oreskovic

first: Emily

last: Wheeler

first: Kristen

middle: E

last: Mengwasser

first: Eric

last: Fujimura

first: Timothy

last: Martin

first: Zuzana

last: Tothova


title: 12-cell-type artificial mixtures validation dataset: An Enhanced DNA Methylation Library for Deconvoluting Peripheral Blood

first: Ze

last: Zhang

address: 375 Longwood Ave

department: Medical Oncology & Population Sciences

institute: Harvard Medical School

type: Methylation profiling by genome tiling array

summary: DNA methylation microarrays have been extensively used for understanding cell type composition in complex tissue samples. Here we expand on existing libraries for reference-based deconvolution of blood DNA methylation data assayed using the Illumina HumanMethylationEPIC array to include 12 different leukocyte subtypes (neutrophils, eosinophils, basophils, monocytes, B cells naïve and memory, CD4+ and CD8+ naïve and memory cells, natural killers, and T regulatory cells). Application of the IDOL algorithm for identifying optimal libraries for the deconvolution of blood-derived DNA methylation data led to to a library consisting of 1200 CpGs. The accuracy of deconvolution estimates obtained using our IDOL-optimized library was evaluated using artificial mixtures with known cellular composition and in samples were both whole-blood DNA methylation data and FACS information were available.  We further showcase potential applications of our expanded library using publicly available cancer, aging, and autoimmune disease data sets.

overall_design: Bisulphite converted DNA from twelve 12-cell-type artificial mixtures, including neutrophils, eosinophils, basophils, monocytes, B cells naïve and memory, CD4+ and CD8+ naïve and memory cells, natural killers, and T regulatory cells, were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4

first: Lucas

last: Salas

first: Devin

last: Koestler

first: Rondi

last: Butler

first: Helen

last: Hansen

first: Annette

last: Molinaro

first: John

last: Wiencke

first: Karl

last: Kelsey

first: Brock

last: Christensen


title: scRNA-seq comparison of B16-GP33 tumor-infiltrating immune cells from IgG, anti-PD-1, anti-PSGL-1, or combination anti-PD-1 and anti-PSGL-1 treated mice

city: Irvine

first: Roberto

last: Tinoco

address: 3444 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: University of California, Irvine

summary: We use scRNA-seq to show the differences in tumor-infiltrating immune cells among IgG, anti-PD-1, anti-PSGL-1, and combination anti-PD-1 and anti-PSGL-1 treated mice. We show that anti-PSGL-1 treatment resulted in an increase in neutrophil and T cells, anti-PD-1 treatment resulted in an increase in macrophages, and the combination resulted in an increase in T cells and macrophages when compared to the tumors of IgG treated mice. Additionally, we show that Tregulatory cells are decreased in the tumors of anti-PSGL-1 and combination treated mice. Further, we find that anti-PSGL-1 treated CD8 T cells show upregulation of activation and survival genes, while combination treatment increased effector gene expression in CD8 T cells. Both anti-PSGL-1 treatment and combination treatment increase effector gene expression in CD4 T cells when compared to IgG. This scRNA-seq study shows the impact of IgG, anti-PD-1, anti-PSGL-1, and combination anti-PSGL-1 and anti-PD-1 antibody tteatment on tumor-infiltrating immune cells in B16-GP33 melnoma tumor bearing mice.

overall_design: scRNA-seq profiling of CD45.2+ tumor infiltrating cells in melanoma tumor bearing mice.

first: Julia

last: DeRogatis

last: Neubert

first: Karla

last: Viramontes

first: Monique

last: Henriquez

first: Christian

last: Guerrero-Juarez


title: HLH-26 regulated genes in C. elegans under exposure to E. faecium

city: Portland

first: Yu

last: Sang

address: 3181 SW Sam Jackson Park Rd

institute: OHSU

summary: To understand the mechanism by which HLH-26 regulated protection against S. enterica infection after exposure to E. faecium, we used RNA sequencing to focus on transcriptional changes induced by E. faecium in hlh-26(ok1453) compared with wild-type animals.

overall_design: Wild-type C. elegans under exposure to E. faecium for 8 hours vs hlh-26(ok1453) C. elegans under exposure to E. faecium for 8 hours

first: Alejandro

last: Aballay


title: Tissue-specific chromatin accessibility cis-regulatory regions in rat white adipose and muscle

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: Chromatin accessibility is a key factor influencing gene expression. We developed a modified protocol, ruptor-ATAC, which with RNA-seq was used to investigate regulatory elements underlying gene expression in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. Integration of both datasets showed that promoter accessibility correlated with RNA expression and identified 44,798 tissue-specific differentially accessible regions (DARs), predominantly localized in intergenic and intron regions. Tissue-specific DARs mapped to differentially expressed genes that were enriched in distinct biological processes. Motif enrichment analysis on DARs predicted binding sites for transcription factors (TFs). Significant up-regulation of 11 TFs recognizing enriched cis-motifs in each tissue indicated their functional relevance. Positive correlation between motif accessibility and target gene expression further supported the role of selected TFs as transcriptional regulators. Our study identifies non-promoter cis-regulatory regions that likely play a major role in the control of tissue-specific gene expression in adipose and muscle.

overall_design: RNA sequencing was performed on 10 gastrocnemius muscle (skeletal muscle) samples and 10 abdominal white adipose tissue (WAT) samples dissected from Fischer 344 x Brown Norway (F344BN) rats. Tissue samples were obtained from 10 individual animals, namely 5 males and 5 females.

first: Venugopalan

last: Nair

first: Mital

last: Vasoya

first: Vishnu

first: Gregory

middle: R

last: Smith

first: Hanna

last: Pincas

first: Collin

last: Douglas

first: Karyn

last: Esser

first: Stuart

last: Sealfon


title: An Enhanced DNA Methylation Library for Deconvoluting Peripheral Blood

first: Ze

last: Zhang

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

overall_design: Refer to individual Series


title: Umbilical cord blood artificial mixtures validation dataset: An Enhanced DNA Methylation Library for Deconvoluting Peripheral Blood

overall_design: Bisulphite converted DNA from 12 umbilical cord blood artificial mixtures with six cell types, including CD8T, CD4T, NK, B cell, monocyte, and granulocyte, were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4

first: Lucas

last: Salas

first: Devin

last: Koestler

first: Rondi

last: Butler

first: Helen

last: Hansen

first: Annette

last: Molinaro

first: John

last: Wiencke

first: Karl

last: Kelsey

first: Brock

last: Christensen


title: Chromatin states and transcription factor binding in SIX1 deficient Rhabdomyosarcoma cells

city: Aurora

first: Heide

middle: L

last: Ford

state: CO

address: 12800 East 19th Ave Rm 6401I

department: Pharmacology

institute: University of Colorado Anschutz Medical Campus

summary: Genetic and shRNA-mediated inhibition of SIX1 expression in RMS cells induces myogenic differentiation and impedes RMS tumor growth. To elucidate the mechanism by which SIX1 loss activates a differentiation program, we performed SIX1, MYOD1, and H3K27ac ChIPseq in two SIX1 knockdown SMS-CTR cell lines and one control SMS-CTR cell line to profile changes in transcriptional activity and myogenic transcription factor binding in fusion-negative Rhabdomyosarcoma.

overall_design: ChIPseq was performed to characterize genome-wide SIX1 and MYOD1 binding as well as H3K27ac deposition in Fusion-Negative Rhabdomyosarcoma cells (SMS-CTR). Two SIX1 knockdown SMS-CTR cell lines (SMS-CTR SIX1 KD5, SMS-CTR SIX1 KD6) and one control SMS-CTR cell line (SMS-CTR SCRAMBLE) were used.

first: Jessica

last: Hsu

first: Etienne

last: Danis

first: Kristin

last: Artinger


title: Transcriptomes of SIX1 deficient and control Rhabdomyosarcoma cells

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Genetic and shRNA-mediated inhibition of SIX1 expression in RMS cells induces myogenic differentiation and impedes RMS tumor growth. To elucidate the mechanism by which SIX1 loss activates a differentiation program, we performed RNAseq in two SIX1 knockdown SMS-CTR cell lines and one control SMS-CTR cell line to profile changes in transcriptome.

overall_design: RNAseq was performed in Fusion-Negative Rhabdomyosarcoma cells (SMS-CTR). Two SIX1 knockdown SMS-CTR cell lines (SMS-CTR SIX1 KD5, SMS-CTR SIX1 KD6) and one control SMS-CTR cell line (SMS-CTR SCRAMBLE) were used. Four replicates of Scramble, three replicates of SIX1 KD5, and two replicates of SIX1 KD6 were used. Due to severe proliferative deficits, only two replicates of the SIX1 KD6 cell line were used.

middle: Y


title: RNA-Seq and ChIP-Seq in SIX1 deficient Rhabdomyosarcoma cells


title: CD4T and CD8T naïve and memory validation dataset: An Enhanced DNA Methylation Library for Deconvoluting Peripheral Blood

summary: DNA methylation microarrays have been extensively used for understanding cell type composition in complex tissue samples. Here we expand on existing libraries for reference-based deconvolution of blood DNA methylation data assayed using the Illumina HumanMethylationEPIC array to include 12 different leukocyte subtypes (neutrophils, eosinophils, basophils, monocytes, B cells naïve and memory, CD4+ and CD8+ naïve and memory cells, natural killers, and T regulatory cells). Application of the IDOL algorithm for identifying optimal libraries for the deconvolution of blood-derived DNA methylation data led to a library consisting of 1200 CpGs. The accuracy of deconvolution estimates obtained using our IDOL-optimized library was evaluated using artificial mixtures with known cellular composition and in samples were both whole-blood DNA methylation data and FACS information were available. We further showcase potential applications of our expanded library using publicly available cancer, aging, and autoimmune disease data sets.

overall_design: Bisulphite converted DNA from 76 glioma patients in different treatment stages, including FCM information for T cells CD4+ and CD8+ naïve and memory, were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4.


title: FlowSorted.BloodExtended.EPIC: An Enhanced DNA Methylation Library for Deconvoluting Peripheral Blood

overall_design: Bisulphite converted DNA from  neutrophils (Neu, n=6), eosinophils (Eos, n=4), basophils (Bas, n=6), monocytes (Mono, n=5), B lymphocytes naive (Bnv, n=4), B lymphocytes memory (Bmem, n=6), T helper lymphocytes naive (CD4nv, n=5), T helper lymphocytes memory (CD4mem, n=4), T regulatory cells (Treg, n=3), T cytotoxic lymphocytes naive (CD8nv, n=5), T cytotoxic lymphocytes memory (CD8mem, n=4), and natural killer lymphocytes (NK, n=4), and 12 DNA artificial mixtures (labeled as MIX in the dataset) were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4


title: Metabolomic and Transcriptomic Signatures of Chemnogenetic Heart Failure

status: Public on Feb 06 2022

first: Fotios

last: Spyropoulos

state: USA

address: 75 Francis Street Thorn 1005

department: Pediatric Newborn Medicine

institute: Brigham and Women's Hospital/Harvard Medical School

summary: In our chemogenetic rat heart failure model, LV and RV transcriptomic analysis was performed by RNA-seq

overall_design: RNA-seq of rat left and right ventricular heart tissue. The LV and RV samples were studied separately and have a separate set of raw data files, separate analysis and expression matrix.


title: Characterizing gene expression responses to biomechanical strain in an in vitro model of osteoarthritis

city: Chicago

first: Anthony

last: Hung

state: IL

address: 920 E 58th St

institute: University of Chicago

summary: Osteoarthritis (OA) is a common chronic degenerative disease affecting articular cartilage and underlying bone at the joints. Genetics and biomechanical stress likely interact to contribute to OA risk, potentially by affecting gene regulation. Population-level gene expression studies of cartilage cells experiencing biomechanical stress may uncover gene-by-environment interactions relevant to OA and human joint health. To build a foundation for such studies, we applied differentiation protocols to develop an in vitro system of chondrogenic cell lines (iPSC-chondrocytes). We characterized gene regulatory response of iPSC-chondrocytes of three humans to cyclic tensile strain treatment using bulk and single-cell RNA (scRNA) sequencing. Using the scRNA data, we were able to determine that iPSC-chondrocytes display some patterns of gene expression found in previously published iPSC-derived chondrocytes and in primary chondrocytes. Furthermore, using the scRNA data we determined that that the efficiency of differentiation does not differ substantially between individuals. Using the bulk RNA sequencing data, we measured the contribution of biological and technical factors to gene expression variation in this system. We further identified robust patterns of gene regulation that differ between strain-treated and control iPSC-chondrocytes. We also found several genes that exhibit inter-individual expression differences in response to mechanical strain, including genes previously implicated in OA. We believe that the in vitro iPSC-chondrocyte CTS model shows great promise when applied to gene expression studies of OA.

overall_design: We collected RNA-seq data from iPSC-derived chondrogenic cells under control conditions and following cyclic tensile strain in 3 individuals. Three replicates of three individuals were conducted, with bulk RNA sequencing conducted from samples from each replicate and single cell RNA sequencing conducted for one of the three replicates.


title: Porcine ZC3H11A is essential for the proliferation of pseudorabies virus (PRV) and porcine circovirus 2 (PCV2) by mediating mRNA export

city: changchun

first: Hongming

last: Yuan

state: Jilin province

address: Lvyuan road

institute: Jilin University

summary:
Purpose:ZC3H11A has been reported to play a role in RNA transport.  The purpose of this study was to detect the differentially expressed genes after ZC3H11A knockout.
Methods: RNA sequencing was performed on PK-15 cell line (WT) and ZC3H11A-/- using Illumina platform, and three repeated RNA sequencing results were obtained.
Results: Using an optimized data analysis workflow,different expression genes were obtained and RNA transport pathway was enriched through KEGG pathway analysis.
Conclusions: In this study, we observed that ZC3H11A interacted with TRanscription and the EXport complex (TREX) and played an important role in mRNA export.

overall_design: PK-15 cell line (WT) and ZC3H11A-/- cells

first: Lin

last: Yang

first: Ziru

last: Wang

first: Hongsheng

last: Ouyang


title: Therapeutic Targeting of EZH2 and BET BRD4 in Pediatric Rhabdoid Tumor [RNA-Seq]

first: Yongzhan

last: zhang

state: Illinois

address: 303 East Superior Street

department: Department of Pediatrics, Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: We proved that histone H3K27me3 and H3K27ac were elevated in AT/RT cells and distributed in distinct chromatin regions to regulate specific gene expression and to promote AT/RT growth. Targeting EZH2 and BRD4 activity is therefore a potential combination therapy for AT/RT.

overall_design: RNA- and chromatin immunoprecipitation-sequencing were used to determine transcriptional and epigenetic changes in AT/RT cells treated with EZH2 and BRD4 inhibitors.

first: Yukitomo

last: Ishi

last: Zhang

first: Ali

first: Takahiro

last: Sasaki

first: Andrea

last: Piunti

first: Amreena

last: Suri

first: Jun

last: Watanabe

first: Kouki

last: Abe

first: Xingyao

last: He

first: Hiroaki

last: Katagi

first: Pankaj

last: Bhalla

first: Manabu

last: Natsumeda

first: Lihua

last: Zou

last: Shilatifard

first: Rintaro

last: Hashizume


title: Therapeutic Targeting of EZH2 and BET BRD4 in Pediatric Rhabdoid Tumor [ChIP-Seq]


title: Therapeutic Targeting of EZH2 and BET BRD4 in Pediatric Rhabdoid Tumor


title: A Hidden Proteome Encoded by circRNAs in Human Placentas: Implications for Uncovering Preeclampsia Pathogenesis

first: Huanqiang

last: Zhao

address: Fangxie Road 419, Huangpu District

institute: Fudan university

summary: Circular RNAs (circRNAs) are consistently overlooked as translational templates due to computational and experimental limitations. Here, we used multi-omics approaches to identify new translational events of circRNAs in human placentas, and assessed the roles of circRNA-encoded proteins in placentation and associated disorders based on the recently proposed protein bait hypothesis. The combination of placental circRNA sequencing and bioinformatics analysis revealed 219607 circRNAs, of which 35% were identified by the Coding Potential Assessment Tool (CPAT) as having >50% coding probability. Ribosomal profiling further identified 528 novel coding circRNAs, including 217 that coded for microproteins verified by LC-MS/MS. Based on these data, we established the Placental Microprotein Bank (PMB) for coding circRNAs and their coded proteins. These proteins have lower molecular weights, higher stable indices and hydrophobicity compared to the canonical proteins, and potentially link to placental development and adverse pregnancy outcomes such as pre-eclampsia. Furthermore, we identified circPRKCB119aa as a novel preeclampsia-related microprotein that enhanced trophoblast autophagy by inhibiting phosphorylation of its cognate linear-spliced isoform protein kinase C (PKC) β. In summary, we discovered a hidden circRNA-encoded proteome in the human placenta, which offers new insights into the mechanisms underlying placentation and its disorders such as, but not limited to, preeclampsia.

overall_design: Three placentas from the first trimester (6~7 weeks of gestation), second trimester (18~20 weeks of gestation) and third trimester (38~40 weeks of gestation), respectively, were collected for high throughput sequencing of circRNAs.

first: Yu

last: Xiong

first: Xirong

last: Xiao

first: Lili

last: Gong

first: Huangfang

last: Xu

first: Lidong

last: Liu

first: Huiqing

last: Lu

first: Yutong

last: Cui

first: Shuyi

last: Shao

first: Jin

first: Jing

last: Ma

first: Qiongjie

last: Zhou

first: Duan

first: Xiaotian

last: Li


title: CRISPR and biochemical screens Identify MAZ as a co-factor in CTCF-mediated insulation at Hox Clusters [CRISPR_set9]

first: Danny

last: Reinberg

state: New York

address: 522 First Avenue, 2nd floor, Room 211

department: Biochemistry

institute: New York University School of Medicine

summary: In this experiment, we sought to analyze the genes positively or negatively selected during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs) with particular focus on the genes enriched for CTCF boundary disruption at HoxA cluster

overall_design: Examination of the genes positively or negatively selected in embryonic stem cells and cervical motor neurons using CRISPR loss-of-function screens, with particular focus on the genes enriched for CTCF boundary disruption at HoxA cluster


title: CRISPR and biochemical screens Identify MAZ as a co-factor in CTCF-mediated insulation at Hox Clusters [ChIP-seq_set7]

summary: In this experiment, we sought to identify the distribution of RAD21 in cervical motor neurons (MNs) that is formed through in vitro differentiation of mESCs.

overall_design: Examination of RAD21 binding in cervical motor neurons using ChIP-seq


title: CRISPR and biochemical screens Identify MAZ as a co-factor in CTCF-mediated insulation at Hox Clusters [CRISPR_set8]

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct


title: CRISPR and biochemical screens Identify MAZ as a co-factor in CTCF-mediated insulation at Hox Clusters [ChIP-seq_set6]

summary: In this experiment, we sought to identify how the distribution of CTCF and MAZ change in WT and MAZ knock-out (KO) cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

overall_design: Examination of CTCF and MAZ binding in embryonic stem cells and cervical motor neurons using ChIP-seq, by knock-out status of MAZ


title: CRISPR and biochemical screens Identify MAZ as a co-factor in CTCF-mediated insulation at Hox Clusters

summary: In this experiment, we sought to identify how the distribution of MAZ change in WT, MAZ HoxA(Δ5|6), and MAZ HoxD(Δ4|8) cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

overall_design: Examination of MAZ binding in embryonic stem cells and cervical motor neurons using ChIP-seq, by status of motif deletion in the cells: WT, MAZ HoxA(Δ5|6), and MAZ HoxD(Δ4|8)


title: CRISPR and biochemical screens Identify MAZ as a co-factor in CTCF-mediated insulation at Hox Clusters [ChIP-seq_set4]

summary: In this experiment, we sought to identify how the distribution of H3K27me3 and H3K4me3 change in WT, MAZ HoxA(delta5|6), MAZ HoxD(delta4|8), and CTCF (delta5|6:6|7) cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

overall_design: Examination of H3K27me3 and H3K4me3 binding in embryonic stem cells and cervical motor neurons using ChIP-seq, by status of motif deletion in the cells: WT, MAZ HoxA(delta5|6), MAZ HoxD(delta4|8), and CTCF (delta5|6:6|7)


title: CRISPR and biochemical screens Identify MAZ as a co-factor in CTCF-mediated insulation at Hox Clusters [ChIP-seq_set3]

summary: In this experiment, we sought to identify how the distribution of CTCF change in WT, MAZ HoxA(Δ5|6), MAZ HoxD(Δ4|8), and CTCF (Δ5|6:6|7) cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs).

overall_design: Examination of CTCF binding in embryonic stem cells and cervical motor neurons using ChIP-seq, by status of motif deletion in the cells: WT, MAZ HoxA(Δ5|6), MAZ HoxD(Δ4|8), and CTCF (Δ5|6:6|7).


title: CRISPR and biochemical screens Identify MAZ as a co-factor in CTCF-mediated insulation at Hox Clusters [4C-seq_set2]

summary: In this experiment, we sought to identify how topological organization changes at HoxA cluster in WT, MAZ HoxA(Δ5|6) and CTCF (Δ5|6:6|7) cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs).

overall_design: Examination of topological organization in embryonic stem cells and cervical motor neurons using 4C-seq, by status of motif deletion in the cells: WT, MAZ HoxA(Δ5|6), and CTCF (Δ5|6:6|7).


title: CRISPR and biochemical screens Identify MAZ as a co-factor in CTCF-mediated insulation at Hox Clusters [CUT&RUN_set1]

summary: In this experiment, we sought to identify how the distribution of CTCF, RAD21, H3K27me3 and H3K4me3 change in WT and double-positive MAZ HoxA(Δ5|6) cervical motor neurons (MNs).

overall_design: Examination of CTCF, RAD21, H3K27me3 and H3K4me3 binding in cervical motor neurons using CUT&RUN, by status of motif deletion in the cells: WT and double-positive sorted MAZ HoxA(Δ5|6).


title: Next Generation Sequencing Facilitates Quantitative Analysis of sh-NC and sh-Etv5 macrophage line Raw264.7 Transcriptomes

city: Guangzhou

first: Rendong

last: Hu

address: Guangzhou Higher Education Mega Centre, Panyu District

institute: South china university of technology

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare sh-NC with sh-Etv5 macrophage line Raw264.7 transcriptome profiling (RNA-seq).

overall_design: Macrophage line Raw264.7 mRNA profiles of negtive ctrl and knockdown Etv5.

first: Liang

first: Min


title: MRNA prolfiles of subcutaneous SK-N-BE(2) xenografts treated with the KIF11 inhibitor 4SC-205

city: Barcelona

first: Marc

last: Masanas

state: - None -

address: Pg Vall d’Hebron 119 129, Mediterranean Building

country: Spain

institute: Vall Hebron Research Institute

summary: The aim of these study is to investiate the expression profile of neuroblastoma SK-N-BE(2) xenografts treated with one single dose of the KIF11 inhibitor 4SC-205 for 24 h. RNASeq libraries were prepared following the TruSeq® Stranded mRNA LT Sample Prep Kit protocol and sequenced on NovaSeq 6000 (Illumina). RNA-seq reads were mapped against human reference genome (GRCh38) using STAR software version 2.5.3a with ENCODE parameters. Genes were quantified using RSEM version 1.3.0. Tumors treated with 4SC-205 presented increased expression of genes involved in the G2/M checkpoint and E2F targets. Genes of mTORC1 pathway were found to be less expressed on treated tumors otherwise. This study demonstrates that KIF11 inhibition using 4SC-205 halts cell cycle progression of cancerous cells of neuroblastoma xenografts.

overall_design: MRNA profiles of SK-N-BE(2) xenografts treated with 4SC-205 for 24 h

first: Miguel

middle: F

last: Segura

first: Anna

last: Santamaria


title: CRISPR and biochemical screens identify MAZ as a co-factor in CTCF-mediated insulation at Hox clusters [MAZ KO]

summary: In this experiment, we sought to analyze how transcriptome of WT and MAZ knock-out (KO) cells change during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

overall_design: Examination of gene expression of ESCs and cervical MNs using ribo-zero RNAseq, by knock-out status of MAZ in triplicates, 2 cell lines (WT and MAZ KO)


title: ADGRG1/GPR56 knockdown in cord blood CD34+ cells

city: Heidelberg

first: Christian

last: Arnold

state: Baden-Württemberg

address: Meyerhofstraße 1

country: Germany

institute: EMBL

summary: ADGRG1/GPR56 was knocked down by two different shRNAs in cord blood CD34+ cells via lentiviral transduction. GFP was used as marker indicating successful transduction.

overall_design: CD34+ cells were pre-stimulated in culture media for two nights, followed by lentiviral transduction. Cells were washed and sorted 72 hours post transduction.

first: Caroline

last: Pabst

first: Lixiazi

last: He

first: Judith

last: Zaugg


title: CRISPR and biochemical screens identify MAZ as a co-factor in CTCF-mediated insulation at Hox clusters [Hi-C]

summary: In this experiment, we sought to analyze how three dimensional genome organization of WT and MAZ knock-out (KO) cells change during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

overall_design: Examination of chromatin architecture of embryonic stem cells and cervical motor neurons using Hi-C, by knock-out status of MAZ in duplicates


title: CRISPR and biochemical screens identify MAZ as a co-factor in CTCF-mediated insulation at Hox clusters [MAZ motif deletion RNA-seq]

summary: In this experiment, we sought to analyze how transcriptome of WT and Maz HoxA(Δ5|6) cells change during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

overall_design: Examination of gene expression of ESCs and cervical MNs using ribo-zero RNAseq, by status of MAZ motif deletion at Hoxa5|6 in triplicates, 2 cell lines (WT and MAZ_HoxA(Δ5|6))


title: Determine differences in chromatin accessibility in primary human AML samples by ATAC-seq.

summary: ATAC-Seq was performed for 35 AML primary specimens from primary AML cells, followed by a detailed ATAC-Seq pipeline for data processing. We provide both raw files as well as various processed files such as individual and consensus peaks.

overall_design: Chromatin accessiblity was analyzed on 35 AML primary specimens using Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) in order to analyze transcription factor activity in combination of mRNA seq data in GPR56 KD scenario.


title: Estrogen receptor alpha ChIP-seq in p53 null mouse mammary gland

city: Houston

first: MURUGESAN

last: PALANIAPPAN

address: One Baylor Plaza

institute: Baylor College of Medicine

summary:
ERα is a major driver for breast cancer initiation and progression.However,the fundamental mechanisms,including global cistromic and genomic transcriptional responses that are required to elicit breast cancer initiation and progression in response to ERα, have not been elucidated.
We used chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) to identify estrogen regulated genes that directly recruit ERα in the p53 null mouse mammary gland

overall_design: Two replicate ERα ChIP samples and one input DNA samples from p53 null mouse mammary glands after mice are treated subcutaneously with 17β Estradiol for 8 hours.

first: Murugesan

last: Palaniappan

first: David

last: Edwards

first: Chad

last: Creighton

first: Daniel

last: Medina

first: Orla

last: Conneely


title: CRISPR and biochemical screens identify MAZ as a co-factor in CTCF-mediated insulation at Hox clusters

first: Danny

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

overall_design: Refer to individual Series


title: Comprehensive molecular classification for adenocarcinoma of gastroesophageal junction between esophageal and gastric adenocarcinomas

city: Seoul

first: Yun-Suhk

last: Suh

address: 101 Daehang-ro, Jongo-Gu

country: South Korea

institute: Seoul National University College of Medicine

summary: Background and aims: The aim of this study was to analyze the molecular characteristics of adenocarcinoma of the gastroesophageal junction (AGEJ) compared to esophageal (EAC) and gastric adenocarcinomas (GCFB) from The Cancer Genome Atlas (TCGA) and Seoul National University (SNU) cohorts using next-generation sequencing.  Methods: Based on mRNA expression of EAC (n=78) and GCFB (n=102) from the TCGA cohort, a molecular classification model using the Bayesian compound covariate predictor classified AGEJ/cardia (n=48) from the TCGA cohort and AGEJ/upper third gastric adenocarcinoma (n=46) from the SNU cohort into the EAC-like or GCFB-like groups. The molecular characteristics between the EAC-like and GCFB-like groups were compared.

overall_design: 46 paired tumor samples-corresponding normal mucosa of SNU cohort (92 samples) were analyzed with RNA sequencing data.

first: Han-Kwang

last: Yang


title: Urinary extracellular vesicle microRNA profiling for detection in patients with interstitial cystitis

status: Public on Feb 05 2022

city: Minato-ku

first: Fumihiko

last: Urabe

department: Urology

institute: The Jikei University School of Medicine

summary: Urinay miRNAs could be a powerful classifier for the detection of patients with interstitial cystitis

overall_design: Urinary microRNA profiles of 20 samples, which consist of 8 of Hunner type intestitial cystitis (HIC) patients, 2 of bladder pain sydrome (BPS) patients, 10 of non-IC/BPS controls.

first: Akira

last: Furuta

first: Taro

last: Igarashi

first: Takahiro

last: Kimura

first: Shin

last: Egawa

first: Hiroki

last: Yamaguchi

first: Kodai

last: Minoura


title: Affymetrix SNP Data array data of pancreatic cancer PDX models

city: Freiburg

first: Hagen

last: Klett

address: Am Flughafen 12

department: Discovery Services Freiburg

institute: Charles River Laboratories

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

summary: Copy number variations were obtained to characterize pancreatic cancer PDX models for tumor research and drug discovery.

overall_design:
Copy numbers were calculated based on SNP6.0 Data using the PICNIC algorithm.
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from PDX tumors.

first: Julia

last: Schüler


title: dsRNA induced IFNβ-MMP13 axis drives corneal wound healing

first: Lan

last: Xihong

state: Shanghai

address: 2005 Songhu Road

department: school of life sciences

institute: Fudan University

summary: Cornea, the outermost transparent layer of the eye, is the first line of defense against external threats. Following injury, the wound healing response is crucial to corneal repair and regeneration, yet its underlying mechanism is poorly understood. Our study was designed to investigate the role of dsRNA and its regulatory network in corneal wound healing.

overall_design: RNA-seq for mouse corneas from three groups: unwounded corneas, wounded corneas treated without RNase III, wounded corneas treated with RNase III.


title: AngII induced responses from non-myocytes in the heart

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: AngII infusion in mouse is a classic model of cardiac hypertrophy. Here we aimed to understand how non-myocytes in the myocardium respond to AngII stimulation.

overall_design: Lyz2-Cre and Lyz2-KLF2-KO mice were subjected to AngII infusion at the dose of 1.0 ug/kg/min for one week. CD45+ and CD31+ cells were sorted from the heart, and subjected to single cell capture by 10X genomics device and followed by RNA-seq using Illumina platform.

first: Xudong

last: Liao

first: Mukesh

last: Jain


title: Targeted scRNA-seq analysis of Wnt signaling in bone marrow

summary: We enriched endothelial cells and other bone marrow cells in both fetal and adult stage to investigate Wnt signaling interaction using targeted scRNA-seq analysis. This analysis facilitate identification of sources of Wnt ligands and detection of Wnt receptor expression in bone marrow. The comparison of fetal and adult stage reveals differences of Wnt signaling in fetal and adult BM.

overall_design: Samples were obtained from C57/B6 wildtype mice. Endothelial cells were enriched by FACS sorting based on expression of marker CD31 and endomucin. Mature hematopoietic cells were depleted from fetal and adult bone marrow cells by lineage antibody conjugated magnetic beads. The obtained cells were directly used for targetted scRNA-seq library preparation.

first: Ralf

middle: H

last: Adams

first: Yang

last: Liu

first: Qi

last: Chen


title: A glycolytic enzyme enoalse negatively regulates plant immunity by repressing intracellular immune receptor NLR genes

city: Ithaca

first: Leiyun

last: Yang

address: 360 Tower road

department: Plant Biology

institute: Cornell University

summary: AtLOS2 gene was isolated from a sensitized genetic screen aiming at the identification of negative regulators of SNC1 gene, a TIR-NLR gene. The whole genome transcriptome (RNA-seq) analysis of the los2-5 mutant revealed 1192 upregulated genes and 1140 downregulated genes in the mutant.

overall_design: Two-week-old plants growing under constant light at 22C were sampled. Three biological replicates were performed for wild type control Col-0 and los2-5 mutant.

first: Jian

last: Hua


title: Chromosome conformation for wild type, eco1-aa, cdc6-mn and eco1-aa cdc6-mn strains arrested in meiotic prophase I

status: Public on Feb 04 2022

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: High-resolution Hi-C in meiotic prophase I arrested cells

overall_design: Purpose: to determine the relative impact of Eco1 and cohesive cohesin on loop extrusion in meiotic prophase I, with a focus on the pericentromere.

first: Lucia

last: Massari

first: Adele

last: Marston


title: Intermediate GATA3 expression renders a noncanonical ILC population in skin essential for hair follicle recycling

city: Beijing

first: Chao

last: Zhong

address: 38 Xueyuan Rd , Haidian District

department: Institute of Systems Biomedicine

institute: Peking University

summary: We find that the expression of GATA3 in skin ILCs is significantly lower than in conventional ILC2s of other tissues, indicating that the regulatory role of GATA3 may be different. Indeed, skin ILCs are still maintained after inducing Gata3 depletion in Gata3fl/flCreERT2 mice, when all ILC2s were gone. In addition, about 70% skin ILCs are found to experience RORγt expression as reflected by RORγt fate-mapping. And, conditional Gata3 depletion in the RORγt fate-mapped skin ILCs does not affect their number as well. Therefore, in contrast to conventional ILC2s, GATA3 is not required for skin ILCs for their maintenance. The RORγt fate-mapped skin ILCs have exhibited ILC3-like features. Single-cell transcriptome analysis further reveals that skin ILCs converge on a Ccr6+ ILC3-like state and an Il1rl1+ ILC2-like state. The regulatory role of GATA3 is crucial in the ILC3-like skin ILCs. It promotes the expression of their featured genes, while suppresses the expression of ILC2-like skin ILC featured genes. These ILC3-like skin ILCs locate in close proximity to hair follicles. During hair follicle recycling they migrate from isthmus to suprabulbar to promote the hair follicle growth. Whereas in absence of Gata3, the ILC3-like skin ILCs exhibit defective migration to the suprabulbar and reduced expression of the featured genes in this process. Together, our study evidence that skin ILCs are alternative to conventional ILC2s. In particular, we shed light on the function of GATA3 in promoting the specific gene expression in ILC3-like skin ILCs and regulating their crucial roles in hair follicle recycling, which will improve our knowledge about the involvement of ILCs in maintaining homeostasis of skin.

overall_design: We want to identify different gene expression in RORγtfm+ and RORγtfm- skin ILCs from RORγt-fm and RORγt-fmΔGata3 mice. We want to  identify different gene expression in skin ILCs between C57BL/6  (WT) and Gata3fl/flCreERT2 mice after tamoxifen treatment to knockout Gata3. We also use scRNA-seq of skin ILC from ear and dorsal skin(Day 0 and Day 10 after depilation) to identify subgroups.

first: Guanqun

last: Ren

first: Mengwei

last: Han

first: Yimo

last: Zhang

first: Wenwen

last: Cheng


title: Transcriptomic effects of mono-(2-ethylhexyl) phthalate and all-trans retinoic acid in the cultured mouse fetal testes

city: Providence

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

summary: We report the results of an RNA-seq analysis conducted as part of an experiment investigating the effects of the phthalate, mono-(2-ethylhexyl) phthalate (MEHP), and all-trans retinoic acid (ATRA) on cultured fetal mouse testes. The goal of the study was to determine whether fetal testis toxicity of MEHP is partially driven by disruption of retinoic acid signaling.

overall_design: Samples are mouse fetal testes isolated on gestational day (GD) 14 and cultured for 24 hours. Samples were treated in tissue culture in one of four media treatment groups: vehicle (1:4000 DMSO), MEHP (1E-4 M), ATRA (1E-6 M), and MEHP + ATRA (co-exposure, 1E-4 M MEHP + 1E-6 M ATRA).

first: Maha

last: Alhasnani

first: Susan

last: Hall


title: Functional Enrichment Analysis of ALYREF

first: weibo

last: zhong

address: 1023-1063 shatai South Road, Baiyun District, Guangzhou

institute: southern medical university

summary: We investigated the biological function and mechanism of ALYREF based on RIP and RNA-seq in C42 cell

overall_design: Examination of RIP for ALYREF and RNA-seq based on si-NC and si-ALYREF

first: Lu

last: jianming

first: Zhong

last: chuanfan

last: weibo


title: MHC class II proteins mediate cross-species entry of bat influenza viruses

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Zoonotic influenza A viruses of avian origin can cause severe disease in individuals, or even global pandemics, and thus pose a threat to human populations. Waterfowl and shorebirds are believed to be the reservoir for all influenza A viruses, but this has recently been challenged by the identification of novel influenza A viruses in bats. The major bat influenza A virus envelope glycoprotein, haemagglutinin, does not bind the canonical influenza A virus receptor, sialic acid or any other glycan, despite its high sequence and structural homology with conventional haemagglutinins. This functionally uncharacterized plasticity of the bat influenza A virus haemagglutinin means the tropism and zoonotic potential of these viruses has not been fully determined. Here we show, using transcriptomic profiling of susceptible versus non-susceptible cells in combination with genome-wide CRISPR-Cas9 screening, that the major histocompatibility complex class II (MHC-II) human leukocyte antigen DR isotype (HLA-DR) is an essential entry determinant for bat influenza A viruses. Genetic ablation of the HLA-DR α-chain rendered cells resistant to infection by bat influenza A virus, whereas ectopic expression of the HLA-DR complex in non-susceptible cells conferred susceptibility. Expression of MHC-II from different bat species, pigs, mice or chickens also conferred susceptibility to infection. Notably, the infection of mice with bat influenza A virus resulted in robust virus replication in the upper respiratory tract, whereas mice deficient for MHC-II were resistant. Collectively, our data identify MHC-II as a crucial entry mediator for bat influenza A viruses in multiple species, which permits a broad vertebrate tropism.

overall_design: Positive selection CRISPR screen with VSV-H18 in U-87MG cells

first: Umut

last: Karakus

first: Silke

last: Stertz


title: RNA m1A methylation regulates glycolysis of cancer cells through modulating ATP5D [Ribo and RNA-seq]

city: guangzhou

first: xie

last: guoyou

address: 大学城中山大学

institute: 中山大学

summary: Studies on biological functions of RNA modifications such as N6-methyladenosine (m6A) in mRNA have sprung up in recent years, while the roles of N1-methyladenosine (m1A) in cancer progression remain largely unknown. We find m1A demethylase ALKBH3 can regulate the glycolysis of cancer cells via a demethylation activity dependent manner. Specifically, sequencing and functional studies confirm that ATP5D, one of the most important subunit of ATP synthase, is involved in m1A demethylase ALKBH3-regulated glycolysis of cancer cells. The m1A modified A71 at the Exon 1 of ATP5D negatively regulates its translation elongation via increasing the binding with YTHDF1/eRF1 complex, which facilitates the release of mRNA from ribosome complex. m1A also regulates mRNA stability of E2F1, which directly binds with ATP5D promoter to initiate its transcription. Targeted specific demethylation of ATP5D m1A by dm1ACRISPR system can significantly increase the expression of ATP5D and glycolysis of cancer cells. In vivo data confirm the roles of m1A/ATP5D in tumor growth and cancer progression. Our study for the first time reveals a crosstalk of mRNA m1A modification and cell metabolism, which expands the understanding of such interplays that are essential for cancer therapeutic application.

overall_design: Ribo-seq and mRNA-seq in Human HeLa WT(n=2) and HeLa ALKBH3-KO(n=2), then caculated the quantity and efficiency of translation

first: Hongsheng

last: Wang

first: Guoyou

last: Xie


title: TAB2 haploinsufficiency

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

institute: Tigem

summary: We identified t a series of 12 individuals from nine families with loss-of-function variants in TAB2 and a multi-system phenotype. This condition emerges as a novel recognizable syndrome with cardiovascular anomalies, facial dysmorphisms and multiple connective tissue features.

overall_design: 6 RNA samples derived from fibroblasts of TAB2 patients  and 5 control samples derived from fibroblats of unaffected individuals were subjected to RNA-Seq analysis.

first: Lucia

last: Micale

first: Marco

last: Castori

first: Silvia

last: Morlino


title: Calibrated Smc3 ChIP-seq for wild type, eco1-aa, cdc6-mn and eco1-aa cdc6-mn strains arrested in meiotic prophase I

first: Daniel

last: Robertson

summary: Genome binding/occupancy profiling of the cohesin subunit Smc3 by high throughput sequencing. S. pombe is included as the calibration genome.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Purpose: to determine the contribution of Eco1 in anchoring on DNA cohesin complexes that are not involved in cohesion but rather on loop extrusion, with a focus on centromere and pericentromere borders.

last: Massari

first: Adele

last: Marston


title: Chromosome conformation for wild type and clb5 clb6 strains arrested before meiotic S phase

summary: High-resolution Hi-C in meiotic pre-S phase cells

overall_design: Purpose: to determine the impact of cohesive cohesin in anchoring cohesin mediated DNA loops before entry into meiosis, with a focus on the pericentromere.


title: Safety, immunogenicity, and efficacy of the IV PfSPZ Vac in Tanzania (BSPZV1)

city: Seattle

first: Raphael

last: Gottardo

state: WA

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutch

summary: This trial will evaluate whether relatively non-immune populations in endemic countries can effectively generate significant cellular and humoral immune responses that confer protection against P. falciparum infection after inoculation of aseptic, purified, vialed, metabolically active, non-replicating (live, radiation attenuated) Plasmodium falciparum sporozoites (PfSPZ Vaccine) administered intravenously (IV).

overall_design: This is a single center, Phase 1, dose escalating, randomized, double blind, controlled trial. Seventy-three healthy male volunteers, aged 18 to 35 years will be recruited. The study will have 5 study groups that will include 49 volunteers who will be intravenously injected with PfSPZ Vaccine, 8 control volunteers who will receive normal saline and 16 additional control volunteers who will be recruited at the time of controlled human malaria infection (CHMI) at 3 and 24 weeks. The control volunteers will help better assess the occurrence of AEs compared to background disease patterns that occur in this tropical area, and the performance of the vaccine.

first: Ying

last: Du

first: Fergal

last: Duffy

first: Jason

last: Carnes

first: Kenneth

last: Stuart


title: FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction

city: Cologne

first: Aleksandra

last: Trifunovic

address: Joseph-Stelzmann-Str. 26

institute: Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases

summary: Mitochondrial integrated stress response emerged as a major adaptive pathway to respiratory chain deficiency, but tissue-specifics of its regulation or how it adapts to different levels of mitochondrial dysfunction are largely unknown. Here we report that diverse levels of mitochondrial cardiomyopathy activate mitoISR, including high production of FGF21, a cytokine with both paracrine and endocrine function, shown to be induced by respiratory chain dysfunction. Remarkably, although being fully dispensable for the cell-autonomous and systemic responses to severe mitochondrial cardiomyopathy, in the conditions of mild-to-moderate cardiac OXPHOS dysfunction, FGF21 regulates a portion of the mitoISR. In the absence of FGF21, a large part of the metabolic adaptation to mitochondrial dysfunction (one-carbon metabolism, transsulfuration and serine and proline biosynthesis) is strongly blunted, independent of the primary mitoISR activator ATF4. Collectively, our work highlights the complexity of mitochondrial stress responses by revealing the importance of the tissue-specificity and dose-dependency of the mitoISR.

overall_design: RNAseq data from RNA extracted from cardiac tissues in WT, FGF21 KO, CLPP KO and double KO mice.

first: Marijana

last: Croon

first: Richard

last: Acton


title: MyoD-Cre driven alterations in K-Ras and p53 lead to a mouse model with histological and molecular characteristics of human rhabdomyosarcoma [RMS_GEMM_tumors]

last: Yustein

state: TX

address: 1102 Bates Ave

department: Pediatrics-Oncology

institute: Texas Children's Hospital

summary: We have developed a new conditional genetically engineered mouse model of rhabdomyosarcoma (RMS) with homologous molecular signature to human RMS that provides valuable pre-clinical models for evaluating novel therapies

overall_design: Mice expressing MyoD promoter-regulated Cre-recombinase were crossed with germline p53Flox or Lox-Stop-Lox (LSL) knock-in alleles expressing oncogenic p53R172H and/or K-RasG12D mutants.

first: Kengo

last: Nakahata

first: Tajhal

last: Patel


title: Resident T Cell Repertoires

city: Aachen

first: Oliver

last: Pabst

address: Pauwelsstrasse 30

institute: RWTH Aachen University

summary: Regulatory T (Treg) are present in lymphoid and non-lymphoid tissues and restrict immune activation, prevent autoimmunity and regulate inflammation. While Treg in non-lymphoid tissues are typically resident, Treg in lymph nodes (LNs) predominantly recirculate and residency of Treg in LNs is poorly studied. Here, we show that 10-20% of all Treg in LNs are memory-like resident cells. Both thymic and peripheral Treg contributed to the pool of resident Treg and their residency did not require continuous TCR signaling. Yet, resident and circulating Treg had distinct TCR repertoires and different LNs contained distinct clonal subpopulations of resident Treg. We speculate that stochastic selection and variation in antigen availability governs commitment of individual T cell clones to the resident pool in each LN. Our results describe a framework for local fine-tuning of immune responses in LNs based on previous adaptive immune responses.

overall_design: TCR repertoire of resident and circulating effector/memory CD4+ T cells in mesenteric lymph node

first: Anne

last: Kaminski

first: Fabio

last: Ticconi

first: Lydia

last: Kopplin

first: Andrea

last: Leufgen

first: Lennart

last: Rüttger

first: Vuk

last: Cerovic

first: Wolfgang

last: Kastenmüller

first: Milas

last: Ugur


title: MyoD-Cre driven alterations in K-Ras and p53 lead to a mouse model with histological and molecular characteristics of human rhabdomyosarcoma

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

overall_design: Refer to individual Series


title: MyoD-Cre driven alterations in K-Ras and p53 lead to a mouse model with histological and molecular characteristics of human rhabdomyosarcoma [RMS_GEMM_cell_lines]

overall_design: Mice expressing MyoD promoter-regulated Cre-recombinase were crossed with germline p53Flox or Lox-Stop-Lox (LSL) knock-in alleles expressing oncogenic p53R172H and/or K-RasG12D mutants.  Resulting tumors were  isolated  and dissociated to establish cell lines.


title: Regulation of mannitol metabolism in Enterococcus faecalis and association with parEF0409 toxin-antitoxin locus function.

city: Vermillion

first: SRIVISHNUPRIYA

last: ANBALAGAN

state: SD

address: 414 East Clark Street

department: Basic Biomedical Sciences

institute: University of South Dakota

summary: RNAseq analysis was performed for Enterococculs faecalis strain OG1RF grown in M9YEG and M9YEM to monitor transcriptional changes. RNAseq analysis was also conducted for mtlR deletion mutant grown in M9YEG to monitor transcriptional changes.

overall_design: RNA was collected from Enterococculs faecalis strain OG1RF grown in M9YEG and M9YEM. RNA was also collected for mtlR deletion mutant grown in M9YEG.  Comparisons were made between the OG1RF grown in M9YEG and M9YEM. Comparisons were also made between OG1RF and mtlR deletion mutant grown in M9YEG.

first: Keith

last: Weaver

first: Srivishnupriya

last: Anbalagan


title: DNA methylation array analysis of high-grade gliomas with pleomorphic and pseudopapillary features

city: Bethesda

first: Drew

last: Pratt

state: Maryland

address: 10 Center Drive, Building 10, Room 2S235

department: Laboratory of Pathology

institute: National Institutes of Health

summary: Genomewide DNA methylation array profiling of 23 previously unpublished CNS tumors resolved into a new entity, high-grade glioma with pleomorphic and pseudopapillary features (HPAP). Tumors demonstrate a variety of histologic diagnoses including glioblastoma (GBM), pleomorphic xanthoastrocytoma (PXA), anaplastic ependymoma, and polymorphous low-grade neuroepithelial tumor of the young (PLNTY). The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue.

overall_design: Bisulfite converted genomic DNA extracted from 23 tumor samples was hybridized to Illumina Infinium EPIC Human DNA Methylation Beadchips

first: D


title: CRISPR activation and interference screens decode stimulation responses in primary human T cells [Supplemental CRISPR]

city: San Francisco

first: Zachary

last: Steinhart

address: 1650 Owens St

department: Gladstone-UCSF Institute of Genomic Immunology

institute: J. David Gladstone Institutes

summary: Regulation of cytokine production in stimulated T cells can be disrupted in autoimmunity, immunodeficiencies, and cancer. Systematic discovery of stimulation-dependent cytokine regulators requires both loss-of-function and gain-of-function studies, which have been challenging in primary human cells. We now report genome-wide CRISPR activation (CRISPRa) and interference (CRISPRi) screens in primary human T cells to identify gene networks controlling interleukin 2 and interferon gamma production. Arrayed CRISPRa confirmed key hits and enabled multiplexed secretome characterization, revealing reshaped cytokine responses. Coupling CRISPRa screening with single-cell RNA-seq enabled deep molecular characterization of screen hits, revealing how perturbations tuned T cell activation and promoted cell states characterized by distinct cytokine expression profiles. Together, these screens reveal genes that reprogram critical immune cell functions, which could inform the design of immunotherapies.

overall_design: Pooled CRISPRa screens followed by sorting for IL-2 and IFN-g high or low expressing bins (CD4+ human T cells)

first: Ralf

last: Schmidt

first: Madeline

last: Layeghi

first: Jacob

middle: W

last: Freimer

first: Raymund

last: Bueno

first: Vinh

middle: Q

last: Nguyen

first: Franziska

last: Blaeschke

first: Chun

last: Ye

first: Alexander

last: Marson


title: CRISPR activation and interference screens decode stimulation responses in primary human T cells [CRISPRa Perturb-seq]

overall_design: Pooled CRISPRa screen coupled with single-cell RNA-seq in human T cells


title: Human Pluripotent Stem Cell-derived Islets Ameliorate Diabetes in Nonhuman Primates

first: Yaqi

last: Wang

state: Beijing

address: No.5 Yiheyuan Road Haidian District

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens


title: Calibrated Smc3 ChIP-seq for wild type, smc3-2R, wpl1Δ and  smc3-2R wpl1Δ strains arrested in meiotic prophase I

first: Daniel

last: Robertson

overall_design: Purpose: to determine the relative contribution of Smc3 acetylation and Wpl1 in retaining and releasing cohesin from chromosomes, with a focus on centromere and pericentromere borders.

first: Lucia

last: Massari

first: Adele

last: Marston


title: Human Pluripotent Stem Cell-derived Islets Ameliorate Diabetes in Nonhuman Primates [monkey_singlecell]

summary: Human pluripotent stem cell-derived islets (hPSC-islets) are a promising cell resource for diabetes treatment. Here, we demonstrate that transplantation of human pluripotent stem cell-derived islets into diabetic nonhuman primates effectively restored endogenous insulin secretion and improved glycemic control. Single-cell RNA sequencing analysis of S6D2 clusters confirmed the existence of the three major pancreatic endocrine cell populations (β cells, α-like cells and δ-like cells) and their proportions, which altogether accounted for 80%. Importantly, hierarchical clustering of S6D2 hCiPSC-islets, 10 wpt kidney grafts and primary human islets showed that the hCiPSC differentiated pancreatic endocrine cells shared similar global gene expression profiles to their native counterparts in primary human islets. Single-cell RNA sequencing analysis on PBMCs revealed the potential immune response of recipient macaque to hCiPSC-islets.

overall_design: Single-cell RNA sequencing analysis on peripheral blood mononuclear cells (PBMCs)  to analyze the potential immune response of recipient macaque to hCiPSC-islets.

first: Yuanyuan

last: Du

first: Zhen

last: Liang

first: Shusen

first: Dong

last: Sun

first: Xiaofeng

first: Liew

last: Yi

first: Shuaiyao

last: Lu


title: Rec8 ChIP-seq for wild type, eco1-aa, wpl1Δ and eco1-aa wpl1Δ strains arrested in meiotic prophase I

summary: Genome binding/occupancy profiling of the cohesin subunit Rec8 by high throughput sequencing.

overall_design: Purpose: to determine the relative contribution of Eco1 and Wpl1 in retaining and releasing cohesin from chromosomes, with a focus on centromere and pericentromere borders.


title: Chromosome conformation for wild type, eco1-aa, wpl1Δ and  eco1-aa wpl1Δ strains arrested in meiotic prophase I

summary: High-resolution Hi-C in meiotic prophase arrested cells

overall_design: Purpose: to determine the impact of Eco1 and Wpl1 on cohesin mediated loop extrusion, with a focus on the pericentromere.


title: Human Pluripotent Stem Cell-derived Islets Ameliorate Diabetes in Nonhuman Primates [human_singlecell]

summary: Pluripotent stem cell-derived islets (hPSC-islets) are a promising cell resource for diabetes treatment. Here, we demonstrate that transplantation of pluripotent stem cell-derived islets into diabetic nonprimates effectively restored endogenous insulin secretion and improved glycemic control. Single-cell RNA sequencing analysis of S6D2 clusters confirmed the existence of the three major pancreatic endocrine cell populations (β cells, α-like cells and δ-like cells) and their proportions, which altogether accounted for 80%. Importantly, hierarchical clustering of S6D2 hCiPSC-islets, 10 wpt kidney grafts and primary islets showed that the hCiPSC differentiated pancreatic endocrine cells shared similar global gene expression profiles to their native counterparts in primary islets. Single-cell RNA sequencing analysis on PBMCs revealed the potential immune response of recipient macaque to hCiPSC-islets.

overall_design: Single-cell RNA sequencing analysis on hCiPSC-islets and islets to analyze all pancreatic endocrine cell types.


title: Transcriptome analyses of uterine RNA from WT and Qa2 deficient mice

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

summary: Since many adaptation processes to pregnancy take place in the uterus, we performed transcriptome analyses of whole uterine lysates. Of 610 differentially regulated genes, 380 were  upregulated in WT uteri and 230 were upregulated in Qa-2- uteri.

overall_design: transcriptome analyses of whole uterine lysates from two WT and two Qa2 deficient mice

first: Natascha

last: Köstlin-Gille

first: Stefanie

last: Dietz


title: Calibrated Smc3 ChIP-seq for wild type, eco1-aa, wpl1-delta and  eco1-aa wpl1-delta strains arrested in meiotic prophase I


title: Influenza virus repurposes the antiviral protein IFIT2 to promote translation of viral mRNAs

status: Public on Feb 03 2022

first: Max

last: Chang

summary: Cells infected by influenza virus mount a large-scale antiviral response and most cells ultimately initiate cell-death pathways in an attempt to suppress viral replication. We performed a CRISPR/Cas9-knockout selection designed to identify host factors required for replication following viral entry. We identified a large class of presumptive antiviral factors that unexpectedly act as important pro-viral enhancers during influenza virus infection. One of these, IFIT2, is an interferon-stimulated gene with well-established antiviral activity but limited mechanistic understanding. As opposed to suppressing infection, we show here that IFIT2 is instead repurposed by influenza virus to promote viral gene expression. CLIP‐seq demonstrated that IFIT2 binds directly to viral and cellular mRNAs in AU‐rich regions, with bound cellular transcripts enriched in interferon‐stimulated mRNAs. Polysome and ribosome profiling revealed that IFIT2 prevents ribosome pausing on bound mRNAs. Together, the data link IFIT2 binding to enhanced translational efficiency for viral and cellular mRNAs and ultimately viral replication. Our findings establish a model for the normal function of IFIT2 as a protein that increases translation of cellular mRNAs to support antiviral responses and explain how influenza virus uses this same activity to redirect a classically antiviral protein into a pro-viral effector.

overall_design: Positive selection CRISPR screen with SC35M influenza in A549 cells

first: Vy

last: Tran

first: Andrew

last: Mehle


title: Mutation-specific reporter for optimization and enrichment of prime editing

city: EA Utrecht

first: Imre

last: Schene

state: Utrecht

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

summary: Prime editing is a versatile genome-editing technique that shows great promise for the generation and repair of patient mutations. However, some genomic sites are difficult to edit and optimal design of prime-editing tools remains elusive. Here we present a fluorescent prime editing and enrichment reporter (fluoPEER), which can be tailored to any genomic target site. This system rapidly and faithfully ranks the efficiency of prime edit guide RNAs (pegRNAs) combined with any prime editor variant. We apply fluoPEER to instruct correction of pathogenic variants in patient cells and find that plasmid-editing enriches for genomic editing up to 3-fold compared to conventional enrichment strategies. DNA repair and cell cycle-related genes are enriched in the transcriptome of edited cells. Stalling cells in the G1/S boundary increases prime editing efficiency up to 30%. Together, our results show that fluoPEER can be employed for rapid and efficient correction of patient cells, selection of gene-edited cells, and elucidation of cellular mechanisms needed for successful prime editing.

overall_design: HEK293T cells were transfected with fluoPEER, PE2, pegRNA, and nicking sgRNA plasmids and FACS sorted after 48 hours into fluoPEER-edited (GFP+RFP+) and fluoPEER-unedited (GFP+RFP-) cells.   The transcriptome of both populations was compared for two replicates for two different prime edit conditions (CTNNB1 6bp-deletion; IARS1 2bp-substitution)

first: Sabine

last: Fuchs

first: Indi

last: Joore


title: Eco1-dependent cohesin acetylation anchors chromatin loops and cohesion to define functional meiotic chromosome domains

first: Daniel

last: Robertson

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae