title: Spatial transcriptomic characterization of the lung parenchyma during COVID-19 pneumonitis

city: Oxford

first: Amy

middle: Rachael

last: Cross

address: John Radcliffe Hospital

department: NDS

institute: University of Oxford

summary:
Severe lung damage in COVID-19 is known to involve complex interactions between diverse populations of immune and stromal cells. The pneumonitis manifesting in COVID-19 and acute respiratory distress syndrome results in spatially heterogenous manifestations of injury, such as infiltrates, loss of epithelial integrity and fibrosis. In this study, we applied a spatial transcriptomics approach to better delineate the cells, pathways and genes responsible for promoting and perpetuating severe tissue pathology in COVID-19 pneumonitis. Guided by tissue histology and multiplex immunofluorescence, we performed a targeted sampling of dozens of regions representing a spectrum of diffuse alveolar damage (mild to severe) from the post-mortem lung of three COVID-19 patients.  These microscopic sites of injury had varying known compositions of CD3+ lymphocytes, CD68+ myeloid cells and panCK+ epithelial cells.
DCC files are the processed sequencing files using the NanoString DND pipeline. The "Initial Dataset.xlsx" is represents raw gene counts for each probe replicate (n=47). "Post Biological Probe QC.xlsx" removes a sample (n=46) with failed sequencing (no rawReads) and conducts biological probe quality controls to collapse probe replicates into a single count per target gene using the GeoMx Analysis suite (version 2.1.0.102).  "qn.exprs.tsv" is the matrix of quantile normalised gene expression by segment (n=46) and  "qn.exprs.corrected.tsv" is the matrix of quantile normalised and batch corrected matrix of gene expression by segment (n=46). Rendered multichannel immunofluorescent microscopy png images corresponding to each area of interest (AOI with the acquistion borders outlined in white) are included.  Further images can be made available upon request.

overall_design: RNA expression was assessed in selected areas within the lung parenchyma from three COVID-19 patients. Tissues were obtained rapidly postmortem, through open biopsy. At least, 14 spatially distinct areas (AOI) per tissue section were sampled to demonstrate the breadth of inflammation and injury within the alveolar region (total AOI = 46).  The areas (AOI) were classified by the severity of alveolar tissue and the presence of proximal SARS-CoV-2 nucelocapsid in aligned non-sequential tissue sections.   These microscopic sites of injury had varying known compositions of CD3+ lymphocytes, CD68+ myeloid cells and panCK+ epithelial cells. The genes measured were included in the NanoString Cancer Transcriptome Atlas (CTA) panel and those included in the COVID-19 spike-in gene panel for added respiratory-related and SARS-CoV-2 genes. The raw count matrix, the quantile normalized expression matrix and the metadata (including the calculated CD3+ and CD68+ cell composition, and the severity of alveolar damage) are provided.  The corresponding immunofluorescence images of each AOI and the whole tissue scan can be provided upon request.

first: A

middle: R

first: S

last: Sansom

first: F

last: Issa


title: Maternal Immune Activation perturbs fetal hematopoietic development and causes persistent changes to postnatal immunity

status: Public on Jan 27 2023

city: SALT LAKE CITY

first: Anna

middle: E

last: Beaudin

state: Utah

country: USA

institute: University of Utah

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Maternal Immune Activation perturbs fetal hematopoietic development and causes persistent changes to postnatal immunity [RNA-Seq]

summary: Adult hematopoietic stem cells (HSCs) respond directly to inflammation and infection, resulting in both acute and persistent changes in quiescence, mobilization, and differentiation.  Here we show that fetal HSCs respond to maternal inflammation in utero, and the fetal response drives long-term changes to postnatal hematopoiesis and immunity. Heterogeneous fetal hematopoietic stem and progenitor cells (HSPCs) show divergent responses to maternal immune activation (MIA), including changes in quiescence, expansion, and immune cell output.  Single cell transcriptomic analysis of fetal HSPCs reveals specific upregulation of inflammation-responsive genes in discrete populations, in response to upregulated IFNα and IL-1α in the fetal liver cytokine milieu. Postnatally, MIA caused the inappropriate expansion and persistence of transient progenitors, concomitant with increased cellularity and hyper-responsiveness of fetal-derived immune cells.  Our investigation demonstrates how inflammation in utero can direct the trajectory of hematopoiesis and immunity by reshaping fetal HSC establishment.

overall_design: 4 samples (2 Saline, 2 pIC)

first: April

middle: C

last: Apostol


title: Microarray expression profiles in S18 and S26 human nasopharyngeal carcinoma cell lines

status: Public on Jan 26 2023

city: guangzhou

first: Yingqin

last: Li

state: guangdong

address: Guangzhou, 510060, P.R. China

country: China

institute: Sun Yat-sen University Cancer Center

summary:
Metastasis accounts for the leading cause of treatment failure in nasopharyngeal carcinoma (NPC). However, the exact mechanisms underlying metastasis remain elusive. S18 and S26 are a pair of NPC cell lines with high and low metastasis abilities, respectively. To evaluate the expression profiles of mRNA in S18 and S26 cells will help to demonstrate genes that contribute the metastasis of NPC.
We performed microarray sequencing to clarify the genes that differentially expressed in S18 and S26 cells.

overall_design: The total RNA of S18 and S26 cells was extracted and hybridized on Affymetrix microarrays.

first: Qian

first: Jun

last: Ma

first: Ying

middle: Q


title: The AtSCL26 Transcription Factor controls cross-talk between GA-and Nitrogen control of root architecture in Arabidopsis thaliana Roots

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

summary: We characterised mutants in the GRAS family transcription factor AtSCL26 in Arabidopsis thaliana using a combination of gene functional analysis, hormone treatments and expression profiling at the cell type level. This has enabled us to implicate AtSCL26 in the cell-specific control of nitrogen-giberellic acid response cross-talk to control root architecture.

overall_design: The whole experiment was carried out in triplicate with 24 microarrays in total (8 experiments).  The response of cortical and epidermal cells, isolated using Fluorescence Activated Cell Sorting (FACS) was analysed after 2 hours of 5mM KNO3 treatment in Arabidopsis thaliana Col0 and atscl26 mutant roots; both genotypes carried GFP reporters marking either epidermal or cortical root cells.  Gene expression was analysed using NimbleGen 12 x 135K microarrays, designed for the TAIR10 genome. Seedlings were grown on low nitrogen (0.1mM KNO3) agar plates for 9 days, then 5mM KNO3 was used as a nitrogen treatment for 2 hours compared to non- treated seedlings kept on low nitrogen plates for 2 hours.  At the end of the treatment, roots were harvested, protoplasts generated and GFP-marked epidermal and cortical cells isolated according to Gifford et al 2008 PNAS. After normalisation two replicates from the complete set were removed since they had low QC values (atscl26 epidermal cells 2hr KCl control treated, biological rep3 and Col0 cortical cells 2hr KNO3 nitrogen treated, biological rep3).

middle: L

first: Anthony

middle: D

last: Carter


title: Integrating methylome and transcriptome signatures expands the molecular classification of the pituitary tumors [RNA-seq]

city: Ribeirão Preto

first: Junier

middle: Marrero

last: Gutiérrez

state: São Paulo

address: Av Bandeirantes, 3900

department: Pediatric

country: Brazil

institute: Ribeirão Preto Medical School-University of São Paulo

summary: Pituitary tumors (PitNETs) tumorigenesis is still not completely understood. Few studies have integrated exome, methylome, and transcriptome analyses. Taking advantage of a comprehensive phenotypic characterized Brazilian cohort, which has heterogeneous ethnic origin, we combined methylome and transcriptome analysis of the three major subtypes of surgically resectable PitNETs. Here, we included RNA-seq and basal patient / tumor data of 65 PitNETs: GH-secreting (acromegaly,n = 15), ACTH-secreting (Cushing disease, n = 7),  and Non-Functioning (n = 43 PitNETs).

overall_design: Retrospective cross-sectional study.

first: Rui

middle: M

last: da Silva-Júnior

first: Ana

last: Bueno

first: Sonir

last: Antonini

first: Margaret

last: de Castro


title: Integrating methylome and transcriptome signatures expands the molecular classification of the pituitary tumors

type: Methylation profiling by genome tiling array

summary: Abnormal DNA methylation contributes to tumor progression and is emerging as a prognostic marker in several types of cancers. Pituitary tumors (PitNETs) tumorigenesis is still not completely understood. Few studies have integrated exome, methylome, and transcriptome analyses. Taking advantage of a comprehensive phenotypic characterized Brazilian cohort, which has heterogeneous ethnic origin, we combined methylome and transcriptome analysis of the three major subtypes of surgically resectable PitNETs (n = 77): GH-secreting (acromegaly, n = 18), ACTH-secreting (Cushing disease, n = 13), and non-functioning (n = 46) PitNETs. Here, we included methylome and basal patient / tumor data.

overall_design: Retrospective cross-sectional study. DNA from 77 microdissected, fresh frozen pituitary tumor samples from patients was extracted using the QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instruction. DNA was commisioned to the University of Southern California Keck Genomics Platform (Los Angeles, CA, USA), where it was bisulfite-converted using tht EZ DNA methylation kit (Zymo Research, Irvine, CA) , as provided by the manufacturer, and hybridized to the Illumina Infinium HumanMethylation850 BeadChip as specified by Illumina.


title: Hedgehog and PDGF signaling intersect during postnatal lung development

city: New York

first: Matthias

last: Kugler

state: NY

address: 550 First Avenue, Medical Science Building, MSB-594

department: Medicine

institute: NYU School of Medicine


title: WDR5 represents a therapeutically exploitable target for cancer stem cells in glioblastoma

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Glioblastomas (GBMs) are heterogeneous, treatment-resistant tumors that are driven by populations of cancer stem cells (CSCs). Despite their importance for tumor growth, few molecular mechanisms critical for CSC population maintenance have been exploited for therapeutic development. We developed a spatially resolved loss-of-function screen in GBM patient-derived organoids to identify essential epigenetic regulators in the SOX2-enriched, therapy resistant niche and identified WDR5 as indispensable for this population. WDR5 is a component of the WRAD complex, which promotes SET1-family-mediated Lys4 methylation of histone H3, associated with positive regulation of transcription. Genetic and pharmacologic inhibition of WDR5 reduced growth and self-renewal of CSCs as well as CSC-mediated tumor growth. Further, WDR5 inhibitors blocked WRAD complex assembly, reduced H3K4 trimethylation, and inhibited tumor growth. These findings highlight the role of WDR5 and the WRAD complex for maintaining the CSC state and provide a rationale for therapeutic development of WDR5 inhibitors for GBM and other advanced cancers.

overall_design: CUT&Tag data from 4 replicates each for DMSO and WDR5 WIN site inhibitor (C16)

first: Kelly

last: Mitchell

first: Sajina

last: Shakya

first: Daniel

middle: J

last: Silver

first: Christopher

last: Goins

first: Lisa

last: Wallace

first: Gustavo

last: Roversi

first: Rachel

last: Schafer

first: Kristen

last: Kay

first: Tyler

last: Miller

first: Adam

last: Lauko

first: John

last: Bassett

first: J

last: D'Amato Kass

first: Anjali

last: Kashyap

first: Erin

last: Mulkearns-Hubert

first: Sadie

last: Johnson

first: Joseph

last: Alvarado

first: Jeremy

middle: N

last: Rich

first: Patrick

last: Paddison

first: Anoop

middle: P

last: Patel

first: Shaun

last: Stauffer

middle: G

last: Hubert

first: Justin

last: Lathia


title: Functional dissection of human mitotic proteins using CRISPR-Cas9 tiling screens

first: Sonali

last: Arora

summary: Kinetochores are large protein assemblies that mark the centromere and bind to mitotic spindle microtubules to ensure accurate chromosome segregation. Like most protein-coding genes, the full multifunctional nature of kinetochore factors remains uncharacterized due to the limited experimental tools for unbiased dissection of human protein sequences. Here, we develop a method that leverages CRISPR-Cas9 induced mutations to comprehensively identify key functional regions within protein sequences that are required for cellular outgrowth. Our analysis of 48 human kinetochore genes revealed hundreds of regions required for cell proliferation, corresponding to known and uncharacterized protein domains. We biologically validated 15 of these regions, including amino acids 387-402 of Mad1, which when deleted compromise Mad1 kinetochore localization and chromosome segregation fidelity. Altogether, we demonstrate that CRISPR-Cas9-based tiling mutagenesis enables de novo identification of key functional domains in protein-coding genes, which elucidates separation of function mutants and allows functional annotation across the human proteome

overall_design: For 4 different cells lines there are 3 samples representing the initial representation of the kinetochore tiling CRISPR library (D5 or D0) and 3 samples representing the final representation after 5 days of outgrowth (D13 or D8)

first: Jacob

middle: A

last: Herman

first: Lucas

last: Carter

first: Jun

last: Zhu

first: Sue

last: Biggins


title: Tumor DNA methylation profiling of pediatric patients with adrenocortical tumors

first: Junier

last: Gutiérrez

summary: Abnormal DNA methylation contributes to tumor progression and is emerging as a prognostic marker in several types of cancers. To investigate whether DNA methylation is associated with Pediatric Adrenocortical Tumor (pACT) presentation and patient prognosis, we analyzed the methylation profile of 57 tumors (Illumina Infinium HumanMethylation850 BeadChip) and patients’ clinicopathological features and outcome.

overall_design: DNA from 57 microdissected, fresh frozen tumor samples from pediatric patients was extracted using the QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instruction. DNA was commisioned to the University of Southern California Keck Genomics Platform (Los Angeles, CA, USA), where it was bisulfite-converted using tht EZ DNA methylation kit (Zymo Research, Irvine, CA) , as provided by the manufacturer, and hybridized to the Illumina Infinium HumanMethylation850 BeadChip as specified by Illumina.

first: Ana

last: Bueno

first: Sonir

last: Antonini


title: Constructing a rat model of stress cardiomyopathy and screening for diagnostic markers using machine learning algorithms

status: Public on Jan 25 2023

city: Hei Long Jiang Province

first: ji

middle: xuan

last: rui

address: Harbin

institute: the First Affiliated Hospital of Harbin Medical University

summary: Background:Epilepsy is a disorder that can manifest as abnormalities in neurological or physical function. Stress cardiomyopathy is closely associated with neurological   stimulation. However, the mechanisms underlying the interrelationship between epilepsy and stress cardiomyopathy are unclear. This paper aims to explore the genetic features and potential molecular mechanisms shared in epilepsy and stress cardiomyopathy.   Methods:By analyzing the epilepsy dataset and stress cardiomyopathy dataset separately, the intersection of the two disease co-expressed differential genes is obtained, the co-expressed differential genes reveal the biological functions, the network is constructed, and the core modules are identified to reveal the interaction mechanism, the co-expressed genes with diagnostic validity are screened by machine learning algorithms, and the co-expressed genes are validated in parallel on the epilepsy single-cell data and the stress cardiomyopathy rat model.   Results: Epilepsy causes stress cardiomyopathy, and its key pathways are Complement and coagulation cascades, HIF-1 signaling pathway, its key co-expressed genes include SPOCK2, CTSZ, HLA-DMB, ALDOA, SFRP1, ERBB3.The key immune cell subpopulations localized by single-cell data are the T_cells subgroup, Microglia subgroup, Macrophage subgroup, Astrocyte subgroup, and Oligodendrocytes subgroup.   Conclusion: We believe epilepsy causing stress cardiomyopathy results from a multi-gene, multi-pathway combination. We identified the core co-expressed genes (SPOCK2, CTSZ, HLA-DMB, ALDOA, SFRP1, ERBB3) and the pathways that function in them (Complement and coagulation cascades, HIF-1 signaling pathway,JAK-STAT signaling pathway), and finally localized their key cellular subgroups(T_cells subgroup, Microglia subgroup, Macrophage subgroup, Astrocyte subgroup,and Oligodendrocytes subgroup). Also, combining cell subpopulations with hypercoagulability as well as sympathetic excitation further narrowed the cell subpopulations of related functions.

overall_design: Male Sprague-Dawley rats, weighing 250 to 300 g, were selected to immobilization stress for 6 hours lasting 7 days to establish stress cardiomyopathy (SCM) model.The anesthetized rats were randomly divided into two groups of normal control and SCM. Ventricle tissues were extracted for RNA sequencing

first: Xuanrui

last: Ji

first: Quanwei

last: Pei

first: Pengqi

last: Lin

first: Dechun

last: Yin


title: mRNA sequence of the glioma cell line U251  after  TEAD3 knockdown

city: Shanghai

first: Zhengyuan

last: Huo

state: Shanghai

address: 389 Xincun Road

department: Department of Neurosurgery

institute: Shanghai Tong Ji Hospital

summary: Glioma is a malignant primary tumour that occurs in the central nervous system.  TEA domain transcription factor (TEAD)  family proteins are the Hippo pathway's ultimate effector molecules.  The function of TEAD3 in gliomas is still unclear.  Therefore, RNA sequencing was performed on TEAD3 knockdown U251 cells and normal U251 cells.     The samples in this study included  normal U251 control group and TEAD3 knockdown group.   Each group contained three samples.  Total RNA was extracted using Trizol reagent following the manufacturer's procedure.   The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number >   7.0 were used to construct sequencing library. Gene Set Enrichment Analysis (GSEA) based on the sequencing results showed that knockdown of TEAD3 in the U251 cell line caused changes in several important pathways, including CTLA4 inhibitory pathway, defective pyroptosis, signaling by Hippo, regulation of TP53 activity, E2F mediated regulation of DNA replication, and FCGR3A mediated phagocytosis.

first: Shaorui

last: Gu

first: YiFang

last: Wu

first: Wenli

last: Wang


title: Characterization and transcriptome analysis of maize small kernel mutant smk7a in different development stages

city: beijing

first: xiaojiao

last: Hu

address: No.12 Zhongguancun South Main Street, Haidian District

institute: Institute of crop science, Chinese academy of agricultural science

summary: The kernel serves as a storage organ for various nutrients and determines the yield and quality of maize. Understanding the mechanisms regulating kernel development is important for maize production. In this study, a small kernel mutant smk7a of maize was characterized. Cytological observation suggested that the development of the endosperm and embryo was arrested in smk7a in the early development stage. Biochemical tests revealed that the starch, zein protein, and indole-3-acetic acid (IAA) contents were significantly lower in smk7a compared with wild-type (WT). Consistent with the defective development phenotype, transcriptome analysis of the kernels 12 and 20 days after pollination (DAP) revealed that the starch, zein, and auxin biosynthesis related genes were dramatically downregulated in smk7a. Genetic mapping indicated that the mutant was controlled by a recessive gene located on chromosome 2. Our results suggest that disrupted nutrition accumulation and auxin synthesis cause the defective endosperm and embryo development of smk7a.

overall_design: We conducted RNA sequencing using the kernels of WT and smk7a mutant collected at 12 and 20 DAP.

first: Jing

first: Xiaojiao


title: Effect of acupuncture on gene expression in cerebral tissue of mice with cerebral hemorrhage

city: Hangzhou

first: Hao

last: Liu

address: 234 Gucui Road, Xihu District, Hangzhou City

institute: Tongde Hospital of Zhejiang Province

summary: The present study aimed to identify and analyze the m6A profiles in the brain tissue of mice with intracerebral hemorrhage after acupuncture treatment.

overall_design: we established ICH mice model. GV20 point was used as the acupuncture point for treating ICH in mice for seven consecutive days. m6A and mRNA sequencing were used to investigate the differences m6 A modification of ICH mice with acupuncture treatment.


title: Cell competition regulates the fate decision of neural stem cells

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Cell competition is a new notion of old theory Darwinian theory in cell level. It is notorious as its function on cancer promotion, actually, cell competition is a critical checkpoint machinery in development, its proper operation roles out suboptimal cells and makes sure the high quality of basic materials make up organism. Although its function has been revealed on other organs, it remains mysterious in brain development. In this paper, we get a compromised cell competitional model by knocking out endothelial Brd4, the lack of Brd4 in endothelial cell induces less neural stem cells deaths and compromised cell competition, endothelial Brd4 regulates cell competition is Testican2 dependent, Testican2 can deposit Sparc. We find a noncanonical role of the canonical negative cell competitional regulator Sparc in the fate decision of neural stem cells, neural stem cells highly expressing Sparc steps forward differentiation. We also find a compromised cell competition in AD patients, by cloning a point mutant of Brd4 found in a group of AD, we reveals that the mutant lose the potential of cell competition promotion. We put forward a new strategy for the treatment of aging related diseases by enhancing cell competitional state.

overall_design: Mice are sorted as two groups based on whether Brd4 is knock out in endothelial cells, RNA sequencing samples are endothelial cells taken from mice brain vascular at E14.5

first: Chenxiao

last: Li

first: Lin

first: Shuang

first: Shukui

last: Zhang

first: Sihan

first: Wenzheng

last: Zou

first: Dongming

first: Mengtian

first: Libo

last: Su

first: Wenwen

first: Yuanyuan

first: Jinyue

last: Zhao

first: Cheng

first: Fen


title: Loss of the immunomodulatory transcription factor BATF2 in humans is associated with a neurological phenotype

city: Bonn

first: Gabor

last: Zsurka

address: Venusberg-Campus 1

department: IEECR

country: Germany

institute: University of Bonn

summary: Epilepsy and mental retardation are known to be associated with pathogenic mutations of a broad range of genes that are expressed in the brain and play a role in neurodevelopment. Here, we report a family with three affected individuals whose clinical symptoms closely resemble a neurodevelopmental disorder. Whole-exome sequencing identified a homozygous stop-gain mutation p.Q19* in the BATF2 gene in the patients. The BATF2 transcription factor is predominantly expressed in macrophages and monocytes, and has been reported to modulate AP-1 transcription factor-mediated pro-inflammatory responses. Transcriptome analysis showed an altered base-level expression of interferon-stimulated genes in the patients’ blood, typical for type I interferonopathies. Peripheral blood mononuclear cells from all three patients demonstrated elevated responses to innate immune stimuli, which could be reproduced in CRISPR–Cas9-generated BATF2-/- human monocytic cell lines. BATF2 is, therefore, a novel disease-associated gene for severe epilepsy and mental retardation, related to dysregulation of immune responses, which underscores the relevance of neuroinflammation for epilepsy.

overall_design: THP-1 human leukemia monocytic cells treated with 9.2s RNA or R848 ligands of TLR7/8 were compared to untreated cells using two independent CRISPR-Cas9-generated BATF2-/- cell lines or wild-type cells. Three replicates were used in experiments 1 and 3. Two replicates were used in experiment 2.

first: Gábor

first: Maximilian

last: Appel

last: Nastaly

first: Kerstin

last: Hallmann

first: Niels

last: Hansen

first: Daniel

last: Nass

first: Tobias

last: Baumgartner

first: Rainer

last: Surges

first: Gunther

last: Hartmann

first: Eva

last: Bartok

first: Wolfram

middle: S

last: Kunz


title: Transcriptional Profiling Identifies Prognostic Gene Signatures for Conjunctival Lymphoma

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

summary: This study characterizes the transcriptional profile and the cellular tumor microenvironment of conjunctival lymphoma and identifies prognostically relevant biomarkers. 10 formalin-fixed and paraffin-embedded conjunctival lymphoma and 8 healthy conjunctival specimens were analyzed by MACE RNA sequencing. The 3,417 upregulated genes in conjunctival lymphoma were involved in processes such as B cell proliferation and Rac protein signaling, whereas the 1,188 downregulated genes contributed most significantly to oxidative phosphorylation and UV protection. The tumor microenvironment, as determined by deconvolution analysis, was mainly composed of multiple B cell subtypes which reflects the tumor’s B cell lineage. However, several T cell types, including T helper 2 cells and regulatory T cells, as well as innate immune cell types, such as anti-inflammatory macrophages and plasmacytoid dendrit-ic cells, were also strongly enriched in conjunctival lymphoma. A 13-biomarker prognostic panel, including S100A8 and S100A9, classified ocular and extraocular tumor recurrence, exceeded prognostic accuracy of Ann Arbor and AJCC staging, and demonstrated prognos-tic value for patient survival in 21 different cancer types in a database of 12,332 tumor pa-tients. These findings may lead to new options of targeted therapy and may improve prog-nostic prediction for conjunctival lymphoma.

overall_design: MACE RNA sequencing of 10 conjunctival lymphoma and 8 healthy conjunctiva samples

first: Julian

last: Wolf

first: Rozina

middle: I

last: Hajdu

first: Thomas

last: Reinhard

first: Günther

last: Schlunck

first: Claudia

last: Auw-Hädrich


title: A role for Δ133p53 in protein turnover at the cell surface

city: Dunedin

first: Alexandra

middle: Boix

last: De Jesus

address: 56 Hanover Street, Central Dunedin, Dunedin 9016

country: New Zealand

institute: University of Otago

summary: To determine the DGE genes upreglated and downregulated in A1,A2, A8, B5, B10 in comparison with NULL (control)

overall_design: DGE between p53 against p53 isoforms

first: Tania

last: Slatter

first: Paulomi

last: Mehta

last: Boix


title: RNA-seq of CEACAM1- and CEACAM1+ regulatory T cells from tumor in patients with renal cell carcinoma

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: We aimed to analyze the transcriptomic differences between CEACAM1- and CEACAM1+ regulatory T cells from tumor.

overall_design: CEACAM1- and CEACAM1+ regulatory T cells (CD4+CD25+CD127- T cells) were sorted from tumor from six patients with renal cell carcinoma.

first: Seung

middle: H

first: Minyong

last: Kang

first: Minwoo

first: Yong

last: Lee

first: Eui-Soon

last: Kim

first: Heejin

last: Nam

first: Eui-Cheol

last: Shin

first: Seong

last: Seo

first: Su-Hyung

last: Park


title: Effects of GSTM1 knockdown on astrocyte transcriptional responses to TNF-alpha stimulation

city: Birmingham

first: Shinichi

last: Kano

state: AL

address: 1720 7th Ave South

department: Psychiatry

institute: University of Alabama at Birmingham

summary: To investigate the role of GSTM1, we knocked down GSTM1 expression in primary mouse astrocytes using lenvirtus vector expressing Gstm1 shRNAmir and then exposed them to TNF-alpha. Non-silencing shRNAmir and non-stimulation served as shRNA and treatment controls, respectively.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for astrocytes with shGstm1 and shControl in 1) no-stimulation, and 2) TNF-alpha stimulation (6 h, 50 ng/ml).

first: Eric

middle: Y

last: Choi


title: RNA-seq of regulatory T cells from peripheral blood and tumor in patients with renal cell carcinoma

summary: We aimed to analyze the transcriptomic differences between regulatory T cells from peripheral blood and tumor.

overall_design: Non-naïve regulatory T cells (CD4+CD25+CD127-CD45RA- T cells) were sorted from peripheral blood and tumor from six patients with renal cell carcinoma.


title: Idiopathic membranous nephropathy and minimal change disease (MCD) transcriptome

city: Bergen

first: Oystein

last: Eikrem

address: Haukelandsveien 22

department: Department of Mecine

country: Norway

institute: Haukeland University Hospital

summary:
Introduction: Minimal change disease (MCD) is a major cause of nephrotic syndrome. With a substantial number of patients requiring long-term immunosuppression leading to significant morbidity, the study aim was to determine MCD glomerular transcriptome to serve as a basis for biomarker discovery and novel drug target identification. Animal work showed podocyte injury induced by IL-7/IL-7R signaling (Zhai S, BBRC, 2018).
Methods: Renal biopsies from adult patients representing the following groups were selected from the Norwegian Kidney Biopsy Registry: MCD (n=14), as well as normal tissue (n=8) and primary membranous nephropathy (MN; n=12) as the two reference groups. RNA for 75 base-pair paired-end RNASeq was obtained by dissecting glomeruli via laser capture microdissection (LCM) from FFPE cross-sections. Systematic delineation of condition-specific alteration in transcriptional landscapes was achieved by combining pathway-centered analyses with methodologies derived from network science and integrating multiple bioinformatics resources.
Results: Compared to normal glomeruli, glomeuli from MCD displayed an inflammatory signature that appeared to be predominantly governed by the IL1 and IL7 systems. While enrichment of IL1 production and secretion was a shared feature of MCD and MN compared to normal tissue, responses involving IL7 pathway activation were unique to MCD. Indeed, IL7R expressed by glomeruli was the most up-regulated gene of to the interleukin-family in MCD vs normal controls. IL7 pathway activation was paralleled by significant enrichment in adaptive immune system processes and transcriptional regulation and depletion in pathways related to energy metabolism and transcription. Downregulation of these organ function-related themes again occurred predominately in MDC and were significantly less pronounced in MN.
Conclusion: Our results demonstrate that archival FFPE-biopsies can be used to generate glomeruli-specific gene expression profiles suitable for systematic delineation of kidney-associated diseases. Here the latter provides a data-driven rationale to experimentally address these MCD-specific features as biomarkers and as novel drug targets. In this context inhibiting activation of the IL7 pathway may be particularly promising.

overall_design:
Comparison of transcriptome of normal controls vs. minimal change nephropathy and idiopathic membranous nephropathy

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

first: Nicolas

last: Delaleu

first: Hans-Peter

last: Marti


title: Effect of DHA in hippocamapal gene expression of wild type and Alzheimer´s disease mice

city: Pamplona

first: Ana

last: Garcia Osta

state: Navarra

address: Juslarrocha 10, 3H

department: neuroscience

country: Spain

institute: Cima

summary: To get insight the molecular mechanism by which DHA prevent dementia, we adminisitered both, aged wild type and Tg2576 mice with a high dose of DHA. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different groups of animals.

overall_design: Comparative gene expression profiling analysis of RNA-seq data between aged wild type or Tg2576 mice with a high dose of DHA and the corresponding untreated controls.

last: García-Osta

first: Sara

last: Badesso

first: Mar

last: Cuadrado-Tejedor


title: mRNA-seq of ubiqutously and pan-neuronally reduce rpia-1 in Caenorhabditis elegans

city: HsinChu

first: Wen-Chi

last: Shen

state: East district

address: No. 101, Section 2, Kuang-Fu Road

department: Biology

country: Taiwan

institute: National Tsing Hua University, Taiwan

summary: Ribose-5-phosphate isomerase A (RPIA) is a rate-limiting enzyme, which connects oxidative phase to non-oxidative phase and mediates redox homeostasis in pentose phosphate pathway (PPP). Here, we report that spatially and temporally limited knockdown of rpia-1 prolongs lifespan and improves healthspan in C. elegans, reflecting the evolutionarily conserved phenotypes observed in Drosophila. We first confirmed that both ubiquitous (in N2) and pan-neuronal (in TU3401) knockdown of rpia-1 enhance tolerance to oxidative stress, reduce polyglutamine aggregation, and improve the deteriorated body bending rate caused by polyglutamine aggregation. Next, we observed that both rpia-1 knockdown conditions enhance lifespan. In addition, rpia-1 knockdown in glutamatergic or cholinergic neurons was sufficient to increase lifespan. Besides the regulation of healthspan through the elevation of NADPH levels, we also identified novel molecular mechanisms that contribute to the longevity effect. Our results showed that rpia-1 reduction was accompanied by induction of autophagic flux, activation of AMPK, and inhibition of TOR signaling. Importantly, the lifespan extension by rpia-1 knockdown required the activation of autophagy and AMPK pathways, and reduced TOR sig-naling. Moreover, the RNA-seq data from the two longlived rpia-1 knockdown strains supported our experimental findings and reveal potential downstream targets, which may play key roles in this intervention. Together, our data disclose the specific spatial and temporal conditions and the underlying molecular mechanisms of rpia-1 knockdown-mediated longevity in C. elegans. These findings may facilitate the development of translational medicine and the improvement of lon-gevity research.

overall_design: Three biological replicates were collected for ubiquitous (in N2) knockdown  at day 5 of adulthood and pan-neuronal (in TU3401) knockdown at day 0 of adulthood.

first: Yu-Ting

last: Lu

first: Chiou-Hwa

last: Yuh

first: Tsui-Ting

last: Ching

first: Chao-Yung

last: Wang

first: Horng-Dar


title: Transcriptomic Analyses Reveal Pre-treatment Cytotoxic Lymphocytes Predict Response to Neoadjuvant Chemoradiotherapy and Survival in Advanced Rectal Cancer.

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

summary: Importance: Neoadjuvant chemoradiotherapy (CRT) is the standard of care for advanced rectal cancer. Yet, predicting response to CRT remains an unmet clinical challenge.    Objective: To investigate the transcriptomic determinants to predict response to neoadjuvant CRT and survival in patients with advanced rectal cancer.    Design: A single-center, retrospective, cohort study.    Setting: A comprehensive cancer center.    Participants: Pre-treatment biopsies from 298 patients with rectal cancer, who were later treated with neoadjuvant CRT between 2004 and 2020, were analyzed by RNA sequencing.    Main measures and outcomes: Transcriptional subtyping was performed by consensus molecular subtype (CMS) classification. Immune cell infiltration was assessed using MCP-counter scores and single-sample gene set enrichment analysis (ssGSEA). Patients with surgical specimens of tumor regression grade (TRG) 3-4 or who were managed by the watch-and-wait approach for more than 3 years were defined as good responders.    Results: Patients classified as CMS1 (6.4%) had a significantly higher rate of good responders; albeit survival was comparable among the four subtypes. Good responders exhibited an enrichment in various immune-related pathways (IFNg and a responses, allograft rejection, IL6 STAT3 signaling during acute phase response, and inflammation), as determined by ssGSEA. MCP-counter scores for cytotoxic lymphocytes were significantly higher for good responders than non-responders (p = 0.0003), and significantly higher for responders than non-responders in GSE109057 (p = 0.0137), GSE87211 (p = 0.0092), and GSE45404 (p = 0.0327) datasets. Cytotoxic lymphocyte MCP-counter score was thus considered an independent predictor of response to CRT, as determined in the multivariable Cox analysis (OR 3.810 [95% CI 1.820-7.970]; p = 0.0004). Multivariable Cox analysis, including post-operative pathological factors, revealed cytotoxic lymphocyte MCP-counter score to be independently associated with recurrence-free survival (HR 0.382 [95% CI 0.158-0.923]; p = 0.0325) and overall survival (HR 0.157 [95% CI 0.030-0.827]; p = 0.0290). ssGSEA showed significantly higher levels of four subpopulations of cytotoxic cells (effector memory CD8 T, natural killer T, natural killer, and activated CD8 T cells) among good responders than non-responders.    Conclusions and Relevance: Cytotoxic lymphocyte score, as computed by RNA sequencing, could be a useful marker for predicting response to CRT and survival among patients with rectal cancer.

overall_design: Messenger RNAs were extracted from 298 rectal cancer samples. Libraries were then prepared with True Seq RNA Access Sample Preparation Kit (Illumina) and sequenced on the Hiseq 2500(Illumina).    ***Raw data are not available for this series due to patient privacy concerns. Furthermore, the raw data will not be available through controlled-access resources such as dbGaP or EGA. The IRB prohibits public access to the raw data.

first: Takashi

last: Akiyoshi


title: Integrating Transcriptomic and ChIP-Seq Reveals Important Regulatory Regions Modulating Gene Expression in Myometrium during Implantation in Pigs [RNA-seq]

city: Wuhan

first: Weiwei

address: Hongshan District

institute: Huazhong Agricultural University

summary: RNA-seq for the uterine circular muscle (CM) and longitudinal muscle (LM) layers at the mesometrial (M) side on days 12 (pre-implantation stage) and 15 (implantation stage) of pregnancy and day 15 of the estrous cycle in pigs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the uterine CM and LM layers at the mesometrial side on days 12 and 15 of pregnancy and day 15 of the estrous cycle in pigs.

first: Caiqin

last: Cao


title: Integrating Transcriptomic and ChIP-Seq Reveals Important Regulatory Regions Modulating Gene Expression in Myometrium during Implantation in Pigs

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

overall_design: Refer to individual Series


title: Exogenous SLFN12 reduces in vivo TNBC proliferation and invasion, increases luminal markers and a gene signature that reducts better breast cancer survival in cohort database analysis

city: Grand Forks

first: Marc

last: Basson

state: ND

address: 1301 N Columbia Rd

institute: University of North Dakota

summary: Our results suggest that increased SLFN12 expression modulates TNBC aggressiveness through a gene signature which could offer new targets for treatment.

overall_design: Human TNBC tumor xenografts with exogenous SLFN12 expression were created and the growth was observed and then RNA-seq was performed to investigate pathways related to SLFN12

first: Sandeep

last: Singhal

first: Sarmad

last: Al-Marsoummi

first: Emilie

middle: E

last: Vomhof-DeKrey

first: Bo

last: Lauckner

first: Trysten

last: Beyer


title: Integrating Transcriptomic and ChIP-Seq Reveals Important Regulatory Regions Modulating Gene Expression in Myometrium during Implantation in Pigs [ChIP -seq]

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the uterine circular muscle (CM) and longitudinal muscle (LM) layers at the mesometrial side on day 15 (implantation stage) of pregnancy, and the uterine CM layer at the mesometrial side on day 15 of the estrous cycle in pigs.

overall_design: Identification of H3K27ac and H3K4me3 modification regions in uterine CM and LM layers at the mesometrial side on day 15 of pregnancy and in uterine CM layer at the mesometrial side on 15 day of the oestrus cycle.

first: Botao

last: Zhang

first: Feiyu


title: Palmitoylation negatively regulates AEG-1 function

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

summary: In vitro studies revealed that AEG-1 is palmitoylated at cysteine at a.a. 75 position. In order to check how palmitoylation regulates AEG-1 function in vivo we generated a knockin moue using CRISPR/Cas9 taking in which cysteine 75 was mutated to serine (AEG-1-C75S). Hepatocytes were isolated from AEG-1-WT and AEG-1C75S littermates, total RNA was isolated and RNA-sequencing was performed.

overall_design: AEG-1-C75S heterozygotes were mated to generate AEG-1-WT and AEG-1-C75S homozygote mice. Hepatocytes were isolated from adult (6-8 wks old mice) and total RNA was extracted 48 h after isolation using QIAGEN RNA extraction kit. Total RNA was subjected to RNA-seq using Illumina platform.

first: Maria

last: Del Carmen Camarena

first: Devanand

last: Sarkar


title: Suppression of RBFox2 by Multiple MiRNAs Contributed to Progressive Heart Failure (RNA-Seq)

city: SHENZHEN

first: MINGYAO

last: GU

address: Xueyuan Avenue, Nanshan District

institute: Shenzhen University

summary: Heart failure is the final stage of various cardiovascular diseases, which seriously threatens human health. Increasing mediators have been found to be involved in the pathogenesis of heart failure, including RNA binding protein RBFox2. It participates in regulation of cardiac function in multiple aspects and plays a critical role in the process of heart failure. However, how RBFox2 itself is regulated remains unclear. Here, we dissected transcriptomic signatures including mRNAs as well as miRNAs in the mouse model of heart failure after TAC surgery. Global and association analyses revealed that large-scale upregulation of miRNAs occurred at heart failure, which was not only responsible for degradation of numerous mRNA transcripts, but also suppressed the translation of key proteins such as RBfox2. With the aid of Ago2 CLIP-seq data, luciferase assays verified that RBfox2 was targeted by multiple miRNAs including let-7, mir-16 and mir-208b, which were critical for cardiac function and upregulated in heart failure stage. Overexpression of these miRNAs suppressed rbfox2 protein and its downstream effects in cardiomyocytes, evidenced by suppressed alternative splicing of Enah gene and impaired E-C coupling via repression of Jph2 protein. Inhibition of let-7, the most abundant of these miRNAs in the heart, could rescue Rbfox2 protein as well as its downstream effects in dysfunctional cardiomyocytes induced by ISO treatment. These findings not only revealed the mechanism leading to RBFox2 depression in heart failure, but also provided an approach to rescue RBFox2 by miRNAs inhibition for the treatment of heart failure.

overall_design: Comparative gene expression profiling analysis of RNA-seq and small RNA data after TAC treatment

first: Chaoliang

last: Wei

first: Mingyao

last: Gu

first: Yuying

last: Zhao


title: Suppression of RBFox2 by Multiple MiRNAs Contributed to Progressive Heart Failure

type: Non-coding RNA profiling by high throughput sequencing


title: Suppression of RBFox2 by Multiple MiRNAs Contributed to Progressive Heart Failure (small RNA-Seq)


title: Losing the maternal effect gene Nlrp2 alters the ovulated mouse oocytes transcriptome and impacts histone demethylase KDM1B expression

city: Houston

first: Ying-Wooi

last: Wan

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We performed RNA sequencing on pools of oocytes after inducing ovarian stimulation in wild-type and Nlrp2-null female mice. We found 231 differentially expressed genes (DEGs) in Nlrp2-null COCs compared to WT COCs (123 up- and 108 downregulated; adjusted p<0.05). The DEGs we identified were enriched for processes involved in neurogenesis, gland morphogenesis, and protein metabolism and for post-translationally methylated proteins. When we compared our RNA sequencing results to an oocyte-specific reference transcriptome that contains many previously unannotated transcripts, we found 228 DEGs, including genes not identified with the first analysis. Intriguingly, 68% and 56% of DEGs from the first and second analyses, respectively, overlap with oocyte-specific hyper- and hypomethylated domains.

overall_design: Transcriptome profiling of Nlrp2-null and WT oocytes

first: Zahra

last: Anvar

first: Imen

last: Chakchouk

first: Momal

last: Sharif

first: Sangeetha

last: Mahadevan

first: Eleni

middle: T

last: Nasiotis

first: Li

last: Su

first: Zhandong

last: Liu

first: Ying

middle: W

first: Ignatia

middle: B

last: Van den Veyver


title: Sperm DNA methylome abnormalities occur both pre- and post-treatment in men with Hodgkin disease and testicular cancer [MCC-Seq]

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

type: Methylation profiling by high throughput sequencing

summary:
Background: Combination chemotherapy has contributed to increased survival from Hodgkin disease (HD) and testicular cancer (TC). However, questions concerning the quality of spermatozoa after treatment have arisen. While studies have shown evidence of DNA damage and aneuploidy in spermatozoa years following anticancer treatment, the sperm epigenome has received little attention. Our objectives here were to determine the impact of HD and TC, as well as their treatments, on sperm DNA methylation. Semen samples were collected from community controls (CC) and from men undergoing treatment for HD or TC, both before initiation of chemotherapy and at multiple times post-treatment. Sperm DNA methylation was assessed using genome-wide and locus-specific approaches.
Results: Imprinted gene methylation was not affected in the sperm of HD or TC men, before or after treatment. Prior to treatment, using Illumina HumanMethylation450 BeadChip (450K) arrays, a subset of 500 probes was able to distinguish sperm samples from TC, HD and CC subjects; differences between groups persisted post-treatment. Comparing altered sperm methylation between HD or TC patients versus CC men, twice as many sites were affected in TC versus HD men; for both groups, the most affected CpGs were hypomethylated. For TC patients, the promoter region of GDF2 contained the largest region of differential methylation. To assess alterations in DNA methylation over time/post-chemotherapy, serial samples from individual patients were compared. With restriction landmark genome scanning and 450K array analyses, some patients who underwent chemotherapy showed increased alterations in DNA methylation, up to two to three years post-treatment, when compared to the CC cohort. Similarly, a higher resolution human sperm-specific assay that includes assessment of environmentally-sensitive regions, or “dynamic sites”, also demonstrated persistently altered sperm DNA methylation in cancer patients post-treatment and suggested preferential susceptibility of “dynamic” CpG sites.
Conclusions: Distinct sperm DNA methylation signatures were present pre-treatment in men with HD and TC and may help explain increases in birth defects reported in recent clinical studies. Epigenetic defects in spermatozoa of some cancer survivors were evident even up to two years post-treatment. Abnormalities in the sperm epigenome both pre- and post-chemotherapy may contribute to detrimental effects on future reproductive health."

overall_design: Sperm samples were collected from Community Control (CC. n=7), Hodgkin Disease (HD, n=7) and Testicular Cancer (TC, n=6) subjects.  Baseline samples were taken prior to the initial of chemotherapy regimens (time 0).  Post-treatment samples were collected at 6, 12, 18, 24, 36, 42 month after chemotherapy sessions concluded (times 1,2,3,4,5,6,7).  Due to drop-out and/or lack of sperm production post-therapy, not all patients were able to provide post-treatment samples.  DNA methylation of sperm DNA was measured using the Illumina HumanMethylation450 BeadChip (platform GPL13534) and a subset was further examined using a custom 5-methyl-cytosine capture sequencing (MCC-Seq)

first: Donovan

last: Chan

first: Kathleen

middle: O

last: Klein

first: Antonim

last: Riera-Escamilla

first: Csilla

last: Krausz

first: Cristian

last: O’Flaherty

first: Peter

first: Bernard

last: Robaire


title: Sperm DNA methylome abnormalities occur both pre- and post-treatment in men with Hodgkin disease and testicular cancer [methylation array]

summary:
Background: Combination chemotherapy has contributed to increased survival from Hodgkin disease (HD) and testicular cancer (TC). However, questions concerning the quality of spermatozoa after treatment have arisen. While studies have shown evidence of DNA damage and aneuploidy in spermatozoa years following anticancer treatment, the sperm epigenome has received little attention. Our objectives here were to determine the impact of HD and TC, as well as their treatments, on sperm DNA methylation. Semen samples were collected from community controls (CC) and from men undergoing treatment for HD or TC, both before initiation of chemotherapy and at multiple times post-treatment. Sperm DNA methylation was assessed using genome-wide and locus-specific approaches.
Results: Imprinted gene methylation was not affected in the sperm of HD or TC men, before or after treatment. Prior to treatment, using Illumina HumanMethylation450 BeadChip (450K) arrays, a subset of 500 probes was able to distinguish sperm samples from TC, HD and CC subjects; differences between groups persisted post-treatment. Comparing altered sperm methylation between HD or TC patients versus CC men, twice as many sites were affected in TC versus HD men; for both groups, the most affected CpGs were hypomethylated. For TC patients, the promoter region of GDF2 contained the largest region of differential methylation. To assess alterations in DNA methylation over time/post-chemotherapy, serial samples from individual patients were compared. With restriction landmark genome scanning and 450K array analyses, some patients who underwent chemotherapy showed increased alterations in DNA methylation, up to two to three years post-treatment, when compared to the CC cohort. Similarly, a higher resolution human sperm-specific assay that includes assessment of environmentally-sensitive regions, or “dynamic sites”, also demonstrated persistently altered sperm DNA methylation in cancer patients post-treatment and suggested preferential susceptibility of “dynamic” CpG sites.
Conclusions: Distinct sperm DNA methylation signatures were present pre-treatment in men with HD and TC and may help explain increases in birth defects reported in recent clinical studies. Epigenetic defects in spermatozoa of some cancer survivors were evident even up to two years post-treatment. Abnormalities in the sperm epigenome both pre- and post-chemotherapy may contribute to detrimental effects on future reproductive health.


title: Sperm DNA methylome abnormalities occur both pre- and post-treatment in men with Hodgkin disease and testicular cancer.


title: Transcriptomic analysis of AGS treatment in human mesothelioma

city: Napoli

first: Stefania

last: Crispi

address: Via Pietro Castellino,111

department: DISBA

country: Italy

institute: CNR

summary:
We analysed the molecular effects on gene modulation exerted by aglianico grape seed extract (AGS) in mesothelioma. Previous results allowed to demonstrate that AGS polar extracts determined apoptosis in three different mesothelioma cell lines including one resistant to conventional chemotherapeutic treatment. In addition this treatment affected tumorigenic and invasive properties of these cells
We used microarrays to identify molecular pathway deregulated by AGS treatment and involved in apoptosis induction.

overall_design: Human malignant mesothelioma MSTO-211H cells were treated with 350 micrograms/ml of AGS  for 48 hours with a double administration at 24 and 48 hours. Cells treated with the vehicle (DMSO) were used controls. RNA extracted from  treated and control cells were used for transcriptomic analysis using Clariom S Array

first: Rossana

last: Cuciniello

first: Francesco

last: Di Meo

first: Maria

last: Sulli

first: Olivia

last: Demurtas

first: Gianfranco

last: Diretto

first: Clizia

last: Villano

first: Riccardo

last: Aversano

first: Domenico

last: Carputo

last: Filosa


title: Transcriptome profiles of macrophages upon infection by isogenic phenotypic variants of Mycobacterium abscessus

status: Public on Jan 31 2023

city: Los Angeles

first: Michael

last: Neely

state: CA

address: 4650 Sunset Blvd

department: Pediatrics

institute: Children's Hospital Los Angeles

summary: Mycobacterium abscessus (Mab) infection can be a deadly infection in patients with chronic lung disease like cystic fibrosis. In vitro and in vivo, Mab may adopt a smooth (S) or rough (R) morphotype, the latter with fewer cell wall glycopeptidolipids. Although there are studies of the host response against constitutive Mab-S and Mab-R, we report the first analysis of early transcriptional events and responses in mouse bone marrow derived macrophages (BMDMs) upon infection with our media-selected, isogenic, interchangeable Mab-S and Mab-R. The early transcriptional events after infection with both the morphotypes showed considerable overlap of the pro-inflammatory genes that were differentially regulated compared to the uninfected macrophages. However, we also observed some signature genes which were upregulated during Mab-S compared to Mab-R infections. Media selected Mab-S and Mab-R behave in a similar fashion to constitutive S and R types with respect to pathogenesis and immune response and will likely be a better model of in vivo infection than multiply passaged, mutated organisms.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of mouse BMDMs infected for 2hrs with Mab-S and Mab-R  and compared with uninfected BMDMs samples (Mab-S infected samples, Mab-R infected samples and uninfected BMDMs sample).

first: Nishant

last: Nandanwar

first: Joy

last: Gibson


title: Gene expression profile at single cell level of crude umbilical cord blood (UCB) and OP9 pre-conditioned UCB.

city: Nishinomiya

first: Yasunori

last: Yoshida

state: Hyogo

address: 1-1, Mukogawa-cho

institute: Hyogo college of medicine

summary: Umbilical cord blood (UCB) transplantation shows pro-angiogenic effect and contributes to symptom amelioration in animal models of cerebral infarction. OP9 is a stromal cell line used as feeder cells to promote hematoendothelial differentiation of embryonic stem cells. We co-cultured UCB 24hr with OP9 (i.e. OP9 preconditioning) and investigated its change in angiogenic properties and underlying mechanisms. Single cell RNA sequencing showed prominent phenotypic shift toward M2 in monocytic fraction of OP9 pre-conditioned UCB.

overall_design: RBC depleted human UCB  was plated on 5-cm Petri dishes at a density of 1x106 cells/mL with OP9 cells ( i.e. OP9 pre-conditioning ). After 24 h culture,adherent and non-adherent cells were subjected to scRNA seq. RBC depleted crude UCB cells were used as a control.

first: Yuki

last: Takeda

first: Kenichi

last: Yamahara

first: Toshinori

last: Takagi

first: Yoji

last: Kuramoto

first: Nobutaka

last: Doe

first: Shinichi

last: Yoshimura

first: Tomohiro

last: Matsuyama

first: Toshihiro

last: Soma

first: Hanae

last: Yamamoto


title: Next generation sequencing analysis of Colletotrichum camelliae transcriptomes in response to tea plants.

city: Changchun

first: Shouan

last: Liu

address: Xi-An-Da Road 5333

institute: Jilin University

summary: Next generation sequencing was performed to identify genes changed in Colletotrichum camelllae upon infection tea plants. The goal of the work is to find interesting genes involved in fungal virulence. The object is to reveal the molecular mechanism of funal virulence.

overall_design: mRNA profiling of Colletotrichum camelliae in response to tea plants.


title: Effect of depletion of Hp1α (Cbx5) and Hp1β (Cbx1) on gene expression of mouse embryonic stem cells (mESCs)

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

summary: To investigate the function of HP1α and HP1β proteins in the regulation of heterochromatin in mESCs, we isolated blastocysts from matings of mice homozygous for Hp1βF/F; Hp1αF/F in a single well of a 96-well plate in ESC medium. After 2 days, when blastocysts hatched, they were trypsinized and cells were seeded in the same well for other 2 days. Expanded mESC clones were further tested for their genotype by PCR. A single clone of Hp1βF/F; Hp1αF/F was transfected with either pCAG-Cre-GFP or pCAG-GFP as a control. GFP positive cells were sorted by flow cytometry and seeded into 10 cm plates. Individual clones were isolated and expanded. Deletion of Hp1β or Hp1α floxed alleles in pCAG-Cre-GFP transfected clones was tested by Western Blotting with appropriate antibodies.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq from 2 different clones with deleted Hp1α and Hp1β and 1 control clone.

first: Mathieu

last: Tardat


title: Differential mRNA expression analysis of H441 cells after BSGL and RSGL treatment

city: Shang Hai

first: zhengke

last: lian

address: 500 Dongchuan Rd

institute: East China Normal University

summary: It has been proved RSGL contains more biological active constituents and shows stronger antitumor effect. We determined gene expression profiling in H441 cells after BSGL and RSGL treatment using RNA-seq analysis to explore the mechinasm for the stronger antitumor effects of RSGL

overall_design: Transcription profiling of H441 cells after BSGL and RSGL treatment

first: Zhengke

last: Lian

first: Jiaxin

last: Hu


title: Effects of adipocyte-conditioned medium on triple-negative breast cancer cells

city: Taipei

first: Yong-Han

last: Su

address: No.1, Chang-Te St., Taipei, Taiwan

institute: National Taiwan University

summary: The disturbance of adipose tissue in obesity highly correlates with cancer progression. To investigate the impacts of obesity on triple-negative breast cancer (TNBC), we performed an in vitro system culturing TNBC cells with human white adipocytes-conditioned medium (hAd-CM). The gene expression profiling between each condition was then assessed by RNA-seq.

overall_design: MDA-MB-231 cells were pre-treated with indicated medium for 3 days. Total RNA was extracted and the differential expression gene profiling was performed using the RNA-seq approach.  MDA-MB-231 cells pre-treated with nutrition medium mixed with DMEM were regarded as the control of the hAd-CM pre-treated groups. Biological duplicates were executed under each condition.

first: Yi-Zhen

last: Wu

first: David

middle: K

last: Ann

first: Ling-Yu

last: Chen

first: Ching-Ying

last: Kuo


title: Gene expression profile at single cell level of amniogenic somatopleure cells (ASCs) from chick embryos

city: Bunkyo-ku

first: Yuka

last: Haneda

state: Tokyo

address: 7-3-1 Hongo

department: Graduate School of Medicine

institute: The University of Tokyo

summary: ASCs were found to contribute not only to the amniotic membrane but also to the cardiovascular system. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of ASCs.

overall_design: Amniogenic somatopleure tissues were collected from E1.5 (st10) chick embryos and dissociate into single cells to analyze using scRNAseq.

first: Akiyasu

last: Iwase

first: Yasunobu

last: Uchijima

first: Youichiro

last: Wada

first: Sachiko

last: Miyagawa-Tomita

first: Hiroki

last: Kurihara


title: A Knock-in Mouse Model of Thymoma with the GTF2I L424H Mutation

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: We previously identified a recurrent mutation L424H in the transcription factor GTF2I in thymic epithelial tumors. The precise role of the GTF2I mutation in these tumors is unclear. Here we describe the generation and characterization of a mouse model in which the Gtf2i L424H mutation was conditionally knocked-in in the Foxn1+ thymic epithelial cells. The Gtf2i mutation impairs development of thymic medulla and maturation of medullary thymic epithelial cells in the young mice and causes tumor formation in the thymus of the aged KI mice. To characterize the molecular features of murine thymomas, we performed digital spatial profiling with GeoMx moue whole transcriptome atlas assay with FFPE thymic tissues of 4 KI and 4 control mice.

overall_design: FFPE thymic tissues of 4 Gtf2i L424H mutation KI and 4 control mice were profiled with the GeoMx whole transcriptome atlas assay. 60 regions were chosen, 95 ROIs were collected from the selected regions based on the expression of markers. They include the epithelial cells (PanCK+), T cells (CD3+), and B cells (B220+) ROIs.

first: Giuseppe

last: Giaccone

first: Yongfeng

last: He

first: Elizabeth

last: A Conner

first: Madeline

last: M.F. Wong

first: Maggie

last: Cam

first: Jing

last: Bian

first: Noemi

last: Kedei

first: Maria

last: O Hernandez


title: Efficient generation of ETX embryoids that recapitulate the entire window of murine egg cylinder development

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

summary: The murine embryonic–trophoblast–extra-embryonic endoderm (ETX) model is an integrated stem cell–based model to study early postimplantation development. It is based on the self-assembly potential of embryonic, trophoblast, and hypoblast/primitive/visceral endoderm-type stem cell lines (ESC, TSC, and XEN, respectively) to arrange into postimplantation egg cylinder–like embryoids. Here, we provide an optimized method for reliable and efficient generation of ETX embryoids that develop into late gastrulation in static culture conditions. It is based on transgenic Gata6-overproducing ESCs and modified assembly and culture conditions. Using this method, up to 43% of assembled ETX embryoids exhibited a correct spatial distribution of the three stem cell derivatives at day 4 of culture. Of those, 40% progressed into ETX embryoids that both transcriptionally and morphologically faithfully mimicked in vivo postimplantation mouse development between E5.5 and E7.5. The ETX model system offers the opportunity to study the murine postimplantation egg cylinder stages and could serve as a source of various cell lineage precursors.

overall_design: We performed single-cell RNA sequencing (scRNA-seq) on ETX embryoids generated with a novel optimized method established in this study.

first: Cathérine

last: Dupont

first: Olivier

middle: M

last: Schäffers

middle: F

first: Eric

last: Bindels


title: Loss of TET2 Impairs Endothelial Angiogenesis via Downregulating STAT3 Target Genes

city: Shanghai

first: Yefei

last: Shi

address: 301 Middle Yanchang Road

institute: Shanghai Tenth People’s Hospital

summary: To investigate the role of TET2 in HUVECs under hypoxia, HUVECs were exposed to an atmosphere of 1% oxygen, 5% CO2 and 94% N2 for 48 h, in which TET2 had been knocked down by siRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of HUVECs transfected with control siRNA or TET2 siRNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUVECs transfected with Ctrl siRNA and TET2 siRNA under hypoxia

first: Bo

last: Li

first: Wenxin

last: Kou

first: Xinru

last: Huang

first: Ming

last: Zhai

first: Shuangjie

last: You

first: Qing

last: Yu

first: Yifan

last: Zhao

first: Jianhui

last: Zhuang

first: Chang

last: Liu

first: Weixia

last: Jian

first: Wenghui

last: Peng


title: Temporal gene expression with 30 days 'spillover' resistance training in the rat tibialis anterior muscle delivered with implantable pulse generators.

city: Gainesville

first: Mark

middle: Robert

last: Viggars

state: Alachua

address: University of Florida, M531

department: Physiology & Aging

institute: University of Florida

summary: Global gene expression patterns were determined from NGS on hypertrophying tibialis anterior muscles after 2, 10, 20 and 30 days resistance training (1 hour post exercise) and control muscles.

overall_design: 4 Animals were used for each timepoint, comparing the stimulated (trained) left tibialis anterior muscle and the unstimulated (contralteral control) right tibialis anterior muscle.

middle: R

first: Hazel

last: Sutherland

first: Jonathan

middle: C

last: Jarvis


title: Genome-wide transcriptional analysis of CD8+ brain TRM during CNS autoimmunity

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

summary: CD8+ TRM are described in autoimmune and chronic inflammatory diseases. However, we still lack knowledge about mechanisms regulating TRM reactivation, in particular in autoimmune diseases. Here, we investigated in a model of TRM-driven central nervous system autoimmunity the transcriptional landscape of self-reactive brain TRM and the requirement of these cells for CD4+ T cell help.

overall_design: Transcriptional activity of steady state (iso), helped (aCD8CD4) and unhelped (aCD8) P14 CD8+ TRM 7 days following tamoxifen administration.

first: Ilena

last: Vincenti

first: Doron

last: Merkler


title: CircGPRC5A(e2) facilitates gastric cancer progression via modulating miR-665/LASP1 axis and activating PI3K/AKT pathway

city: Beijing

first: Yixun

last: Lu

state: Haidian

address: Fuxing Road

department: Department of General Surgery

institute: Chinese PLA General Hospital

summary: Accumulating evidence has shown that circRNAs played critical roles in cancer and oncology. However, the role and mechanisms of circRNAs in gastric cancer (GC) remains not fully understood. CircRNA microarray analysis is one of reliable and convenient methods to detect differentially expressed circular RNAs. The aims of this study are to investigate the differentially expressed circRNAs in GC via human circRNA microarray analysis, and illuminate the role and underlying mechanisms of hsa_circ_0025506, i.e., circGPRC5A(e2), in GC.

overall_design: Three pairs of fresh frozen gastric cancer and adjacent normal tissues from gastric adenocarcinoma patients (pathological stage III) were collected and circRNA microarray analysis was performed with the Human circRNA Arrays V2.0.

first: Hongqing

last: Xi

first: Xinxin

last: Wang

first: Bo

last: Wei

first: Lin

last: Chen


title: RNA sequencing of glk1 glk2 double mutants  under LD conditions at ZT4

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

institute: Korea University

summary: We sequenced mRNA of WT (Col-0) and glk1 glk2 double mutants under LD conditions. RNA was extracted from seedlings of 1.02 developmental stage at ZT4 and proceeded for library preparation

overall_design: RNA extracted followed by high-throughput transcriptome sequencing of WT (Col-0) and glk1 glk2 double mutants  under LD conditions at ZT4.

first: Hendry

last: Susila

first: Ji

last: Ahn


title: Induced Torpor: An Experimental Model to Investigate the Effects of Chronic Low-Dose Radiation Exposure on Zebrafish Liver

city: Belfast

first: Thomas

last: Cahill

address: 19 Chlorine Gardens

institute: Queens university Belfast

summary: We hypothesised that induction of a torpor-like state would confer a radioprotective effect given the evidence that hibernation extends survival times in irradiated squirrels compared to active controls. To test this hypothesis, a torpor-like state was induced in zebrafish using melatonin treatment and cold temperatures, and radiation exposure was administered twice over the course of 10 days. The protective effects of induced-torpor were assessed via RNA sequencing of mRNA extracted from the liver.  A systems-level analysis was performed on the transcriptomic data to characterise the cellular phenotypes in radiation (28.5-rad), temperature+melatonin (18.5-mel), temperature+radiation (18.5-rad), and temperature+melatonin+radiation (18.5-mel-rad) groups compared with a control group (28.5-Ctrl). The results revealed that the torpor group experiences a reduction in metabolic genes, and increased pro-survival, antiapoptotic and DNA repair genes. The radiation group had changes to lipid metabolism and absorptions, a wound healing response and an immune response. While the induced torpor group showed a response to stress including changes to metabolism and perturbation of the circadian rhythm, it also maintained the pro-survival, anti-apoptotic and DNA repair genes seen in the torpor group suggesting a conferred radio-protective effect.

overall_design: Transcriptomic analysis of zebrafish liver assessing the protective effects of induced torpor on the harmful effects of low dose radiation

first: Gary

last: Hardiman

first: Willian

middle: A

last: da Silveira

first: Ludivine

last: Renaud

first: Tucker

last: Williamson

first: Hao

first: Dongjun

last: Chung

first: Ian

last: Overton

first: Sherine

last: Chan


title: RNA Sequencing Analyzes Chondrocyte Transcriptomes of Wild-type, miR-26a -/- and Cartilage-specific miR-23a/b clusters Knockout Mice

city: Hiroshima

first: Shigeru

last: Miyaki

state: Hiroshima

address: 1-2-3, kasumi Minami-ku

department: Medical Center for Translational and Clinical Research

institute: Hiroshima University

summary: To reveal the potential regulation target genes of miR-26a and miR-23a/b clusters in articular chondrocytes, we performed RNA-seq using RNA samples from cultured chondrocytes, which were primarily isolated from 3-week-old wild-type, miR-26a -/- or miR-23a/b cluster flox/flox;Col2a1-cre mice. Single-read libraries were prepared and sequenced by Illumina Nextseq 500. Proteins from the same sample were extracted for LC-MS/MS analysis. After data processing, differential expressed genes were screened out for exploring potential miRNA regulation targets.

overall_design: Transcriptomic profiles of articular chondrocytes from wild-type, miR-26a -/- (with or without miR-26a mimic transfection after isolated) and cartilage-specific miR-23a/b clusters knockout mice (each one)

first: Chenyang

last: Ding


title: Multiple copies of microRNA binding sites in long 3’UTR variants regulate axonal gene expression

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

summary: Rapid responses to changes over space and time within highly polarized cells, such as motor neurons, depend on local translation and post-transcriptional regulation in distinct subcellular compartments such as axons. MicroRNAs (miRNAs) can regulate this process in a mechanism that is not yet fully understood. Here, using live cell imaging and RNA sequencing analysis, we demonstrated how miRNAs can differentially control hundreds of transcripts at the subcellular level. We confirmed that the length of the miRNA target-sequence regulates both mRNA stability and protein translation rates; longer seed regions have an increased inhibitory effect. Interestingly, transcriptome analysis of the motor neuron subcellular compartments did not reveal any differences in seed length between axonal and somata mRNAs. However, we recognized that long 3’UTRmRNA variants are enriched in axons and contain more sequence repeats, particularly for binding a few specific miRNA. Finally, as proof of concept, we demonstrated that the long 3’UTR mRNA variant of the motor protein kif5b is enriched explicitly in motor neuron axons and contains multiple sequence repeats for binding miR-129-5p. This subsequently results in the differential post-transcriptional regulation of kif5b and its synthesis in axons. Thus, we suggest that the number of miRNA binding sites at the 3’UTR of the mRNA, rather than the miRNA seed length, regulates the axonal transcriptome. These new insights clarify how globally expressed miRNA can adaptively interact with their targets at the subcellular level, while possibly driving multiple cellular functions.

overall_design: Examination of miR-1-3p or control sequence OE for 0h, 2h or 4h in 293T cells.

first: Luba

last: Farberov

first: Ariel

last: Ionescu

first: Yazeed

last: Zoabi

first: Eran

last: Perlson

first: Noam

last: Shomron


title: Neuronal Dot1ll is a broad mitochondrial gene-repressor associated with human brain aging via H3K79 hypermethylation

city: Amsterdam

first: Marten P.

middle: Piet

last: Smidt

address: Sciencepark 904

department: SILS

institute: UvA

summary: Role of Dot1l in the transcriptional programming of midbrain dopamine neurons

overall_design: Examination of three groups: 1) Pitx3-Cre/+;Dot1l-+/+;Rosa-lox-stop-lox-YFP  2) Pitx3-Cre/+;Dot1l-Floxed/+;Rosa-lox-stop-lox-YFP 3) Pitx3-Cre/+;Dot1l-Floxed/Floxed/;Rosa-lox-stop-lox-YFP. Material is FACS sorted (YFP) to isolated the Pitx3-Cre positive cells ( YFP positive) (midbrain dopamine neurons) for differential gene expression analysis at developmental stage E15.75.

first: M

middle: P

first: H

middle: J

last: van Heesbeen


title: Small RNA next genration sequencing of miRNAs in Withaferin A treated MDA-MB-231 cells.

city: Bathinda

first: Shashank

last: Kumar

state: Punjab

address: VPO Guddha

department: Biochemistry

country: India

institute: CENTRAL UNIVERSITY OF PUNJAB

summary: In this study, we reporte the altered miRNAs expression in the human triple negative breast cancer cell line (MDA-MB-231)  in response to withaferin A at IC50 (2 µM) concentration.

overall_design: Withaferin A is a major pharmacological active constituent of Withania somnifera (Solanaceae) plant. In this study we were aimed to identify the diffentially expressed known/novel miRNAs using next generation sequencing (NGS) in withaferin A treated MDA-MB-231 cells.  For this, Human breast TNBC (MDA-MB-231) cells were cultured in the Dulbecco’s Modified Eagle Medium (DMEM) media supplemented with 10% (v/v) heat-inactivated FBS, 100 U/ml of penicillin, and 100 mg/ml of streptomycin and maintained in 5% CO2 at 37 degre celcius in a humidified atmosphere of 95% air in CO2 incubator. A total of 1x105 MDA-MB-231 cells were seeded in 35mm treated culture dishes containing 1ml of DMEM culture media and sub-cultured at every 3–4 days.  The cultured MDA-MB-231 cells were treated with WA (2 µM) for 24 h as experimental group and without WA treated MDA-MB-231 cells were taken as control group. Three samples were assigned for each group.


title: Titin truncating variantsin hiPSC-cardiomyocytes inducepathogenic proteinopathy, sarcomeredefect and contractile dysfunction independent of the core contractilemachinery

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

state: California

address: 1120 VETERANS BLVD.

country: USA

institute: AMGEN, INC.

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

overall_design: Refer to individual Series


title: Titin truncating variantsin hiPSC-cardiomyocytes inducepathogenic proteinopathy, sarcomeredefect and contractile dysfunction independent of the core contractilemachinery [scRNA-seq]

summary: Titintruncating variants(TTNtv) have been identified as the single largestgenetic cause of dilated cardiomyopathy(DCM). In this studywe modeled the disease phenotypes of TTNtv-induced DCM in hiPSC-CMsusing CRISPR/Cas9 genome editing and tissue engineering technologies. Transcriptomic, cellular and micro-tissue studies revealed that TTNtv hiPSC-CMs displayed pathogenic proteinopathy, sarcomere defects, aberrant Na+channel activities and, most importantly, contractile dysfunction. These phenotypes establish a dual mechanism of poison peptide effect and haploinsufficiency that collectively contribute to DCM pathogenesis. On the other hand, TTNtv cellular defects did not interfere with normal function of the core contractile machinery, actin-myosin-troponin-Ca2+complex, and preserved the therapeutic mechanism of sarcomere modulators. Treatment of TTNtv cardiac micro-tissues with investigational sarcomere modulators augmented contractility and resulted in sustained transcriptomicchanges that promotereversalof DCM disease signatures, as revealed by single-cell RNA-seqanalysis.Taken together, our findings depict the underlying pathogenic mechanisms of TTNtv-induced DCMand demonstrate the validity of sarcomere modulators as potentialtherapeutic agentsfor this disease.

overall_design: Single cell RNAseq was performed on wt and TTNtv/+ cardiomyocyte containing cardiac microwire cultures with and without AMG3360355 (troponin modulator) or AMG2591713 (myosin activator) treatment.

first: Guanyi

last: Huang

first: Devin

last: Wakefield

first: Xin

last: Luo

first: Jingli

last: Zhang

first: Patrick

last: Vigneault

first: Jinghong

last: Wang

first: Anjali

last: Bisaria

first: Oliverio

last: Oliver

first: Hong

last: Zhou

first: Chi-Ming

last: Li

first: Songli

first: Christopher

last: Hale


title: Neuronal Dot1ll is a broad mitochondrial gene-repressor associated with human brain aging via H3K79 hypermethylation II

first: Marten P.


title: Transcriptome (RNA-seq) analysis of the retina of crumbs 2a (crb2a m289/m289) zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.

city: London

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

institute: UCL

summary: The crumbs cell polarity complex plays a crucial role in apical-basal epithelial polarity. When human CRB1 is mutated, it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa, with no established genotype-phenotype correlation. Using the oko meduzym289/m289 (crb2a-/-) zebrafish model, we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient-derived retinal organoids, with disruption to cell cycle modulation and epigenetic transcriptional control. Hence, using reduced representation bisulphite sequencing (RRBS) we explored differential DNA methylation, identifying hypermethylated pathways involving biological adhesion, Hippo and transforming growth factor beta (TGFbeta) signalling. Functional epigenetic modules (FEM) were highlighted through the integration of RNA-seq and RRBS, confirming cell cycle involvement and disturbance of TGFbeta, BMP, Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development.

overall_design: We used RNA-seq to identify differentially expressed genes between the zebrafish model of CRB, crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a-/- and control wildtype. Biological replicates were taken.

first: Nicholas

last: Owen


title: Discovery of Novel Genes and Pathways through Comparative Transcriptomics Approach to Elucidate Genes Expressed in Durian (Durio zibethinus Murr) D24 Varieties Fruit Pulp Development and Ripening.

city: Sunway

first: Nurul

middle: Arneida

last: Husin

state: Selangor

address: Jalan Lagoon Selatan

country: Malaysia

institute: Monash University

summary: In this study, RNA Seq analysis was performed for the comprehensive understanding of the transcriptome of the durian, Durio zibethinus Murr. using Illumina HiSeq Platform. In comparison with the durian reference genome, the studies identified 3,438 novel exons and 1,197 novel loci. The total number of novel transcripts were 280. Ninety-seven novel transcripts did not show any similarity with any sequences available in the Genebank’s nucleotide database. Comparison of the top five ranked gene abundances between three differential groups YS/MS, YS/RS and MS/RS showed a difference in their genes and the function. Several key genes involved in sugar metabolism, sulfur production, and ripening process were further studied and visualised using IGV to view changes in their expression profile. 1,4-alpha-glucan-branching enzyme 2-1, chloroplastic/amyloplastic-like, hexokinase-3-like, UDP-sugar pyrophosphorylase-like were detected among the genes responsible for sugar and starch metabolism in durian fruit. The highest expression of genes involved in sugar and starch metabolism pathway was in the mature stage. There is almost similar level of gene expression involved in sugar metabolism in young and ripening stage. Methionine gamma-lyase-like (MGL) and PAP-specific phosphatase HAL2-like genes responsible for sulphur production and the metabolism in durian showed a rapid change in expression (about two times) from the young stage to mature and ripening stage. Interestingly, 1-aminocyclopropane-1-carboxylate oxidase (ACO) genes responsible for ethylene biosynthesis for fruit ripening were showed a significant increase in young stage compared to other stages. Glucose and ribitol dehydrogenase-like were among the top gene abundance identified in the ripening stage, and responsible in carbohydrate metabolism and acquisition of desiccation tolerance. Endochitinase 1-like was the gene in all three stages and responsible in carbohydrate binding site. The categorization of differently expressed transcripts among the three groups to Gene Ontology (GO) and KEGG pathway indicates the highest number of assigned genes to cellular process, metabolic process, cellular metabolic process, cellular nitrogen compound metabolic process; (biological_process), binding, catalytic activity, ion binding (molecular_function) and intracellular, cell part, cell (cellular_component). KEGG pathway mapping was finally carried out to classify the genes into different metabolic pathway. The percentage of the mapped reads to the KEGG pathway was 96.50% (YS/MS), 60.20% (YS/RS) and 35.30% (MS/RS). KEGG pathway distributions of highly expressed genes were mapped to the pathway in a group of nucleotide metabolism, carbohydrate metabolism, lipid metabolism, amino acid metabolism, metabolism of other amino acids, metabolism of cofactors and vitamins, biosynthesis of other secondary metabolites, glycan biosynthesis and metabolism, metabolism of terpenoids and polyketides, and energy metabolism. Comparison of the output of the top 10 highly significant genes between four statistical methods; CLC, CuffDiff, DESeq2, and EdgeR showed the similarity and dissimilarity between the pipelines. The highest similarity of the significant genes was observed when compared using DESeq2 and EdgeR methods.  As a whole, the studies conducted successfully revealed several genetic attributes of durian (D24) cultivar. The information also serves as a preliminary genomics expression data which could serve as the foundation in creating a new durian variety that is drought-resistance, and has longer shelf-like and has low-sugar fruits suitable for diabetics and glucose intolerant patients.

overall_design: Total of 9 samples; 3 biological replicates collected from three different stages of growth; young, mature and ripening,

first: Sadequr

last: Rahman

first: Rohini

last: Karunakaran

first: Subhash

last: Bhore


title: Titin truncating variantsin hiPSC-cardiomyocytes inducepathogenic proteinopathy, sarcomeredefect and contractile dysfunction independent of the core contractilemachinery [bulk RNA-seq]

first: Tracy

last: Yamawaki

overall_design: wt and TTNtv/+ hIPSC-cardiomyocytes at 30,90,150 days post differentiation in triplicate.

first: Guanyi

last: Huang

first: Devin

first: Xin


title: Comparative Transcriptomic Signature of the Simulated Microgravity Response in C. elegans

city: Newark

first: Irem

last: Celen

state: DE

address: 15 Innovation Way

institute: University of Delaware

summary: N2 worms were cultured in ground control conditions for three weeks, exposed to simulated microgravity for four days. Next, the maintained impact in the gene expression after the exposure was investigated after return to ground condition on days four, eight, and twelve.

overall_design: The animals were cultured in CeHR medium for three weeks after synchronization for allowing acclimatization to liquid conditions and reducing the effects of liquid cultivation on gene expression profiles. The ground control animals were maintained in CeHR medium in 20 mL scintillation. Then, the worms were exposed to clinostat-simulated microgravity for four days and the maintained impacts were observed at four, eight, and twelve days after placing the worms back to ground control conditions

first: Jung

middle: H

last: Doh

first: Chandran

last: Sabanayagam


title: Reduced representation bisulfite sequencing (RRBS) of the retina of crumbs 2a (crb2a m289/m289) zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.

country: United Kingdom

overall_design: We used RRBS to identify differentially methylated regions/genes between the zebrafish model of CRB, crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a-/- and control wildtype. Biological replicates were taken.

first: Maria

last: Toms

first: Yuan

last: Tian


title: A systematic exploration on Ginsenoside Rg5 reveals proresolving functions in airway mucous cells.

city: Gwangju

first: YouMin

last: KIM

address: 123, Cheomdangwagi-ro, Buk-gu

department: DEPARTMENT OF BIOMEDICAL SCIENCE AND ENGINEERING

institute: Gwangju Institute of Science and Technology

summary: Ginsenoside Rg5 reveals proresolving functions in airway mucous cells through inhibition of ROS production and promoting anti-inflammation factors

overall_design: Two replicates of Rg5 and PMA treatment

first: Bum-Ho

last: Bin

first: Jihawn

last: Park

first: You

last: Kim

first: Hyojin

last: Heo

first: Mi-Gi

last: Lee

first: Dongmin

last: Jang


title: Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification [WGBS]

status: Public on Jan 24 2023

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

summary: Epigenetic mechanisms govern developmental cell fate decisions, but how DNA methylation coordinates with chromatin structure and three-dimensional DNA folding to enact cell-type specific gene expression programmes remains poorly understood. Here, we use mouse embryonic stem and epiblast-like cells deficient for 5-methyl cytosine or its oxidative derivatives (5-hydroxy-, 5-formyl- and 5-carboxy-cytosine) to dissect the gene regulatory mechanisms that control cell lineage specification at the exit of pluripotency. Genetic ablation of either DNA methyltransferase (Dnmt) or Ten-eleven-translocation (Tet) activity yielded largely distinct sets of dysregulated genes, revealing divergent transcriptional defects upon perturbation of individual branches of the DNA cytosine methylation cycle. Unexpectedly, we found that disrupting DNA methylation or oxidation interferes with key enhancer features, including chromatin accessibility, enhancer-characteristic histone modifications, and long-range chromatin interactions with putative target genes. In addition to affecting transcription of select genes in pluripotent stem cells, we observe impaired enhancer priming, including a loss of three-dimensional interactions, at regulatory elements associated with key lineage-specifying genes that are required later in development, as we demonstrate for the key hematopoietic genes Klf1 and Lyl1. Consistently, we observe impaired transcriptional activation of blood genes during embryoid body differentiation of knockout cells. Our findings identify a novel role for the dynamic turnover of DNA methylation at the exit of pluripotency to establish and maintain chromatin states that epigenetically prime enhancers for later activation during developmental cell diversification.

overall_design: Mouse embryonic stem cells (mESC, cultured in 2i/Lif) were differentiated to epiblast like stem cells (EpiLC) or embryoid bodies (EB). Four cell lines were used: A triple knock-out of Tet1, Tet2 and Tet3 (TET_KO) and the corresponding parental wild-type line (TET_WT); a triple knock-out of Dnmt1, Dnmt3a and Dnmt3b (DNMT_KO) and the corresponding parental wild-type line (DNMT_WT). Conditions were generally assessed in triplicate.

first: Aled

last: Parry

first: Christel

last: Krueger

first: Tim

last: Lohoff

first: Steven

last: Wingett

first: Stefan

last: Schoenfelder

first: Wolf

last: Reik


title: Comparative transcriptomic analyses of Spring OilSeed Rape (SOSR)accessions in response to warm temperature.

city: Pozuelo de Alarcón

first: Isabel

last: Díaz

state: Madrid

address: Campus Montegarcedo

department: Interacción de las Plantas con el Medio

institute: CBGP-INIA-UPM

summary: Elevated growth temperatures are negatively affecting crop productivity and increasing yield losses. Root traits associated with improved adaptation to rising temperatures are a promising approach to generate new varieties better suited to face the environmental constrains caused by climate change. In this study, we identified various Brassica napus roots traits altered in response to warm temperature. Thus, different combination of changes in specific root traits results in an extended and deeper root system. This overall root growth expansion facilitates root adaptation by maximizing root-soil surface interaction and increasing its ability to explore extended soil areas. We associated these traits to coordinated cellular events, including changes in cell division and elongation rates, that drive the increase in root growth triggered by warm temperature. Comparative genome wide transcriptomic analysis revealed the main genetic determinants of these RSA changes and uncovered the necessity of a tight regulation of the heat shock stress response to adjust root growth to warm temperature. Our work provides a phenotypic, cellular and genetic framework of root response to warming temperatures that will help to harness root adaptation mechanisms for crop yield improvement under the future climatic scenario.

overall_design: RNA sequencing (RNA-seq) of root tips from two selected accessions (Drakkar and Duplo) grown at optimal (21ºC) vs warm (29ºC) temperatures on a pouch and wick system.

first: Marta

last: Boter

first: Jennifer

last: Poza

first: Jose

last: Jarillo

first: Manuel

last: Piñeiro

first: Monica

last: Pernas


title: Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification [ATAC]


title: Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification [RNASeq]


title: Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification [PCHIC]


title: Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification [HMCP]


title: Extracellular vesicle-mediated RNA transfer contributes to inter-cellular communication in the liver tumor microenvironment

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

summary: Extracellular vesicles and their contents are gaining recognition as important mediators of intercellular communication through the transfer of bioactive molecules such as non-coding RNA. We evaluated the contribution of EV miRNA in intercellular communication between hepatocellular cancer cells and hepatic stellate cells. EV-based miRNA was comprehensively assessed in both cell types individually. Using co-cultures of both HCC and HSC cells in transwell and 3D spheroids culture, we established EV-based miR-126-3p as a potential EV-based miRNA mediator of HSC to HCC communication through which tumor cell migration, invasion and three-dimensional growth in spheroids could be influenced. Manipulation of miR-126-3p by enforced expression or inhibition using pre-miR-126-3p or antimiR-126-3p respectively did not alter cell viability, proliferation, or sensitivity to either sorafenib or regorafenib. In contrast, migration was decreased in HepG2 cells with enforced expression of miR-126-3p. Knockdown of miR-126-3p in HepG2 resulted in a significant increase in ADAM9 expression and in LX-2 cells increased collagen accumulation and the compactness of spheroids but did not alter the number or size of spheroids. The restoration of miR-126 in 3D-co-culture of HepG2 and LX2 cells with precursor showed significant alleviated expression of ADAM9 and VEGF, While the silencing of miR-126 was elevated the expression of ADAM9 and VEGF. These studies implicate miR-126-3p in functional effects on migration, invasion, and spheroid growth in HCC cells in the presence of HSC, and thus demonstrate the presence of functional EV RNA based intercellular signaling between HSC and HCC cells that may be relevant to tumor cell behavior.

overall_design: To evaluate functional role of extracelluar vesicle RNA contribution in the liver tumor microenvironment and to identify extracelluar vesicle RNA as biomarkers of tumor microenvironment.

first: Anurahda

last: Moirangthem

first: Piyush

last: Gondaliya

first: Irene

last: Yan

first: Adil

last: Sayyad

first: Julia

last: Driscoll


title: Polyomic elucidation of the 9,10-anthraquinone biodegradation pathway by a newly isolated oxy-PAH degrading specialist from PAH-contaminated soil

city: Barcelona

first: Sara Nienke

last: Jiménez Volkerink

address: Av Diagonal 643

department: Genetics, Microbiology and Statistics

institute: University of Barcelona

summary: We report the isolation of the first bacterial strain, Sphingobium sp. AntQ-1, with the ability to grow on the oxy-PAH anthraquinone as sole carbon and energy source. We combine genomic, transcriptomic and metabolomic analysis to comprehensively elucidate the anthraquinone metabolic pathway and to identify key degradative genes.

overall_design: For the transcriptomic analysis, we performed a comparative RNA-seq experiment comparing the expression of cultures of Sphingobium sp. AntQ-1 grown either with anthraquinone or with acetate as control condition. Cells were grown in liquid mineral medium supplemented with vitamin B12 containing either anthraquinone or acetate as sole carbon sources. At the mid-exponential phase, cells were harvested for total RNA extraction. For each growth condition, RNA-seq analysis was done on three biological replicates of distinct rRNA-depleted RNA preparations.

first: Sara

middle: N

last: Jimenez Volkerink

first: Joaquim

last: Vila

first: Cristina

last: Minguillon

first: Maria

last: Jordan Ramos

first: Sudarshan

last: Shetty

first: Hauke

last: Smidt

first: Magdalena

last: Grifoll


title: Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification [ChIP]

first: Simon

last: Andrews

overall_design: Mouse embryonic stem cells (mESC, cultured in 2i/Lif) were differentiated to epiblast like stem cells (EpiLC) or embryoid bodies (EB). Four cell lines were used: A triple knock-out of Tet1, Tet2 and Tet3 (TET_KO) and the corresponding parental wild-type line (TET_WT); a triple knock-out of Dnmt1, Dnmt3a and Dnmt3b (DNMT_KO) and the corresponding parental wild-type line (DNMT_WT). Conditions were generally assessed in triplicate.generally assessed in triplicate.-ype line (DNMT_WT). Conditions were generally assessed in triplicate.

first: Aled

last: Parry

first: Christel

last: Krueger

first: Tim

last: Lohoff

first: Steven

last: Wingett

first: Stefan

last: Schoenfelder

first: Wolf

last: Reik