title: Genome-Wide CRISPR Screen Identifies Pharmacogenomic Determinants of Blinatumomab Resistance in Acute Lymphoblastic Leukemia [ChIP-seq]

city: Memphis

first: Jun

last: Yang

state: Tennessee

address: 262 Danny Tomas Pl, MS 313

institute: St Jude Children's Research Hospital

summary: Blinatumomab is an efficacious immunotherapeutic agent in B-cell acute lymphoblastic leukemia (ALL). However, pharmacogenomic basis of leukemia response to blinatumomab is unclear. Using genome-wide CRISPR, we comprehensively identified leukemia intrinsic factors of blinatumomab sensitivity, i.e., the loss of CD58 as a top driver for resistance, in addition to CD19. CD58 expression varied across 20 ALL moleuclar subtypes, with marked downregulation linked to PAX5 P80R mutation in leukemia. Genome editing confirmed the effects of this mutation on CD58 expression and blinatumomab sensitivity in B-ALL, with validation in patient leukemic blasts. We described a PAX5-driven enhancer at the CD58 locus, which was disrupted by PAX5 P80R. Without CD58 in B-ALL, blinatumomab-induced T cell activation was abolished with transcriptomic/ epigenomic reprogramming. Finally, we screened 1,639 transcription factor genes to systematically identify regulators of CD58/CD19 expression. In conclusion, we identified novel genetic mechanisms of blinatumomab resistance in B-ALL, suggesting strategies for genomics-guided treatment individualization.

overall_design: ChIP was performed on 697 parental and PAX5 edited clones, including 697-PAX5-P80R/FS, 697-PAX5-WT/FS, and 697-PAX5-WT/WT. The following antibodies were used for ChIP assays: anti-PAX5 (Abcam, ab15164), anti-H3K27Ac (CST, 8173S), and anti-H3K4me3 (CST, 9751).

first: Yizhen

last: Li


title: Genome-Wide CRISPR Screen Identifies Pharmacogenomic Determinants of Blinatumomab Resistance in Acute Lymphoblastic Leukemia [ATAC-seq]

status: Public on Dec 21 2022

middle: J

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ATAC-seq was performed on: 1) 697 parental and PAX5 edited clones, including 697-PAX5-P80R/FS, 697-PAX5-WT/FS, and 697-PAX5-WT/WT; 2) T cells that were incubated with Parental or CD58-KO Nalm6 for 48 hours with 1 ng/mL blinatumomab treatment.

first: Xujie

last: Zhao


title: Genome-Wide CRISPR Screen Identifies Pharmacogenomic Determinants of Blinatumomab Resistance in Acute Lymphoblastic Leukemia [RNA-seq]

type: Expression profiling by high throughput sequencing

overall_design: Total RNA was purified from human pan T cells that were incubated with leukemia cells (Parental, CD58 knock out, or CD19 knock out Nalm6 cells) with or without blinatumomab treatment by using Qiagen Rneasy Mini Kit and subsquently used for RNA-sequencing.


title: Aberrant activation of p53/p66Shc-mInsc axis increases asymmetric divisions and attenuates proliferation of aged mammary stem cells.

city: Milano

first: Pier Giuseppe

last: Pelicci

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

summary:
Mammary gland aging is due to aberrant activation of p66Shc, which induces p53/p44 signaling, leading to failure of symmetric divisions, decreased proliferation and reduced regenerative potential of MaSCs.
Age-related changes in mammary epithelial cells derived from C57BL/6J WT and p66Shc knockedout mice cultured as stem cell-enriched mammospheres.

overall_design: Bulk RNA-sequencing analysis on total RNA extracted from passage 2 mammosferes derived from 3 young (2 month-old) and 3 aged (12 month-old) C57BL/6J WT and p66Shc knock-out (p66-/- C57BL/6J) mice.

first: Chiara

last: Priami

first: Giulia

last: De Michele

first: Lucilla

last: Luzi

first: Enrica

last: Migliaccio

first: PierGiuseppe

middle: G


title: Genome-Wide CRISPR Screen Identifies Pharmacogenomic Determinants of Blinatumomab Resistance in Acute Lymphoblastic Leukemia

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

overall_design: Refer to individual Series


title: Persistent post-COVID-19 smell loss is associated with inflammatory infiltration and altered olfactory epithelial gene expression

city: Durham

first: John

last: Finlay

state: NC

address: 40 Duke Medicine Circle

institute: Duke University

summary: We show that humans with lasting PASC olfactory loss harbor cellular and molecular changes in the olfactory epithelium, the peripheral organ for smell. Biopsy analyses using single cell RNA-sequencing, obtained from 6 patients 4-16 months following infection, identified a dysruption of olfactory epithelium homeostasis with infiltration of unique immune cell populations.

overall_design: Single cell 3' RNAseq of olfactory epithelium from 6 adult human patients with lasting olfactory dysfunction post COVID (PASC) (based on psychophysical olfactory assessment, with SIT scores 17-29) using the 10X Genomics Chromium platform and sequenced on Illumina Nextseq 500 compared to previously published control datasets (Oliva et al., 2021) (Durante et al., 2020).

first: Bradley

last: Goldstein


title: Drug tolerant persisters in erlotinib treated EGFR-mutated lung adenocarcinoma arise from pre-existing tumor cells and survive in an adapted stromal microenvironment

city: Toronto

first: Ming-Sound

last: Tsao

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Research

country: Canada

institute: University Health Network

summary:
Targeted therapies require life-long treatment, as drug discontinuation invariably leads to tumor recurrence. Recurrence is thought to mainly be driven by minor subpopulations of drug tolerant persister (DTP) cells that survive the cytotoxic drug effect. In lung cancer, DTP studies have mainly been conducted using tumor cell line models.
We conducted an in vivo DTP study using a lung adenocarcinoma (LUAD) patient-derived xenograft (PDX) tumor driven by an epidermal growth factor receptor (EGFR) mutation. Daily treatment of tumor-bearing mice for 5-6 weeks markedly shrunk the tumors and generated DTPs, which were analyzed by bulk population transcriptome.

overall_design: Microarray transcriptome profiling was performed on 4 baseline (BL) and 4 DTP tumors; total RNAs from xenografts were amplified by DASL kit and hybridized to  Illumina HT12v4 chip

first: Ming-soung

first: Quan


title: Drug tolerant persisters in erlotinib treated EGFR-mutated lung adenocarcinoma arise from pre-existing tumor cells and survive in an adapted stromal microenvironment [RNA-seq]

summary: Targeted therapies require life-long treatment, as drug discontinuation invariably leads to tumor recurrence. Recurrence is thought to mainly be driven by minor subpopulations of drug tolerant persister (DTP) cells that survive the cytotoxic drug effect. In lung cancer, DTP studies have mainly been conducted using tumor cell line models.

overall_design: single Cell RNAseq was performed on  Baseline(BL) and  DTP tumor


title: Single cell transcriptomic and spatial landscapes of the developing human pancreas - spatial transcriptomics

city: London

first: Oladapo

middle: Edward

last: Olaniru

address: Hodgkin building, Guy's campus

department: Department of Diabetes

country: United Kingdom

institute: King's College London

summary: The progress made in directed differentiation of stem cells has shown that understanding human pancreas development can provide cues for generating unlimited amounts of insulin-producing beta cells for transplantation therapy in diabetes. However, current differentiation protocols have not been successful in reproducibly generating functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. Here, we present detailed transcriptomic analysis of the various cell types of the developing human pancreas, including their spatial gene patterns. We integrated single cell RNA sequencing with spatial transcriptomics at multiple developmental timepoints and revealed distinct temporal-spatial gene cascades in the developing human pancreas.

overall_design: Human fetal pancreases at 12, 15, 18 and 20 post-conception weeks were subject to 10x Visium spatial transcriptomics

middle: E

first: Ulrich

last: Kadolsky

first: Shichina

last: Kannambath

first: Heli

last: Vaikkinen

first: Kathy

last: Fung

first: Pawan

last: Dhami

first: Shanta

last: Persaud


title: Single cell transcriptomic and spatial landscapes of the developing human pancreas

overall_design: Human fetal pancreases at 12, 13, 14, 15, 18, 19 and 20 post-conception weeks were subject to single cell RNA-seq analysis


title: Successful Sulphide-driven Partial Denitrification: efficiency, stability and resiliency in SRT-controlled conditions

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary: The aim of the present work was to maximise  NO2- conversion over NO3- reduction coupled with complete sulphide (HS-) oxidation, by the selective control of influent S/N ratio and sludge retention time (SRT). A 2.5-L chemostat was operated for 115 days and three operational phases were tested at decreasing SRT of 40, 23 and 13 h, testing S/N ratios in the range of 0.5-1 gS/gN. Successful sulphide-driven PAD was achieved and lead to average NO2- conversion efficiencies as high as 77±17% at all the conditions tested, with the highest value of 99% at the lowest S/N of 0.58 gS/gN and SRT of 23 h. Respirometric tests showed that NO3- uptake rate was stable at 90±10 mgN/gVSS/h, either when NO3- was present as sole electron acceptor or at NO2- levels as high as 120 mgN/l; on the contrary, NO2- uptake rates were very sensitive to the applied conditions. Metabarcoding analyses revealed that the microbial community was highly enriched in Sulphur Oxidizing Bacteria (SOB>80%) and strict and stable S-limiting conditions appeared to favour Thiobacillus over Sulfurimonas genus. A preliminary assessment of N2O potential emission was also performed. To the best of our knowledge, this is the first work evaluating the synergic effect of SRT and influent S/N ratio on nitrite accumulation in highly SOB-enriched systems and the NO2- conversion efficiencies achieved are among the highest reported in literature.

overall_design: Lab-scale chemostat seeded with enriched Sulphur Oxidizing Biomass and fed with sythetic mineral medium rich in sulphide and nitrate

first: Cecilia

last: Polizzi

first: David

last: Gabriel

first: Giulio

last: Munz


title: The clinical and molecular characteristics of progressive hypothalamic/optic pathway pilocytic astrocytoma [850k array]

first: Jason

last: Chiang

address: 262 Danny Thomas Pl

department: Pathology

institute: St. Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary: Unresectable hypothalamic/optic pathway pilocytic astrocytoma (PA) can be challenging to manage due to repeated progressions despite multiple lines of therapy. To identify clinical and biologic factors associated with tumor progression, we retrospectively identified 72 unresectable, non-NF1-associated, hypothalamic/optic pathway PA. Tumors were classified as low- (6.9%), intermediate- (43.1%), and high-risk (50%) based on their response to treatment. High-risk tumors were defined as those that progressed after three or more lines of chemotherapy/targeted therapy, progressed after radiation, developed metastatic disease, or died of disease. DNA methylation profiling and transcriptome analysis (RNA sequencing) were performed on treatment-naïve tumors with available tissue, and the findings were validated by immunohistochemistry (IHC) on additional tumor tissue. The median follow-up of the entire cohort was 12.3 years. High-risk tumors were associated with male sex (M:F = 2.6:1), younger age at diagnosis (median 3.2 years vs. 6.7 years, P = 0.005), and high incidence of KIAA1549-BRAF fusion (81.5% vs. 38.5%, P = 0.0032). High-risk tumors demonstrated decreased CpG methylation and increased RNA expression in many mitochondrial genes and genes downstream of E2F and NKX2.3 transcription factors. Transcriptome analysis identified transcription factor TBX3 and proto-oncogene serine/threonine protein kinase PIM1 as common downstream targets of both E2F and NKX2.3 and potential drivers of tumor progression. IHC confirmed increased expression of TBX3 and PIM1 in high-risk tumors. PIM1 is known to increase the stability and transcriptional activity of MYC, and gene enrichment analysis identified enrichment of MYC targets. Signaling pathways known to be implicated in pilocytic astrocytoma, such as MAPK and PI3K/AKT/mTOR, were also enriched, as well as pathways related to mitochondrial biogenesis and oxidative phosphorylation. Our results support the model in which the p53-PIM1-MYC axis and TBX3 act alongside MAPK and PI3K/AKT/mTOR pathways to promote tumor progression in hypothalamic/optic pathway PA, highlighting potential new targets for combination therapy and refining disease prognosis.

overall_design: Genome-wide methylation profiling of FFPE tumor samples using microarray

first: Sahaja

last: Acharya

first: Xiaoyu

last: Li

first: Daniel

middle: C

last: Moreira

first: Asim

last: Bag

first: Ibrahim

last: Quaddoumi


title: The clinical and molecular characteristics of progressive hypothalamic/optic pathway pilocytic astrocytoma


title: miRNA expression profiling in early-stage epithelial ovarian cancer

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: Early-stage epithelial ovarian cancer (eEOC) patients have a generally favorable prognosis but heterogeneous behavior at recurrence. Accurate prediction of the risk of relapse is still a major concern, essentially to avoid overtreatment. We have identified a robust miRNA-based signature named MiROvaR able to predict early disease recurrence in case materials of mostly advanced-stage EOC patients.   We challenged MiROvaR in the eEOC sub-setting (stage IA-IIB) and it proved to accurately classify eEOC patients according to their risk of relapse.

overall_design: We retrospectively selected patients diagnosed with early stage ovarian cancer who underwent comprehensive surgical staging at our institution and whose FFPE blocks were available. 89 cases of stages from IA to IIB were included. After profiling on Agilent SurePrint 8x60K human miRNA arrays, 87 cases were eligible for data analysis. The historical retrospective case material (1993-2015) has been entirely revised by the specialized pathologist who is in charge of the gynecological oncology diseases classification at INT.  Classyfing process followed the current clinical practice in accordance with the current criteria asssessed in 2014 by FIGO and WHO. Clinical variables: Age (yr) at diagnosis; grade/stage, according to FIGO (2014); histology according to WHO (2014)


title: SARS-CoV-2 Neurotropism and Single Cell Responses in Brain Organoids Containing Innately Developing Microglia

city: Stockholm

first: Carl

middle: M

last: Sellgren

address: Solnavagen 1

country: Sweden

institute: Karolinska Institute

summary: Here, we derive human brain organoids with innately developing microglia to investigate the cellular responses to SARS-CoV-2 infection on a single cell level. We find evidence of limited tropism to SARS-CoV-2 for all major cell types and observe extensive neuronal cell death that also include non-infected cells. Single cell transcriptome profiling reveals distinct responses in microglia and astrocytes that share features with cellular states observed in neurodegenerative diseases

overall_design: IPSC-derived cerebral organoids were infected with live SARS-CoV-2 and single cells were collected from three pooled orgnoids for each condition: control, 24 and 72 hour post-infection. Each condition comprised of two replicates.

first: Susmita

last: Malwade


title: Gene expression profile of B cells from OPN-competent and deficient Faslpr autoimmune mice

first: claudia

last: Chiodoni

state: Italy

address: Via Amadeo 42

department: Department of experimental oncology

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: We performed gene expression profile on splenic CD19+ cells from autoimmune Faslpr/lpr and OPN-/-Faslpr/lpr mice to investigate the dynamics at the basis of the more incident transformation characterizing OPN-deficient animals. GEP on splenic CD19+ from BALB/c and OPN-/- mice was performed as control.

overall_design: CD19+ cells were separated through immunomagnetic beads (anti-CD19) from the splenic cell suspension of  5 month-Faslpr/lpr and OPN-/-Faslpr/lpr mice. CD19+ from BALB/c and OPN-/- animals were analysed as controls. After check of purity, RNA was extracted and GEP was performed.

first: Mario

middle: P

last: Colombo

first: Celeste

last: Rizzello

first: Claudia

last: Milani


title: FASN inhibition as a potential treatment for endocrine-resistant breast cancer

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: The aim of the experiment was to investigate the effect of TVB-3166 treatment in primary patient-derived breast tumor explants. RNA sequencing was performed in response to treatment with TVB-3166 or vehicle control. RNA sequencing analyses revealed that TVB significantly altered the mRNA expression of 219 genes as compared to the control.

overall_design: Patient-derived explants were treated with either vehicle or 200 nM TVB-3166 for 72 hours. Total RNA was isolated using Rneasy mini kit (Qiagen) according to manufacturesr's instructions, and sequencing libraries were prepared for each sample and sequenced with read length of 76bp using Illumina HiSeq platform.

first: Aleksandra

last: Gruslova

first: Andrew

last: Brenner


title: Genome-wide maps of chromatin state in cultured male germline stem cells with retinoic acid treatment [scATAC-seq]

city: Hong Kong

first: Tin-Lap

last: Lee

address: LKSIBSB, CUHK, Shatin, Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: We report the application of single-cell ATAC-seq to reconstruct the epigenetic program and differentiation trajectory associated with the retinoic acid (RA)-induced differentiation in cultured male germline stem cells (GSCs). We also identified key transcription factors and regulatory elements regulated by RA.

overall_design: Chromatin accessibility profiles of retinoic acid-treated GSCs.

first: Jinyue

last: Liao

first: Hoi Ching

last: Suen


title: RNAseq analysis of wildtype and Slc7a5 knockout CD4+ T cells from the knee joints of arthritic mice

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

institute: University of Liverpool

summary: We report differences in gene expression between wildtype and Slc7a5 knockout CD4+ T cells obtained from mouse knee joints with antigen induced arthritis

overall_design: Wildtype and Slc7a5 knockout CD4+ T cells were sorted from mouse knee joint with antigen induced arthritis (n=4 per group). RNA was isolated using the Qiagen RNeasy microkit  and sequenced on the Illumina platform.

first: Joy

last: Ogbechi

middle: L

first: Louise

last: Topping

first: Richard

middle: O

last: Williams


title: Impact of schizophrenia GWAS loci converge onto distinct pathways in cortical interneurons vs glutamatergic neurons during development

city: New York City

first: Jaroslav

last: Bendl

state: New York

address: One Gustave L. Levy Place, Department of Genetics and Genomics Sciences, Box 1210

department: Genetics and Genomics Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Genome binding/occupancy profiling was carried out by high throughput sequencing in human developmental cortical interneurons and developmental glutamatergic neurons derived from healthy control vs schizophrenia iPSCs

overall_design: Open chromatin profiles (ATAC-seq assay) in human developmental cortical interneurons (MGE organoid) and glutamatergic neurons (CO organoid) derived from healthy control vs schizophrenia iPSCs

first: Dongxin

last: Liu

first: Sangmi

last: Chung

first: John

middle: F

last: Fullard

first: Panos

last: Roussos


title: Chronic alcohol-induced dysbiosis of the gut microbiota and gut metabolites impairs sperm quality

city: Chongqing

first: li

last: hui

address: Xinqiao Street, Shapingba District

country: China

institute: Xinqiao Hospital of Army Medical University

summary: Purpose: To explore whether chronic alcohol consumption affects sperm quality by inducing changes in the gut microbiota.

overall_design: In this study, we established a mouse model of chronic alcohol consumption by allowing male C57 mice to freely ingest 10% ethanol for 8 weeks. We then collected the faecal microbiota of the male mice in the chronic drinking group (alcohol) and the control group (control) and transplanted them into the transplant groups (the alcohol-faecal microbiota transplantation [FMT] group and the control-FMT group). Next, we collected faecal, testes, and blood samples from each group. The Suiplus semen analysis (SSA) system was used to analyse sperm quality; 16S ribosomal RNA sequencing and non-targeted metabolomics were performed to evaluate the gut microbiota and its metabolites; a cytokine antibody array was used to evaluate the levels of inflammatory cytokines in mouse blood and testicular cells; RNA sequencing was performed to analyse the gene expression in mouse testes; and testicular blood flow was evaluated by ultra-high resolution imaging system.

first: Hui

last: Li


title: Identification of a novel antitumor CD4+ T cell cluster orchestrating antitumor immunity

city: Hidaka-City, Saitama

first: Satoshi

last: Yamasaki

department: Department of Respiratory Medicine

country: Japan

institute: Saitama Medical University

summary: scRNAseq-based unsupervised clustering and clonotyping revealed that Th1/17 and CCR6 SP clusters formed metacluster Th7R, which was distinct from Th1 or Th17, characterized by high expression of the IL-7 receptor. Use of this cluster to assess antitumor CD4+ T cell immunity from the peripheral blood and to predict the efficacy of immune checkpoint inhibitors will pave the way for novel antitumor immunotherapy strategies for patients.

overall_design:
Investigating how differences in gene expression and TCR repertoires of T cells in blood affect the response of pembrolizumab therapy. All samples in this dataset were obtained from patients before receiving pembrolizumab therapy.
GEX and TCR samples with the same P* identifier were obtained from the same set of cells.

first: Hiroshi

last: Kagamu

first: Shigehisa

last: Kitano

first: Ou

last: Yamaguchi

first: Atsuhito

last: Mouri

first: Ayako

last: Shiono

first: Fuyumi

last: Nishihara

first: Yu

last: Miura

first: Kosuke

last: Hashimoto

first: Hisao

last: Imai

first: Kyoichi

last: Kaira

first: Kunihiko

last: Kobayashi

first: Tatsuhiro

last: Shibata

first: Katsuhisa

last: Horimoto


title: Next Generation Sequencing Analysis of OX40hi Treg and OX40lo Treg cells from mouse tumors and spleens

city: New York

first: Ning

last: Yang

state: NY

institute: MSKCC

summary: Based on RNA-seq technology, we studies gene expression profiles in Treg cells isolated from mouse tumors and spleens. We identified differential gene expressions comparing OX40hi Treg with OX40lo Treg cells from tumors and spleens. The difference of Trges in tumors and spleens were also identified.

overall_design: Foxp3-GFP mice were intradermally implanted with B16 cells at 5x10^5 cells at the right side. After 7-10 days, tumors and spleens were dissected and digested into single cells. After staining with antibodies against CD45, CD3, CD4 and OX40, OX40hiGFP+ and OX40loGFP+ cells were sorted in BD FACSAria cell sorter.

first: Adrian

middle: Y

last: Tan

first: Liang

last: Deng


title: The clinical and molecular characteristics of progressive hypothalamic/optic pathway pilocytic astrocytoma [RNA-Seq]

first: Jason

last: Chiang

overall_design: RNA-seq from 20 FFPE tumor samples

first: Sahaja

last: Acharya

first: Xiaoyu

last: Li

first: Daniel

last: Moreira

first: Asim

last: Bag

first: Ibrahim

last: Quaddoumi


title: RNA-Seq of mice omenta after intraperitoneal (IP) or systemic delivery (IV) of tumor-specific T cells

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

country: Spain

institute: FIMA

summary: We sought to investigate if and how the alternative delivery methods could differentially impact the gene expression profiles in the tumor microenvironment.

overall_design: Mice were injected intraperitoneally with B16-OVA cell line which homes to the omentum. 6 days post tumor challenge, we treated mice with tumor-specific T cells electroporated with IL-12-coding mRNA either IP or IV. 18h after treatment we isolated omenta and extracted RNA to further continue with sequencing.

first: Claudia

middle: A

last: Di Trani

first: Celia

last: Gomar

first: Joan

middle: R

last: Cabrera

first: Leire

last: Arrizabalaga

first: José

last: Gomariz

first: Francesco

last: Marchese


title: The EMT-regulator ZEB1 shapes bone marrow immunological niches in AML suppressing T-cell activity and fostering Th17 expansion

first: Barbara

last: Bassani

address: via G. Antonio Amadeo, 42

department: Department of Research

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano

summary: We performed gene expression profiling to evaluate potential differences between Zeb1 expressing and Zeb1 silenced cells

overall_design: C1498 cells were treated overnight with lentiviral particles containing plasmid expressing a short hairpin RNA (shRNA) sequence against ZEB-1 (seq C, or seq D or a negative control construct, Scr) and green fluorescence protein (GFP). Two weeks after infection, GFP+ cells were isolated and used for RNA extraction and hybridization on microarrays.

first: Giorgia

last: Simonetti

first: Sabina

last: Sangaletti


title: Cellular and molecular characterization of iPSC-derived human RPE cells from normal and Smith-Lemil-Opitz syndrome patients

city: Buffalo

first: Michael

last: Farkas

address: 3495 Bailey Ave, Bldg 20, Mail Stop 151

department: Ophthalmology

institute: State University of New York at Buffalo

summary: Comparison of transcriptomes from two SLOS cell lines of differing disease severity and a control cell line to analyze associated transcriptome changes

overall_design: RNASeq analysis of control cell line and 2 SLOS cell lines

middle: H

first: Elizabeth

middle: D

last: Au

first: Lara

last: Skelton

first: Sriganesh

last: Rao

first: Steven

last: Fliesler


title: Characterization by RNAseq of malignant pleural mesothelioma cell lines and their response to palbociclib

status: Public on Dec 20 2022

city: Bruxelles

first: Sabine

last: Paternot

address: 808 Route de Lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

summary: Malignant pleural mesothelioma (MPM) is an aggressive cancer with limited therapeutic options. In this study, we evaluated the impact of CDK4/6 inhibition by palbociclib in established MPM cell lines using a variety of approaches including RNA sequencing. Palbociclib used alone sufficed to strongly and durably inhibit the proliferation of 4 of 6 cell lines. In a parallel study, the efficacy of palbociclib was confirmed in a large panel of patient-derived cell lines indicating a unique sensitivity of MPM to CDK4/6 inhibition. Importantly, insensitivity to palbociclib was mostly explained by the lack of active T172-phosphorylated CDK4, which was associated with the high p16 levels that accompany RB1 defects or inactivation, and also (unexpectely) CCNE1 overexpression in the presence of WT RB1. Prolonged treatment with palbociclib irreversibly inhibited proliferation despite re-induction of cell cycle genes upon drug washout. A senescence-associated secretory phenotype (SASP) including various potentially immunogenic components was also irreversibly induced. Our study strongly supports the clinical evaluation of CDK4/6 inhibitory drugs for MPM treatment including in several combinatorial therapies.

overall_design: 6 cell lines were treated for 9-10 days with 0,1 % DMSO or 1 µM palbociclib. Experiment was performed in duplicate or triplicate except for Met5A which was analyzed only once. For the four sensitive cell lines, the reversibility of the cell cycle arrest imposed by palbociclib was also investigated after a drug washout of 48 hours. This experiment was performed once. Met5A cells were also used in untreated conditions for characterization.

first: Pierre

last: Roger

first: Eric

last: Raspé

first: Maxime

last: Tarabichi


title: Circulating microRNA profiling in diffuse intrinsic pontine gliomas

first: Loris

last: De Cecco

summary: Diffuse midline glioma (DMG) identifies gliomas originating in the thalami, brainstem, cerebellum and spine. Within this entity, tumours that infiltrate the pons, called diffuse intrinsic pontine gliomas (DIPGs), have a rapid onset and devastating neurological symptoms. Radiotherapy is the only intervention that is able to modify the disease course, albeit not in a curative way.  In recent years, liquid biopsies have represented the next step in clinical diagnostics due to their easily accessible nature. The purpose of this study is to profile circulating miRNA expression to disclose a potential prognostic signature with clinical impact.

overall_design: Blood samples were collected at the baseline prior to treatment, kept at 4 C for 30 minutes and processed within 1 h after collection by centrifugation at 1600 x g at 4 C for 10 min.  Serum was aliquoted in vials and stored at -80 C.  The miRNA expression was profiled using the miRNA microarray (Agilent) designed on miRBase 19.0; 2006 miRNAs were profiled in serum specimens from 47 patients enrolled in two clinical studies combining nimotuzumab with concomitant radiation and vinorelbine. Cases were divided in a training set (n=23) and an independent validation set (n=24). Having progression free survival as endpoint, a semi supervised learning approach was applied to disclose a prognostic signature.


title: Role of ASCL1 in human neural development

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

summary: As a proneural gene, ASCL1 was reported to be important to neurogenesis. To better illustrate the role of ASCL1 in human telencephalon development, we genetically engineered an ASCL1 knockout (KO) hESC line and ASCL1 rescue (RE) hESC line, and then preformed RNA sequencing when WT, KO and RE were differentiated into neural progenitors in vitro. Our results showed that ASCL1 KO hESCs could be regularly maintained in vitro, and could be efficiently specified into neuroectoderm cells and following telencephalic neural progenitors. Remarkably, dorsal progenitors-derived from ASCL1 KO hESCs failed to differentiate into DCX positive neuroblasts. In addition, dorsal and ventral progenitors retained higher expression of VZ/ESVZ genes but had much lower expression of LSVZ genes after KO of ASCL1. Re-introducing of ASCL1 in KO hESCs through a doxycycline (Dox) inducible overexpression system reversed the gene expression changes induced by cortical progenitors with ASCL1 KO. Taken all these together, our results revealed a pivotal role of ASCL1 in both dorsal and ventral telencephalic development by progressing the cycling progenitors within the ESVZ to post-mitotic early born neurons in the LSVZ in human telencephalon.

overall_design: The mRNA of wild type (WT) and ASCL1 knock out (KO) neural progenitors with dorsal and ventral identies, and  ASCL1 rescue (RE) dorsal neural progenitors in a background of ASCL1 knock out were extracted with triplicated at Day25 in vitro differentiation and sequenced on an Illumina HiSeq 2500 platform.

first: Du

last: Yanhua

first: Ma

last: Lin

first: Li


title: Regulatory T-cell-derived molecular signature predicts two-year outcome in biliary atresia and intrahepatic cholestasis

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: We investigated bile-acid induced gene expression patterns in regulatory T-cells, and applied those gene sets to gene expression profiles of liver samples obtained from children with biliary atresia and intrahepatic cholestasis.  Patient subgroups identified using the regulatory T-cell gene sets were then assessed for association with two-year outcome in patients with biliary atresia.

overall_design:
mRNA profiles of 19 infants with biliary atresia (n=9) and intrahepatic cholestasis (n=10)
----------------------------
Authors state "the raw fastq files have been lost with no chance of recovery".

first: Alex

last: Miethke

first: Ramesh

last: Kudira


title: Comparative skin cancer atlas and interactome: A multi-modal spatial approach to uncovering the cells  and interactions underlying skin cancer diversity

city: Brisbane

first: Quan

last: Nguyen

state: Queensland

address: 22 Burns Street, Indooroopilly

country: Australia

institute: Institute for Molecular Bioscience

summary: The three major skin cancer types - squamous cell carcinoma (SCC), basal cell carcinoma (BCC), and melanoma - account for >70% of all cancer. Although these cancers all derive from the outer skin layer (epidermis), variability in cell type composition and interactions causes substantial cross-cancer differences in disease initiation and invasive and metastatic potential. A knowledgebase of cell type composition and cell-to-cell interactions within the three skin cancers is needed to aid the assessment of risks and prognosis upon patient presentation. Here we integrated six distinct yet complementary spatial single-cell technologies to build the largest cell atlas and interactome of SCC, BCC, and melanoma to date. First, we performed single-cell RNA sequencing (scRNAseq) on >50,000 cells from 11 paired healthy and SCC patient biopsies. GeoMx spatial proteomics data independently validated the presence of rare immune cell types defined by scRNAseq. Visium and CosMx transcriptomic analyses were performed for all three skin cancer types to map spatial neighbourhoods and construct a cell-to-cell interaction atlas. We independently validated two key LR interactions, PD1_PDL1 and IL34_CSF1R, using Opal Multiplex Polaris and RNAscope data. Downstream analysis of IL34_CSF1R signalling zones suggested enrichment of IL34-related antigen presenting pathways in melanoma. Overall, we present a valuable database and analysis approaches to reveal potential biomarkers of initiation and progression of the most lethal type (melanoma) and the most common types (SCC and BCC) of skin cancer.

overall_design: Overall, samples from 12 human skin cancer patients were profiled by spatial and single cell multi-omics.  Adjacent tissue sections from the same tissue blocks (FFPE - Formalin Fixed Paraffin Embedded blocks, or OCT- Optimal Cutting Temperature blocks) were used.

first: Laura

last: Grice

first: Guiyan

last: Ni

first: Xinnan

last: Jin

first: Minh

last: Tran

first: Onkar

last: Mulay

first: Duy

last: Pham

first: Emily

last: Killingbeck

first: Mark

middle: T

last: Gregory

first: Siok

last: Teoh

first: Tuan

last: Vo

first: Min

last: Zhang

first: Zachary

last: Reitz

first: Katharina

last: Devitt

first: Liuliu

last: Pan

first: Arutha

last: Kulasinghe

first: Yung-Ching

last: Kao

first: Michael

last: Leon

first: Sarah

last: Murphy

first: Hiromi

last: Sato

first: Jazmina

last: Gonzalez Cruz

first: Snehlata

last: Kumari

first: Hung

middle: N

last: Luu

last: Warren

first: H

last: Soyer

first: Mitchell

middle: S

last: Stark

first: Kiarash

last: Khosrotehrani

first: Ian

last: Frazer

first: Youngmi

last: Kim


title: Analysis of effects of polyrotaxane on macrophages

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

summary: We analyzed effects of polyrotaxane (PRX) on LPS-stimulated bone marrow-derived macrophages (BMDMs).

overall_design: RNA-seq profiling of effects of PRX on the BMDM transcriptome.

first: Yumiko

last: Oishi


title: Analysis of genes regulated by AS2 and TOP1

city: Kanazawa

first: Hiro

last: Takahashi

state: Ishikawa

address: Kakuma-machi

institute: Kanazawa University

summary: AS2 encode AS2-domain containing protein and may regulate transcription. AS2 is involved in the determination of axes of leaves of Arabidopsis thaliana. Type IB DNA topoisomerase (TOP1α) gene has genetic interaction with AS1 and AS2 and is involved in repression of leaf polarity genes. To know the gene regulation in the leaf development, expression profile among wild-type  and as2 mutant treated with and without 10-hydroxyl substituted camptothecin (10H-CPT), a specific TOP1 inhibitor, were  compared

overall_design: Shoot apices that contain leaf primordia were selected.

first: Ayami

last: Nakagawa

first: Chiyoko

last: Machida


title: Differences in the intrinsic chondrogenic potential of human mesenchymal stromal cells and iPSC-derived multipotent cells

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

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

overall_design: Refer to individual Series


title: Molecular mechanism of mice embryonic diapause induction by nutrient deprivation

status: Public on Dec 18 2022

first: Jiajia

last: Ye

address: Qiangye road 500

institute: Chinese Academy of Sciences

summary: To thoroughly characterize the diapaused blastocyst induced by ovariectomy, maternal starvation, and nutrient deprivation, we executed RNA-sequencing  analyses for ND blastocysts at E4.5, DIA, Sta, K-PC, and K+0.02 blastocysts at E5.5.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ND blastocysts at E4.5, DIA, Sta, K-PC, and K+0.02 blastocysts at E5.5 (E4.5, DIA, Sta, K-PC, and K+0.02)


title: Microarray data of synovial tissues during initial high tibial osteotomy and plate removal surgery in human knee OA

city: Kyoto

first: Shigeo

last: Yoshida

state: Kyoto

address: 54, Kawahara-cho, Shogoin, Sakyo-ku

department: Orthopaedics

institute: Kyoto University

summary: This study aimed to determine whether alignment correction by high tibial osteotomy can change the biological intra-articular microenvironment of osteoarthritic  knees.

overall_design: mRNA were obtained from three independent donors during initial high tibial osteotomy and plate removal surgery

first: Kohei

last: Nishitani


title: Distinct Fibroblast Progenitor Subpopulation Expedites Regenerative Mucosal Healing by Immunomodulation

status: Public on Dec 19 2022

city: Philadelphia

first: Kang

middle: I

last: Ko

state: Pennsylvania

address: 240 S. 40th Street

department: Department of Periodontics

institute: University of Pennsylvania

summary: Oral fibroblasts are speculated to exhibit superior healing capacity. We used scRNA-seq to investigate oral fibroblast heterogeneity in mouse and human palate tissues.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Soft tissues from the hard palate from two C57BL/6 mice were pooled to generate scRNA-seq data. Human palatal rugae from two patients were used to generate scRNA-seq data.

first: Brett

last: DerGarabedian

first: Zhaoxu

last: Chen

first: Rahul

last: Debnath

first: Annette

first: Brittany

last: Link

first: Jonathan

last: Korostoff

first: Dana

last: Graves


title: Transcriptome analysis of the over-expression of OsMYB14, an R2R3-MYB Transcription Factor in Rice

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

type: Expression profiling by genome tiling array

summary:
The profiling was conducted with the Rice 3'-Tiling 135k Microarray designed from 31,439 genes deposited at IRGSP, RAP2 database (http://rapdb.lab.nig.ac.jp).
In this research, we have searched for genes responsible for over-expression of OsMYB14, an R2R3-MYB transcription factor in rice, Oryza sativa cv IlMi

overall_design: A total of 6 chips were used for microarray. Total RNA was extracted from flag leaves and panicles at 6 days before heading (DBH) of the transgenic (23 line) and WT plants and used for the microarray experiments

first: Joung


title: Stage-specific embryonic antigen 4 is a specific marker for high-efficient enrichment of porcine SSCs

city: Yangling

first: Pengfei

last: Zhang

state: Shaanxi,

address: 22# Xinong Road

department: College of Animal Science and Technology

institute: Northwest A&F University

summary: Purpose: To understand the Unique transcriptome features of the SSEA4-positive spermatogonial population.

overall_design: mRNA profiles of SSEA-positive spermatogonia and undifferentiated spermatogonia sorted from 90-day old pigs were generated by deep sequencing, in triplicate, using Illumina Hiseq-4000 sequencer

first: Wenxian

last: Zeng


title: Long non-coding RNA TILR constitutively represses TP53 and apoptosis induction in lung cancer II

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

summary: Recent evidence suggests that non-coding RNAs play an integral regulatory role in numerous functions in lung cancer development. Here, we report identification of a novel lncRNA, herein termed TP53-inhibiting lncRNA (TILR), which plays a role as a constitutive negative regulator of p53 expression and hence its functions including activation of downstream genes such as p21 and MDM2 and induction of apoptosis. Proteomic search for TILR-associated protein revealed the association with PCBP2, and the mid-portion of TILR was required for both PCBP2 and p53 mRNA binding. In addition, depletion of PCBP2 faithfully phenocopied effects of TILR silencing. We also found that TILR suppressed p53 expression post-transcriptionally as well as via a positive feedback loop between p53 and the Fanconi anemia pathway genes. Taken together, our findings clearly demonstrate that TILR constitutively inhibits p53 expression in cooperation with PCBP2, maintaining p53 transcriptional activity at a level sufficiently low for avoidance of spurious apoptosis induction.

overall_design: Microarray analysis using a Agilent-039494 SurePrint G3 Human GE v2 8x60K array was conducted. Biological replicates: 3 control replicates, 3 transfected replicates.

first: Mika

last: Iwai

first: Taisuke

last: Kajino

first: Masahiro

last: Nakatochi

first: Kiyoshi

last: Yanagisawa

first: Hisanori

last: Isomura

first: Yukako

last: Shimada

first: Motoshi

last: Suzuki

first: Ayumu

last: Taguchi


title: Long non-coding RNA TILR constitutively represses TP53 and apoptosis induction in lung cancer

overall_design: Microarray analysis using a Whole Human Genome Microarray 4x44K G4112F (Agilent-014850) was conducted


title: Transcriptomics and Metabolomics Reveal Liver Metabolic Changes and Phytochemical Deposition Occurring after Tomato Consumption in Mice

city: Houston

first: Michael

middle: P.

last: Dzakovich

state: TX

address: 1100 Bates Ave.

department: Pediatrics

institute: USDA-ARS Children's Nutrition Research Center

summary: Tomato consumption is associated with many health benefits including lowered risk for developing certain cancers. However, the effects of tomato consumption on gene expression and the chemical profile of mammalian liver are not well defined.

overall_design: C57BL/6 mice (n=11-12/group) were fed a macronutrient matched diet containing either 10% red tomato, 10% tangerine tomato, or no tomato powder for 6 weeks after weaning. RNA-Seq followed by gene set enrichment analyses indicated that tomato type and consumption, in general, altered expression of phase I and II xenobiotic metabolizing genes.

first: Mallory

last: Goggans

first: Jennifer

last: Thomas-Ahner

first: Nancy

last: Engelmann Moran

first: Steven

middle: K

last: Clinton

first: David

last: Francis

first: Jessica

last: Cooperstone


title: Changes of gene levels in medial prefrontal cortex of CUS depressive model mice induced by running exercise

city: Chongqing

first: Qin

last: Lu

address: Shi you lu street

institute: Chongqing medical university

summary: Although there were a few differentially expressed genes (DEGs), the kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed enriched GABAergic synapse pathways

overall_design: We performed seq-RNA sequencing to understand running exercise on the transcriptome level  in mPFC of mice exposed to chronic unpredicted stress.

first: Lu

last: Qin


title: Biomimetic strategy for cartilage formation: synergy of stem cell micro-aggregates and supramolecular peptide nanofibers

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

summary: Recapitulation of embryonic developmental events is receiving increasing recognition as a strategy to induce robust tissue regeneration. In this work, we aimed to explore the critical events of cartilage formation by combining adult human bone marrow-derived mesenchymal stromal cells (hBMSCs) with supramolecular nanofibrous hydrogel. The micro-aggregation led to the altered global transcriptional profiles of hBMSCs and enhanced chondrogenic commitment early in 24h. Furthermore, the supramolecular nanofiber structure formed by peptide amphiphiles (PAs) maintained the cell cohesion and favored the deposition of cartilaginous matrix, thus facilitating the progression of differentiation. Upon subcutaneous implantation, the hBMSCs microaggregates-laden PA hydrogel demonstrated evident ectopic cartilage formation. Notably, RNA-sequencing data illustrated that the PA hydrogel facilitated the in vivo chondrogenesis progression of the encapsulated donor cells, and also activated the chondrogenesis in the host tissue via paracrine signaling. We conclude that PA hydrogel delivering microaggregates of hBMSCs could recapitulate the critical developmental events during cartilage development. This bioinspired approach will offer the potential to regenerate functional and durable tissues for the functional recovery of traumatic injuries of the cartilaginous skeleton .

overall_design: Microaggregation of hBMSCs was induced by using in-house designed micro-well culture system and the obtained hBMSCs aggregates (3D) were cultured in vitro for 72hrs either in proliferation media or chondrogenic differentiation media. The same density of hBMSCs cultured in monolayer (2D) was set-up as control. 2000 microaggregates were harvested after 12, 24 and 72hrs to extract RNA for RNA sequencing. For in vivo samples, hBMSCs were loaded with or without supramolecular peptide amphiphles (PA) hydrogel and cultured for 3weeks in vitro in chondrogenic media before subcutaneous implantation in immunodeficient mice. After 1 week,explants (n=3) were harvested, total RNA was extracted, and RNA sequencing was performed.

first: Wei

last: Ji

first: Yingying

last: Wang


city: Beijing

first: Jianwen

last: Chen

state: Beijing

address: 28th, Fu Xing road, Hai Dian district

institute: First Medical Center of Chinese PLA General Hospital

summary:
The Role of EGR1 in hypoxia/reoxygenation (H/R) injuried mice primary renal tubular epithelial cells
Purpose: we performed comparative RNA-seq analyses to identify differentially expressed genes between Knockdown of Egr1 and negtive control in hypoxia/reoxygenation (H/R) injuried mice primary renal tubular epithelial cells.
Methods:we grew mouse primary renal tubular epithelial cells to approximately 50% confluence, transfected using EndoFectin™ Max (GeneCopoeia, China). H/R was used to mimic IRI in vitro. Briefly, cells were incubated in glucose-free medium in a tri-gas incubator (94% N2, 5% CO2 and 1.0% O2) at 37 °C for 6 hours. Subsequently, cells were incubated in complete medium under normal conditions for 18 hours for reoxygenation. Cells were then collected by 1ml TRIzol (Invitrogen, Carlsbad), and sent to Annoroad Corporation (Beijing, China) for high throughout Illumina NovaSeq 6000 sequencing (GPL24247) (Illumina, San Diego, CA, USA).
Results: To determine the possible pathways and downregulated genes of Egr1 in protecting mice primary renal tubular epithelial cells from injury, we conduct the transcriptomotic sequencing. After sequence, the clean reads rate of all samples were ≥98%.The quality of the assembled transcriptome is good enough for functional annotation and further analysis.
Conclusions: We performed RNA-sequencing (RNA-Seq) on isolated mouse renal tubular epithelial cells of 3 groups, negtive control(Sham group) treated with H/R (H/R group) or Egr1 overexpression plasmid (Egr1OV group). Egr1-responsive genes showed significant enrichment in proliferation pathway.

first: Jian-Wen

first: Men-Jie

last: Huang

first: Xiang-Mei


title: Transient upregulation of EGR1 signaling enhances kidney repair by activating SOX9+ renal tubular cells


title: Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [BS-seq]

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: Plants develop mutualistic association with beneficial rhizobacteria. To understand this important phenomenon, early mechanisms for establishing the mutualism are critical. Here we report that active DNA demethylation in plants controls root secretion of myo-inositol, which triggers and further facilitates colonization of the beneficial rhizobacteria Bacillus megaterium strain YC4, thereby allowing for plant growth-promotion. YC4 promotes plant growth but the beneficial effects were lost in the Arabidopsis mutant rdd that is defective in active DNA demethylation. Roots of rdd failed to associate with YC4, meanwhile the level of myo-inositol in root exudates was drastically reduced in rdd. Supplementation of myo-inositol to rdd restored YC4 colonization and plant growth-promotion, while plants with defective myo-inositol monophosphatase also failed in establishing mutualism with YC4. myo-Inositol not only induced chemotaxis of YC4 but also increased YC4 biofilm production, consistent with the transcriptional regulation of YC4 by myo-inositol. In addition, myo-inositol preferentially attracts Bacillus megaterium among the examined bacteria species. Regardless of YC4 inoculation, myo-inositol biosynthesis and catabolism genes are down- and up-regulated, respectively, in rdd compared to wild type plants. The differential expression of myo-inositol homeostasis genes is correlated with local DNA hypermethylation, whereas genetic disruption of the RNA-directed DNA methylation pathway abolished these epigenetic marks and reset the corresponding gene expression patterns, resulting in restored YC4 colonization and plant growth-promotion. Importantly, that active DNA demethylation controls myo-inositol-mediated mutualism between YC4 and plants was also demonstrated in Solanum lycopersicum. Our results uncover an important function of myo-inositol in plant-microbe interactions and its dependence on plant epigenetic regulation.

overall_design: MethylC-Seq:4 samples examined, Col-0_M (mock), Col-0_T (treated), rdd_M, rdd_T(each sample has 2 replicates); Arabidopsis mRNA seq: 4 samples examined, Col-0_M(mock), Col-0_T(treated),rdd_M, rdd_T (each sample has 3 biological replicates); YC4-R4 bacteria mRNAseq: 2 samples examined, 6H_C (mock), 6H_T (treated)(each sample has 3 replicates)

first: Juan

last: Vílchez

first: Yu

last: Yang

first: Li

last: Peng

first: Hailing

last: Zi


title: Phosphorylation of the Argonaute ALG-1 regulates microRNA binding during C. elegans development

city: Basel

first: Foivos

last: Gypas

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

type: Non-coding RNA profiling by high throughput sequencing

summary: Here, we report a new phosphorylation site on ALG-1 that modulates its ability to bind miRNAs. Mutating ALG-1 S642 into a phosphomimetic residue strongly impairs binding to miRNAs. Furthermore, this mutation causes embryonic lethality which are not observed in animals depleted of alg-1 suggesting that it may consequently impair the normal function of its homolog alg-2. Quantification of miRNAs in the phosphorylation mutants of alg-1 reveals that the miRNA passenger strands are strongly increased but not preferentially loaded into ALG-1, indicating that the defects in miRNA binding may also lead to an accumulation of miRNA duplexes.

overall_design: Quantification of miRNA expression in Alg1 mutants.

first: Smita

last: Nahar

first: Helge

last: Grosshans


title: Sirt3 Promotes Chondrogenesis, Chondrocyte Mitochondrial Respiration and the Development of High-Fat Diet-Induced Osteoarthritis in Mice

city: Oklahoma City

first: Timothy

middle: M

last: Griffin

state: OK

address: 825 NE 13th St

department: Aging and Metabolism

institute: OMRF

summary: Cartilage is characterized by mature chondrocyte metabolic heterogeneity in a zone-dependent manner. In this study, we used single cell mRNA sequencing (scRNA-seq) to evaluate the corresponding functional and metabolic phenotypic heterogeneity of in vitro cultured primary juvenile murine chondrocytes

overall_design: Single cell RNA sequencing to explore heterogeneity in primary cultured chondrocytes from knee joints of C57BL/6J mice


title: Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [bacteria RNA-seq]

city: Shanghai


title: Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria

sample_organism:
Priestia megaterium
Arabidopsis thaliana


title: Whole brain transcriptome of wild-type or Nav1.8CreROSA26DTA mice upon LPS sepsis

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

institute: AIST

summary: To check changes in transcriptome in whole brain upon LPS sepsis, mice were injected with PBS or LPS and gene expression was analyzed. Nav1.8CreROSA26DTA mice lack Nav1.8-positive nociceptor.

overall_design: Whole brains were prepared from wild-type or Nav1.8CreROSA26DTA mice injected with PBS or LPS.

first: Kenta

last: Maruyama


title: A KO mouse model for the lncRNA Lhx1os produces motor neuron alterations  and locomotor impairment

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

institute: Sapienza University of Rome

summary: Here we describe a conserved motor neuron specific long non-coding RNA, Lhx1os, whose knock-out in mice produces motor impairment and post-natal reduction of mature motor neurons (MNs). The endoplasmic reticulum (ER)-stress response pathway resulted specifically altered with the downregulation of factors involved in the Unfolded Protein Response (UPR). Lhx1os was found to bind the ER-associated PDIA3 disulfide isomerase and to affect the expression of the same set of genes controlled by this protein, indicating that the two factors act in conjunction to modulate the UPR. Altogether, the observed phenotype and function of Lhx1os indicate its important role in the control of MN homeostasis and function.

overall_design: Expression profile of WT and Lh1os KO mice spinal cord tissues by high-throughput sequencing .

first: Silvia

last: Galfrè

first: Adriano

last: Setti

first: Vittorio

last: Padovano

first: Flaminia

last: Pellegrini

first: Carmine

last: Nicoletti

first: Davide

last: Mariani

first: Julie

last: Martone


title: Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [TAIR-RNA-seq]

first: Huiming

last: Zhang

overall_design: Arabidopsis mRNA seq: 4 samples examined, Col-0_M(mock), Col-0_T(treated),rdd_M, rdd_T (each sample has 3 biological replicates)

first: Juan

last: Vílchez

first: Yu

last: Yang


title: Blood milieu in acute myocardial infarction reprograms human macrophages for trauma repair

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

summary: Acute myocardial infarction (AMI) is accompanied by a systemic trauma response that impacts on the whole body, including blood. In this study, we addressed whether macrophages, key players in trauma repair, sense and respond to these changes. For this, healthy human monocyte-derived macrophages were exposed to 20% human AMI (n=50) or control (n=20) serum and analyzed by transcriptional and multiparameter functional screening followed by network-guided data interpretation and drug repurposing. Results were validated in an independent cohort at functional level (n=47 AMI, n=25 control) and in a public dataset. AMI serum exposure resulted in an overt AMI signature, enriched in debris cleaning, mitosis, and immune pathways. Moreover, we identified gene networks associated with AMI and with poor clinical prognosis in AMI. Network-guided drug screening on the latter unveiled Prostaglandin E2 (PGE2) signaling as target for clinical intervention in detrimental macrophage imprinting during AMI trauma healing. Our results demonstrate pronounced context-induced macrophage reprogramming by the AMI systemic environment, to a degree decisive for patient prognosis. This offers new opportunities for targeted intervention and optimized cardiovascular disease risk management.

overall_design: Primary human CD14+-derived macrophages growing in 96-wells were exposed to different stimuli for 24h (n=4-6 per condition). Cells were washed, lysed, pooled per condition, and RNAsequencing was performed.

first: Margaux

last: Fontaine

first: Erik

last: Biessen

first: Lieve

last: Temmerman


title: Single-cell RNA Sequencing reveals functional difference of ASCL1-expressing and NEUROD1-expressing SCLC cells

city: Los Angels

first: Xuexi

state: California

address: AHSP A9404, 8700 Beverly Blvd

department: Medicine

institute: Cedars Sinai Medical Center

summary: Small cell lung cancer (SCLC) is a particularly aggressive, lethal and widely metastatic lung cancer. Surgical specimens of SCLC are rare and difficult to obtain due to their early metastasis. In this study, we generated single cell lung suspensions of SCLC tissues. ScRNA-seq was performed on CD45 and CD31 negative live cells sorted by FACS. Purified cells were clustered to evaluate the cancer cell sub-clusters.

overall_design: To  study the mechanism of lung cancer tumorigenesis and progression , we isolated individual cells (CD45/CD31-) from two freshy resected human primary SCLC, single cell RNA-sequencing was performed on the purified  cells.

first: X

first: Z

last: Liu


first: Jianwen

last: Chen

summary:
The Role of SOX9 in hypoxia/reoxygenation (H/R) injuried mice primary renal tubular epithelial cells
Purpose: we performed comparative RNA-seq analyses to identify differentially expressed genes between Knockdown of Sox9 and negtive control in hypoxia/reoxygenation (H/R) injuried mice primary renal tubular epithelial cells.
Methods:we grew mouse primary renal tubular epithelial cells to approximately 50% confluence, transfected using EndoFectin™ Max (GeneCopoeia, China) 12h before suffering to H/R injury. H/R was used to mimic IRI in vitro. Briefly, cells were incubated in glucose-free medium in a tri-gas incubator (94% N2, 5% CO2 and 1.0% O2) at 37 °C for 6 hours. Subsequently, cells were incubated in complete medium under normal conditions for 18 hours for reoxygenation. Cells were then collected by 1ml TRIzol (Invitrogen, Carlsbad), and sent to Annoroad Corporation (Beijing, China) for high throughout Illumina NovaSeq 6000 sequencing (GPL24247) (Illumina, San Diego, CA, USA).
Results: To determine the possible pathways of Sox9 in protecting mice primary renal tubular epithelial cells from injury, we conduct the transcriptomotic sequencing. After sequence, the clean reads rate of all samples were ≥98%.The quality of the assembled transcriptome is good enough for functional annotation and further analysis.
Conclusions: We performed RNA-sequencing (RNA-Seq) on isolated mouse renal tubular epithelial cells of two groups, treated with H/R and transfected with siNC (H/R+siNC group) or siSox9 (H/R+siSox9 group). SOX9-responsive genes showed significant enrichment of the WNT signaling pathway in primary tubular epithelial cells.

first: Jian-Wen

first: Men-Jie

last: Huang

first: Xiang-Mei


title: Differential susceptibility of retinal neurons to the loss of mitochondrial biogenesis factor Nrf1

status: Public on Dec 17 2022

first: Chai-An

last: Mao

state: Texas

address: 6431 Fannin Street, MSB7.242

department: Ophthalmology And Visual Scien

institute: University of Texas McGovern Medical School

summary: The retina, the accessible part of the central nervous system, has served as a model system to study the relationship between energy utilization and metabolite supply. When the metabolite supply cannot match the energy demand, retinal neurons are at risk of death. As the powerhouse of eukaryotic cells, mitochondria play a pivotal role in generating ATP, produce precursors for macromolecules, maintain the redox homeostasis, and function as waste management centers for various types of metabolic intermediates. Mitochondrial dysfunction has been implicated in the pathologies of a number of degenerative retinal diseases. It is well known that photoreceptors are particularly vulnerable to mutations affecting mitochondrial function due to their high energy demand and susceptibility to oxidative stress. However, it is unclear how defective mitochondria affect other retinal neurons. Nuclear respiratory factor 1 (Nrf1) is the major transcriptional regulator of mitochondrial biogenesis, and loss of Nrf1 leads to defective mitochondria biogenesis and eventually cell death. Here, we investigated how different retinal neurons respond to the loss of Nrf1. We provide in vivo evidence that the disruption of Nrf1-mediated mitochondrial biogenesis results in a slow, progressive degeneration of all retinal cell types examined, although they present different sensitivity to the deletion of Nrf1, which implicates differential energy demand and utilization, as well as tolerance to mitochondria defects in different neuronal cells. Furthermore, transcriptome analysis on rod-specific Nrf1 deletion uncovered a previously unknown role of Nrf1 in maintaining genome stability.

overall_design: Retinal mRNA profiles of 4 weeks old wild-type and Rho-iCre:Nrf1f/f retinas were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000. Male and female retinas were sequenced separately.

first: Takae

last: Kiyama


title: scRNA-Seq of Cdkn2a mutant murine Epithelioid Hemangioendothelioma tumors

status: Public on Dec 16 2022

city: Cleveland

first: Brian

middle: P

last: Rubin

address: 9620 Carnegie Ave NE2-215

department: Cancer Biology

institute: Cleveland Clinic

summary: Epithelioid hemangioendothelioma (EHE) is a rare vascular sarcoma that is associated with a TAZ-CAMTA1 fusion in greater than 90% of cases and loss of CDKN2A in human EHE tumors is associated with late stage disease. Murine EHE tumors were created by conditionally expressing TAZ-CAMTA1 and conditionally knocking out Cdkn2a within vascular endothelium. Resultant tumors were used for single cell RNA sequencing and compared against age matched wild type mice tissue.

overall_design: scRNA Sequencing of Cdkn2a mutant Epithelioid Hemangioendothelioma Tumors in Mouse

first: Caleb

last: Seavey


title: Transcriptomic changes of HepG2 cell line in response to treatment with boric acid

city: Ankara

first: Aysegul

last: Tombuloglu

address: Universiteler Mah.

department: Medical Informatics

country: Turkey

institute: Middle East Technical University

summary:
Boric acid is the common physiological form of Boron in human body. There is an ongoing effort to illuminate its biological effects via in vitro and in vivo experimental settings.
Many of the biological effects of boric acid are known to be concentration dependent. In this study, genome-wide transcriptional effects of boric acid treatment on HepG2 cell line at IC50 level was investigated.

overall_design: RNA was harvested from either HepG2 cells  treated with 24 mM boric acid (IC50 level) for 24 hours or untreated HepG2 cells. RNA samples obtained from treated cells (n=3) and untreated cells (n=3) were hybridized to Affymetrix HuGene 1.0st arrays.

first: Hulya

last: Copoglu


title: PAX5 controls lineage transitions between neuroendocrine and non-neuroendocrine states during carcinoma progression

summary: Single cell lung suspensions of SCLC tissues were generated. scRNA-seq was performed on CD45 and CD31 negative live cells sorted by FACS. Purified cells were clustered to evaluate the cancer cell sub-clusters.

overall_design: To study the intratumoral heterogeneity, we isolated individual cells (CD45/CD31-) from one freshly resected human primary SCLC, removed inflammatory infiltrate and endothelial cells, and performed single cell analysis using the 10x Genomics Chromium platform.

first: Zhe


title: Systemic environment in acute myocardial infarction programs human macrophages for trauma repair

first: Han

summary: In this study human primary monocyte-derived macrophages from healthy volunteers (pool of 6-8 donors) were exposed for 24 h to a 1:5 dilution of human patient serum. Patient sera were obtained either from control patients (n=20) or patients suffering an acute myocardial infarction (AMI, n=47, selected from POSTEMI trial, S. Limalanathan et al. J Am Heart Assoc 2014). All exposed macrophages were analyzed by RNA sequencing. The study revealed that macrophages significantly alter their gene expression profile in response the AMI-serum exposure, and adapt phagocytic, metabolic and cell cycling programs.

overall_design: Primary monocytes were isolated from human PBMCs by CD14+ beads and differentiated into macrophages using recombinant human M-CSF 100ng/ml for seven days with one medium change. Patient or control serum was added directly into the growth medium of fully differentiated macrophages and incubated for 24h. Cells were washed, lysed and RNA sequencing was performed.

first: Margaux


title: NarGHJI mediated virulence in Staphylococcus aureus

city: Hefei

first: Yujie

last: Li

state: Anhui

address: 1129 Huizhou Ave

institute: University of Science and Technology of China

summary:
To investigate the function NarGHJI in the regulation of the expression of virulence factors, we constructed a narGHJI mutant by targeted deletion of narG in MRSA isolate USA300 LAC
We then performed gene expression profiling analysis using data obtained from RNA-seq of of two different strains at early exponential (OD600 = 0.5).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type strain USA300 LAC and narG knockout mutant.

first: Ting

last: Pan

first: Ruobing

last: Cao

first: Wei

first: Zhien

last: He

first: Baolin

last: Sun


title: Effect of antiviral drugs on gene expression in the control of CMV infection in passion fruit

city: Guiyang

first: liqun

last: Zhang

state: Guizhou

address: Jiaxiu South Road, Huaxi District

institute: GZ university

summary: To investigate the resistance mechanism of control drugs in resisting CMV virus, we established an indoor CMV- Passion fruit seedling in vivo screening model, treated with different antiviral commercial agents, and then we performed gene expression profiling on RNA-seq data of the best effective drug treatment group.

overall_design: Gene expression profiling of RNA-seq data of the 5% amino-oligosaccharide agent-treated group with higher efficacy against CMV virus compared with the CK group

first: Zhi

last: Zhao


title: An iTSC-derived placental model of SARS-CoV-2 infection reveals ACE2-dependent susceptibility in syncytiotrophoblasts

city: Clayton

first: Monika

last: Mohenska

state: VIC

address: 15 Innovation Walk

institute: Monash University

summary: We have developed an in vitro model of SARS-CoV-2 infection of placental cell types using induced trophoblast stem cells (iTSCs). This model allowed us to show that STs but not EVTs are infected. Importantly, infected STs lack the expression of key differentiation genes, lack typically observed differentiated morphology and produce significantly lower human chorionic gonadotropin (HCG) compared to non-infected controls. We also show that an anti-ACE2 antibody prevents SARS-CoV-2  infection and restores normal ST differentiation and function. We highlight the establishment of a platform to study SARS-CoV-2 infection in early placental cell types, which will facilitate investigation of antiviral therapy to protect the placenta during early pregnancy and development.

overall_design: Examination of the effects of SARS-CoV2 on placental cell types.

first: Jose

last: Polo

first: Joseph


title: Single-Cell Analysis of NASH mouse livers

city: Berkeley

first: Danica

last: Chen

address: 335 Morgan Hall

institute: University of California, Berkeley

summary: We performed single-cell RNA-sequencing of the livers from WT and SIRT7 KO mice.

overall_design: scRNA-sequencing of the livers from WT and SIRT7 KO mice.

first: W

middle: C

last: Mu

first: Chih

last: Wang


title: Gene Expression Profiling of livers in an NASH Mouse Model

summary: We used microarray to study the global transcriptomic changes in the livers of SIRT7 KO mice, which develop spontaneous nonalcoholic fatty liver disease.

overall_design: Total RNA was isolated from the livers of wild type and SIRT7 KO mice using an RNA isolation kit (Qiagen). Microarray hybridizations were performed at the University of California, Berkeley Functional Genomics. Laboratory using Affymetrix GeneChip mouse 430As according to the instructions of the manufacturer (Affymetrix).

first: Rika

last: Ohkubo


title: SIRT7 liver

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

overall_design: Refer to individual Series


title: RNA-Seq of livers of Gata4LKO and control mouse on LXR agonist GW3965

city: Dallas

first: Lara

last: Bideyan

address: 5323 Harry Hines Blvd., MC: 9077 Y6.314

department: Internal Medicine

institute: UT Southwestern

summary: GATA4 is a transcription factor known for its crucial role in the development of many tissues, including liver; however, its role in adult liver metabolism is unknown. Here, using high-throughput sequencing technologies, including assay for transposase-accessible chromatin with sequencing (ATAC-Seq), we identified GATA4 as a transcriptional regulator of metabolism in liver. GATA4 expression is elevated in response to refeeding, and its occupancy is increased at enhancers of genes linked to fatty acid and lipoprotein metabolism. Knocking out GATA4 in adult liver (Gata4LKO) decreased transcriptional activity at GATA4 binding sites especially during feeding. Gata4LKO mice have reduced plasma HDL cholesterol and increased liver triglyceride levels. The expression of a panel of genes involved in cholesterol export and triglyceride hydrolysis was downregulated and the expression of those involved in lipid uptake were upregulated in Gata4LKO liver, We further demonstrate that GATA4 collaborates with LXR liver. GATA4 shares a number of binding sites and direct transcriptional targets with LXRs, and loss of GATA4 impairs the hepatic transcriptional response to LXR agonist. Collectively, these results show that hepatic GATA4 contributes to the transcriptional control of hepatic and systemic lipid homeostasis.

overall_design: RNA-Seq of frozen liver tissue from GW3965 vs DMSO treated GATA4 Liver KO (Gata4 floxed/floxed; AAV8-Tbg-Cre) or Control (Gata4 floxed/floxed; AAV8-Empty) mice. Nine-week-old mice on Gata4LKO and control mice, 1 week after AAV injection, were gavaged with 40 mg/kg GW3965 prepared in canola oil (Collins et al. 2002) at 17 h, and then 8 h before before sacrifice. Mice were 4 h fasted at the time of killing. Dimethylsulfoxide in canola oil was used as vehicle control.

first: Peter

last: Tontonoz


title: RNA-Seq of Epithelioid Hemangioendothelioma cell lines

first: Brian

last: Rubin

state: OH

summary: Epithelioid hemangioendothelioma (EHE) is a rare vascular sarcoma that is associated with a WWTR1-CAMTA1 fusion gene in greater than 90% of cases. Cell lines were generated from WWTR1-CAMTA1 positive murine EHE tumors which also harbor a loss of CDKN2A. RNA sequencing was performed on cell lines.

overall_design: RNA Sequencing of Epithelioid Hemangioendothelioma Cell Lines

first: Caleb

last: Seavey


title: RNA-Seq of livers of Gata4LKO and control mouse on western diet

overall_design: RNA-Seq of frozen liver tissue from fasted or refed GATA4 Liver KO (Gata4 floxed/floxed; AAV8-Tbg-Cre) or Control (Gata4 floxed/floxed; AAV8-Empty) mice on Western Diet for 3 weeks.


title: Towards Optimization of Precision Oncology in Metastatic Uterine Tumors

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

institute: Health Research Institute of Santiago (IDIS)

summary: Precision oncology and its diagnostic tools are essential for developing personalized cancer treatments. The purpose of this study was to integrate data on the digital patterns of reticulin fiber scaffolding and the immune cell infiltrate, transcriptomic and epigenetic profiles in aggressive uterine adenocarcinoma (uADC), uterine leiomyosarcoma (uLMS) and their respective lung metastases (LM-uADC and LM-uLMS), with the aim of obtaining key tumor microenvironment (TME) biomarkers that can help improve metastatic prediction and shed light on potential therapeutic targets.

overall_design: Total genomic DNA (gDNA) from 10-μm FFPE tissue sections of the invasive tumor front (ITF) from uADC and uLMS primary tumors and their respective lung metastasis (LM-uADC and LM-uLMS) were pocessed on the Infinium MethylationEPIC array (850K). Samples that passed the quality controls using RnBeads package in R environment, were analyzed to asses their DNA methylation profile. The DNA methylation data from u-ADC and u-LMS primary tumors used in this study has been previously deposited on GEO with the accession number GSE171142.

first: Rafael

last: Lopez-Lopez


title: ATAC-Seq of fasted and refed WT mouse liver

overall_design: Assay for transposase-accessible chromatin with sequencing (ATAC-Seq) in fresh liver tissue from fasted or refed mice.


title: Analysis of allogeneic and syngeneic CD4+ T cells reveals novel target genes and related pathway in acute graft-versus host disease

city: Suzhou

first: Qiao

last: Cheng

state: Jiangsu Province

address: Shizi Street

department: Institute of Blood and Marrow Transplantation (IBMT)

institute: The First Affiliated Hospital of Soochow University

summary: The goals of the study are to compare differently expressed genes in allogeneic and syngeneic CD4+ T cells isolated from splenocytes of allogeneic (donor: C57BL/6, host: Balb/c) and syngeneic (donor:  Balb/c, host: Balb/c) HSCT mice.

overall_design: RNA sequence was performed with allogeneic and syngeneic CD4+ T cells (n = 3 for each group) to identify the  differently expressed genes and related pathway.

first: Dong

first: Xiaoxuan

last: Lai

first: Yin

last: Liu

first: Hui

last: Zheng

first: Depei

last: Wu

first: Yang

last: Xu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of aGVHD mice  tranferred Wild Type or OTUD1-/- cells.

summary: Donor OTUD1 deficiency significanltly ameliorates the severity of aGVHD mice. We used single cell RNA sequencing (scRNA-seq) to analyze the immune cells in aGVHD mice transferred wild type or OTUD1-deficient cells.

overall_design: Spleens were isolated from aGVHD mice transferred wild type or OTUD1-deficient cells, then, the spleens were prepared as single cell suspensions and  analyzed using scRNAseq.


title: Hepatic GATA4 regulates cholesterol and triglyceride homoestasis


title: Analysis of allogeneic and syngeneic CD3+ T cells reveals novel target genes and related pathway in acute graft-versus host disease

summary: The goals of the study are to compare differenely expressed genes in allogeneic and syngeneic CD3+ T cells isolated from splenocytes of allogeneic (donor: C57BL/6, host: Balb/c) and syngeneic (donor:  Balb/c, host: Balb/c) HSCT mice.

overall_design: RNA sequence was performed with allogeneic and syngeneic CD3+ T cells (n = 3 for each group) to identify the  differenely expressed genes and related pathway.


title: RNA-Seq of fasted and refed WT mouse liver

overall_design: RNA-Seq of frozen liver tissue from fasted or refed mice.


title: H3K27Ac ChIP-Seq of fasted and refed Gata4LKO and control mouse liver

overall_design: ChIP-Seq of acetylation of histone H3 Lysine 27 (H3K27Ac) of frozen liver tissue from fasted or refed GATA4 Liver KO (Gata4 floxed/floxed; AAV8-Tbg-Cre) or Control (Gata4 floxed/floxed; AAV8-Empty) mice.


title: Analysis of allogeneic and syngeneic CD8+ T cells reveals novel target genes and related pathway in acute graft-versus host disease

summary: The goals of the study are to compare differenely expressed genes in allogeneic and syngeneic CD8+ T cells isolated from splenocytes of allogeneic (donor: C57BL/6, host: Balb/c) and syngeneic (donor:  Balb/c, host: Balb/c) HSCT mice.

overall_design: RNA sequence was performed with allogeneic and syngeneic CD8+ T cells (n = 3 for each group) to identify the  differenely expressed genes and related pathway.


title: RNA-Seq of fasted and refed Gata4LKO and control mouse liver

overall_design: RNA-Seq of frozen liver tissue from fasted or refed GATA4 Liver KO (Gata4 floxed/floxed; AAV8-Tbg-Cre) or Control (Gata4 floxed/floxed; AAV8-Empty) mice.


title: Optimized Repli-seq: An improved DNA Replication Timing Analysis by Next Generation Sequencing

city: Minneapolis

first: Juan Carlos

last: Rivera-Mulia

state: MN

address: 420 Washington Ave SE

department: Department of Biochemistry, Molecular Biology and Biophysics

institute: University of Minnesota Medical School

summary: DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we developed an improved method to measure RT genome-wide that enables high resolution analysis of low input samples.

overall_design: Genome-wide replication timing profiles were constructed from H9, U2OS and MEF cell lines.

first: JuanCarlos


title: Gene expression profiling of Zebrafish larvae treated with bepridil

first: Xinrui

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary:
Purpose: Bepridil is a commonly used drug for angina pectoris and arrhythmia. However, its toxicity and other potential effects on embryonic development remain unknown. In this study, we revealed the physical and developmental toxicity of bepridil on zebrafish models and human myocardial H9c2 cells.
Methods: The AB line zebrafish embryos were treated with different concentrations of bepridil at 24 hpf. The mRNA profiles of zebrafish larvae at 120 hpf in 0, 250, 750 and 1295 ng/mL bepridil groups were generated with deep sequencing, in triplicate, using Illumina sequencing platform (HiSeqTM 2500). RNA integrity was analyzed through the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara). The RNA integrity number ≥ 7 was subjected to the following analysis. Genes with adjusted P-value < 0.05 and foldChange >2 were defined as differentially expressed genes (DEGs).
Results: About 45 million sequence reads were mapped to the zebrafish genome in each group. The RNA-seq data confirmed that low-dose of bepridil treatment induced an obvious xenobiotic stimulus and drug catabolic process. The enriched DEGs of GO and KEGG workflow showed negative regulation of proteolysis and peptidase in 250 and 750 ng/mL bepridil groups, which eventually led to the metabolic disorders of lipids and a variety of essential amino acids. As a long-term acting calcium antagonist, bepridil caused partial changes (Generatio, 61/426) of calcium signaling channel in 120 hpf zebrafish larvae after 1295 ng/mL (LC10) treatment. However, the cardiac muscle contraction and adrenergic of cardiomyocytes were affected significantly in the same group. Besides, the overall DEGs were highly correlated to cell proliferation and differentiation of the zebrafish. In brief, the transcriptome results were similar to our in vivo phenotype data. The liver metabolism and cardiovascular function of zebrafish would be affected by bepridil during early embryonic development.
Conclusions: Our study reveals the potential embryotoxicity of bepridil, a traditional antiarrhythmic drug, in zebrafish embryos. The transcriptomes of zebrafish larvae were progressed with biological replicates (n = 3) and generated through RNA-seq. Our results reveal the detailed biological and metabolic responses of bepridil to embryonic development, which has guiding significance for the clinical medication of prenatal heart patients.

overall_design: Zebrafish larvae mRNA profiles of 120 hpf individuals in 0, 250, 750 and 1295 ng/mL bepridil treatment groups

first: Yalan

last: Wei

first: Yuqing

last: Lei

first: Hua

last: Cao


title: Identification of a novel ER-NFκB driven stem-like cell population associated with poor outcome of ER+ breast cancer patients

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

summary: Up to 40% of patients with Estrogen Receptor positive (ER+) breast cancer experience relapse. Breast cancer stem cells (BCSCs) are known to be involved in therapy resistance, relapse, and development of more aggressive and metastatic tumors. Therefore, there is an urgent need to identify genes/pathways that drive stem-like cell properties in ER+ breast tumors. Using single-cell RNA sequencing and bioinformatic approaches, with additional follow-up studies, we identified a unique quiescent stem-like cell population that is driven by ER and NFkB in multiple ER+ breast cancer models. Moreover, a gene signature derived from this stem-like population is expressed in endocrine therapy-resistant and metastatic cell populations and predictive of poor patient outcome. These findings indicate a novel role for ER and NFkB crosstalk in BCSCs biology and understanding the mechanism by which these pathways promote stem properties may be exploited to improve outcomes for ER+ breast cancer patients at risk of relapse.

overall_design: scRNA-seq (10XGenomics)

first: Svetlana

middle: E

last: Semina

first: Jonna

last: Frasor


title: Transposase-accessible chromatin regions of MDA-MB-453 cells expressing ectopic wild-type, Y537S, or K303R ER alpha.

city: Koto-ku

first: Tomoyoshi

last: Nakadai

state: Tokyo

institute: Cancer Institute of JFCR


title: Transcriptomic analysis of primary human lung cells and tissue samples highlights cellular crosstalk during infections with influenza A virus

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps University Marburg

summary: We used RNA sequencing to comprehensively map the expression of coding and non-coding RNAs in primary human alveolar epithelial type II cells (AECIIs), alveolar macrophages (AMs), human lung tissue, and the  epithelial cell line A549 during infection with IAV strain H3N2 Panama

overall_design: Infected and uninfected samples of each cell type were compared in biological triplicates.

first: Katja

last: Hönzke

first: Andreas

last: Hocke


title: Genome-wide analysis of ectopically expressed wild-type, Y537S, or K303R ER alpha-binding genomic regions in MDA-MB-453 cells.

summary: We analyzed the wild-type, Y537S, or K303R ER alpha-binding genomic regions ectopically expressed in MDA-MB-453 cells by ChIP-seq, and identified K303R-related disordered ERa binding and chromatin opening at Fox motif regions.

overall_design: MDA-MB-453 cells expressing wild-type, Y537S, or K303R ER alpha cultured under +/- doxycycline and +/- E2 conditions were subjected to standard ChIP-seq analysis.

first: Reo

last: Maruyama


title: Genome-wide analysis of transposase-accessible chromatin regions of MDA-MB-453 cells expressing ectopic wild-type, Y537S, or K303R ER alpha.

summary: We analyzed the chromatin state of MDA-MB-453 cells expressing wild-type, Y537S, or K303R ER alpha by ATAC-seq, and identified K303R-related disordered chromatin opening which has Fox-binding motifs.

overall_design: MDA-MB-453 cells expressing wild-type, Y537S, or K303R ER alpha cultured under +/- doxycycline and +/- E2 conditions were subjected to standard ATAC-seq analysis.


title: Chromatin condensation is independent from nuclear condensation in late-stage terminal erythropoiesis revealed from the dynamic three-dimensional genomic organizations [Hi-C]

city: CHICACO

first: Feng

last: Yue

state: ILLINOIS

address: 303 E. Superior Simpson Querrey

institute: Northwestern University Feinberg School of Medicine

summary: Mammalian terminal erythropoiesis involves chromatin and nuclear condensation followed by enucleation. Late-stage erythroblasts undergo caspase-mediated nuclear opening formation that is important for nuclear condensation through partial release of histones. It remains unknown whether nuclear opening and histone release influence the three-dimensional (3D) genomic organization during terminal erythropoiesis. Here, we compared the genome wide 3D organization, chromatin accessibility, and transcriptome of the cultured mouse erythroid progenitors with and without the blocking of nuclear opening during differentiation. We found that terminal differentiation from the basophilic to orthochromatic stages of erythroblasts involves compaction and establishment of long-range interactions of the heterochromatin regions, which is associated with globally increased accessibility and upregulation of erythroid-related genes. Surprisingly, blocking of nuclear opening did not have a significant impact on 3D genomic organization, chromatin accessibility, or transcriptome despite the inhibition of histone release and nuclear condensation. Inhibition of nuclear opening also significantly affected enucleation. We further demonstrated this through a caspase-3 and 7 double knockout mouse model, which showed significant defects in nuclear opening and condensation with a compromise of enucleation in fetal erythroid progenitors. However, loss of these effector caspases had minimal effects on the red cell indices and survival of the recipient animals in a fetal liver cell transplantation model. Overall, these results indicate that nuclear opening and histone release may not be necessary for chromatin condensation and global transcriptome but are critical for nuclear condensation and efficient enucleation. These data also underline the robustness of enucleation despite the dysplastic or less condensed nucleus.

overall_design:
RNA-Seq, ATAC-seq and genome-wide chromatin conformation capture (Hi-C) in mouse erythroblast precursors cells collected at time 0 and compared to cells treated with Z-VAD or DMSO at 24 h and collected at 30 h.
This submission contains Hi-C data.

first: Honghao

last: Bi

first: Dongmei

last: Wang

first: Juan

first: Yijie

first: Haiyan

last: Bao

first: Xu

last: Han

first: Peng

last: Ji


title: The three-dimensional genomic organization changes in terminal erythropoiesis reveal independence of chromatin condensation from nuclear condensation [ATAC-Seq]

address: Ward Building Room 3-230/45, 303 E Chicago Avenue

department: Pathology

institute: Northwestern University

overall_design: Fetal liver cells cultured in EPO containing medium for 24h and treated with caspase inhibitor or DMSO for 6h.

last: Liu


title: The three-dimensional genomic organization changes in terminal erythropoiesis reveal independence of chromatin condensation from nuclear condensation [RNA-Seq]

overall_design: Fetal liver cells cultured in EPO containing medium for 24h and treated with caspase inhibitor or DMSO for 6h. Cells were then harvested for RNA-seq.


title: PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [RNAseq]

city: Shanghai

first: Xuan

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health,  Chinese Academy of Sciences

summary: The three-dimensional (3D) genome structure of human malaria parasite Plasmodium falciparum is highly organized and plays important roles in regulating coordinated expression patterns of specific genes such as virulence genes which are involved in antigenic variation and immune escape. However, the molecular mechanisms that control 3D genome of the parasite remain elusive. Here by analyzing genome organization in P. falciparum, we identify high-interacting regions (HIRs) with strong chromatin interactions telomeres and virulence genes loci. Specifically, HIRs are highly enriched with repressive histone marks (H3K36me3 and H3K9me3) and form the transcriptional repressive center. Deletion of PfSETvs, which controls H3K36me3 level, results in marked reduction of both intra-chromosomal and inter-chromosomal interactions for HIRs. Importantly, such chromatin reorganization coordinates with dymamic changes in epigenetic feature in HIRs and specifically activation of var genes. Our results uncover a fundamental mechanism that the epigenetic factor PfSETvs controls the 3D organization of heterochromatin in regulating the transcription activities of var genes family in P. falciparum.

overall_design: we generate Hi-C maps for wild-type and PfSETvs-KO samples at Ring stage in P.falciparum. Analysis of these datasets together with H3K9me3 and H3K36me3 and gene expression data allow us to uncover the changes in 3D genome with the epigenome changes and  regulation of antigenic variation in the parasite.

first: Gang

last: Wei


title: Gut microbiota promotes stem cell differentiation   through stromal niches in early postnatal development

city: Hangzhou

first: Lijiang

last: Fei

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: At birth, newborns are exposed to gut microbiota, which plays a critical role in host physiology. A reduced level of microbial diversity has been associated with necrotizing enterocolitis (NEC), one of the most deadly diseases in premature infants, but the underlying disease mechanisms are still poorly understood. Although the epithelial turnover of germ free mice is significantly delayed compared to conventionally raised mice, it remains unclear how gut microbiota exposure in the early postnatal period promotes stem cell renewal and differentiation. By analyzing genetic and experimental mouse models and performing single cell analysis, we demonstrate that gut microbiota promotes stem cell differentiation through the activation of critical stromal niche components. Our single cell analysis reveals that gut microbiota controls the size and heterogeneity of macrophage populations that secrete Wnt ligands, thereby maintaining the proliferation of intestinal telocytes, a recently identified gut mesenchymal stem cell niche. We show that stem cell differentiation, when impaired by antibiotic treatment promotes NEC, while treatment with Lactobacillus, which in NEC is dramatically less abundant, rescues NEC-like pathology through the activation of macrophage and telocyte niches. Our work highlights the mechanisms of how gut microbiota-facilitate mesenchymal niche proliferation which supports stem cell differentiation in early postnatal development.

overall_design: Identification and comparision of the Lgr5 cell differentiation in gut microbiota composition change

first: Ji-Eun

last: Kim


title: Compendium of functional regulatory variants in human neuropsychiatric disease (RNA-Seq)

city: Stanford

first: Margaret

last: Guo

state: CA

address: 269 Campus Dr. CCSR Room 2150

institute: Stanford University

summary:
Abstract: Noncoding variants of presumed regulatory function contribute to neuropsychiatric disease heritability. 4442 noncoding variants connected to risk for 10 neuropsychiatric disorders, including autism spectrum disorder, attention deficit hyperactivity disorder, bipolar disorder, borderline personality disorder, major depression, generalized anxiety disorder, panic disorder, post-traumatic stress disorder, obsessive-compulsive disorder, and schizophrenia, were studied within developing human neural cells. Integrating epigenomic and transcriptomic data with massively parallel reporter assays identified 637 disease-associated single-nucleotide variants (daSNVs) with altered transcription-regulating activity. Expression-gene mapping, network analyses, and chromatin looping identified 619 candidate disease-relevant target genes modulated by these daSNVs. Specific daSNV-associated molecular pathways mapped to prevalent mental health symptoms. These data provide a framework resource to study inherited pathogenic risk for human neuropsychiatric disorders.
Purpose: To place disease-associated single nucleotide variants (daSNVs) in genomic context within human neural cells, matched RNA-seq, chromatin accessibility profiling via ATAC-seq, and enhancer-promoter looping via H3K27ac HiChIP was performed in ES cells and at day 2 (N-D2), 10 (N-D10), and 28 (N-D28) of neuronal differentiation. Additionally, anterior (A-NPC) and posterior (P-NPC) neuronal stem cells were generated and studied. Matched sequencing was also performed on primary human astrocytes from adult brains. Processed data for all cell types can be found in this repository. Raw data D10 and D28 RNA seq samples can be found here. Raw data for D0, D2, A-NSC, A-D2, P-NSC, and P-D2 data can be found here: https://www.biorxiv.org/content/10.1101/2020.12.02.398677v1.abstract. Raw data for Astrocytes can be found with the Donohue, et al. "The combinatorial cis-regulatory vocabulary of cell type-specific gene regulation in homeostasis and disease".

overall_design: ES-derived neuronal and primary astrocyte mRNA profiles in vitro


title: Comparative analysis of the DNA methylation landscape in CD4, CD8, and B memory lineages

city: Lebanon

first: Lucas

middle: A.

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

summary: There is considerable evidence that epigenetic mechanisms and DNA methylation are critical drivers of immune cell lineage differentiation and activation. However, there has been limited coordinated investigation of common pathways in distinct cell types for immunological processes such as immune activation.  Further, it remains unclear if the memory cell subtypes differentiate distinctly by cell lineages. We used the Illumina EPIC array to characterize the DNA methylation similarities and differences in B cell, CD4 T, and CD8 T naïve and memory cells states. Our data describe considerable overlap in CpG dinucleotides and genes with altered DNA methylation in the process of naïve to memory activation across the three lineages, clearly suggesting that common pathways exist for immune memory generation. Further, our analyses revealed specific CpG dinucleotides and genes in CD4 T and CD8 T central to effector memory differentiation. Finally, we identified unique DNA methylation patterns in TEMRA CD8 T cells compared to other CD8 T memory cell subtypes.

overall_design: Bisulphite converted, EPIC arrayed DNA from naïve and memory B and T lymphocytes:  B naïve (n=6), B memory (n=7), CD4 naïve (n=6), CD4 central memory (n=6), CD4 effector memory (n=6), CD8 naïve (n=12), CD8 central memory (n=5), CD8 effector memory (n=4), CD8 TEMRA (n=5).

first: Ze

last: Zhang

first: Rondi

last: Butler

first: Devin

last: Koestler

first: Shelby

last: Bell-Glenn

first: Gayathri

last: Warrier

first: Annette

last: Molinaro

first: Brock

last: Christensen

first: John

last: Wiencke

first: Karl

last: Kelsey


title: RNA-seq data of 20 pairs of colorectal tumor with matched adjacent normal colorectal tissue

city: Beijing

first: Jiabo

last: Di

address: Fucheng Road 52

institute: Peking University Cancer Hospital

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression. The goals of this study is to compare gene expressions in colorectal tumor versus adjacent normal colorectal tissue.

overall_design: In total 20 pairs of colorectal tumor with matched adjacent normal colorectal tissue were sent to RNA sequencing. Adjacent normal tissue was used as germline control.

first: Xiangqian

last: Su