title: Elucidation of focal adhesion kinase as a modulator of migration and invasion and as a potential therapeutic target in chronic lymphocytic leukemia (miRNA-Seq)

city: BRIGHTON

first: Chris

last: Pepper

address: Falmer

department: Brighton and Sussex Medical School

institute: University of Sussex

summary: The retention and re-migration of Chronic Lymphocytic Leukemia cells into cytoprotective and proliferative lymphoid niches is thought to contribute to the development of resistance leading to subsequent disease relapse. The aim of this study was to elucidate the molecular processes that govern CLL cell migration to elicit a more complete inhibition of tumor cell migration. We compared the phenotypic and transcriptional changes induced in CLL cells using two distinct models designed to recapitulate the peripheral circulation, CLL cell migration across an endothelial barrier and the lymph node interaction between CLL cells and activated T cells. Initially, CLL cells were co-cultured with CD40L-expressing fibroblasts and exhibited an activated B-cell phenotype and their transcriptional signatures demonstrated the upregulation of pro-survival and anti-apoptotic genes and overrepresentation of the NF-κB signaling pathway. Using our dynamic circulating model we were able to study the transcriptomics and miRNomics associated with CLL migration. More than 3000 genes were altered when CLL cells underwent transendothelial migration, with overrepresentation of adhesion and cell migration gene sets. From this analysis an upregulation of the FAK signaling pathway was observed. Importantly, ptk2 (FAK) gene expression was significantly upregulated in migrating CLL cells (ptk2 Fold-change= 5.0). Here we demonstrate that TLR9 agonism increased levels of p-FAK (p<0.05) which could be prevented by pharmacological inhibition of FAK with defactinib (p<0.01). Furthermore, a reduction in CLL cell migration and invasion was observed when FAK was inhibited (p<0.05), supporting a role for FAK in both CLL migration and tissue invasion. Taken together, our data highlights the potential for combining FAK inhibition with current targeted therapies as a more effective treatment regime for CLL.

overall_design: MiRNA-Seq for Migratory vs Circulatory CLL cells using an in vitro circulating model system

first: Thomas

last: Burley

first: Andrew

last: Hesketh

first: Giselda

last: Bucca

first: Emma

last: Kennedy

first: Eleni

last: Ladikou

first: Ben

last: Towler

first: Simon

last: Mitchell

first: Colin

middle: P

last: Smith

first: Christopher

last: Fegan

first: Rosalynd

last: Johnston

first: Andrea


title: Elucidation of focal adhesion kinase as a modulator of migration and invasion and as a potential therapeutic target in chronic lymphocytic leukemia

status: Public on Mar 22 2022

country: United Kingdom

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Sex-Specific Transcriptomic Signatures in Brain Regions Critical for Neuropathic Pain-Induced Depression

status: Public on Apr 03 2022

city: Guang Zhou

first: dai

middle: wei

last: ping

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Road

country: China

institute: Sun Yat-sen University

summary: Neuropathic pain is a chronic debilitating condition with a high comorbidity with depression. Clinical reports and animal studies have suggested that both the medial prefrontal cortex (mPFC) and the anterior cingulate cortex (ACC) are critically implicated in regulating the affective symptoms of neuropathic pain. Neuropathic pain induces long-term structural, functional and biochemical changes in both regions, which are thought to be regulated by multiple waves of gene transcription. However, the similarity and differences in the transcriptomic profiles changed by neuropathic pain between these regions are largely unknown. Furthermore, women are more susceptible to pain and depression than men. The molecular mechanisms underlying this sexual dimorphism remain to be explored. Here, we performed RNA sequencing and analyzed the transcriptomic profiles of the mPFC and ACC of female and male mice at 2 weeks after spared nerve injury (SNI), an early time point when the mice began to show mild depressive symptoms. Our results show that the SNI-induced transcriptomic changes in female and male mice are largely distinct. Interestingly, the female mice exhibit more robust transcriptomic changes in the ACC than male, whereas the opposite pattern occurs in the mPFC. Cell type enrichment analyses reveal that the differentially expressed genes involve genes enriched in both neurons and various types of glia. We further performed Gene Set Enrichment Analysis (GSEA), which reveal significant de-enrichment of myelin sheath development in both female and male mPFC after SNI. In the female ACC, gene sets for synaptic organization and mitochondria function are enriched, and gene sets for extracellular matrix are de-enriched after SNI, while such signatures are absent in male ACC. Collectively, these findings reveal sexual dimorphism at the transcriptional level induced by neuropathic pain, and provide novel therapeutic targets for chronic pain and its associated affective disorders.

overall_design: Transcriptomic profiles of the mPFC and the ACC in female and male mice at 2 weeks after spared nerve injury

first: Weiping

last: Dai

first: Shuying

last: Huang

first: Yuan

last: Luo

first: Xin

last: Cheng

first: Pei

last: Xia

first: Mengqian

last: Yang

first: Panwu

last: Zhao

first: Yingying

last: Zhang

first: Wei-Jye

last: Lin

first: Xiaojing

last: Ye


title: Elucidation of focal adhesion kinase as a modulator of migration and invasion and as a potential therapeutic target in chronic lymphocytic leukemia (RNA-Seq II)

first: Chris

last: Pepper

overall_design: RNA-Seq CD40L expressing fibroblast co-culture with CLL cells

first: Thomas

middle: A

last: Burley

first: Andrew

last: Hesketh

first: Giselda

last: Bucca

first: Emma

last: Kennedy

first: Eleni

middle: E

last: Ladikou

first: Ben


title: Transcriptome landscape of pig embryo implantation site at single-cell resolution.

status: Public on Mar 18 2022

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

summary: Porcine conceptus together with its surrounding endometrial tissues were profiled using the 10x platform to identify intercellular crosstalk and global expression changes associated with embryo implantation in each cell type

overall_design: The study included pregnant include endometrium tissue (n=1) of non-pregnant pig, maternal-fetal tissue (n=1) and peri-blood (n=1) of pig on gestational day 15.


title: Elucidation of focal adhesion kinase as a modulator of migration and invasion and as a potential therapeutic target in chronic lymphocytic leukemia (RNA-Seq I)

overall_design: RNA-Seq for Migratory vs Circulatory CLL cells using an in vitro circulating model system

last: Towler

first: Simon

last: Mitchell

first: Colin

last: Smith

first: Christopher

last: Fegan

first: Rosalynd

last: Johnston

first: Andrea


title: RNA-seq in FHC cell lines.

city: Zhengzhou

first: Zhuoyu

last: Gu

address: Jianshe East Road

institute: The First Affiliated Hospital, Zhengzhou University

summary:
Purpose: The goals of this study are to invsetigate the primary biological process of hnRNPK.
Methods: Samples (FHC cells transfected with control or hnRNPK shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated.
Results: In FHC, metabolism was regulated hnRNPK.
Conclusions: RNA-seq in FHC cell lines revealed that hnRNPK mainly regulated metabolism.

overall_design: mRNA profiles of FHC hnRNPK knockdown cells


title: In silico discovery of the blood cell interactome [Affymetrix]

status: Public on Mar 21 2022

city: Oslo

first: Sjur

last: Reppe

address: Kirkeveien 166

department: Medical biochemistry

country: Norway

institute: OSLO UNIVERSITY HOSPITAL

summary:
The aim of the present study identify putative macromolecular interactions in human peripheral blood based on significant correlations at the transcriptional level.
We found that significant transcript correlations within the giant matrix reflect experimentally documented interactions involving select ubiquitous blood relevant transcription factors (CREB1, GATA1, and the glucocorticoid receptor (GR, NR3C1)).

overall_design: We performed transcriptional profiling of peripheral blood from Norwegian women (50–86 years, n=105) representing a cohort with varying bone mineral densities (BMDs) and free of primary diseases and medication known to affect the skeleton.

first: Kaare

middle: M

last: Gautvik


title: Chromosomal duplications increase gene dosage and mRNA level in C. elegans

city: New York

first: Sevinc

last: Ercan

state: NY

address: 100 Washington Square East

department: Biology

country: USA

institute: New York University

summary: Isolation of copy number variations and chromosomal duplications at high frequency in Caenorhabditis elegans suggested that this organism tolerates dosage problems. Here we addressed if this tolerance is due to a genome-wide compensation mechanism acting at the level of mRNA expression. We characterized several chromosomal duplication strains using DNA-seq and analyzed gene expression in two duplication and a fosmid integration strain using mRNA-seq. Our results show that on average, increased gene dosage leads to increased mRNA expression, pointing to a lack of genome-wide dosage compensation. Different genes within the same duplicated region show variable changes in mRNA expression, suggesting feedback regulation of individual genes. Transcriptional repression by somatic dosage compensation and germline silencing contribute to the level of mRNA increase from a large X chromosomal duplication. In sum, our results show a lack of genome-wide dosage compensation mechanism acting at the mRNA level in C. elegans and highlight the role of epigenetic and individual gene regulation contributing to the varied consequences of increased gene dosage.

overall_design: DNA-seq and RNA-seq in large duplication strains to look at copy number variation and effect of DCC recruitment on the transcriptional output of duplicated segments in CNV. Comparison between strains that recruit DCC and those that do not.

first: Bhavana

last: Ragipani

first: Sarah

last: Albritton

first: Ana

last: Morao

first: Diogo

last: Mesquita

first: Maxwell

last: Kramer


title: A prognostic hypoxia gene signature with low heterogeneity within the dominant tumour lesion in prostate cancer patients.

status: Public on Apr 01 2022

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

institute: Oslo University Hospital

summary:
Background: Hypoxia gene signatures measured in a biopsy are promising biomarkers in prostate cancer. We determined the ability of a previously developed signature to correctly classify tumours as more or less hypoxic and investigated how intratumour heterogeneity affected its biomarker performance.
Methods: The 32-gene signature was determined from gene expression data of 141 biopsies from the dominant (index) lesion of 94 patients treated with prostatectomy. Hypoxic fraction was measured by pimonidazole immunostaining of whole-mount and biopsy sections and used as reference standard for hypoxia.
Results: The signature was correlated with hypoxic fraction in whole-mount sections, and the parameters showed almost the same association with tumour aggressiveness. Gene- and pimonidazole-based classification of patients differed considerably. However, the signature had low intratumour heterogeneity compared to hypoxic fraction in biopsies and showed prognostic significance in three independent cohorts.
Conclusion: The biopsy-based 32-gene signature from the index lesion reflects hypoxia-related aggressiveness in prostate cancer.

first: Unn

middle: B

last: Salberg

first: Vilde

last: Skingen

first: Christina

middle: S

last: Fjeldbo

first: Tord

last: Hompland

first: Ljiljana

last: Vlatkovic

first: Knut

middle: H

last: Hole

first: Therese

last: Seierstad


title: In silico discovery of the blood cell interactome [microRNA]

summary:
The aim of the present study identify putative macromolecular interactions in human peripheral blood based on significant correlations at the transcriptional level.
We found that significant transcript correlations within a giant matrix including also mRNAs from the same project reflect experimentally documented interactions

first: Kare


title: Activation of the YAP-TEAD4-HHEX transcriptional complex by Casein Kinase 2 promotes tumorigenesis in colorectal cancer

status: Public on Mar 15 2022

city: Shanghai

first: Zhehui

last: Zhu

state: Shanghai

address: Kongjiang Road 1665, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing


title: Maternal H3K36 and H3K27 HMTs protect germline development via regulation of the transcription factor LIN-15B

status: Public on Mar 16 2022

city: Santa cruz

first: Chad

middle: Steven

last: Cockrum

state: CA

address: 329 sinsheimer labs

institute: University of California at Santa Cruz

summary: Maternally synthesized products play critical roles in development of offspring. A premier example is the C. elegans H3K36 methyltransferase MES-4, which is essential for germline survival and development in offspring. How maternal MES-4 protects the germline is not well understood, but its role in H3K36 methylation hinted that it may regulate gene expression in Primordial Germ Cells (PGCs). We tested this hypothesis by profiling transcripts from nascent germlines (PGCs and their descendants) dissected from wild-type and mes-4 mutant (lacking maternal and zygotic MES-4) larvae. mes-4 nascent germlines displayed down-regulation of some germline genes, up-regulation of some somatic genes, and dramatic up-regulation of hundreds of genes on the X chromosome. We demonstrated that up-regulation of 1 or more genes on the X is the cause of germline death by generating and analyzing mes-4 mutants that inherited different endowments of X chromosome(s). Intriguingly, removal of the THAP transcription factor LIN-15B from mes-4 mutants reduced X mis-expression and prevented germline death. lin-15B is X-linked and mis-expressed in mes-4 PGCs, identifying it as a critical target for MES-4 repression. The above findings extend to the H3K27 methyltransferase MES-2/3/6, the C. elegans version of Polycomb Repressive Complex 2. We propose that maternal MES-4 and PRC2 cooperate to protect germline survival by preventing synthesis of germline-toxic products encoded by genes on the X chromosome, including the key transcription factor LIN-15B.

overall_design: We profiled transcripts from Primordial Germ Cells (PGCs) and Early Germ Cells (EGCs) dissected from wild-type and mutant L1 or L2 larvae, respectively. We used pairwise differential expression analyses (mutant vs wild type) to compare samples of mes-4(bn73), mes-3(bn199), mrg-1(qa6200), and met-1(bn200) null M-Z- mutants to samples of wild type. Samples of PGCs and EGCs were sequenced in 2 batches: "pgcs_egcs_batch01" on an Illumina HiSeq 2500 and "pgcs_egcs_batch02" on an Illumina NovaSeq 6000. Principal Component Analysis (PCA) did not reveal batch effects in the top 2 principal components among samples that had some replicates sequenced in 1 batch and some replicates sequenced in the other batch. Thus, we did not batch-correct samples of PGCs and EGCs. All samples of PGCs and EGCs were used to calculate normalization scaling factors (using the pooling and deconvolution approach in the R package "scran") and to perform quality control. In this study, the samples of PGCs dissected from drh-3(bn197) hypomorphic mutant L1s were only used for normalization and quality control; they were not used for differential expression analysis. Our drh-3(bn197) allele is genetically linked to glh-1::GFP::3xFLAG on chromosome 1 and produces the same protein as the drh-3(ne4253) hypomorphic allele (Gu et al., 2009). All worms strains, including "wild-type", carry a germline-specific glh-1:GFP:3xFLAG marker that was used to isolate germ cells. We also profiled transcripts from distal halves of gonads dissected from mes-4(bn73) M+Z-, mes-4 (bn73) M+Z-; lin-15B(n744) M-Z- mutant and wild-type adult hermaphrodites. Samples of adult gonads were sequenced in 2 batches: "adgerm_batch01" and "adgerm_batch02", both on an Illumina NovaSeq 6000. We performed pairiwse differential expression analyses comparing samples of mutants to samples of wild type that were sequenced in the same batch.

first: Susan

last: Strome


title: Regionally distinct trophoblast regulate barrier function and invasion in the human placenta

city: San Francisco

first: Bryan

last: Marsh

address: 35 Medical Center Way, RMB 912E, None

institute: University of California, San Francisco

summary: Single Cell RNA-sequencing data from four human placental samples

overall_design: Single Cell RNA-sequencing data collected from both the Placental Villi/Basal Plate and Smooth Chorion regions from four human placental samples (8 total samples).

first: Robert

last: Blelloch

middle: J

last: Fisher


title: Whole genome bisulfite sequencing (WGBS) using porcine parthenogenetic embryos and biparental controls

status: Public on Mar 14 2022

city: Columbus

first: Jinsoo

last: Ahn

state: OH

address: 2029 Fyffe Rd

institute: The Ohio State University

type: Methylation profiling by high throughput sequencing

summary: The objective of this study was to, using porcine parthenogenetic embryos, investigate imprinting status of genes within the H19/IGF2 locus in chromosome 2.

overall_design: Analyses of paternal or maternal hypermethylation in porcine embryos.

first: Seongsoo

last: Hwang

first: Kichoon

last: Lee


title: The effect of insulin-like growth factor 1 and insulin on neutrophil polarization

status: Public on Mar 13 2022

city: Düsseldorf

first: Rianne

last: Nederlof

address: Universitätsstraße 1

department: Institut für Herz-und Kreislaufphysiologie

country: Germany

institute: Heinrich-Heine University

summary: We analyzed bone marrow derived neutrophils after they were left untreated, or treatment with LPS/IFNgamma (pro-inflammatory), IL4 (anti-inflammatory), insulin-like growth factor 1 and insulin to detect transcriptional changes after the different treatments.

overall_design: Neutrophils were isolated from bone marrow from femurs and tibias of C57Bl/6J mice (n=4) by Percoll gradient centrifugation, dissolved in medium (DMEM with 3% FCS, 1mM HEPES and 1% PenStrep) and plated in a 6-well plate 5-6 x 10*6 cells per well. Cells were left untreated or treated with 20 ng/mL IL-4, 10 ng/mL LPS and 2 ng/mL IFNγ, 10 ng/mL IGF1 or 10 or 100 ng/mL insulin for 4 hours at 37°C.

first: Sophia

last: Reidel

first: André

last: Spychala

first: Patrick

last: Petzsch

first: Karl

last: Köhrer

first: Axel

last: Gödecke


title: Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers [ATAC HD]

status: Public on Mar 08 2022

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: ATAC-seq was used to study the chromatin landscape of T cell subsets from PBMCs healthy donors.

overall_design: CD8 and CD4 Immune cell subsets were sorted from young and older healthy donors PBMC samples and chromatin accessibility was assayed for comparison across age and between various Immune cell subsets

first: Josephine

last: Giles

first: Sasi

last: Manne

last: Wherry


title: Gene Regulatory Networks for the characterization of the effects of the catalytic inhibition of DNA topoisomerase II

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

summary: The inference of Gene Regulatory Networks (GRN) enables in silico generation of biological models, which are capable of integrat- ing large amounts of diverse biological information. These often base on gene expression data. In this project, several GRNs were reconstructed out of RPE-1 cells RNAseq data in order to identify cellular processes affected by antitumoral drug merbarone. Merbarone catalytically inhib- its the enzyme Topoisomerase II. Additionally, it is intended to provide an overview and a general pipeline for GRN inference and reconstruc- tion, from transcription data preprocessing to network validation and analysis.

overall_design: RNA-seq experiments in human RPE cells were generated upon different times of merbarone treatment: 1) 4h merbarone treatment (2 replicates) and 2) 8h merbarone treatment (2 replicates).

first: Andrés

last: Herrero-Ruiz

first: Pedro

last: Martínez-García

first: Silvia

last: Jimeno-González

first: Fernando

last: Delgado Chaves

first: Francisco

last: Gómez-Vela

first: Federico

last: Divina

first: Miguel

last: Garcı́a-Torres

last: Cortés-Ledesma


title: Skin transcriptomics predict outcome after ionizing radiation exposure with potential dosimetric applications in a mouse model

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: Increased use of nuclear reactors and radioactive materials for energy production and proliferation of nuclear weaponry increases risk of radiation exposure or nuclear accidents. Development of radiation countermeasures for the diagnosis, prognosis, and radiation treatment are trailing behind, and knowledge of the deleterious radiation effects on health and responses to exposure at the molecular, cellular, and systems biology level are still not fully understood. In this work, skin biopsies collected at h2, d4, d7, d21, and d28 from mice exposed to 1, 3, 6, 20Gy of whole-body x-ray ionizing radiation were used in a transcriptomic approach to evaluate the potential of radiation-induced transcriptional alterations in diagnosis and prognosis of a radiation event. Mice exposed to 20Gy were euthanized under the humane endpoint of an IACUC approved study protocol at d7 while mice that received 1, 3, 6Gy survived the full 28 days time course. Sammon plot analysis showed a clear separation of samples based on survival and timepoints within lethal (20Gy) and in the sublethal (1, 3, 6Gy) IR doses. Differences in the numbers, regulation mode, and fold change of significantly differentially transcribed genes (SDTGs, p < 0.05 and FC > 2) were identified between lethal and sublethal doses. Down and upregulation dominated transcriptomes during the first post-exposure week, respectively. Numbers of SDTGs and percentages of upregulated SDTGs revealed stationary transcription and low upregulation percentages after lethal dose in contrary to transcription responses that were dynamic and largely upregulated after exposure to sublethal doses. Longitudinal variations in numbers of up/downregulated SDTGs suggested delayed and extended responses with increasing IR doses in the sublethal range with lethal-like responses in late time points suggesting more than a single-phase response. This was supported further by the distributions of common and unique genes across the TPs within each dose. Several genes with potential use as markers for radiation exposure and dosimetric applications were identified. Pathways enrichment analysis showed strong modulations of immune responses, fibrosis development, detoxification responses, hematological responses, skin reactions, neurological system disruptions, maintenance of gastric mucosa, and cell survival, migration, and proliferation pathways. The majority of the identified pathways were predicted activated after sublethal and inactivated after lethal exposures, particularly during the first post-exposure week.

overall_design: In this work, skin biopsies collected at h2 (d0), d4, d7, d21, and d28 from mice exposed to 1, 3, 6, 20Gy of whole-body x-ray ionizing radiation were used in a transcriptomic approach to evaluate the potential of radiation-induced transcriptional alterations in diagnosis and prognosis of a radiation event.

first: Abdulnaser

last: Alkhalil

first: John

last: Clifford

first: Stacy

last: Miller

first: Marti

last: Jett

first: Rasha

last: Hammamieh

first: Lauren

middle: T

last: Moffatt

first: Jeffrey

middle: W

last: Shupp


title: Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers [ATAC melanoma]

first: E

last: WHERRY

summary: ATAC-seq was used to study the chromatin landscape of CD8 T cells in locally advanced melanoma patients treated with neo-adjuvant/adjuvant Pembrolizumab

overall_design: CD8 naive and Non naive cells were sorted from  PBMC and tumor samples from advanced melanoma patients treated with neo-adjuvant/adjuvant Pembrolizumab and chromatin accessibility was assayed for comparison analysis

first: Josephine

last: Giles

first: Sasi

last: Manne

last: Wherry


title: HHEX ChIP-seq from human HCT116

first: Zhehui

last: Zhu

summary: HHEX ChIP-seq on human HCT116

overall_design: HCT116 cells were passaged in low density with 1x10^6 cells per 10 cm plate, when cells were completely adhered, and then harvested for ChIP.

first: Yuegui

last: Guo

first: Chen-Ying

last: Liu


title: Identification of differential expressed genes after HHEX/YAP/TAZ/TEAD knockdwon in colorectal cancer cells

summary: We have identified HHEX as an oncogene to promote proliferation in colorectal cancer. To elucidate the potential mechanism of HHEX in colorectal cancer, RNA-seq analysis was performed in HCT116 cells to analyze differential expressed genes after HHEX knockdown.

overall_design: HCT116 cells transiently expressing siNC control, siHHEX_1, siHHEX_2, siHHEX_3, siYAP/TAZ_1, siYAP/TAZ_2 or siTEAD1/2/3/4.


title: In silico discovery of the blood cell interactome

first: Sjur

last: Reppe

type:
Expression profiling by array
Expression profiling by RT-PCR

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

overall_design: Refer to individual Series


title: RNA-seq using porcine parthenogenetic embryos and biparental controls

first: Jinsoo

last: Ahn

overall_design: Analyses of paternal or maternal allele-specific expression in porcine embryos.

first: Seongsoo

last: Hwang

first: Kichoon

last: Lee


title: Porcine parthenogenetic embryos and biparental controls


title: ANRIL regulates multiple molecules of pathogenetic significance in diabetic nephropathy

status: Public on Mar 06 2022

city: London

first: Subrata

last: Chakrabarti

state: Ontario

address: 1151 Richmond St

department: Pathology and Lab Medicine

country: Canada

institute: Univeristy of Western Ontario

summary:
Background: Hyperglycemia-induced transcriptional alterations lead to aberrant synthesis of a large number of pathogenetic molecules leading to functional and structural damage to multiple end organs including the kidneys. Diabetic nephropathy (DN) remains a major cause of end stage renal disease. Multiple epigenetic mechanisms, including alteration of long non-coding RNAs (lncRNAs) may play a significant role mediating the cellular transcriptional activities. We have previously shown that lncRNA ANRIL may mediate diabetes associated molecular, functional and structural abnormalities in DN. Here we explored downstream mechanisms of ANRIL alteration in DN.
Methods: We used renal cortical tissues from ANRIL knockout (KO) mice and wild type (WT) mice, with or without streptozotocin (STZ) induced diabetes for RNA sequencing. The differentially expressed genes were identified using edgeR and DESeq2 computational methods. KEGG and Reactome pathway analyses and network analyses using STRING and IPA were subsequently performed.
Results:   Diabetic animals showed hyperglycemia, reduced body weight gain, polyuria and increased urinary albumin. Both albuminuria and polyuria were corrected in the KO diabetic mice. RNA analyses showed Diabetes induced alterations of a large number of transcripts in the wild type (WT) animals. ANRIL knockout (KO) prevented a large number of such alterations. The altered transcripts include metabolic pathways, apoptosis, extracellular matrix protein synthesis and degradation, NFKB related pathways, AGE-RAGE interaction pathways etc. ANRIL KO prevented majority of these pathways.
Conclusion: These findings suggest that as ANRIL regulates a large number of molecules of pathogenetic significance, it may potentially be a drug target for DN and other chronic diabetic complications.

overall_design: The purpose of this study was to identify the transcripts and relevant pathways that are altered in a clinically relevant animal model of diabetic nephropathy. Using an ANRIL knockout model, the study further investigated which of these transcripts and pathways are regulated by ANRIL

first: Parisa

last: Shooshtari

first: Biao

last: Feng

first: Saumik

last: Biswas

first: Michael

last: Levy

first: Hanxin

last: Lin

first: Zhaoliang

last: Su


title: Transcriptomic Analysis of the Major Orphan Ichthyosis Subtypes Reveals Shared Immune and Barrier Signatures

first: Ana

last: Pavel

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary: In this study we performed the first global RNA-seq analysis in 54 ichthyosis patients (7 Netherton syndrome/NS, 13 epidermolytic ichthyosis/EI, 16 lamellar ichthyosis/LI, 18 congenital ichthyosiform erythroderma/CIE) and 40 healthy controls. Differentially expressed genes (DEGs) were defined based on fold changes/FCH>2 and false discovery rate/FDR<0.05 criteria. We found robust and significant Th22/Th17 skewing in all subtypes (e.g. IL-17A/C/F, S100A7/8/9/12; p<0.001) with modest changes in Th2 pathway, primarily in NS, and Th1 skewing in CIE.

overall_design: RNA-seq data was profiled from skin biopsies of 54 ichthyosis patients (7 Netherton syndrome/NS, 13 epidermolytic ichthyosis/EI, 16 lamellar ichthyosis/LI, 18 congenital ichthyosiform erythroderma/CIE) and 40 healthy controls.

first: Madeline

last: Kim

first: Daniela

last: Mikhaylov

first: Stephanie

last: Rangel

first: Helen

last: He

first: Yael

last: Renert-Yuval

first: Ester

last: Del Duca

first: Kunal

last: Malik

first: Thy

last: Huynh

first: Erin

last: Ibler

first: Mary

last: Sun

first: Ning

last: Zhang

first: Yeriel

last: Estrada

first: James

middle: G

last: Krueger

first: Amy

last: Paller

first: Emma

last: Guttman-Yassky


title: Transcriptome Alterations in ASMT Knockout-Induced Depression-Like Behaviors and Exercise Effects

city: shanghai

first: Wenbin

last: Liu

address: 500 Dongchuan Road

institute: East China Normal University

summary: Sleep disorder caused by abnormal circadian rhythm is one of the main symptoms and risk factors of depression. N-acetylserotonin methyltransferase (ASMT), the last rate-limiting enzyme of melatonin (MT, a known hormone regulating circadian rhythms), has been reportedly associated with depression. Exercise can regulate circadian rhythm and play an important role in depression treatment. Recently, gene chip has been widely used in depression research. In the present study, we showed that ASMT knockout induced depression-like behaviors, which were ameliorated by swimming exercise. Moreover, swimming exercise increased serum levels of MT and 5-HT in ASMT knockout mice. In addition, transcriptome analysis identified 10 differentially expressed genes (DEGs) in KO mice compared with WT mice, and 29 DEGs in KO mice after swimming exercise. Among the DEGs, the direction and magnitude of change in Eps8l1 and Plcb2 were confirmed by qRT-PCR partly. Subsequent bioinformatic analysis showed that p53 signaling pathway, long-term depression and estrogen signaling pathway were enriched significantly. In the protein-protein interaction (PPI) networks, Mpp1 and Pidd1 were hub genes. These findings may provide new targets for the treatment of circadian rhythm-associated depression.

overall_design: Mice were randomly assigned to four groups: wild-type control group (WT), ASMT-knockout control group (KO), wild-type exercise group (WE), and ASMT-knockout exercise group (KE).

first: Weina

first: Zhengtang

last: Qi

first: Zhuochun

last: Huang

first: Jie

last: Xia

first: Zhiming

last: Cui

first: Lingxia

last: Li


title: The androgen receptor-lncRNASAT1-Akt-p15 axis mediates androgen-induced cellular senescence in prostate cancer cells

status: Public on Mar 04 2022

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

summary: The bipolar androgen therapy (BAT) to treat prostate cancer includes cycles of supraphysiological androgen levels (SAL) under continuous androgen deprivation therapy (ADT). We showed previously that SAL induces cellular senescence in androgen-sensitive PCa cells and ex vivo in PCa tumor samples from patients that underwent radical prostatectomy. Here, we show that SAL induces cellular senescence in both, castration sensitive (CSPC) LNCaP and castration resistant PCa (CRPC) C4-2 cells through the cell cycle inhibitor p15. Treatment with the Akt inhibitor (Akti) potently inhibited SAL-induced expression of p15 and cellular senescence in both cell lines. Proximity ligation assays (PLA) combined with high-resolution laser-scanning microscopy indicate that SAL promotes interaction of endogenous androgen receptor (AR) with endogenous Akt in cytoplasm as well as in nucleus after 72 hours hormone treatment. This suggests that the AR interacts with Akt also in a long-term manner. Transcriptome sequencing (RNA-seq) comparing the SAL-induced transcriptomes of LNCaP with C4-2 cells as well as of Akti treated cells revealed landscapes for cell senescence. Interestingly, one of the identified genes is the lncRNASAT1. SAL treatment of native patient tumor samples ex vivo results in upregulation of lncRNASAT1. The lncRNASAT1 is down-regulated in PCa tumor tissues compared to non-tumor tissues of same patients indicating a tumor suppressive function. Knockdown indicates that the lncRNASAT1 is crucial for SAL-induced cancer cell senescence and regulates LNCaP cell proliferation being an upstream factor for pAkt and for p15. Further, knockdown of lncRNASAT1 inhibits LNCaP cell proliferation by low androgen levels but enhances proliferation by SAL. This suggests that lncRNASAT1 serves as a tumor suppressor with SAL. Interestingly, immunoprecipitation of AR detected lncRNASAT1 as an AR interacting partner that regulates AR target gene expression. Thus, we identified a novel pathway of androgen signaling as the AR- lncRNASAT1- Akt- p15INK4b- axis to mediate SAL-induced cellular senescence.

overall_design: Transcriptional profile of C-42 and LNCaP cells upon androgen treatment in combination with Akt inhibitor.

first: Kimia

last: Mirzakhani

first: Marzieh

last: Ehsani

first: Seyed

first: Francesco

last: Neri

first: Aria

last: Baniahmad


title: Characterization of novel natural compound derivatives with cancer-selective cytotoxicity (RNA-seq dataset 2)

summary: Colorectal cancer is one of the most frequent and lethal cancer in the world. Current therapeutic approaches are still not fully successful, yet cause numerous and severe side effects for the patient. We screened chemically synthesized derivatives from two natural compounds (a-Mangostin and Paeonol) as potential novel chemicals that increase cancer cell selectivity over non-transformed human cells. We found two of them that efficiently induced cell cycle arrest and apoptosis in human cancer cells and organoids derived from tumor tissue without affecting the viability of human non-cancer cells and intestinal organoids derived from healthy tissue. Our findings increase the knowledge about cancer-specific compounds and propose two natural compound derivatives as potential novel chemotherapeutics.

overall_design: Transcriptional profile of colon cancer cell lines upon treatment of two cancer-selective novel natural compounds

first: Suneetha

last: Nunna

first: Ying-Pei

first: Anna

last: Krepelova

first: Annunziata

last: Francesco

first: Lisa

last: Adam

first: Sandra

last: Käppel

first: Ming-Hua

last: Hsu


title: Transcriptomic analysis in human bronchial epithelial cells after rhinovirus (RV) and influenza (IAV) virus infection for 48 hours

status: Public on Mar 01 2022

city: Hong Kong

first: Renee Wan Yi

last: Chan

state: Select a State

address: 1 Shing Cheong Road, Kowloon Bay, Hong Kong

department: Paediatrics

country: Hong Kong

institute: Chinese University of Hong Kong

summary: RNA-seq analysis to study the antiviral effect induced by RV and influenza A virus

overall_design: RNA-seq analysis using well differentiated human bronchial epithelial cells (HBEC) infected with rhinovirus A16 (RV) and influenza A virus A/Oklahoma/447/2008 (H1N1)

first: R

first: K

middle: Y

last: Tao


title: Exposure of PBMCs to SARS-CoV-2, as opposed to SARS-CoV, induces cell-intrinsic type I innate immunity responses in several immune cell types in the absence of productive infection

city: Berlin

first: Dylan

last: Postmus

state: Berlin

address: Charitépl. 1

department: Institute of Virology

institute: Charité – Universitätsmedizin Berlin

summary: We investigate the response of peripheral blood mononuclear cells (PBMCs) to SARS-CoV and SARS-CoV-2 exposure.

overall_design: RT-qPCR, western blotting and single cell RNA sequencing was peformed on PBMCs exposed ex vivo to SARS-CoV and SARS-CoV-2 virus or mock exposed.

first: Julia

last: Kazmierski

first: Kirstin

last: Friedmann

first: Cornelius

last: Fischer

first: Jenny

last: Jansen

first: Anja

last: Richter

first: Laure

last: de Jarcy

first: Christiane

last: Schüler

first: Madlen

last: Sohn

first: Sascha

last: Sauer

first: Christian

last: Drosten

first: Antoine-Emmanuel

last: Saliba

first: Leif

last: Sander

first: Christine

last: Goffinet

first: Daniela

last: Niemeyer


title: Biomarkers for canine Leptospira vaccine potency

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

summary: We used RNAseq to investigate innate immune responsiveness in canine 030-D cell line induced by inactivated L. interrogans serogroups Canicola and Icterohaemorrhagiae, and two bivalent, non-adjuvanted canine Leptospira vaccines containing the same serogroups. We identified more than 900 DEGs associated with pathways related to innate immune responses in common to these three stimuli. Several molecules including CXCL-10, SAA, and complement factor C3 were identified that could serve as targets for development of a biomarker-based in vitro assay to assess Leptospira vaccine quality. In vitro assay could replace the current animal vaccine-challenge potency assay and contribute to reduction of animal use in vaccine manufacturing.

overall_design: 39 samples comprising 6 stimuli (including medium-only control) and 3 time-points. Each condition was performed in triplicate.

first: Andreja

last: Novak

first: Arjen

last: Sloots


title: Characterization of novel natural compound derivatives with cancer-selective cytotoxicity (RNA-seq dataset 3)

first: Seyed Mohammd Mahdi

last: Rasa

first: Suneetha

last: Nunna

first: Ying-Pei

last: Huang

first: Seyed

first: Anna

last: Krepelova

first: Annunziata

last: Francesco

first: Lisa

last: Adam

first: Sandra

last: Käppel

first: Ming-Hua

last: Hsu

first: Francesco

last: Neri


title: RNA sequencing of pro-B from Skiv2l-deficient B cells

city: DALLAS

last: Yan

state: TEXAS

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: To identify differentially expressed mRNAs in Skiv2l-deficient pro-B cells.

overall_design: FACS-sorted pro-B cells from bone marrow of 3 Skiv2lfl/fl-Cd79a-Cre mice and 3 Skiv2lfl/fl controls.

first: Kun

last: Yang


title: Analysis of Clec1a role in the development of experimental autoimmune encephalomyelitis

city: Noda

first: Yulia

last: Makusheva

state: Chiba

address: Yamazaki 2669

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

summary: Clec1A, a member of C-type lectin receptor family, has a carbohydrate recognition domain in its extracellular region, but no known signaling motif in the cytoplasmic domain. Clec1a is highly expressed in endothelial cells and weakly in dendritic cells. Although this molecule was reported to play an important role in the host defense against Aspergillus fumigatus by recognizing 1,8-dihydroxynaphthalene-melanin on the fungal surface, the roles of this molecule in un-infected animals remain to be elucidated. In this study, we found that Clec1a–/– mice develop milder symptoms upon induction of experimental autoimmune encephalomyelitis (EAE), an animal model for multiple sclerosis. The maximum disease score was significantly lower, and demyelination and inflammation of the spinal cord were much milder in Clec1a–/– mice compared to wild-type mice. No abnormality was detected in the immune cell composition in the draining lymph nodes and spleen on day 10 and 16 after EAE induction. Recall memory T cell proliferation after restimulation with myelin oligodendrocyte glycoprotein peptide (MOG35-55) in vitro was decreased in Clec1a–/– mice, and antigen presenting ability of Clec1a–/– dendritic cells was impaired. Interestingly, RNA-Seq and RT-qPCR analyses clearly showed that the expression of inflammatory cytokines including Il17a, Il6 and Il1b was greatly decreased in Clec1a–/– mice after induction of EAE, suggesting that this reduced cytokine production is responsible for the amelioration of EAE in Clec1a–/– mice. These observations suggest a novel function of Clec1A in the immune system.

overall_design: Lymph node mRNA profiles of wild type (WT) and Clec1a–/–  mice. Samples were collected 1) in steady state, 2) at day 10 after EAE induction, 3) at day 16 after EAE induction. Total of six samples of draining lymph nodes, one biological replicate of each one, were analyzed.

first: Xiao-Qi

last: Ye

first: Ce

last: Tang

first: Yoichiro

last: Iwakura


title: ELK3 modulates the antitumor efficacy of natural killer cells against triple negative breast cancer by regulating mitochondrial dynamics [ChIP-seq]

status: Public on Mar 03 2022

city: Seongnam-si

first: Joo Dong

last: Park

state: Gyeonggi-do

address: 335, Pangyo-ro

department: Biomedical Science

country: South Korea

institute: CHA University

summary: We demostrated that ELK3-Mid51 axis in TNBCs mediate mitochondrial dynamics determines concentration of reactive oxygen species that is linked to the immune sensitivity to cytotoxicity of NK cells.

overall_design: To screen downstream targets of ELK3, ELK3KD-231 were transfected with pLenti-cMyc-Flag-ELK3. We performed chromatin immunoprecipitation assay using anti-Flag.

first: Joo

middle: D

first: Kyung-Soon


title: ELK3 modulates the antitumor efficacy of natural killer cells against triple negative breast cancer by regulating mitochondrial dynamics [RNA-seq]

overall_design: The gene expression profiles of wild-type MDA-MB231 cells and ELK3 knockdown cells with those that were transfected with control vector or plasmid expressing wild-type ELK3


title: Evaluation of transcriptional changes of bone marrow derived macrophages (BMDM) in response to necrotic pancreatic acinar cells

city: Greifswald

first: Janine

last: Golchert

address: Felix-Hausdorff-Str. 8

department: Department of Functional Genomics

institute: University Medicine Greifswald

summary: To investigate the activation and polarisation of BMDMs during the course of pancreatitis, BMDMs were co-incubated with CCK-stimulated acinar cells (+/- the serine protease inhibitor nafamostat) for 6h in an in vitro experiment. The LPS treatment served as a positive control.

overall_design: We used BMDMs isolated from C57Bl/6 mice which were maintained in the presence of 20ng MCSF over 7d until they were confluent. Co-incubation was performed with freshly prepared acinar cells from C57Bl/6 mice over 6h +/- Nafamostat. BMDMs were carefully washed before RNA Isolation. Transcriptome analyses were performed using individual RNA samples.

first: Georg

last: Homuth

first: Matthias

last: Sendler


title: Characterization of novel natural compound derivatives with cancer-selective cytotoxicity (RNA-seq dataset 1)

first: Seyed Mohammd Mahdi

last: Rasa

first: Suneetha

last: Nunna

first: Ying-Pei

last: Huang

first: Seyed

first: Anna


title: Characterization of novel natural compound derivatives with cancer-selective cytotoxicity


title: Single-cell analysis of hepatoblastoma identifies distinct tumor cell signatures that predict susceptibility to chemotherapy using patient-specific tumor spheroids

first: Hanbing

last: Song

address: 513 Parnassus Ave, HSE

department: Department of Medicine

institute: UCSF

summary:
Method: In this study we use single cell RNA sequencing (scRNA-seq) to distinguish HB tumor cells from non-tumor cells and to identify distinct tumor cell types that account for the heterogeneity of HB. We also use a novel method to grow HB tumor cells as patient-specific spheroids (PDS) and show how this can be used to predict treatment response and identify novel therapeutic targets.
Results: This study establishes that tumor heterogeneity can be defined by the relative proportions of five distinct subtypes of tumor cells. Notably, patient-derived HB spheroid cultures predict differential responses to treatment based on the transcriptomic signature of each tumor, suggesting a path forward for precision oncology for these tumors.
Conclusions: These results define HB tumor heterogeneity with single-cell resolution and demonstrate that patient-derived spheroids can be used to evaluate responses to chemotherapy.

overall_design: Single-cell RNA sequencing based on Seq-Well S^3 protocol of nine hepatoblastoma patients tumor tissues with matched normal samples and spheroid samples grown from the tumor tissues.

first: Simon

last: Bucher

first: Deviana

last: Burhan

first: Franklin

first: Amar

last: Nijagal

first: Bruce

last: Wang


title: ELK3 modulates the antitumor efficacy of natural killer cells against triple negative breast cancer by regulating mitochondrial dynamics

first: Joo Dong


title: Cmarr/miR-540-3p axis promotes cardiomyocyte maturation transition by orchestrating Dtna expression

first: Yukang

last: Wu

address: siping road 1239

institute: tongji university

summary: Here, our study showed that a heart-rich lncRNA, Cmarr, which is specifically upregulated during heart development, promoted the maturation transition of ESC-CMs. Cmarr interacted with miR-540-3p to increase the expression of Dtna (a key component of DGC), thus served as a new regulator of the DGC-YAP complex and cardiomyocyte maturation. Our study further identified that Cmarr could recover Dtna expression in the MI heart and attenuate the cardiac remodeling.

overall_design: RNA-seq and miRNA-seq of heart tissues

first: Xudong

last: Guo


title: Genome-wide maps of chromatin state in Huh 7 cells

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

summary: We report the application of chromatin immunoprecipitation sequencing (ChIPseq) and ATAC for high-throughput profiling of histone modifications in Huh 7 cells.

overall_design: ChIP-seq were performed with antibodies against acetylated H3K27 (H3K27ac), H3K4me1, and H3K4me3 and evaluated the open chromatin regions by assay for transposase-accessible chromatin with sequencing (ATAC-seq) to detect the genome-wide maps of chromatin state in HCC cells.

first: Zhiao

last: Chen


title: The effect of high altitudes and time-of-day on human whole-blood transcriptome

city: Rehovot

first: Saar

last: Ezagouri

address: Rehovot

country: Israel

institute: Weizmann Institute of Science

summary: High altitude exposes humans to hypobaric and hypoxic conditions, which induce various physiological and molecular changes. Recent evidence, mostly from animal models, points towards interaction between circadian rhythms and the hypoxic response, however their human relevance is largely unknown. To examine the interaction between elevated altitude-low oxygen and daily rhythms, we analyzed the effect of different high altitudes in conjunction with day-time on human whole blood transcriptome. We found that high altitude vastly affects the blood transcriptome and unexpectedly, does not necessarily follow a monotonic response to altitude elevation. We observed daily variance in gene expression, which was largely dependent on altitude. Moreover, using digital cytometry approach we estimated the relative changes in abundance of different cell types and found the several immune cell types were responding in a time- and altitude-dependent manner. Taken together, our data shed new light on the transcriptional response to high altitude and its interaction with daily rhythms.

overall_design: RNA sequencing of human whole blood samples collected in 4h intervals, throughout 24h at 3 different altitudes: Sea level (SL, Granoble, France), Puno (PU, Peru 3,800m), La Rinconada (RI, Peru 5,100m).

first: Gal

last: Manella

first: Benoit

last: Champigneulle

first: Jonathan

last: Gaucher

first: Monique

last: Mendelson

first: Emeline

last: Lemarie

first: Emeric

last: Stauffer

first: Aurélien

last: Pichon

first: Connor

last: A Howe

first: Stephane

last: Doutreleau

first: Marina

last: Golik

first: Samuel

last: Vergès

first: Gad

last: Asher


title: Nutrigenomics in Animal Feeding: Digital Gene Expression Analysis in Poultry Fed Tenebrio molitor Larvae Meal

status: Public on Feb 28 2022

city: Grugliasco

first: Dominga

last: Soglia

state: Torino

address: largo Braccini 2

department: Veterinary science

country: Italy

institute: Università degli Studi di Torino

summary: The purpose of this study was to investigate the effects of high levels of Tenebrio molitor dietary inclusion (15%) on molecular mechanisms that influence poultry health in a broiler chicken diet.

overall_design: The global gene expression of four tissues (breast, liver, jejunum, and caecum) was evaluated using the RNA-Seq approach.

first: Irene

last: Viola

first: Joana

last: Nery

first: Achille

last: Schiavone


title: RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription

city: New York

first: Abderhman

last: Abuhashem

address: Rockefeller Research Labs, 430 E 67th St

department: Developmental Biology Program

institute: Sloan-Kettering Institute for Cancer Research

summary: ChIP-seq experiments of NELFB (HA), NELFE, and Spt5 in mESCs under serum/LIF conditions. The experiments where performed with and without dTAG degradation of NELFB

overall_design: Duplicates per conditions. Cells were treated for 30 mins with 500nM dTAG-13, then collected for ChIP-seq protocol.

first: Anna-Katerina

last: Hadjantonakis


title: Transcriptome analysis of cardiac organoids derived from Duchenne Muscular Dystrophy patient-derived inudced pluripotent stem cells

city: Leuven

first: Yoke Chin

last: Chai

state: Leuven

address: Herestraat 49, ON5

department: Development & Regeneration

country: Belgium

institute: KU Leuven

summary: Duchenne muscular dystrophy (DMD) is a rare genetic disease that leads to progressive muscle weekness and loss of mobility. Dilated cardiomyopathy is the major cause of death however the pathogenesis remains unclear. This is partly due to the limited accessiblity to human samples, the intrinsic limitations of 2D cell cultures and animal models that do not fully recapitulate human disease phenotypes. We aim at developing patient-derived human 3D cardiac models with DMD-relevances to aid disease modeling, drug discovery and regenerative medicine.

overall_design: Bulk RNAseq of cardiac organoids derived from DMD-hiPSC and its isogenic-corrected control lines via CRISPR/Cas genome editing. (n = 3)

first: Vittoria

last: Marini

first: Fabiola

last: Marino

first: Nefele

last: Giarratana

first: Enrico

last: Pozzo

first: Robin

last: Duelen

first: Álvaro

middle: C

last: Calabuig

first: Maurilio

last: Sampaolesi

first: Yoke


title: Spatial charting of single-cell transcriptomes in tissues

status: Public on Feb 25 2022

city: Houston

first: Anil

middle: K

last: Sood

state: TX

address: 6767 Bertner Ave

department: genetics

institute: MDACC

summary: We performed single-cell RNA sequencing and spatial transcriptomics experiments on two ductal carcinoma in situ tissues and applied CellTrek to identify tumor subclones that were restricted to different ducts, and specific T cell states adjacent to the tumor areas. Our data show that CellTrek can accurately map single cells in diverse tissue types to resolve their spatial organization.

overall_design: We developed a computational method called CellTrek that combines single-cell RNA sequencing and spatial transcriptomics datasets to achieve single-cell spatial mapping through coembedding and metric learning approaches.

first: Runmin

last: Wei

first: Siyuan

last: He

first: Nicholas

last: Navin


title: Swine cecum development at single cell level

status: Public on Feb 27 2022

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: Different time point piglet cecum scRNA-seq

overall_design: scRNA-seq of pig cecum at different time points

first: Shen

last: Li

first: Hongu

last: Zhang

first: Wei

last: Ge

first: Liang

last: Chen

first: Qingshi

last: Meng


title: Production of vascularised kidney organoids with anatomically appropriate tubular organization and connection, solely from embryonic stem cells

city: Edinburgh

first: Mona

last: Elhendawi

state: Midlothian

address: 7 George Square

institute: The University of Edinburgh

summary:
Organoids generated from pluripotent stem cells typically possess accurate micro anatomy but lack the higher order organization of an organ, which limits how well they mimic real organs. In this study we present a method for engineering kidney organoids solely from mouse embryonic stem cells (mESC), with much improved higher-order anatomy. mESC were differentiated to ureteric bud (iUB), nephron (iNP) and stromal lineages (iSP); pure progenitor populations were sorted and their expression profiles were compared to their embryonic day (E) 11.5 and 12.5 counterpart.
Results: Comparative analysis showed the similarity of iUB progenitors to both E11.5 and E12.5 UB cells. However, both iNP and iSP were distinct from their ex-fetu counterparts.

overall_design: RNA profiles of the iUB, iNP, and iSP were compared to that of the E11.5 and E12.5 equivalant. 36 samples were included and are divided into nine groups (each group has four different repeats)

first: Anwar

last: Palakkan

first: Julia

last: Tarnick

first: Martin

last: Waterfall

first: May

last: Sallam

first: Fokion

last: Glykofrydis

first: Jamie

last: Davies


title: Induction of potassium channel regulator KCNE4 in the submandibular lymph nodes of a melanoma metastasis model

status: Public on Feb 23 2022

city: Fukuoka

first: Tomoko

last: Tanaka

address: 7-45-1 Nanakuma, Jonan-ku

institute: Fukuoka University

summary: The process of metastasis starts even before the tumor cells actually metastasize to the lymph nodes. In this study, mice were injected with B16-F10 murine melanoma cells to generate a tongue submandibular lymph node (SLN) metastasis model in which to investigate genes of interest.

overall_design: B16-F10 or PBS was injected into the tongue of C57BL/6 mice, and submandibular lymph nodes (SLNs) were collected 3 days later. Sample; SLNs of mice implanted with B16-F10, Control; SLNs of mice injected with PBS.

first: Ryosuke

last: Mano


title: Prediction of sex-determination mechanisms in avian primordial germ cells using RNA-seq analysis

status: Public on Feb 24 2022

city: Midlothian

first: Kennosuke

last: Ichikawa

address: Easter Bush Campus

department: The Roslin Institute

summary: Avian sex is determined by various factors, such as the dosage of DMRT1 and cell-autonomous mechanisms. While the sex-determination mechanism in gonads is well analyzed, the mechanism in germ cells remains unclear. In this study, we explored the gene expression profiles of male and female primordial germ cells (PGCs) during embryogenesis in chickens to predict the mechanism of sex-determination. Male and female PGCs were isolated from blood and gonads with a purity > 96% using flow cytometry and analyzed using RNA-seq. Prior to settlement in the gonads, female circulating PGCs (cPGCs) obtained from blood displayed sex-biased expression. Gonadal PGCs (gPGCs) also displayed sex-biased expression, and the number of female-biased genes detected was higher than male-biased genes. The female-biased genes in gPGCs were enriched in some metabolic processes. To reveal the mechanisms underlying the transcriptional regulation of female-biased genes in gPGCs, we performed stimulation tests. Stimulation with retinoic acid against cultured gPGCs derived from male embryos resulted in the upregulation of several female-biased genes. Overall, our results suggest that sex determination of avian PGCs possess aspects of both cell-autonomous and somatic cell regulation. Moreover, it appears that sex determination occurs earlier in females than in males.

overall_design: Examination of 3 different developmental stage for each sex. Biological replicates = 2

first: Yoshiaki

last: Nakamura

first: Hidemasa

last: Bono

first: Ryo

last: Ezaki

first: Mei

last: Matsuzaki

first: Hiroyuki

last: Horiuchi


title: Gene expression profiles of PRMT1 knockdown adipocytes

city: Guangzhou

first: Qi

last: Zhu

state: Guangdong

address: Sun Yat-sen University, Guangzhou, Guangdong, 510006, China

department: School of Life Sciences

institute: Sun Yat-sen University

summary: We attempted to analyze the effect of PRMT1 knockdown in adipogenesis.3T3-L1 preadipocytes were used to investigate aipogenesis in vitro. Analysis of the transcriptomics from siNC and siPRMT1 3T3-L1 cells at MDI induction for 24 h and 72 h provides new insight into the collective roles of PRMT1 in mitotic clonal expansion and adipocyte differentiation.

overall_design: mRNA profiles of siNC and siPRMT1 3T3-L1 cells at MDI induction for 24 h and 72 h.

first: Dinghui

last: Wang

first: Feng

last: Liang


title: Transcriptional heterogeneity in primary and metastatic gastric cancer revealed using single-cell RNA sequencing

status: Public on Feb 22 2022

city: Hangzhou

first: penghui

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

institute: Pharmaceutical Informatics Institute

summary: Deciphering intra- and inter-tumoral heterogeneity is essential for understanding gastric cancer (GC) biology and identifying effective therapeutic targets. We used single-cell RNA sequencing (scRNA-seq) to reveal the transcriptional heterogeneity of diverse cells within primary and metastatic GC and their roles in disease progression.

overall_design: We performed unbiased scRNA-seq analysis of 42,968 cells from 10 fresh human tissue samples from six patients. Primary tumor and adjacent non-tumoral samples and six metastases from different organs or tissues (liver, peritoneum, ovary, lymph node) were evaluated. Validation experiments were performed using histological assays and bulk transcriptomic datasets.

first: Haiping

last: Jiang

first: Dingyi

last: Yu

first: Penghui


title: Hepatoprotective effects of semaglutide, lanifibranor and dietary intervention in the GAN diet-induced obese and biopsy-confirmed mouse model of NASH

status: Public on Feb 21 2022

city: Hørsholm

first: Martin

middle: Rønn

last: Madsen

state: Please Select

address: Hørsholm Kongevej 11

department: Computation Biology

country: Denmark

institute: Gubra

summary: Non-alcoholic steatohepatitis (NASH) has emerged as a major challenge for public health because of high global prevalence and lack of evidence-based therapies. Most animal models of NASH lack sufficient validation regarding disease progression and pharmacological treatment. The Gubra-Amylin NASH (GAN) diet-induced obese (DIO) mouse demonstrate clinical translatability with respect to disease etiology and hallmarks of NASH. This study aimed to evaluate disease progression and responsiveness to clinically effective interventions in GAN DIO-NASH mice. Disease phenotyping was performed in male C57BL/6J mice fed the GAN diet high in fat, fructose and cholesterol for 28-88 weeks. GAN DIO-NASH mice with biopsy-confirmed NASH and fibrosis received low-caloric dietary intervention, semaglutide (30 nmol/kg/day, s.c.) or lanifibranor (30 mg/kg/day, p.o.) for 8 and 12 weeks, respectively. Within-subject change in NAFLD Activity Score (NAS) and fibrosis stage was evaluated using automated deep learning-based image analysis. GAN DIO-NASH mice showed clear and reproducible progression in NASH, fibrosis stage and tumor burden with high incidence of hepatocellular carcinoma. Consistent with clinical trial outcomes, semaglutide and lanifibranor improved NAS, while only lanifibranor induced regression in fibrosis stage. Dietary intervention also demonstrated substantial benefits on metabolic outcomes and liver histology. Differential therapeutic efficacy of dietary intervention, semaglutide and lanifibranor was supported by quantitative histology, RNA sequencing, and blood/liver biochemistry. In conclusion, the GAN DIO-NASH mouse model recapitulates various histological stages of NASH and faithfully reproduces histological efficacy profiles of compounds in advanced clinical development for NASH. Collectively, these features highlight the utility of GAN DIO-NASH mice in preclinical drug development.

overall_design: Experiment 1: 8 and 12 week treatment with Lanifibranor and Semaglutide in GAN DIO-NASH mice. Experiment 2: 12 weeks of chow-reversal intervention in GAN DIO-NASH mice.

first: Mathias

last: Møllerhøj

first: Henrik

last: Hansen


title: Genome-wide mapping of H3K27 tri-methylation in PRC2 components of Pyricularia oryzae

status: Public on Feb 20 2022

first: Chuyu

last: Lin

address: 866#, Yuhangtang Road

department: College of Agriculture and Biotechnology

institute: Zhejiang University

summary: We report different roles of three PRC2 components, KMT6, P55 and SIN3 played in distribution of genome-wide H3K27 tri-methylation of Pyricularia oryzae. Polycomb repressive complex 2 (PRC2), which is composed of Ezh(Kmt6), Su(z)12, Esc(Eed) and accessory subunits RbAp48/Nurf55(P55), catalyzes the methylation of histone H3 at lysine 27. Loss of P55 caused severe global defects in the normal distribution of H3K27me3 and transcriptional reprogramming on the H3K27me3-occupied genes. Furthermore, we found that the Sin3 histone deacetylase complex was required to sustain H3K27me3 occupancy and stably maintain gene repression by directly interacting with P55.

overall_design: Examination of H3K27 tri-methylation of different PRC2 components of Pyricularia oryzae. Two biological replicates were performed.

first: Zeng

last: Tao


title: Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes

status: Public on Feb 17 2022

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road, 260 EMRB

department: Biochemistry

institute: University of Iowa

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

overall_design: Refer to individual Series


title: Integrative small and long RNA-omics analysis of human healing and non-healing wounds discovers cooperating microRNAs as therapeutic targets

status: Public on Feb 16 2022

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

summary:
We identified pathologically relevant miRs that exhibited abnormal VU expression and displayed their targets enriched explicitly in the VU gene signature.
The biological function of these miRNAs in human epidermal keratinocytes or fibroblasts during wound repair remains unclear.
To study the genes regulated by miR-96-5p, miR-218-5p, miR-424-5p, miR-450b-5p, miR-516b-5p or miR-7704, we transfected miRNA mimics into human primary epidermal keratinocytes or fibroblasts to overexpress respective miRNA expression.
We performed a global transcriptome analysis of keratinocytes or fibroblasts upon miRNA overexpression using Affymetrix arrays.

overall_design: Gene expression profiling of keratinocytes or fibroblasts transfected with either miRNA mimics control (n = 3) or respective miRNA mimics (n =3 for each miRNA) for 24 hours was carried out by using human Clariom™ S assay (ThermoFisher Scientific) at the Bioinformatics and Expression Analysis (BEA) core facility at Karolinska Institutet.

middle: X

last: Landén

first: Zhuang

last: Liu

first: Letian

last: Zhang


title: The wound activated ERF15 transcription factor drives Marchantia polymorpha regeneration by activating an oxylipin biosynthesis feedback loop

status: Public on Feb 19 2022

city: Zwijnaarde

first: Lieven

last: De Veylder

address: Technologiepark 71

institute: VIB-UGent Center for Plant Systems Biology

summary: The regenerative potential in response to wounding varies largely along species. Within the plant lineage, the liverwort Marchantia polymorpha displays an extraordinary regeneration capacity. However, its molecular pathways controlling the initial regeneration response post wounding is currently unknown. In Arabidopsis, the transcription factor ETHYLENE RESPONSE FACTOR 109 (ERF109) plays an essential role in tissue regeneration. Here, we demonstrate that the Marchantia MpERF15 transcription factor gene represents a functional ortholog of ERF109, being instantly activated following wounding and being essential for gemmaling regeneration following tissue incision. MpERF15 is a downstream target of the MpCOI1 oxylipin receptor, but differently from Arabidopsis ERF109 its wound responsiveness is COI1 independent. At the other hand, and again differently from ERF109, MpERF15 drives oxylipin biosynthesis by controlling the upstream MpAOS2 and MpAOC biosynthesis genes. The resulting rise in the oxylipin dnOPDA levels results in an increase in gemma cell number and apical notch organogenesis, giving rise to highly disorganized and compact thalli. Our data pinpoint MpERF15 as a key factor activating an oxylipin biosynthesis amplification loop following wounding that eventually results in re-activation of cell division and regeneration, and suggest that the genetic networks controlling oxylipin biosynthesis in response to wounding might have been reshuffled over evolution.

overall_design: Three biological replicates of Tak-1 or Mperf15ko 14-day-old thalli wounded after 1h were compared with three biological replicates of Tak-1 or Mperf15ko thalli under unwounded control conditions.

first: Yuanke


title: Expression and 5' end mapping data for Mycobacterium tuberculosis with deletion of Rv2752c/rnj

city: Boston

first: Scarlet

middle: Sara

last: Shell

state: MA

address: 665 Huntington Ave, SPH 1 Room 802

department: Immunology and Infectious Diseases

institute: Harvard School of Public Health

summary: We used three M. tuberculosis strains (WT H37Rv, an RV2752c deletion mutation, and the mutant complemented with an Rv2752c overexpression construct), extracted RNA from log phase cultures, and made RNAseq expression libraries as well as 5'-end-directed libraries.

overall_design: Comparison of gene expression and 5' end abundance in the presence, absence, and overexpression of Rv2752c (encoding RNase J). Two replicates were used for each strain. Expression libraries and 5' end mapping libraries were made from the same RNA samples.

first: Sarah

last: Fortune

first: Maria

last: Martini

first: Nathan

last: Hicks


title: Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer [RNA-seq]

status: Public on Feb 15 2022

city: LEBANON

first: Diwakar

middle: Pattabiraman

last: Pattabiraman

state: NH

address: 1 Medical Center Drive

department: Molecular and Systems Biology

institute: Geisel School of Medicine at Dartmouth

summary: The Epithelial-to-Mesenchymal Transition (EMT) is a dynamic cellular program that is frequently used by cancer cells to increase migratory and invasive cell characteristics. It is a key contributor to both heterogeneity and chemo-resistance and metastasis in many solid tumors, including triple negative breast cancer. In particular, the intermediate or hybrid EMT state has increased tumor initiating and stem-like properties. Here, we have identified multiple distinct EMT states derived from the human breast cell line, SUM149PT, including three unique intermediate states, possessing distinct migratory, tumor initiating, and metastatic qualities. We have used this model to interrogate the epigenetic landscape of these distinct EMT states in a multi-omics approach, identifying and RUNX2 as relevant in regulating the intermediate state, as well as to develop a novel multiplexed staining approach to evaluate E-M heterogeneity (EMH) and overall EMT score in orthotopic tumors as well as patient tumor samples. This model reveals insights into the complex EMT spectrum of cell states, the networks that control them, and how EMT plasticity contributes to tumor heterogeneity in breast cancer.

overall_design: Single-end RNA-sequencing of three replicates per cell line (7). No treatments

first: Meredith

last: Brown

middle: R

first: Owen

middle: M

last: Wilkins


title: Pkd1 and Pkd2 mRNA cis-inhibition drives polycystic kidney disease progression [Pkd1]

status: Public on Feb 11 2022

city: Dallas

first: Ronak

last: Lakhia

state: Texas

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UTSW

summary: We report the findings of deletion of the miR17 binding motif from Pkd1 mRNA

overall_design: examination of RNA from whole kidney lysates from control and cystic

first: Vishal

last: Patel


title: Pkd1 and Pkd2 mRNA cis-inhibition drives polycystic kidney disease progression [Pkd2]

summary: We report the findings of deletion of the miR17 binding motif from Pkd2 mRNA

overall_design: examination of RNA from whole kidney lysates


title: Monocyte and macrophage lipid accumulation results in downregulated type-I interferon responses I

status: Public on Feb 10 2022

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

institute: Amsterdam UMC - locatie AMC

summary: Macrophages are critical components of atherosclerotic lesions and their pro- and anti-inflammatory responses influence atherogenesis. Type-I interferons (IFNs) are cytokines that play an essential role in antiviral responses and inflammatory activation and have been shown to promote atherosclerosis. Although the impact of type-I IFNs on macrophage foam cell formation is well-documented, the effect of lipid accumulation in monocytes and macrophages on type-I IFN responses remains unknown. Here we examined IFN stimulated (ISG) and non-ISG inflammatory gene expression in mouse and human macrophages that were loaded with acetylated LDL (acLDL), as a model for foam cell formation. We found that acLDL loading in mouse and human macrophages specifically suppressed expression of ISGs and IFN-β secretion, but not other pro-inflammatory genes. The downregulation of ISGs could be rescued by exogenous IFN-β supplementation. Activation of the cholesterol-sensing nuclear liver X receptor (LXR) recapitulated the cholesterol-initiated type-I IFN suppression. Additional analyses of murine in vitro and in vivo generated foam cells confirmed the suppressed IFN signalling pathways and suggest that this phenotype is mediated via downregulation of interferon regulatory factor binding at gene promoters. Finally, RNA-seq analysis of monocytes of familial hypercholesterolemia (FH) patients also showed type-I IFN suppression which was restored by lipid-lowering therapy and not present in monocytes of healthy donors. Taken together, we define type-I IFN suppression as an athero-protective characteristic of foamy macrophages. These data provide new insights into the mechanisms that control inflammatory responses in hyperlipidaemic settings and can support future therapeutic approaches focusing on reprogramming of macrophages to reduce atherosclerotic plaque progression and improve stability.

overall_design:
Familial hypercholesterolemic patients and healthy subjects: the study population, design, and further processing of these human study subjects and their samples have been extensively described (Stiekema et al., 2021). Briefly, untreated FH patients who indicated to start lipid-lowering therapy (statin, PCSK9 antibody, and/or ezetimibe) according to their treating physician were included. The healthy controls were age, sex, and body mass index (BMI) matched with the FH patients. After inclusion, FH patients fasted for at least 9 hours before blood samples were drawn for lipid measurements and monocyte isolation. This was repeated after 12 weeks of lipid-lowering therapy.

RNA-Seq raw data is made available through the European Genome-phenome Archive (EGA) due to patient privacy concerns:
https://ega-archive.org/datasets/EGAD00001008967

first: Hung-Jen

last: Chen

first: Cindy

middle: P

last: van Roomen

first: Guillermo

last: Griffith

first: Ricky

last: Siebeler

first: Annette

middle: E

last: Neele

first: Jeffrey

last: Kroon

first: Marten

middle: A

last: Hoeksema

first: Menno

last: de Winther


title: Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer


title: Partial Tendon Injury at the Tendon-to-Bone Enthesis Activates Skeletal Stem Cells

status: Public on Feb 14 2022

city: Tucson

first: Kellen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

summary: Partial tendon-to-bone interface (TBI) injuries heal in a mechanically inferior manner and redevelop healthy uninjured tissue morphology. The origin of the cells involved in tendon-to-bone healing remains unknown. We employed a rigorous approach to evaluate if mouse skeletal stem cells (mSSC) play a role in tendon-to-bone healing after partial-injury. Using fluorescence-activated cell sorting we identified that found that they are present within the TBI. Using a TBI-injury rainbow lineage tracing mouse model, we demonstrated that injury-responsive cells within the TBI and calcaneus proliferate polyclonally following partial-tendon injury at the TBI. These injury-responsive clonal cells express skeletal marker SP7. We quantified the differences in mSCC frequency after TBI-injury and found that mSSC respond to injury with a higher frequency and have associated changes in gene expression, with the specific down-regulation of the TGFβ signaling pathway. Exogenous delivery of TGFβ after injury was found to reduce the mSSC response after injury. These findings suggest that mSSC may facilitate tendon-to-bone healing by downregulating TGFβ signaling within the mSSC niche.

overall_design: RNA-seq was performed in sham control, uninjured, and partially injured mSSCs at post injury day 7.

first: Ashley

last: Titan

first: Michael

last: Longaker

last: Januszyk


title: Transcriptional atlas of the cytokine drivers and cellular contributors mediating enhanced SARS-CoV-2 lung pathology in hamsters after non-protective immunization

status: Public on Feb 08 2022

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

summary: Since December 2019, the novel human Coronavirus SARS-CoV-2 has spread globally, causing millions of deaths. Unprecedented efforts have enabled development and authorization of a range of vaccines, which reduce transmission rates and confer protection against the associated disease COVID-19. These vaccines are conceptually diverse, including e.g. classical adjuvanted whole-inactivated virus, viral vectors, and mRNA vaccines.  We have analysed two prototypic model vaccines, the strongly TH1-biased measles vaccine-derived candidate MeVvac2-SARS2-S(H) and a TH2-biased Alum-adjuvanted, non-stabilized Spike protein side-by-side, for their ability to protect Syrian hamsters upon challenge with a low-passage SARS-CoV-2 patient isolate. The MeVvac2-SARS2-S(H) vaccine protected the hamsters from severe disease. In contrast, the protein vaccine induced vaccine-associated enhanced respiratory disease (VAERD) with massive infiltration of eosinophils into the lungs. Global RNA-Seq analysis of hamster lungs revealed reduced viral RNA and less host dysregulation in MeVvac2-SARS2-S(H) vaccinated animals, while S protein vaccination triggered enhanced host gene dysregulation when compared to unvaccinated control animals. Of note, mRNAs encoding the major eosinophil attractant CCL-11, the TH2 response-driving cytokine IL-19, as well as TH2-cytokines IL-4, IL-5, and IL-13 were exclusively up-regulated in the lungs of S protein vaccinated animals, consistent with previously described VAERD induced by RSV vaccine candidates. IL-4, IL-5, and IL-13 were also up-regulated in S-specific splenocytes after protein vaccination. Using scRNA-Seq, T cells and innate lymphoid cells were identified as the source of these cytokines, while CCL11 and IL-19 mRNAs was found in interstitial macrophages displaying an activated phenotype. Interestingly, the amount of viral reads in this macrophage population correlated with the abundance of Fc-receptor reads. These findings suggest that VAERD is triggered by induction of TH2-type helper cells secreting IL-4, IL-5, and IL-13, together with stimulation of macrophages dependent on Fc-receptor mediated uptake of virus complexed with non-neutralizing antibodies. Via this mechanism, uncontrolled eosinophil recruitment to the infected tissue occurs, a hallmark of VAERD immunopathogenesis. These effects could effectively be treated using dexamethasone and were not observed in animals vaccinated with MeVvac2-SARS2-S(H).  Taken together, our data validate the potential for, and identify the transcriptional mediators that underlie VAERD and their cellular origins, in the context of protein-based TH2-biased COVID-19 vaccines. Dexamethasone, which is already in use for treatment of severe COVID-19, may alleviate such VAERD, but in-depth scrutiny of any next-generation protein-based vaccine candidates is required, prior and after their regulatory approval.

overall_design: To identify determinants underlying the differential protection or pathology arising from TH1- or TH2-biased vaccination approaches, we performed RNA-Seq profiling of hamster lung tissue. Lung transcriptomes from SARS-CoV-2 infected hamsters were compared to infected animals previously immunized with either TH1- or TH2-biased vaccines. We subjected RNA of four animals per group (four groups) to NextSeq 550 Illumina RNAseq using a single-end 86 bp setting.

first: Aileen

last: Ebenig

first: Samada

last: Muraleedharan

first: Julia

last: Kazmierski

first: Arne

last: Auste

first: Martina

last: Anzaghe

first: André

last: Gömer

first: Dylan

last: Postmus

first: Patricia

last: Gogesch

first: Marc

last: Niles

first: Roland

last: Plesker

first: Csaba

last: Miskey

first: Michelle

last: Serra

first: Angele

last: Breithaupt

last: Hörner

first: Carina

last: Kruip

first: Rosina

last: Ehmann

first: Zoltan

last: Ivics

first: Zoe

last: Waibler

first: Stephanie

last: Pfaender

first: Emanuel

last: Wyler

first: Markus

last: Landthaler

first: Alexandra

last: Kupke

first: Geraldine

last: Nouailles

first: Christine

last: Goffinet

first: Richard

middle: J

last: Mühlebach


title: Pkd1 and Pkd2 mRNA cis-inhibition drives polycystic kidney disease progression

first: Ronak

last: Lakhia

first: Vishal

last: Patel


title: Rumen fluid miRNAome of dry cows transitioned from forage to 65% grain diet

status: Public on Feb 03 2022

city: Vienna

first: Cátia

last: Pacífico

state: Vienna

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

summary: This study aimed to explore the changes in miRNAome in the rumen fluid during diet transition from forage to high-grain.

overall_design: Rumen fluid was collected from 4 ruminally-canulated non-lactating Holstein cows fed a 100% baseline forage diet (FD) and then transitioned to high-grain (HG; 65% concentrate) feeding.

first: Catia

last: Pacifico

first: Susanne

last: Kreuzer-Redmer


title: RNA sequencing analysis for cellular metabolic pathway in MARCHF6 Knock-Out HeLa cell lines

status: Public on Feb 01 2022

city: Pohang

first: Cheol-Sang

last: Hwang

state: Gyeongbuk

address: 77, Cheongam-ro

department: Department of Life Sciences

institute: POSTECH

summary: Analysis of cellular metobolic differences between wild-type and MARCHF6-/- from HeLa cell lines.

overall_design: Total RNA was obtained from HeLa wild type  and HeLa MARCHF6 KO cell lines in triplicate and then RNA-seq was perform.

first: Sang-hyeon

last: Mun

first: The

last: Nguyen

first: Cheol-sang


title: Interaction between PPARγ and mTORC1 in the regulation of inguinal white adipose tissue transcriptome

first: NORC

last: Boston

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

summary: Purpose: To investigate the involvement of mTORC1 as a mediator of the actions of the PPARγ ligand rosiglitazone in subcutaneous inguinal white adipose tissue transcriptome; Methods: Mice bearing regulatory associated protein of mTOR (Raptor) deletion and therefore mTORC1 deficiency exclusively in adipocytes (adiponectin Cre recombinase) and littermate controls were fed a high-fat diet supplemented or not with the PPARγ agonist rosiglitazone (30 mg/kg/day) for 8 weeks and evaluated for inguinal white adipose tissue transcriptome (Rnaseq); Results: 3,2425 genes had their correspondent mRNA levels altered by either adipocyte Raptor deficiency or rosiglitazone administration or their combination. Among those, 408 genes modulated by rosiglitazone required mTORC1. Conclusion: PPARγ and mTORC1 are essential partners in the regulation of a cluster of genes in inguinal white adipose tissue.

first: Maynara

middle: L

last: Andrade

first: William

middle: T

last: Festuccia


title: Human Blood Brain Barrier treated by Insulin

status: Public on Feb 05 2022

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

summary: This study aims to map the dynamics of insulin-responsive pathways in polarized human cerebral microvascular endothelial cell (hCMEC/D3) monolayers, a widely used BBB cell culture model, to elucidate molecular mechanisms underlying BBB dysfunction in AD.

overall_design: RNA-Sequencing (RNA-Seq) was performed on hCMEC/D3 monolayers with and without insulin treatment at various time points.

first: Krishna

last: Kalari


title: Metabolic reprogramming in livers from LKB1 KO mice

status: Public on Jan 28 2022

city: Bethesda

first: Natalie

last: Porat-Shliom

state: MD

address: Building 10, Room 12C207 MSC 1

department: Thoracic and GI Malignancies Branch

institute: National Cancer Institute

summary:
The goals of this study was to compare hepatic transcriptome profiling (RNA-seq) in wild type (WT) and Liver Kinase B1 knock out (LKB1 KO) mice
Methods: hepatocyte mRNA profiles of 10-weeks-old WT and LKB1 KO mice were generated, in triplicate, using Illumina NextSeq technology. The sequence reads that passed quality filters were analyzed at the gene level.

overall_design: Three 6 weeks old wild type (WT) and 3 LKB1 fl/fl mice were injected with AAV8 Cre. Livers were harvested for analysis 4 weeks after.

first: Suehelay

last: Acevedo-Acevedo

first: Alexei

last: Lobanov


title: RNA sequencing of primary Sjögren’s syndrome neutrophils

status: Public on Jan 25 2022

city: Beijing

first: Yu

last: Peng

address: No. 1, Shuaifu yuan

institute: Peking Union Medical College Hospital

summary:
Objective Neutrophils and aberrant NETosis have been implicated in the pathogenesis of diverse autoimmune diseases, however, their roles in primary Sjögren’s syndrome (pSS) remain unclear. We aimed to reveal the potential roles of neutrophils and neutrophil extracellular traps (NETs) in this study.
Methods pSS patients were enrolled according to the corresponding diagnostic criteria. NETosis markers were measured in plasma and small salivary gland using ELISA and immunofluorescence. The gene signatures of neutrophils were assessed by RNA-Seq and RT-PCR. Reactive oxygen species (ROS), mitochondrial ROS (mitoROS) production and JC-1 was measured by flow cytometry.
Results NETosis markers including cell free-DNA (cf-DNA), myeloperoxidase (MPO) in plasma and small salivary gland from pSS patients were significantly higher than healthy controls (HCs) and were associated with disease activity. RNA sequencing and RT-qPCR revealed activated Type I IFN signaling pathway and higher expression of type I interferon related genes in pSS neutrophils. Further stimulating with IFN-α 2a in vitro significantly induced ROS production and JC-1 monomer percentage  in pSS neutrophils.
Conclusions Our data suggest the involvement of neutrophils and enhanced NETosis in pSS patients. Further mechanism study in vitro revealed that type I IFN activation in pSS neutrophils led to mitochondrial damage and related ROS production which finally result in the generation of NETs.

overall_design: RNA sequencing of 7 pSS patients and 6 healthy controls

first: Xunyao

last: Wu

first: Shulan

last: Zhang

first: Yunyun

last: Fei


title: GD2-CAR T-cell therapy for H3K27M-mutated diffuse midline gliomas

status: Public on Feb 07 2022

city: Stanford

first: Michelle

last: Monje

state: CA

address: 265 campus drive, SIM1 G3035

department: Neurology

institute: Stanford University

summary: Diffuse intrinsic pontine glioma (DIPG) and other H3K27M-mutated diffuse midline gliomas (DMGs) are universally lethal central nervous system (CNS) tumors that occur most commonly in children and young adults1. Average life expectancy is ten months from diagnosis, and 5-year survival is less than 1%2. Palliative radiotherapy is the only established treatment3, and neither cytotoxic nor targeted pharmacological approaches have demonstrated anti-tumor responses or improved prognosis to date3,4. We previously discovered that the disialoganglioside GD2 is highly and uniformly expressed on H3K27M+ DMG cells and demonstrated that intravenously (IV) administered GD2.4-1BB.z chimeric antigen receptor (CAR) T-cells eradicated established DMGs in patient-derived orthotopic murine models5, thereby providing the rationale for a first-in-human/first-in-child Phase 1 clinical trial (NCT04196413). Because CAR T-cell-induced inflammation and edema of the brainstem can result in obstructive hydrocephalus, increased intracranial pressure, and dangerous tissue shifts, a number of neurocritical care precautions were incorporated in the clinical trial design and management plan. Here we present the clinical experience from the first four patients with H3K27M+ DMG treated with GD2-CAR T-cells at dose level 1 (DL1; 1e6 GD2-CAR T-cells/kg administered IV). Patients who exhibited clinical benefit were eligible for subsequent administrations of GD2-CAR T-cells. Given preclinical evidence for increased CAR T-cell potency6, and the potential for diminished immunogenicity with locoregional administration, second doses were administered intracerebroventricularly (ICV) through an Ommaya catheter to three patients. As predicted from preclinical models, toxicity was largely related to the neuroanatomical location of the tumors and was reversible with intensive supportive care. Although GD2 is expressed at low levels in normal neural tissue, no evidence of on-target, off-tumor toxicity was observed. Three of four patients exhibited clinical and radiographic improvement, underscoring the promise of this approach for H3K27M+ DMG therapy. Correlative studies of serum and CSF revealed marked proinflammatory cytokine production following GD2 CAR T cell administration and single cell transcriptomic analysis of 65,598 single cells from CAR T cell products and patient CSF has begun to reveal differences that correlate with the heterogeneity between subjects and routes of administration.

overall_design:
10X mRNA sequencing of human patient CAR-T cell products and longitudinal sampling of cerebrospinal fluid during CAR-T therapy.
NOTE FROM SUBMITTER: Due to patient privacy concerns, we are withholding raw sequencing data files.

first: Shawn

last: Gillespie

first: Zina

last: Good


title: Acetylation-specific interference by anti histone H3K9ac intrabody results in precise modulation of gene expression

status: Public on Jan 30 2022

city: PISA

first: antonino

last: cattaneo

address: piazza dei calieri, 7

institute: Scuola Normale Superiore

summary: The goal of this study is to compared the global gene expression changes driven by the histone PTM-selective interference with those induced by the inhibition of the corresponding modifying enzymes.  We chose site-specific histone H3 acetylation as a target for this comparison, and we investigated the transcriptomic response in yeast cells, either expressing the intrabody anti-H3K9ac scFv-58F  or treated with HATs inhibitors (Curcumin and CPTH2)

overall_design: Three yeast strains were used: the pL200-58F-HA strain, stably expressing the scFv-58F-HA, the pL200-645-HA strain expressing an unrelated intrabody scFv-645-HA (an anti neuroligin-2 intrabody) and a pL220-HA strain, carrying the empty vector pL220.   Inhibition of histone H3 acetylation was obtained by treating the control yeast strain pL220-HA with either Curcumin (200 µM) or CPTH2 (400 µM) in SD-L media for 1 hour (see Fig. S1).   The baseline control was represented by pL220-HA cells treated with the same concentration of DMSO (0.4%) used to dissolve the drugs.   Total RNA was extracted from pL220-HA grown either in presence of Curcumin or CPTH2,  as well as from pL200-HA, pL200-58F-HA or pL220-645-HA (the two intrabody-expressing strains), and RNA samples underwent RNA-sequencing (RNA-seq) analysis. Differential gene expression (DEG) analysis was performed, comparing either the two HATi-treated or the two intrabody-expressing conditions against the DMSO-treated baseline control condition.

first: Simonetta

last: Lisi

first: Matteo

last: Trovato

first: Ottavia

last: Vitaloni

first: Marco

last: Groth

last: Fantini

first: Paola

last: Tognini

first: Michele

last: Chirichella

first: Sara

last: Cornuti

first: Mario

last: Costa

first: Antonino

last: Cattaneo


title: Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer [ATAC-seq]

first: Diwakar

last: Pattabiraman

overall_design: Paired-end RNA-sequencing of 2 replicates per cell line (7). No treatments or controls

first: Meredith

middle: S

last: Brown

first: Owen

last: Wilkins


title: Intercellular transfer of miR-200c-3p impairs the angiogenic capacity of cardiac endothelial cells

status: Public on Jan 31 2022

city: Maastricht

first: Jana

last: Hegenbarth

state: Limburg

address: Universiteitssingel 50

department: Department of Molecular Genetics

institute: Maastricht University

summary: We identify miR-200c-3p as a microRNA to be enriched in cardiomyocyte (CM)-derived EVs under conditions of hypertrophic stress. This miRNA is transferred from CMs to cardiac endothelial cells (ECs) where it will impair endothelial cell function.RNA sequencing was performed to identify the mechanisms and genes that are under direct or indirect control of miR-200c and that could explain the phenotypes observed.

overall_design: Endothelial cells were transfected with either a scrambled precursor molecule (control) or a precursor molecule specific for miR-200c-3p. The two groupd were compared regarding gene expression (mRNA)

first: L

last: Ottaviani

first: R

last: Juni

last: de Abreu

first: M

last: Sansonetti

first: V

last: Sampaio-Pinto

first: J

last: Halkein

first: JC

first: N

last: Ring

first: K

last: Knoops

last: Kocken

first: C

last: de Jesus

first: A

last: Ernault

first: H

last: el Azzouzi

first: F

last: Rühle

first: S

last: Olieslagers

last: Fernandes

last: Ferreira

last: Braga

last: Stoll

first: D

last: Nascimento

last: de Windt

first: P

last: da Costa Martins


title: Systemic Delivery of an AAV9 Exon Skipping Vector Significantly Improves or Prevents Features of Duchenne Muscular Dystrophy in the Dup2 Mouse Model

status: Public on Jan 29 2022

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

summary:
Purpose: Duchenne muscular dystrophy (DMD) is typically caused by mutations that disrupt the DMD reading frame, but nonsense mutations in the 5’ part of the gene lead to the utilization of an internal ribosomal entry site (IRES) in exon 5, resulting in expression of a highly functional N-truncated dystrophin. We have developed an AAV9 vector expressing U7 small nuclear RNAs targeting DMD exon 2 and tested it in a mouse model containing a duplication of exon 2, in which skipping of both exon 2 copies results in IRES-induced expression, and skipping of only one exon 2 leads to wild-type dystrophin expression.
Methods: One-time intravascular injection of an AAV9 vector expressing U7 small nuclear RNAs targeting Dmd exon 2 at either P0-P1 or at 2 months of age results in efficient exon skipping and dystrophin expression, and significant protection from functional and pathologic deficits.
Results: In mice treated neonatally, dystrophin immunofluorescence reached 49-85% of normal signal intensity and 76-99% dystrophin-positive fibers, with near-complete correction of dystrophic pathology, and these beneficial effects showed no significant signs of declining for at least 6 months. RNA sequencing (RNA-Seq) and Ribosome Profiling (RPF-Seq) indicated that treatment restored a ‘non-dystrophic’ gene expression profile by reversing the direction and magnitude of differentially expressed genes previously identified in dystrophic skeletal muscle from DMD patients. The dystrophin transcript showed clearly increased RPF reads in the treated sample, indicating that the treatment specifically increased dystrophin translation.
Conclusions: The results demonstrate the robustness, durability, and safety of exon 2 skipping following delivery of scAAV9.U7snRNA.ACCA, supporting its clinical use.

overall_design: Skeletal muscle mRNA and ribosome footprinting profiles from Dmd Dup2 mice treated with an AAV9 exon skipping vector


title: Viability of discarded human livers during normothermic machine perfusion is associated with activation of repair mechanisms

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

summary:
Background and Aims: Liver transplantation provides an effective cure for end-stage liver disease but is hampered by a severe organ shortage. Normothermic machine perfusion (NMP) of donor livers allows dynamic preservation in addition to viability assessment prior to transplantation. Little is known about the injury and repair mechanisms induced during NMP. Therefore, we examined gene and protein expression changes in a cohort of discarded human livers during NMP, stratified by liver viability.
Approach and Results: 6 human livers from donation after circulatory death (DCD) underwent 12 hours of NMP, of which 3 met viability criteria. We applied bulk transcriptomics to evaluate differences in gene expression relating to injury, repair, and regenerative responses among livers based on viability. Viable livers demonstrated robust activation of innate immunity after 3 hours of NMP followed by enrichment of pro-repair and pro-survival mechanisms. Nonviable livers demonstrated delayed and persistent enrichment of innate immune responses. Viable livers demonstrated effective induction of autophagy, the cellular repair and homeostasis pathway, compared to nonviable livers. Enrichment of pro-survival signaling was also broader in these livers.
Conclusions: NMP of discarded DCD human livers results in ischemia-reperfusion injury, but importantly activates autophagy as a means of cellular repair. More pronounced activation of autophagy was seen in livers that met viability criteria for transplantation. Therapeutic targeting of the autophagy mechanism may allow rehabilitation of nonviable livers for transplantation.

overall_design: Human liver mRNA profils of fatty and lean liver samples subjected to 0, 3 or 6 hours of normothermic machine reperfusion

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