title: Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes in MM.1S cells treated with DMSO, All-trans retinoic acid (ATRA), carfilzomib (Cfz), and their combinations

first: Qiang

last: Wang

state: Texas

address: 6550 FANNIN STREET

institute: HOUSTON METHODIST RESEARCH INSTITUTE

summary:
ATRA is important for sensitizing MM cells to Cfz. To determine what signalling pathways are affected by ATRA+Cfz in MM cells, MM.1S MM cell line was pulsed with Cfz and then cultured with DMSO or 10µM ATRA for 12 h. Total RNAs of 2 x 106 MM.1S cells for each sample were extracted by RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to Cancer Genomics Center at The University of Texas  (Houston, TX) for genearray followed by data analysis.
We use gene experssion profiling data to determine differential expression of genes in MM cells in culture with DMSO, ATRA, Cfz or ATRA+Cfz.

overall_design: Examination of gene-profiling data in MM cells repsonse to control, ATRA, Cfz or ATRA+Cfz treatment.


title: RNA sequence of gene expression in tumor-infiltrating Tc1 and Tc9 cells

status: Public on Dec 31 2021

city: Houston

first: Liuling

last: Xiao

address: 6670 Bertner Ave

country: USA

institute: Houston Methodist Research Institute

type: Expression profiling by high throughput sequencing

summary: we use RNA sequence to detect the global gene expression in tumor-infiltrating Tc1 and Tc9 cells after being adoptively transferred in vivo

overall_design: Tumor-infiltrating Tc1 and Tc9 cells were sorted by flow cytometry sorter to detect their mRNA profiles.


title: Detection and validation of RNA H19-induced UHMK1 expression as a clinical pancreatic cancer progression marker

city: Heidelberg

first: Yiqiao

last: Luo

state: Deutschland

address: Im Neuenheimer Feld 365

country: Germany

institute: Section Surgical Research

summary: Long non-coding RNA H19

overall_design: mRNA was isolated by the use of the RNeasy Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions with lipotransfected NC or siH19-2. Microarray analyses was performed at the Microarray-Analytic Center of the Medical Faculty Mannheim, using Clariom™ D Assays (Thermo Fisher Scientific, Dreieich, Germany).

first: Shanshan

last: Han

first: Bin

last: Yan

first: Huihui

last: Ji

first: Jury

last: Gladkich

first: Ingrid

last: Herr


title: Defining the mammalian coactivation of hepatic 12-hour clock and lipid metabolism

first: Huan

last: Meng

address: One Baylor Plaza BCM 130

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Expression data from distal colon tissues of WT and Gm31629-/- mice

city: Changsha

first: Xu

last: Feng

state: Hunan

address: 87# Xiangya Road

department: Department of Endocrinology, Endocrinology Research Center

country: China

institute: Xiangya Hospital of Central South University

summary: Mucosal healing is a key treatment goal for inflammatory bowel disease, and epithelial regeneration is required for an intact gut epithelium. Long noncoding RNAs are involved in the development of inflammatory bowel disease. Here, we investigated the role of a novel long noncoding RNA, Gm31629, in epithelial regeneration. We used RNA-seq to to detail the global programme of gene expression in distal colon tissues from WT and Gm31629-/-.

overall_design: WT and Gm31629-/- mice were subjected to 3% DSS treatment in drinking water for 7 days and sacrificed on day 8. Distal colon tissues were dissected and total RNA was extracted for eukaryotic RNA-seq and associated analysis.

first: Xiaowei

last: Liu

first: Xiang-Hang


title: Time course SRC-3 ChIP-Seq and XBP1s ChIP-Seq in the C57BJ/L6 WT, SRC-3 WT versus KO, and Xbp1 WT versus LKO mice under chow and fasting conditions

summary: We report the hepatic SRC-3 and XBP1s cistrome at 4-hour interval timecourse zeitgeber times (ZTs) in the liver of the C57BJ/L6 WT mice under chow and fasting conditions; we also chose liver samples at CT24, ZT0 and ZT8 for comprehensive SRC-3 and XBP1s ChIP-Seq to interrogate the genomic binding profiles of hepatic SRC-3 and XBP1s in vivo.

overall_design: Livers were harvested at 4-hour interval for a total of 24 hours from the male C57BJ/L6 mice under the zeitgeber condition of 12h:12h light:dark cycle


title: Single nuclei ATAC-seq (10X Genomics Chromium) of FACS enriched cortical and hippocampal interneurons from P30 mouse brains

city: Bethesda

first: Timothy

middle: J

last: Petros

state: MD

address: 35 Convent Drive Building 35A, Room 3B-1002

department: NICHD

institute: NIH

summary: While epigenetic modifications are critical for cell state changes throughout development, a detailed characterization of chromatin accessibility during neurogenesis has not been explored. We collected single-cell chromatin accessibility profiles of ~40,000 cells from 4 distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many of which were restricted to distinct progenitor cell types or brain regions. By integrating snATAC-Seq and transcriptome data, we characterized changes of chromatin accessibility at enhancers and promoters that were tightly coupled to transcript abundance throughout neurodevelopment. Integrating our chromatin accessibility profiles from embryonic and adult interneurons with the iPSYCH2012 GWAS dataset revealed several disease-associated polymorphisms overlapped accessible regions in embryonic cells and MGE-derived mature interneurons. These findings highlight the coordination between chromatin accessibility and gene expression as neural progenitors mature during embryogenesis, and open the door for future studies to define critical enhancer-promoter interactions that direct cell fate decisions.

overall_design: FACS enriched cortical and hippocampal interneuron nuclei from P30 mouse brains. 2 replicates per region.

first: C

middle: T

last: Rhodes

first: A

last: Mitra


title: RNA sequencing in arthritic joints of wild type and Sema3B deficient mice

city: Vigo

first: Samuel

last: Garcia

address: Estrada Clara Campoamor 341

department: Rheumatology & Immune-mediated Diseases (IRIDIS) group

country: Spain

institute: Galicia Sur Health Research Institute (IIS Galicia Sur)

summary: We found that the severity of the K/BxN serum-transfer arthritis model is higher in Sema3B deficient (Sema3b-/-) mice. Here we analyzed by RNAseq the tranciptional differences in the joints of these mice group.  We used four groups: 1) WT control (non-arthritic); 2) Sema3b-/- control; 3) WT arthritis day 9; 4) Sema3b-/- artritis day 9.

overall_design: Forepaws mRNA profiles of control and arthrititic  wild type (WT) and Sema3b-/- mice

last: García Pérez

first: Norman

last: Jiménez Otero


title: Time course hepatic RNA-Seq in the SRC-3 WT versus KO mice

summary: We report the hepatic total gene expression (starting at ZT0 and proceeding every four hours for two complete 12-hour cycles) in the liver of SRC-3 WT and KO mice.

overall_design: Livers were harvested at 4-hour interval for a total of 24 hours under the zeitgeber condition of 12h:12h light:dark cycle


title: IL-36 is a hallmark of Netherton syndrome with type I IFN, Th2 and Th9 responses distinguishing its dual clinical manifestations

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: Netherton syndrome (NS) is a rare recessive skin disorder caused by loss-of-function mutations in SPINK5 encoding the protease inhibitor LEKTI. NS patients suffer from a severe skin barrier defect, display inflammatory skin lesions and superficial scaling with atopic manifestations. They can present with typical ichthyosis linearis circumflexa (NS-ILC) or scaly erythroderma (NS-SE). Here we employed a combination of several molecular profiling methods to comprehensively characterize the skin, immune cells and allergic phenotypes of NS-ILC and NS-SE patients. This integrated multi-omic approach revealed abnormal epidermal proliferation and differentiation and IL-17/IL-36 signatures in lesional skin and blood in both NS endotypes. While the molecular profiles of NS-ILC and NS-SE lesional skin were very similar, non-lesional skin of each disease subtype displayed distinctive molecular features. NS-SE non-lesional and lesional epidermis showed activation of the type I IFN signaling pathway, which is involved in skin homeostasis and inflammation. NS-ILC lesional skin differed from NS-ILC non-lesional skin by increased complement activation and neutrophil infiltration. Serum cytokine profiling and immunophenotyping of circulating lymphocytes showed a Th2-driven allergic response in NS-ILC, whereas NS-SE patients displayed mainly a Th9 axis with increased CCL22/MDC and CCL17/TARC serum levels. This study identifies IL-17/IL-36 as predominant signaling axes in both NS endotypes and unveils distinct molecular features characterizing NS-ILC and NS-SE. These results identify new therapeutic targets and could pave the way for precision medicine of NS.

overall_design: Transcriptome of non-lesional and lesional skin from 13 NS patients with 2 clinical manifestations NS-ILC (n=9) and NS-SE (n=4)

first: Claire

last: Barbieux

middle: C

first: Johann

middle: E

last: Gudjonsson

first: Alain

last: Hovnanian


title: Single nuclei RNA-seq (10X Genomics Chromium) of FACS enriched cortical and hippocampal interneurons from P30 mouse brains

overall_design: FACS enriched cortical and hippocampal interneuron nuclei from P30 mouse brains.


title: Reduced SCRIB expression compromises endometrial stromal cells decidualization

city: Shanghai

first: Yaoming

last: Peng

state: 上海

address: Shanghai Medical College Fudan University

department: obstetric and gynecology

institute: Fudan university

summary: To identify the molecular pathway regulated by Scribble (SCRIB) in primary hunan endometrial stromal cells (ESCs) decidualization, high-throughput RNA-seq was performed to analyze the transcriptome profile in si-Ctrl or si-SCRIB  transfected decidualized ESCs (dESCs).

overall_design: mRNA profiles of si-Ctrl or si-SCRIB tranfected dESCs.

first: Haiou

first: Congjian

last: Xu


title: Western and Heart Healthy Dietary Patterns Differentially Affect the Expression of Genes Associated with Lipid Metabolism, Interferon Signaling and Inflammation in the Jejunum of Ossabaw Pigs

city: Boston

first: Alice

middle: H

last: Lichtenstein

state: MA

address: 711 Washington St

department: Jean Mayer USDA Human Nutrition Research Center on Aging

institute: Tufts University

summary: Overall diet quality and statin therapy are important modulators of inflammation and CAD progression, yet their effects on jejunum is not well understood. Our objective was to examine the effects and interaction of  dietary patterns and statin therapy on jejunal mucosa gene expression in the Ossabaw pig.

overall_design: Thirty-two Ossabaw pigs (16 boars, 16 gilts) were randomized using a 2x2 factorial design into four groups: Hearty Healthy diet (HHD); Heart Healthy diet + atorvastatin (HHD+S); Western diet (WD, also noted as Atherigenic [ARST] below); and Western diet + atorvastatin (WD+S). Heart Healthy diet (high in unsaturated fat, unrefined grain, fruits/vegetables [HHD]) or Western diet (high in saturated fat, cholesterol, refined grain [WD]), with or without atorvastatin.

first: Shumao

last: Ye

first: Nirupa

middle: R

last: Matthan

first: Stefania

last: Lamon-Fava

first: Gloria

last: Solano-Aguilar

first: Jerrold

last: Turner

first: Maura

last: Walker

first: Zhi

last: Chai

first: Sukla

last: Lakshman

first: Joseph

middle: F

last: Urban Jr


title: DNMT1 reads heterochromatic H4K20me3 to reinforce DNA methylation of transposons

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

summary: DNA methylation and trimethylated histone H4K20 (H4K20me3) constitute two important epigenetic mechanisms that frequently cooperate in silencing repetitive elements of the mammalian genome. However, it remains elusive how these two modifications crosstalk. Here, we report the specific readout of heterochromatin marks H4K20me3 by the first bromo-adjacent-homology (BAH1) domain of maintenance DNA methyltransferase DNMT1. Engagement of BAH1-H4K20me3 ensures heterochromatin targeting of DNMT1, and cooperates with the previously reported readout of H3K9me3/H3 ubiquitination by the RFTS domain to allosterically stimulate DNMT1’s activity at both global and focal levels. Interplay between RFTS and BAH1 domains profoundly impacts the maintenance of DNA methylation and genomic resistance to radiation damage. Together, our study provides a heterochromatin-regulated model for DNMT1 in which multivalent recognition of repressive histone modifications by DNMT1 directly influence the cellular landscape of DNA methylation and genomic stability.

overall_design: H4K20me3 CUT&RUN was performed in Dnmt1 KO ES cell overexpressed with wild type or W796A DNMT1.


title: Germline RUNX1 Variation and Predisposition to Childhood Acute Lymphoblastic

city: Memphis

first: Jun

middle: J.

last: Yang

state: TN

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital


title: ChIP-Seq for human placenta

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

summary: We generated ChIP-Seq (H3K4me1, H3K4me3 and H3K27ac) data for term human placenta. Together with RNA-Seq and epigenomic data generated for placentas of rhesus macaque and mouse, we aim to understand the evolution of gene expression and regulatory elements among the placentas of different mammalian species.

first: Ming-an

first: Gernot

last: Wolf

first: Todd

last: Macfarlan


title: Frequent mutations of FBXO11 identify BCL6 as a therapeutic target in Burkitt Lymphoma

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: BCL6 is a key oncogene in lymphoma pathogenesis. The expression of BCL6 in lymphoid cells can be deregulated by several mechanisms, including chromosomal translocations, somatic mutations in the promoter regulatory regions or reduced proteasome-mediated degradation. FBXO11 was recently identified as a major ubiquitin ligase involved in the degradation of BCL6 and is frequently inactivated in diffuse large B-cell lymphoma (DLBCL). In this work, we found that FBXO11 is frequently mutated in Burkitt lymphoma (BL) but rarely mutated in other BCL6-positive lymphomas, such as follicular lymphoma (FL). All mutations tested impaired FBXO11 mediated BCL6 degradation and FBXO11 knock-out completely stabilized BCL6 levels in human BL cell lines. Conditional deletion of one copy or both copies of FBXO11 in c-Myc-driven B cell lymphoma in mice accelerated lymphomagenesis, genetically confirming that FBXO11 is a haplo-insufficient oncosuppressor in lymphoma. In both FBOX11 WT and deficient BL mouse and human cell lines, blockade of BCL6 via a specific degrader or BCL6 inhibitors, impaired lymphoma growth in vitro and in vivo, an effect further enhanced by co-inhibition of c-Myc activity. Overall these findings not only establish FBXO11 as one of the most frequently mutated genes in BL, but also elucidate its biological functions in lymphomagenesis and thereby identify BCL6 as a specific therapeutic target in BL.

overall_design: Comparative analysis between WT and FBXO11 knock-out Burkitt lymphoma (BL) cell lines.

first: Chiara

last: Pighi

first: Taek

last: Cheong

first: Mara

last: Compagno

first: Enrico

last: Patrucco

first: Maddalena

last: Arrigoni

first: Martina

last: Olivero

first: Qi

first: Cristina

last: Lopez

first: Bruno

middle: M

last: Grande

first: Teresa

last: Poggio

first: Fernanda

last: Langellotto

first: Lisa

last: Bonello

first: Riccardo

last: Dall’Olio

first: Luca

last: Molinaro

first: Laura

last: Saucek

first: Claudia

last: Voena

first: Paola

last: di Celle

first: Louis

last: Staudt

first: Reiner

last: Siebert

first: Alberto

last: Zamò

first: Roberto

last: Chiarle


title: STAT3 induces breast cancer growth and progression via IL-6, STC1 and MMP13 secretion by Cancer Associated Fibroblasts

first: Aurora

last: Savino

state: Piemonte

address: via Nizza, 52

institute: Università di Torino

summary: In the tumor microenvironment, Cancer Associated Fibroblasts (CAFs) become activated by cancer cells and increase their secretory activity to produce soluble factors that contribute to tumor cells proliferation, invasion and dissemination to distant organs. The pro-tumorigenic transcription factor STAT3 and its canonical inducer, the pro-inflammatory cytokine IL-6 act conjunctly in a positive feedback loop that maintains high levels of IL-6 secretion and STAT3 activation in both tumor and stromal cells. Here, we demonstrate that STAT3 is essential for the pro-tumorigenic functions of murine breast cancer CAFs both in vitro and in vivo, and identify a STAT3 signature significantly enriched for genes encoding for secreted proteins. Among those, IL-6, ANGPTL4, STC-1 and MMP13 were validated as STAT3-dependent mediators of CAF pro-tumorigenic functions by different approaches. CAFs activities were moreover impaired by IL-6 Receptor blocking antibodies and by MMP13 inhibition, supporting the feasibility of a therapeutic approach based on inhibiting STAT3-induced CAF-secreted proteins. The usefulness of such an approach is supported by the observation that an equivalent CAF-STAT3 signature in humans is expressed at high levels in breast cancer stromal cells and characterizes patients with a shorter disease specific survival, including those with basal-like disease.

overall_design: In order to identify STAT3 transcriptional targets potentially mediating CAFs pro-oncogenic properties, we compared the mRNA expression profiles of primary CAFs, derived from NeuT transgenic mammary tumors, silenced or not for STAT3.

first: Lidia

last: Avalle

last: Raggi

first: Emanuele

last: Monteleone

first: Luisa

last: Statello

first: Andrea

last: Camperi

first: Simona

last: Aversano Stabile

first: Niccolò

last: De Marzo

first: Francesca

last: Marino

first: Chiara

last: Guglielmi

last: Zanini

first: Marco

last: Forni

first: Danny

last: Incarnato

first: Salvatore

last: Oliviero

first: Valeria

last: Poli


title: Transcriptome data involved in female Chinese tongue sole (Cynoglossus semilaevis)

city: Qingdao

last: Wang

state: Shandong

address: 106 Nanjing Road

institute: Yellow Sea Fisheries Research Institute, Chinese Academy Fishery Science

summary: In the present study, five important somatotropic and reproductive tissues including brain, pituitary gland, liver, gonad and muscle from 6 large females and 6 small males were used for transcriptomic analysis. A mean of 23,389,128 high quality clean reads were obtained from each library and 109, 698, 1,325, 2,299 and 2,141 differentially expressed genes (DEGs) separately recognized from brain, pituitary gland, liver, gonad and muscle between small and large female individuals (fold change ≥ 2 and q < 0.05). These DEGs’ enrichment analysis suggests that the up-regulation of neuroactive ligand-receptor interaction, cell cycle, DNA replication and MAPK signaling pathway in large female group may be involved in the regulation of growth differences.

overall_design: Examination of five important somatotropic and reporductive tissues including brain, pituitary gland, liver gonad and muscle from 6 small females and 6 large females individuals

first: Songlin

last: Chen


title: Nucleoporin-93 overexpression overcomes trafficking bottlenecks in metastasis of breast cancer

city: San Francisco

first: Binyamin

last: Zuckerman

state: California

institute: UCSF

summary: The integrative computational analysis we developed has assigned NUP93 with important roles in progression of mammary cancer, which we confirmed in animals. Surprisingly, NUP93 emerges from these studies as a master driver of metastasis. This conclusion was supported by functional characterization of two groups of naturally occurring mutant alleles. Remarkably, mammary cells overexpressing NUP93 display over-activation of multiple growth factor pathways, including the WNT/beta-catenin pathway. This route has previously been associated with colorectal tumors, but recent network-based analysis linked it to breast cancer (Koval and Katanaev, 2018). We conclude that NUP93 integrates and enhances not only WNT but also additional growth factor signals. Thus, by seizing an essential step common to multiple signaling routes, NUP93 acquires robust oncogenic attributes. Beyond the identification of augmented nuclear transport as a new hallmark of cancer, our study exposes tumor vulnerabilities and offers not only a new target for intervention but also a pharmacological strategy tailored to the subset of NUP93 overexpressors.

overall_design: WCE RNA was extracted from MDA-MB-231 cells treated with either control or NUP93-targetting siRNA, in two biological replicates. In addition, MCF7 cells were similarly treated fith siRNAs and fractionated to obtain WCE, cytosolic and nuclear fractions. RNA was extracted from all fractions (two biological replicates), and all samples were subjected to RNA-seq after PolyA selection.

first: Nishanth

middle: B

last: Nataraj

first: Igor

last: Ulitsky

first: Yosef

last: Yarden


title: Transcriptional profiling of pancreatic somatostatin and beta-cells from zebrafish [bulk RNA-seq]

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

summary: Pancreas contains a collection of different types of endocrine cells. Each endocrine cell secretes a specific hormone. Using reporter lines for two hormones, insulin and somatostatin1.1, we observe the presence of bi-hormonal cells in zebrafish pancreas. To characterize the cells at transcriptional level, we performed next-generation RNA-Sequencing on FACS sorted cells expressing sst1.1, ins, or both sst1.1 and ins.

overall_design: We used fluorescence-activated cell sorting (FACS) coupled with next generation RNA-Sequencing to profile sst1.1+ somatostatin, ins+ beta- and sst1.1+ ins+ cells from 30 dpf animals. Cells were sorted directly into lysis buffer and cDNA prepared using Smart-Seq2. Sequencing was performed on llumina NextSeq500. Reads were splice-aligned to the zebrafish genome, GRCz11, using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene.

middle: P


title: Transcriptional profiling of pancreatic somatostatin and beta-cells from zebrafish [scRNA-seq]


title: RNA-sequencing of adipocyte and stromal vascular cells (SVCs) of epididymal and inguinal adipose tissue from normal chow diet (NCD)-fed mice

city: Seoul

first: Jae Bum

last: Kim

address: Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: In mammals, white adipose tissues are largely divided into visceral epididymal adipose tissue (EAT) and subcutaneous inguinal adipose tissue (IAT) with distinct metabolic properties. To investigate molecular mechanisms underlying depot-specific metabolic roles, we report the transcriptomes of adipocytes and SVCs derived from NCD-fed mouse epididymal adipose tissue (EAT) or inguinal adipose tissues (IAT).

overall_design: Examination of 12 samples derived from EAT and IAT

first: Injae

last: Hwang

first: Hahn

last: Nahmgoong

first: Yong

middle: G

last: Jeon

first: Jae


title: Cannabinoid receptor 1 deficiency alters expression of stress-related genes in microglia

city: Bonn

first: Eva

middle: Carolina

last: Beins

address: Venusberg-Campus 1

institute: University of Bonn

summary: Microglia (CD11b+ cells) were isolated from brain tissue of stress-naïve wild type and CB1-deficient (Cnr1-/-) mice using magnetic cell separation and gene expression analysed using 3' mRNA sequencing. Differential gene expression showed that Cnr1-/- microglial transcriptomes do not fundamentally differ from those of wild type controls. Only seven differentilly expressed genes remained significant after correcting for multiple testing. The top hit was Fkbp5 (encoding FK506 binding protein 5 (FKBP5), a regulator of glucocorticoid receptor activity.

overall_design: Microglial mRNA profiles of wild type and CB1-deficient (Cnr1-/-) mice

first: Andreas

last: Zimmer


title: Transcriptional profiling of pancreatic somatostatin and beta-cells from zebrafish

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

overall_design: Refer to individual Series


title: ATAC sequencing of zebrafish pancreatic beta-cells

summary: Pancreatic beta-calls are responsible for regulating the blood glucose levels via secretion of hormone insulin. To elucidate the chromatin state in zebrafish beta-cells, we performed ATAC-Sequencing.

overall_design: Two replicates of beta-cells. For control, one replicate of hepatocytes was generated. ATAC-Seq was performed on 50k FACS sorted cells obtained from 3 mpf animals. For beta-cells, Tg(ins:Brainbow1.0) was used, while for hepatocytes, Tg(fabp10:dsRed, ela3l:GFP)gz12, also known as 2CLIP (2-color liver pancreas), was used.


title: Characterisation of gene expression of cancer-associated and normal fibroblasts from lobular and ductal breast cancer patients

city: Carrington Crescent

first: Andrew

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

summary: The purpose of this study was to characterise gene expression differences between cultured human cancer-associated fibroblasts and normal fibroblasts from lobular and ductal breast cancer patients.

overall_design: Cultured human fibroblasts from female breast cancer tumours.


title: Acetyl-lysine Reader CECR2 Drives Breast Cancer Metastasis by Coordinating Macrophage Polarization and Immune Suppression

city: New Haven

first: Qin

last: Yan

state: CT

address: Department of Pathology, PO Box 208023

institute: Yale School of Medicine


title: Hypoxia-induced genes in mouse spermatogonia

city: Kyoto

first: Takashi

last: Shinohara

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

summary:
Purpose: We tried to identify genes that regulate hypoxic response in mouse spermatogonial stem cells. We report the chareacterization of genes expressed under 1% oxygen.
Results: We found 228 differentialy expressed genes between cells cultured under hypoxia (1% oxygen) and those under normoxia (20% oxygen).

overall_design: Germline stem (GS) cells from mouse testes were established under 20% oxygen.  The cells were then passaged to a new culture plates and cultured under 1% oxygen for 2 days.

first: Hiroko

last: Morimoto

first: Takuya

last: Yamamoto


title: Acetyl-lysine Reader CECR2 Drives Breast Cancer Metastasis by Coordinating Macrophage Polarization and Immune Suppression [cell line]

summary:
Purpose: Advanced breast cancer leads to significantly higher mortality due to metastasis. The goal of this work is to screen and study the deregulated epigenetic regulators to identify the novel targets for the treatment of metastatic breast cancer.
Methods:RNA-Seq analysis of matched primary and metastatic breast samples to detect the deregulated epigenetic regulators. Live imaging system was applied to modulate metastatic tumor growth in vivo.
Results: we identified that deregulated CECR2 was associated with breast cancer metastasis by RNA sequencing analysis of the matched primary and metastatic breast cancer samples from 13 patients. CECR2 knockout significantly decreased breast cancer metastasis in both immunocompromised and immunocompetent mice models. RNA-seq analysis showed that gene set "response to NF-κB signaling" was significantly decreased by CECR2 depletion in breast cancer cells.  Mechanistically, CECR2 formed a complex with RELA on NF-κB target gene promoters to activate target gene expression. Furthermore, CECR2 played a key role in tumor associated macrophage recruitment and polarization, which regulates the antitumor immunity in microenvironment.
Conclusions: our work identified and characterized a novel epigenetic regulator CECR2 in regulating breast cancer metastasis, and can serve as a potential target for the treatment of metastatic breast cancer.

overall_design: RNA-seq analysis of LM2 cells with control sgRNA, CECR2 sgRNA-1 or CECR2 sgRNA-2 to determine the effects of CECR2 knockout (by CRISPR/Cas9 system). Duplicate samples are used.

first: Meiling

last: Zhang

first: Zongzhi

middle: Z

last: Liu


title: Acetyl-lysine Reader CECR2 Drives Breast Cancer Metastasis by Coordinating Macrophage Polarization and Immune Suppression [metastasis]

overall_design: RNA-seq analysis of 13 paired breast tumor samples; in vitro and in vivo functional study; molecular mechanism study


title: Evaluation of BMP2/miRNA expression systems (hybrid vectors) for potent therapeutic efficacy in bone tissue regeneration

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

summary: Reconstruction of bone defects and compensation of deficient repair mechanisms represent important goals within the field of regenerative medicine and require novel safe strategies for translation into the clinic. Therefore, we generated a nonviral osteogenic gene therapeutic (hybrid) vector system, combining an improved bone morphogenetic protein 2 (BMP2) gene cassette and pro-osteogenic microRNAs. The hybrid vectors were tested for their functionality and osteogenic differentiation potential in C2C12 and C3H/10T1/2 via alkaline phosphatase enzyme activity assay, enzyme-linked immunosorbent assay and reverse transcription quantitative polymerase chain reaction analysis of miRNA and osteogenic marker expression. In a mouse ectopic bone formation model, osteoinduction in transfected muscle tissue was analysed via micro computed tomography scans and histological staining. All tested hybrid vector systems led to an increase in BMP2 protein overexpression in C2C12 and C3H/10T1/2, when compared with miRNA-lacking constructs. Incorporated miRNAs were found to be efficiently upregulated. Distinct intra- and extracellular localization preferences were observed. The hybrid vector consisting of BMP2 and miR-590 revealed highest potential  of inducing osteogenic differentiation. The favourable effect of combining overexpression of BMP2 and miRNAs has been shown in vitro and in vivo. Induction of mineralization was observed in an ectopic bone mouse  model, although high variability in terms of size and shape indicates potential for improvement regarding plasmid administration and retention. We believe this study contributes in a valuable way to the preclinical knowledge of nonviral gene therapy for tissue regeneration. Also, we hope to encourage additional research on multi-target gene therapeutic approaches.

overall_design: Twelve samples were analyzed via RNAseq, consisting of 4 groups with three replicas each. One group served as reference (BMP2), other 3 groups were different hybrid vectors.

first: Teresa

last: Brenner

first: Katja

last: Posa-Markaryan

first: Simon

last: Sperger

first: Ara

last: Hacobian


title: BRCA1 and BRCA2 classification of ovarian cancer

city: Amsterdam

first: Philip

last: Schouten

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

type: Genome variation profiling by genome tiling array

summary: Inactivating germline BRCA1 and BRCA2 mutations confer a defect in homologous recombination DNA repair which was found to leave traces in tumor DNA copy number aberration (CNA) profiles. In analogy to previously trained breast cancer CNA classifiers that predicted association with BRCA1 and BRCA2 mutated cancer and benefit of high dose double strand break inducing chemotherapy, we trained BRCA1 and BRCA2 classifiers on CNA profiles of 50 BRCA1 mutated, 10 BRCA2 mutated and 13 non-familial ovarian cancers and investigated whether tumor type and mutation type independent classifiers could be trained. The cross validated area under the curve of the receiver/operator characteristic curve of ovarian cancer BRCA1 and BRCA2 classifiers were 0.67 (95% CI: 0.55-0.78) and 0.91 (95% CI: 0.79-1). These classifiers identified the majority of the samples with germline and somatic BRCA1 and BRCA2 mutations and BRCA1 promoter hypermethylation in the Cancer Genome Atlas (TCGA) dataset. Combining tumor type or mutated gene did not yield higher AUCs than single gene classifiers, although the ovarian BRCA1+BRCA2 classifier identified most BRCA1 and -2 mutated cases, including those in the TCGA dataset, and a combined breast and ovarian cancer BRCA1 classifier may improve response prediction to double strand break inducing chemotherapy.

overall_design: Shrunken centroid classifiers trained by 10 fold crossvalidation on BRCA1 vs. control and BRCA2 vs. control samples.

first: Daniel

last: Vis

first: Ewald

last: van Dijk

first: Esther

last: Lips

last: Scheerman

first: Carolien

last: van Deurzen

first: Patricia

last: Ewing-Graham

first: Agnes

last: Jager

first: Els

last: Berns

first: Petra

last: Nederlof

first: Lodewyk

last: Wessels

first: Sabine

last: Linn


title: Natural C. elegans microbiota protects against infection via production of a cyclic lipopeptide of the viscosin group

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

summary: Caenorhabditis elegans is associated in nature with a species-rich, distinct microbiota, which was characterized only recently. Thus, our understanding of the relevance of the microbiota for nematode fitness is still at its infancy. One major benefit that the intestinal microbiota can provide to its host is protection against pathogen infection. However, the specific strains conferring the protection and the underlying mechanisms of microbiota-mediated protection are often unclear. Here, we identify natural C. elegans microbiota isolates that increase C. elegans resistance to pathogen infection. We show that isolates of the Pseudomonas fluorescens subgroup provide paramount protection from infection with the natural pathogen Bacillus thuringiensis through distinct mechanisms. We found that the P. lurida isolates MYb11 and MYb12 (members of the P. fluorescens subgroup) protect C. elegans against B. thuringiensis infection by directly inhibiting growth of the pathogen both in vitro and in vivo. Using genomic and biochemical analyses, we further demonstrate that MYb11 and MYb12 produce massetolide E, a cyclic lipopeptide biosurfactant of the viscosin group, which is active against pathogenic B. thuringiensis. In contrast to MYb11 and MYb12, P. fluorescens MYb115-mediated protection involves increased resistance without inhibition of pathogen growth and most likely depends on indirect, host-mediated mechanisms. This work provides new insight into the functional significance of the C. elegans natural microbiota and expands our knowledge of bacteria-derived compounds that can influence pathogen colonization in the intestine of an animal.

overall_design: mRNA profiles of wild type (WT) C.elegans exposed to either Bacillus thuringiensis B-18247 (Dilution at 1:100), B-18407 (Dilution at 1:100) or None (Control) fed by E. coli OP50, P. lurida isolates MYb11 or P. fluorescens MYb115 at 12h or 24h were generated by deep sequencing (3 replicates), using Illumina HiSeq2000.

first: Kohar

last: Kissoyan

last: Dierking


title: Hepatocytes :MH vs. ProliHH vs. PHH vs. HLC

status: Public on Dec 30 2021

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary:
Hepatocytes isolated from DILI patient's liver (#2064) were cultured for a long term using irrMEF and EMUKK-05, and comprehensive gene expression was compared between Puromycin-treated and non-treated groups. In addition, comprehensive gene expression analysis of human mature hepatocytes, primary cultured cells, and ips cell-derived hepatocyte-like cells were performed as controls.
Two-condition experiment, Proliferating hepatocytes (ProilHH) vs. puromycin-treated ProliHH. Primary human hepatocytes (PHH) and isolated humen mature hepatocytes (MH) and human iPSC-derived hepatocyte-like cells (HLC) as controls.

overall_design: Hepatocytes were isolated from the livers of human DILI patients and frozen after primary culture. The cells were cultured for a long turm of time in MEF feeder and EMUKK-05 medium (ProliHH), and the gene expression changes between the puromycin- and non-puromoted groups were analyzed. Puromycin was used as a selective agent for hepatocytes.

first: Saeko

last: Akiyama

first: Noriaki

last: Saku

first: Shoko

last: Miyata

first: Kenta

last: Ite

first: Masashi

last: Toyoda

first: Tohru

last: Kimura

first: Masahiko

last: Kuroda

first: Atsuko

last: Nakazawa

first: Mureo

last: Kasahara

first: Hidenori

last: Nonaka

first: Akihide

last: Kamiya

last: Kiyono

first: Toru

last: Kobayashi

first: Yasufumi

last: Murakami


title: Boosting NAD+ blunts toll-like receptor-4 induced type I interferon in control and systemic lupus erythematosus monocytes

city: Bethesda

first: Komudi

last: Singh

address: Building 10

institute: NIH

summary: This is a pilot study to evaluate the effects of NR supplementation on monocytes function, registered in ClinicalTrials.gov with registration number: NCT02812238 and approved by the National Heart and Lung Institute IRB.

overall_design: Healthy volunteers were screened prior to signing consent and subjects were then randomly assigned to a 7-day supplementation of either NR (1000 mg daily) or a matching placebo. After one week of therapy, subjects underwent a 24-hour fast followed by an early-morning fixed 500-calorie meal. Blood draw was taken before and 3hrs. after feeding

first: Michael

middle: N

last: Sack

first: Jing

last: Wu


title: Correction of a Factor VIII genomic inversion with designer recombinases

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

summary: Despite advances in nuclease-based genome editing technologies, correcting human disease-causing genomic inversions remains a challenge. Here, we describe the potential use of a recombinase-based system to correct a 140 kb int1h inversion frequently found in patients diagnosed with Hemophilia A. With the use of directed molecular evolution, we developed a linked heterodimeric recombinase system (RecF8) achieving 30% inversion of the target sequence in human tissue culture cells. Transient RecF8 treatment of endothelial cells, differentiated from int1h patient derived iPSCs, resulted in prominent correction of the inversion and restored Factor VIII mRNA expression. Our data suggest that the development of designer-recombinases represent an efficient and specific mean towards treatment of large gene inversions causing monogenic diseases.

overall_design: ChIP-Seq based examination of RecF8 recombinase binding sites in a human cell line.

first: Teresa

last: Rojo-Romanos

first: Felix

last: Lansing


title: Chronic Benzene Exposure Aggravates Pressure Overload-Induced Cardiac Dysfunction

city: Louisville

first: Igor

last: Zelko

state: Kentucky

address: 302 E. Muhammad Ali Blvd, Cardiovascular Innovation Institute bld., Room 310

department: Medicine

institute: University of Louisville

summary: Benzene is a ubiquitous environmental pollutant abundant in household products, petrochemicals and cigarette smoke. Benzene is a well-known carcinogen in humans and experimental animals; however, little is known about the cardiovascular toxicity of benzene. Recent population-based studies indicate that benzene exposure is associated with an increased risk for heart failure. Nonetheless, it is unclear whether benzene exposure is sufficient to induce and/or exacerbate heart failure. We examined the effects of benzene (50 ppm, 6 h/day, 5 days/week, 6 weeks) or HEPA-filtered air exposure on transverse aortic constriction (TAC)-induced pressure overload in male C57BL/6J mice. Our data show that benzene exposure had no effect on cardiac function in the Sham group; however, it significantly compromised cardiac function as depicted by a significant decrease in fractional shortening and ejection fraction, as compared with TAC/Air-exposed mice. RNA-seq analysis of the cardiac tissue from the TAC/benzene-exposed mice showed a significant increase in several genes associated with adhesion molecules, cell-cell adhesion, inflammation, and stress response. In particular, neutrophils were implicated in our unbiased analyzes. Indeed, immunofluorescence studies showed that TAC/benzene exposure promotes infiltration of CD11b+/S100A8+/myeloperoxidase+-positive neutrophils in the hearts by 3-fold. In vitro, the benzene metabolites, hydroquinone and catechol, induced the expression of P-selectin in cardiac microvascular endothelial cells by 5-fold and increased the adhesion of neutrophils to these endothelial cells by 1.5-2.0-fold. Benzene metabolite-induced adhesion of neutrophils to the endothelial cells was attenuated by anti-P-selectin antibody. Together, these data suggest that benzene exacerbates heart failure by promoting endothelial activation and neutrophil recruitment.

overall_design: C57BL6 male mice were instrumented with transverse aortic constriction (TAC) surgery or sham surgery to simulate heart failure conditions. After 1 week recovery mice vere exposed to HEPA filtered air or 50 ppm benzene (6 hrs/day, 5 days/week) for 6 weeks. At the end of exposure, the RNA from mouse hearts (6 samples per group) from four experimental groups was extracted and differential gene expression was analyzed using RNAseq.

first: Sanjay

last: Srivastava

first: Steven

last: Jones

first: Shizuka

last: Uchida


title: Transcriptome Analysis of Pterygium and Pinguecula Reveals Genomic Instability Associated with Chronic Inflammation

city: Córdoba

first: Jose

last: Echenique

state: Córdoba

address: Edificio Integrador, Medina Allende S/N, Ciudad Universitaria

department: Clinical Biochemistry

country: Argentina

institute: School of Chemistry Sciences, National University of Cordoba

summary:
Background: Damage due to ultraviolet (UV) light from the sun is implicated in the development of two proliferative lesions of the ocular surface: pterygium and pinguecula. In this study, RNA-sequencing technology was used to investigate underlying molecular mechanisms.
Methods: Pterygium and pinguecula specimens were collected at the time of surgical removal, along with adjacent specimens of healthy conjunctiva. RNA was extracted and sequenced. Data from individual samples were grouped as 1) healthy conjunctiva, 2) pterygia-highly exposed to UV (pterygia-E), 3) pterygia-normally exposed (pterygia-NE) and 4) pinguecula. Pairwise comparison was made of differentially expressed genes (DEGs). Randomly selected DEGs were validated in independent tissue specimens by RT-PCR. Gene sets were further analyzed by Ingenuity Pathway Analysis (IPA), and by assembly of cell type, tissue differentiation and pathological process markers.
Results: Transcripts from 18,630 genes were identified. Pterygium exhibited 69% similarity, and pinguecula exhibited 73% similarity to healthy conjunctiva. Pinguecula and pterygia exhibited 95% similarity to each other and pterygia-E and pterygia-NE exhibited 98% similarity to each other. Among the most interesting DEGs were four tumor suppressor genes downregulated in pterygia-E and pterygia-NE: C10orf90, RARRES1, DMBT1, and SCGB3A1. C10orf90 and RARRES1 were also downregulated in pinguecula. Comparison of pterygia-E and pterygia-NE uncovered evidence of genomic instability due to failure to repair DNA damage, and associated with inflammation and the immune response; these changes were also observed in pinguecula, but to a lesser extent, and are consistent with atypia and dysplasia documented pathologically. IPA overwhelmingly linked DEGs to cancer and predicted activation of 12 different upstream regulators known to mediate epithelial cell proliferation. Cell type markers were present for all epithelial and stroma cell types quiescent stem cells of both epithelia and stroma were lacking. Cell-type and differentiation marker expression indicated well-differentiated epithelial components of mixed conjunctival, limbal, and corneal cell-types with mucosal differentiation. Upregulation of MUC6 in all three lesions suggested the presence of a glandular cell type. In all three lesions, genes characteristic of palmoplantar epidermis: KRT9 and TRPV3, were upregulated, suggesting transdifferentiation due to stress. Markers of cornification characteristic of inflammation were also upregulated. Matrix metalloproteinase expression was only slightly changed, suggesting the lesions were not invasive, however fibrovascular proliferation was evidenced.
Conclusions: A hallmark of cancer, genomic instability begins in the precancerous stage, and can be caused by failure to repair DNA damage due to UV light exposure. This can be exacerbated by inflammation due to products of DNA damage. Our findings suggest that pinguecula and pterygia, while benign lesions, are both on the pathological path towards cancer.

overall_design: RNAseq analyses of transcripts extracted from  pinguecula, UV-exposed pterygia, normally-exposed pterygia  and healthy conjunctiva.

first: Maria

last: Suarez

first: Juan

last: Lopez

first: Esteban

last: Medina

first: Mariano

last: Iros

first: M

last: Fini

first: Horacio

last: Serra


title: Transcriptomic analysis of adult mouse spinal cord tissue in the control of HDAC4 during inflammatory pain

city: Heidelberg

first: Daniela

last: Mauceri

address: Im neuenheimer Feld 366

department: Neurobiology

institute: Heidelberg University

summary: The goal of this study was to evaluate the role of HDAC4 in spinal sensitization. We analyzed gene expression changes associated with the subcellular localization of HDAC4 in the spinal cord dorsal horn following CFA-induced inflammatory pain. The analysis was performed in basal conditions and after intraplantar injection of CFA to the hind paw of mice that received intraspinal injection of rAAV-constructs influencing the subcellular localization of HDAC4.

overall_design: mRNA profiles of dorsal spinal cord segments L3-5 from 3-month-old mice after intraspinal delivery of expression constructs encoding for LacZ (control), HDAC4 wt, or HDAC4 3SA, sequenced by RNA-seq. Profiles in basal conditions (intraplantar saline injection, 24 h) or 24 hours after intraplantar CFA injection. Each condition is in triplicate.

first: Christian

last: Litke


title: The aberrant upregulation of exon 10-inclusive SREK1 through SRSF10 acts as an oncogenic driver in human hepatocellular carcinoma

city: Hangzhou

first: Jianxiang

last: Chen

state: Zhejiang

address: No.58,Haishu Rd, Cangqian,

department: Pharmacy Institute and Department of Hepatology

institute: Hangzhou Normal University

summary: The deregulation of alternative splicing (AS) has recently been implicated as a relevant source of molecular heterogeneity in cancer. However, the targets and intrinsic mechanisms on regulatory network of splicing in hepatocarcinogenesis are largely unknown. Here, we report a functional impact of the splice variant of Splicing Regulatory Glutamic Acid and Lysine Rich Protein 1 (SREK1) and its upstream regulator, Serine/arginine-rich splicing factor 10 (SRSF10) on sustaining the oncogenic signal.

overall_design: To identify the alternative spliced targets of SRSF10 in HCC cells, we did the stable knockdown for the SRSF10 (3B-2, LM3-2) and Scramble control (3B-1, LM3-1) in Hep3B and HCCLM3 cells by lentivirus-mediated shRNA delivery. The RNA was extracted and sent for mRNA sequencing to identify the splicing targets regulated by SRSF10.

first: Cunjie

last: Chang

first: Muthukumar

last: Rajasekaran

first: Yiting

last: Qiao

first: Heng

last: Dong

first: Yu

last: Wang

first: Hongping

last: Xia

first: Amudha

last: Deivasigamani

first: Minjie

last: Wu

first: Karthik

last: Sekar

first: Hengjun

last: Gao

first: Mengqing

last: Sun

first: Yugin

first: Qian

last: Li

first: Lin

last: Tao

first: Zhen

last: Yan

first: Menglan

first: Shasha

first: Shujuan

last: Zhao

first: Dajing

first: Lina

first: Fan

last: Yang

first: Haojin

first: Baodong

first: Ling

last: Su

first: Liang

last: Xu

first: Ye

first: Veerabrahma

last: Seshachalam

first: Gongxing

first: Jayantha

last: Gunaratne

first: Wanjin

last: Hong

first: Junping

last: Shi

first: Gongying

first: David

middle: S

last: Grierson

first: Benoit

last: Chabot

first: Tian

last: Xie

first: Kam

last: Hui


title: miRNA profiling of human Sertoli cells-derived extracellular vesicles

status: Public on Dec 28 2021

city: Beijing

first: Xiao-Hui

last: Tan

address: 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

summary: We performed an analysis of identification and quantification of microRNA (miRNA) expression profiles of EVs from human Sertoli cells, aiming to obtain the profiling of the miRNAs in these EVs to explore their possible roles in the development of testis

overall_design: Examination of one sample from EVs derived from human Sertoli cells

first: Rui-Li

last: Guan


title: Indisulam targets RNA splicing and metabolism to serve as a novel therapeutic strategy for high risk neuroblastoma

city: London

first: Clare

last: Eckold

state: London

address: 10 Logan Place

institute: (None)

summary: Neuroblastoma is the most common solid tumour in childhood. Prognosis remains poor for high risk cases despite the use of multimodal treatment, highlighting the urgent need for novel therapeutic strategies. Analysis of cell line drug sensitivity data suggested that among solid tumours neuroblastoma could be the most sensitive to treatment with indisulam (E7070). Indisulam is a clinical aryl sulphonamide and selective promoter of DCAF15-E3-ubiquitin ligase dependent degradation of the RNA splicing factor and transcriptional coactivator RBM39. Here, we demonstrate for the first time that indisulam is highly efficacious in vitro and in vivo in experimental models of neuroblastoma. Indisulam induced rapid depletion of RBM39, accumulation of splicing errors in mRNA and growth inhibition in a DCAF15-dependent manner. Global analysis of protein and RNA alterations in IMR32 cells demonstrated a significant overlap between mis-spliced RNA and decrease in protein levels. Pathway analysis indicated an enrichment for genes involved in cell cycle and one-carbon metabolism, including CDK4 and TYMS. Finally, indisulam induces mitochondrial dysfunction, metabolome perturbations, alterations to redox balance and NAD/NADH ratio in vitro. Metabolic changes were validated in IMR32 xenografts in vivo. Collectively, our data suggest that high-risk neuroblastomas, which are frequently MYCN/MYC-driven, may be particularly susceptible to the dual targeting of metabolism and RNA splicing with anticancer sulfonamides such as indisulam

overall_design: RNA was extracted from IMR-32 cells which were treated with two doses of indisulam at two time points

first: Arti

last: Sikka

first: Anke

last: Nijhuis

first: Hector

last: Keun


title: Synthetic introns enable mutation-dependent targeting of cancer cells

city: Seattle

first: Khrystyna

middle: Dilai

last: North

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Research Center

summary: Many cancers carry recurrent change-of-function mutations in RNA splicing factor genes, which induce sequence-specific changes in RNA splicing. Here, we describe a method to harness this change in RNA splicing activity to drive splicing factor mutation-dependent gene expression in cancers and selectively eliminate these tumors. We engineered synthetic introns which were efficiently spliced in leukemia and breast epithelial cells bearing the most common SF3B1 mutations, but unspliced in wild-type cells—and vice versa—to yield mutation-dependent protein production. A massively parallel screen of 8,881 distinct introns delineated ideal intronic size, mapped essential sequence elements, and revealed the basis of mutation-dependent splicing. Synthetic introns enabled mutation-dependent expression of herpes simplex virus thymidine kinase and subsequent ganciclovir-mediated elimination of leukemia and breast epithelial cells bearing SF3B1 mutations, while leaving wild-type cells unaffected. This approach significantly decreased the growth of otherwise lethal leukemia xenografts and correspondingly improved host survival. The modular, compact, and specific nature of synthetic introns thereby provide a means to exploit cancer-specific changes in RNA splicing for genotype-dependent gene expression and gene therapy.

overall_design: Analysis of synthetic intron splicing in SF3B1 MUT vs SF3B1 WT cells

middle: D

first: Salima

last: Benbarche

first: Omar

last: Abdel-Wahab

first: Robert

middle: K

last: Bradley


title: Arabidopsis thaliana 6-day-old dark-grown hypocotyls; Col-0 and shr (LOF)

city: Seoul

first: Souvik

last: Dhar

state: Gwanak gu

address: 1, Gwanak ro

institute: Seoul National University

summary: Transcriptional profiling of hypocotyl comparing wild type with shr mutant. We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SHORT-ROOT on growth and development of Arabidopsis shoot system (hypocotyl) by global transcriptome analysis and to identify the key players in the regulatory pathway.

overall_design: Two-condition experiments, Col-0 and shr. Biological triplicates: 3 Col-0 and 3 shr.

first: Eun

last: Yoon

first: Jun

last: Lim


title: RNA Seq analysis of dark-grown hypocotyl comparing wild type with shr mutant.

summary: Genome-wide transcriptome analysis of hypocotyl comparing wild type with the shr-2 mutant. We used Hiseq2500 sequencing platform to identify the key players in the SHORT-ROOT-mediated hypocotyl growth and developmental pathway.

overall_design: Two-condition experiments, Col-0 and shr. Biological duplicates: 2 Col-0 and 2 shr.


title: Methylome inheritance and enhancer dememorization construct an epigenetic gate safeguarding embryonic programs

status: Public on Dec 29 2021

first: Wei

address: Zhongguancun street, Haidian

department: THU-PKU Center for Life Sciences

institute: Tsinghua University

type: Methylation profiling by high throughput sequencing

summary: Unlike that of mammals, the total DNA methylome of many cold-blooded vertebrates is globally inherited from gametes to early embryos. In zebrafish, this is however accompanied by sweeping “dememorization” of enhancers prior to fertilization for sperm and just after fertilization for oocyte, as they undergo full methylation and are not demethylated again until phylotypic stage. The significance of both global methylome inheritance and enhancer dememorization in early embryos remains largely unknown. Adding to the puzzles, the zygotic mutant zebrafish of dnmt1, the major DNA methylation maintenance methyltransferase, surprisingly can develop to term. To solve the role of DNA methylation in early development, we generated zebrafish embryos derived from dnmt1-knocking down oocytes using a recently developed method OMIS (Oocyte Microinjection in situ), which successfully eliminated DNA methylation before zygotic genome activation. dnmt1-deficient embryos failed to initiate epiboly and died around gastrulation. This is in part caused by activation of immune response and p53-regulated apoptosis, likely triggered by the derepression of transposable elements. Single cell RNA-seq further revealed defective differentiation in these mutants. DNA methylation is also required for the establishment of repressive histone marks H3K27me3 and H2AK119ub. Strikingly, the loss of DNA methylation leads to extensive derepression of somatic genes and enhancers, which acquire ectopic H3K27ac, accessible chromatin, and H3K4me3. These somatic enhancers are preferentially CG-rich and are bound by CG-containing TFs. By contrast, embryonic enhancers are generally CG-poor, methylation-insensitive, and are bound by CG-less TFs. Hence, the global DNA methylome inheritance is essential for vertebrate early development, and enhancer dememorization resets an epigenetic gate that separates embryonic and somatic programs.

overall_design: By employing MethylC-seq, total RNA-seq, scRNA-seq, CUT&RUN, ChIP-seq, and ATAC-seq in control and dnmt1 mKD embryos at oocyte, 256-cell, dome and shield stages in zebrafish, we interrogated the function of DNA methylome and its inheritance in early zebrafish development.

first: Xiaotong

last: Wu

first: Bingjie

last: Zhang

first: Hongmei


title: RNA-Seq approaches to understand the role of ARNO/Cyth2 on IL-1beta-stimulated synovial fibroblasts.

status: Public on Dec 25 2021

city: Glasgow

first: Miguel

last: Pineda

address: 120 university avenue

institute: University of Glasgow

summary:
The aim of this study was to explore the role of ARNO, also known as Cyth2, in synovial fibroblasts using NGS-derived transcriptome analysis (RNA-seq). Synovial fibroblasts were isolated from mouse synovium, and stimulated with IL-1beta for 12 hours in healthy cells and cells where Cyth2 expression was knocked-down by silencing RNA.
Methods: Synovial fibroblasts were extracted from the synovium of healthy mice and expanded in vitro, RNA was extracted from naïve, IL-1β stimulated and  IL-1β stimulated ARNO knock-down synovial fibroblast.
Methods:  Whole Transcriptome Profiling of synovial fibroblasts  were generated by deep sequencing, in triplicate, using Illumina NextSeq™ 500 platform.  Libraries were prepared using polyA selection (TruSeq stranded mRNA kit).
Methods: The sequence reads that passed quality filters were  aligned to mouse reference genome (GRCM38) using Hisat2 version 2.1.0.  we mapped about 30 million sequence reads per sample (75 bp, paired-end)
Methods: Featurecounts version 1.4.6 was used to quantify reads counts. Data quality control, non-expressed gene filtering, median ratio normalization (MRN) implemented in DESeq2  package and identification of differentially expressed (DE) genes were done  using the R bioconductor project DEbrowser.
Results: Firstly, We detected  differentially expressed (DE) genes among three conditions, which pass the threshold of >4 fold, adjp <0.01. Then, we detected DE genes in IL-1β stimulated ARNO knock-down synovial fibroblast compared to IL-1β stimulated synovial fibroblast, which pass the threshold of >2 fold, adjp <0.01. DE genes reflect decreased cellular inflammatory response after ARNO knockdown
Conclusions: Our results reflect an ARNO-mediated inflammatory response in synovial fibroblast, provides new opportunitties for targeting fibroblast in chronic arthritis and joint disease.

overall_design: Our results show the transcriptome profile of naïve, IL-1β stimulated and IL-1β stimulated ARNO knock-down synovial fibroblast expanded in vitro


title: Genome-Scale Patterns in The Loss of Heterozygosity Incidence in Saccharomyces cerevisiae

status: Public on Dec 27 2021

city: Krakow

first: Hanna

last: Tutaj

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

summary: We applied extensive assays--repeated over several genetic backgrounds and environments--to reveal some general features of the loss of heterozygosity (LOH) in yeast. We found that LOH: was most frequent in homozygotes, was more densely distributed on shorter chromosomal arms, depended on the presence of some repetitive elements but not the intensity of transcription, occured also in absence of growth although at a low rate. Our findings uncover new features of LOH and help to interpret those already known.

overall_design: Examination of transciption levels of BY4743 Saccharomyces cerevisiae strain in six different conditions; 2 biological replicates for each sample

first: Adrian

last: Pirog

first: Katarzyna

last: Tomala

first: Ryszard

last: Korona


title: Transcriptome analysis of the effects of different anti-browning agents on the rooting of tissue cultured seedlings

status: Public on Dec 24 2021

city: Hefei

first: manman

last: Wang

address: 103 Meishan Road

institute: Anhui University of Chinese Medicine

summary: This study intends to improve the induction rate of peony seedlings by using different anti-browning agents and different combinations, and clarify the relationship between anti-browning agents and seedling rooting through transcriptome sequencing methods.

overall_design: Tissue mRNA profiles of add AC, PVP, AC/PVP and CK

first: Xia

last: Chen

first: Chao

last: Yu

first: Xiangtao

last: Zhu


title: A male-derived non-ribosomal peptide pheromone controls female schistosome development II

status: Public on Dec 23 2021

city: Dallas

first: James

last: Collins

state: TX

address: 5323 Harry Hines Blvd.

department: Pharmacology

institute: UT Southwestern

summary: βAlanyl-tryptamine (BATT) is a peptide secreted by male S. mansoni upon pairing with a female parasite. Treatment of synthetic BATT on virgin females wihtout any pairing is sufficient to induce sexual development and egg depostiion.

overall_design: RNA sequencing of virgin  female schistosome parasites after 8 days of culturing in ABC169 media supplemented with 5 µM BATT or βAlanine

first: Rui

middle: J


title: Epigenetic basis of oncogenic-Kras mediated epithelial-cellular proliferation and plasticity [Mint-ChIP)

status: Public on Dec 22 2021

city: Durham

first: Preetish

last: Kadur Lakshminarasimha Murthy

state: NC

address: 101 Science Dr

institute: Duke University

summary: We perfromed Mint-ChIP using anti-FOSL1 antibody on Kras mutant mouse lung epithelial cells.

overall_design: Mint-ChIP on mouse lung tumour cells.

middle: L

last: Murthy

last: Xi

first: Yoshihiko

last: Kobayashi


city: Denver

first: Hara

last: Levy

state: CO

address: 1400 Jackson Street

department: Pediatrics

institute: National Jewish Health

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
We used microarrays to look at differential gene expression in PBMC samples from proband, proband's parents, and healthy controls
We used microarrays to look at the differential gene expression in THP-1 monocyte/macrophages after incubation with plasma from CF probands, proband's parents, healthy controls

platform_organism:
Homo sapiens
synthetic construct

overall_design:
Expression data from CF proband and parent PBMCs; expression data from THP-1 monocytes/macrophages incubated with CF proband and parent plasma
Expression array with pairwise comparisons between groups with differential comparison

first: Joanne

last: Domenico


title: HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network [miRNA-Seq]

city: Harbin

first: Yuhong

state: Heilongjiang

address: NO 23 Youzheng Street

institute: First Hospital of Harbin Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To explore the potential integrated molecular network by long non-coding RNA HOXA11-AS in keloid fibroblast
Methods:  Using primary cultured keloid-derived fibroblasts (sample 0), small interfering RNAs were designed and transfected into two keloid fibroblast samples (samples 1 and 2) to knockdown HOXA11-AS. One nonspecific transfection control (sample 3) and one blank control (sample 4) were used to remove nonspecific overlap from the studied group. The lncRNAs, messenger RNAs (mRNAs), and microRNAs (miRNAs) of five samples were sequenced to identify differentially expressed (DE) profiles in HOXA11-AS-knockdown keloid fibroblasts in samples 1 and 2, which facilitated removal of overlap with the nonspecific controls (samples 3 and 4). Using stepwise bioinformatic analysis, DE lncRNA and mRNAs characterized by close and natural antisense relationship were constructed into an interactive network by bioinformatic analysis. Based on this network, a lncRNA–mRNA–protein interaction network was extended by integration of the human protein–protein interaction (PPI) network. The Page Rank algorithm was used to score each mRNA in the extended LMN network to reveal significant functioning genes. Next, screened genes were validated by real-time PCR and western blot ting. Validated genes were used to construct a competing endogenous network based on DE miRNA profiles.
Results: SNED1, NIPAL3, and VTN were detected significantly changed in HOXA11-AS-knockdown keloid fibroblasts. Only NIPAL3 was predicted to be involved in an intergated network for HOXA11-AS via three competing endogenous miRNAs (hsa-miRNA-19a-3p, hsa-miR-141-3p, and hsa-miR-140- 5p).
Conclusion: An interactive molecular network of HOXA11-AS–three miRNAs–NIPAL3 was predicted in keloid fibroblasts

overall_design: Using primary cultured keloid-derived fibroblasts (sample 0), small interfering RNAs were designed and transfected into two keloid fibroblast samples (samples 1 and 2) to knockdown HOXA11-AS. One nonspecific transfection control (sample 3) and one blank control (sample 4) were used to remove nonspecific overlap from the studied group. Comparison between sample 1 and sample 0, sample 2 and sample 0,sample 3 and sample 0 as well as between sample 4 and sample 0 was respectively performed for differentially experessed (DE) profiles of lncRNA, mRNA or miRNA.

first: Xiaojie

last: Sun

first: Qiang

first: Wei


title: HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network

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

overall_design: Refer to individual Series


title: Epigenetic basis of oncogenic-Kras mediated epithelial-cellular proliferation and plasticity [scRNA-seq]

summary: We perfromed scRNA-seq on normal and Kras mutant mouse lung epithelial cells.

overall_design: scRNA-seq on mouse lung epithelial cells.

last: Lakshminarasimha Murthy


title: Epigenetic basis of oncogenic-Kras mediated epithelial-cellular proliferation and plasticity [RNA-Seq]

summary: We perfromed RNA-seq on normal and Kras mutant mouse lung epithelial cells.

overall_design: RNA-seq on mouse lung epithelial cells.

first: Diana

last: Arguijo


title: Epigenetic basis of oncogenic-Kras mediated epithelial-cellular proliferation and plasticity [ATAC-seq]

summary: We perfromed ATAC-seq on normal and Kras mutant mouse lung epithelial cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ATAC-seq on mouse lung epithelial cells.

last: K Lakshminarasimha Murthy


title: Transcriptional signatures of clonally derived Toxoplasma tachyzoites

status: Public on Dec 20 2021

city: Stanford

first: Terence

last: Theisen

state: California

address: Fairchild Science Building D305

institute: Stanford Univeristy

summary: Toxoplasma gondii has numerous, large, paralogous gene families that are likely critical for supporting its unparalleled host range: nearly any nucleated cell in almost any warm-blooded animal. The SRS (SAG1-related sequence) gene family encodes over 100 proteins, the most abundant of which are thought to be involved in parasite attachment and, based on their stage-specific expression, evading the host immune response. For most SRS proteins, however, little is understood about their function and expression profile. Single-parasite RNA-sequencing previously demonstrated that across an entire population of lab-grown tachyzoites, transcripts for over 70 SRS genes were detected in at least one parasite. In any one parasite, however, transcripts for an average of only 7 SRS genes were detected, two of which, SAG1 and SAG2A, were extremely abundant and detected in virtually all. These data do not address whether this pattern of sporadic SRS gene expression is consistently inherited among the progeny of a given parasite or arises independently of lineage. We hypothesized that if SRS expression signatures are stably inherited by progeny, subclones isolated from a cloned parent would be more alike in their expression signatures than they are to the offspring of another clone. In this report, we compare transcriptomes of clonally derived parasites to determine the degree to which expression of the SRS family is stably inherited in individual parasites. Our data indicate that in RH tachyzoites, SRS genes are variably expressed even between parasite samples subcloned from the same parent within approximately 10 parasite divisions (72 hours). This suggests that the pattern of sporadically expressed SRS genes is highly variable and not driven by inheritance mechanisms, at least under our conditions.

overall_design: RNASeq of purified, clonally derive RH Toxoplasma tachyzoites

middle: C

first: John

last: Boothroyd


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes

status: Public on Dec 16 2021

city: Ottawa

first: Adrian

last: Pelin

state: Ontario

address: 501 Smyth Rd.

country: Canada

institute: Ottawa Hospital Research Institute

summary:
Purpose: Next-generation sequencing (NGS) will be used to quantify whole transcriptome changes during genetic perturbations and viral infections
Methods: RNA was harvested in Trizol 488 (Thermo Fisher). RNA was extracted using the manufacturer’s protocol and quantified by nanodrop. PANC1 wild-type or ARID1A knockout total RNA was sequenced by The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children (Toronto, Canada) using the Illumina HiSeq2500 platform to generate single-end 100 bp reads. Adapters were trimmed using Trimmomatic and adapter-free reads were mapped to the human genome (hg19).
Results: We have identified ARID1A KO to make cells more suceptible to viral infection due to decreased basal level of expression of ISGs
Conclusions: Our study represents the first look at the role of ARID1A in the context of viral infection.

overall_design: PanC1 mRNA profile during VSV infection of WT or ARID1A KO

first: Carolina

last: Ilkow


title: Gene expression based outcome of CT-26 tumor in C57/BL6 mice after treatment with anti-PD-1 antibody, GITR-L, combination or Bispecific molecules

city: Redwood City

first: Kyle

last: Halliwill

address: 1500 Seaport Blvd

institute: Abbvie Inc

summary: Co-stimulatory receptors such as GITR play key roles in regulating the effector functions of T cells. Agonistic anti-GITR antibodies have been investigated as a cancer immunotherapy with demonstrated efficacy in pre-clinical models. In human clinical trials, however, GITR agonist antibodies have shown limited therapeutic effect which may be due to a suboptimal receptor clustering-mediated signaling. To overcome this potential limitation, a rational protein engineering approach is needed to optimize GITR agonist-based immunotherapies. Here we show a novel bispecific molecule consisting of an anti-PD-1 antibody fused with a multimeric GITR ligand (anti-PD-1-GITR-L) that induces a PD-1-dependent and FcγR-independent GITR clustering, resulting in an enhanced activation, proliferation, and memory differentiation of primed antigen-specific GITR+PD-1+ T cells. The anti-PD-1-GITR-L bispecific is a PD-1 directed GITR-L construct that has a different mechanism of action (MoA) than the co-administration of anti-PD-1 plus GITR-L and demonstrated a dose-dependent immunologically driven tumor growth inhibition in syngeneic, genetically engineered and xenograft humanized mouse tumor models. Combination of anti-PD-1-GITR-L with TGFβ inhibition or chemotherapy (gemcitabine), respectively, resulted in tumor remission in immunogenically cold and checkpoint blockade resistant mouse models. Dose-dependent correlations between target saturation and Ki67 and TIGIT up-regulation on memory T cells have been observed following a single dose of anti-PD-1-GITR-L bispecific in mice and non-human primates. Anti-PD-1-GITR-L thus represents a novel bispecific approach for directing GITR agonism for cancer immunotherapy.

overall_design: 5 mice per treatment arm were treated using 3 doses of test agents on days 7, 9 and 11 after tumor inoculation (tumors approx 100mm3 day 7). Test articles are isotype control 0.3mg/kg, anti-muPD-1 0.3mg/kg, isotype-muGITR-L 0.43mg/kg, 1:1 combination (anti-muPD-1 0.3mg/kg plus isotype-muGITR-L 0.43mg/kg), and anti-muPD-1-muGITR-L bispecific 0.43mg/kg. FFPE samples collected days 8 and 10 for FFPE production of tumors and draining lymph nodes. RNA run on NanoString mouse PanCancer immune profiling panel C3400.

first: Hamsell

last: Alvarez Jares

first: Susan

last: Rhodes


title: Single-cell mRNA sequencing of anti-PD-1 GITR-L bispecific antibody treated CT26 mouse tumor model infiltrating leukocytes

overall_design: Two tumor samples per treatment group were sequenced for single-cell gene expression via the 10x workflow

last: Jares

first: Zoltan

last: Dezso


title: Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

summary: Using 10x Genomics Chromium Single Cell 3’ RNAseq platform, we sequenced human stem cell derived pancreatic islet cells during different stages of development and maturation process. We optimized a protocol for pancreatic endocrine differentiation, particularly focusing on the final, extended maturation stage during which significant reorganization of the cytoarchitecture of islet-like aggregates took place correlating with a remarkable maturation of glucose-induced insulin secretion. The transcriptomic changes during the time-course were combined with detailed physiological studies including dynamic insulin secretion assays, respirometry measurements, electrophysiological profiling as well as imaging of calcium and cAMP signaling and exocytosis.

overall_design: 18 scRNAseq samples were analyzed.

first: Diego

last: Balboa

first: Tom

last: Barsby

first: Väinö

last: Lithovius

first: Jonna

last: Saarimäki-Vire

first: Muhmmad

last: Omar-Hmeadi

first: Oleg

last: Dyachok

first: Hossam

last: Montaser

first: Per-Eric

last: Lund

first: Mingyu

last: Yang

first: Hazem

last: Ibrahim

first: Anna

last: Näätänen

first: Vikash

last: Chandra

first: Helena

last: Vihinen

first: Eija

last: Jokitalo

first: Jarkko

last: Ustinov

first: Anni

middle: I

last: Nieminen

first: Emilia

last: Kuuluvainen

first: Ville

last: Hietakangas

first: Pekka

last: Katajisto

first: Joey

last: Lau

first: Per-Ola

last: Carlsson

first: Sebastian

last: Barg

first: Anders

last: Tengholm

first: Timo

last: Otonkoski


title: RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins

status: Public on Dec 18 2021

city: Moscow

first: Alexey

middle: A.

last: Gavrilov

address: 34/5 Vavilova street

country: Russia

institute: Institute of Gene Biology of the Russian Academy of Sciences

summary: Nuclear noncoding RNAs are key regulators of gene expression and chromatin organization. Here we present RedChIP, a technique combining RNA-DNA proximity ligation and chromatin immunoprecipitation for identification of RNAs associated with genomic regions occupied by a protein of interest. We identify a spectrum of cis and trans acting lincRNAs enriched at Polycomb and CTCF binding sites, which may be involved in Polycomb mediated gene repression and chromatin looping.

overall_design:
The RedChIP experimental procedure for mapping RNA-DNA interactome mediated by protein of interest is based on Red-C protocol with protein immunoprecipitation step followed by high-throughput sequencing of the chimeric RNA-DNA molecules.
BioProject: PRJNA728474; SRA Study accession: SRP319077

middle: A

first: Rinat

last: Sultanov


title: The transcriptome profile of MOSJ-Dkk1 cells treating with DkkMo in vitro and in vivo.

status: Public on Dec 19 2021

city: Temple

first: Carl

last: Gregory

state: Texas

address: 5701 Airport Road

department: Molecular and Cellular Medicine

institute: Texas A&M Health Sciences Center

summary: Next-generation sequencing (NGS) has revolutionized the systems-based analysis of cellular pathways. Our aim is to use RNA-seq to reveal the mechanisms by which DkkMo suppresses tumor expansion both in vitro and in vivo.

overall_design: In vitro sample was from MOSJ-Dkk1 cultures. in vivo sample was from mouse MOSJ-Dkk1 xenograft. High throughput sequencing was performed on a NovaSeq 6000 system, recovering 70 million(in vitro) and 150 million(in vivo) raw reads per sample in 150 bp paired-end format respectively. The reads were aligned to the GRCm38.98 reference genome

first: Simin

last: Pan


title: Gene expression analysis in recessive dystrophic epidermolysis bullosa skin highlights drug repurposing opportunities to improve wound healing

first: Chrysanthi

last: Ainali

state: England

address: Strand

institute: KING'S COLLEGE LONDON

summary: The molecular basis to the chronic inflammation and scarring in RDEB skin has been partially characterized but the current data on cytokine, chemokine, matrix and cell pathologies in RDEB skin have yet to yield new interventional therapies for patients. Here we performed a detailed assessment of RDEB wound gene expression in combination with a reverse transcriptomics analysis which indicate genes and drugs that could promote wound healing in RDEB.

overall_design: We collected 4mm punch biopsies of whole skin from the edge of chronic wounds in RDEB subjects (EBw), 6 samples from intact/normal skin from the same RDEB individuals (EBn), and 6 samples from healthy controls (HC) matched for age, sex, ethnicity, body site, and time of biopsy. Samples were homogenised using a hand-held Polytron in lysis buffer, and RNA was extracted and quantified. Gene expression profiling was performed using the Illumina whole-genome expression array HumanHT-12 v4.0 Expression BeadChip.

first: John

last: McGrath

first: Alexandros

last: Onoufriadis


title: Epigenetic basis of oncogenic-Kras mediated epithelial-cellular proliferation and plasticity

first: Preetish

last: Kadur Lakshminarasimha Murthy


title: Blood-based miRNA biomarkers as correlates of brain-based miRNA expression

status: Public on Dec 14 2021

city: San Antonio

first: Melanie

middle: Anita

last: Carless

address: One UTSA Circle

institute: The University of Texas at San Antonio

summary: To better understand the relationship between peripheral blood- and brain-based epigenetic activity, we conducted a pilot study on captive baboons (Papio hamadryas) to investigate correlations between miRNA expression in peripheral blood mononuclear cells (PBMCs) and 14 different cortical and subcortical brain regions, represented by two study groups comprised of 4 and 6 animals. Using next-generation sequencing, we identified 362 miRNAs expressed at ≥10 read counts in 80% or more of the brain samples analyzed. Nominally significant pairwise correlations (one-sided P<0.05) between peripheral blood and mean brain expression levels of individual miRNAs were observed for 39 and 44 miRNAs in each group. When miRNA expression levels were averaged across animals within the groups, pairwise correlations between PBMCs and individual brain regions are all highly significant (P<2.2x10^-16), although correlations between brain regions are markedly stronger (rs=0.86-0.99) than those between blood and brain (rs=0.47-0.57). Principal component analysis revealed differentiation in miRNA expression between peripheral blood and the brain regions for the first component (accounting for ~75% of variance). Linear mixed effects modeling attributed most of the variance in expression to differences between miRNAs (>70%), with non-significant 7.5% and 13.1% assigned to differences between blood and brain-based samples in the two study groups. Hierarchical UPGMA clustering revealed two major co-expression branches that are evident in both groups, with one comprised of miRNAs hyper-expressed in blood relative to the brain samples, exhibiting an enrichment of miRNAs expressed in immune cells (CD14+, CD15+, CD19+, CD3+, and CD56+ leukocytes) among the top blood-brain correlates. In the other major branch, hypo-expression in the blood samples was observed, with enrichment for miRNAs associated with Alzheimer’s Disease among its top correlates. Although some differentiation was observed between tissue types, these preliminary findings reveal wider correlated patterns between blood- and brain-expressed miRNAs, suggesting the utility of blood-based miRNA profiling for investigating by proxy the epigenetic underpinnings of neurological and neuroinflammatory processes in the brain.

overall_design: miRNAseq characterization and comparison of peripheral blood mononuclear cells and brain samples obtained from captive baboons.

first: Mark

last: Kos


title: Afatinib and Pembrolizumab for Recurrent or Metastatic Head and Neck Squamous Cell Carcinoma (ALPHA Study): A Phase II Study with Biomarker Analysis

status: Public on Dec 10 2021

city: Taipei

first: Hsiang-Fong

last: Kao

state: Please Select

address: No.57, Ln. 155, Sec. 3, Keelung Rd.,

department: Medical Oncology

country: Taiwan

institute: National Taiwan University Cancer Center

summary:
Afatinib may augment pembrolizumab therapy and improve the ORR in HNSCC patients.
The paired tissue analysis showed that afatinib, an epidermal growth factor (EGFR) tyrosine kinase inhibitor, may enhance antigen presentation, natural killer cell–mediated cytotoxicity, and immune reactions. We also identified unaltered methyl-thioadenosine phosphorylase (MTAP) levels, EGFR amplification, and high programmed death-ligand 1 expression as possible predictive biomarkers for therapeutic outcomes.

overall_design: A phase II, single arm study using pembrolizumab and afatinib for platinum-refractory head and neck squamous cell carcinoma patients. Pre-treatment and post-treatment biopsy were used for analysis.

first: Jean-San

last: Chia

first: Ruey-Long

last: Hong


title: Transcriptional profiling of mouse Th17 cells treated with bacterial metabolites 3-oxo-lithocholic acid [3-oxoLCA] and isolithocholic acid [isoLCA]

city: Boston

first: Eunha

last: Kim

state: MA

address: 77 Ave Louis Pasteur

department: Immunology

country: USA

institute: Harvard Medical School

summary: We report transcriptional profiling of mouse Th17 cells activated and expanded in vitro in the presence of Th17-inhibitory bacterial metabolites 3-oxoLCA and isoLCA.

overall_design: Naïve CD4 T cells  from C57BL/6J mice were activated and expanded in Th17 polarization condition for 3 days in vitro. 3-OxoLCA and isoLCA were added 18 hours after T cell receptor (TCR) activation by anti-CD3 and anti-CD28 antibodies.

first: Donggi

last: Paik

first: Jun

middle: R

last: Huh


title: PCW-1001, a novel pyrazole compound, modulates the expression of DNA damage response genes

status: Public on Dec 15 2021

city: Seoul

first: Minsung

last: Kang

address: 75 Nowon-ro

institute: Korea institute of radiological and medical sciences

summary: As pyrazole and its derivatives have a wide range of biological activities, including anticancer activity, the design of novel pyrazole derivatives has emerged as an important research field. This study describes a novel pyrazole derivative that exerts antitumor and radiosensitizing activities in breast cancer both in vitro and in vivo. We synthesized a novel pyrazole compound N,N-dimethyl-N'-(3-(1-(4-(trifluoromethyl)phenyl)-1H-pyrazol-4-yl)phenyl)azanesulfonamide (PCW-1001) and showed that it inhibited several oncogenic properties of breast cancer both in vitro and in vivo. PCW-1001 induced apoptosis in several breast cancer cell lines. Transcriptome analysis of PCW-1001-treated cells showed that it regulated the DNA damage response, suggesting its potential use in radiotherapy. Indeed, PCW-1001 enhanced the radiation sensitivity of breast cancer cells by modulating the expression of DNA damage response genes. Therefore, our data describe a novel pyrazole compound, PCW-1001, with antitumor and radiosensitizer activities in breast cancer.

overall_design: MCF7 cells were treated with DMSO and 10 μM PCW-1001 for 24 h, and afterward, cell lysates were analyzed using the nCounter®PanCancer Pathways Panel (770 genes) in accordance with the manufacturer’s protocol. Quantitative changes in mRNA levels were analyzed and clustered using the nSolver software (NanoString Technologies).

first: Ah-Young

first: Jae-Sung


title: Single cell transcriptome analysis of distal adult human lung airway cells

city: San Francisco

first: Jaymin

last: Kathiriya

state: CA

address: 513 Parnassus Ave

institute: University of California San Francisco

summary: To comprehensively study the heterogeneity within distal airway epithelium, we performed single cell transcriptomic analysis of the normal human donor lung samples. Our analysis reveals that secretory (club) and basal cells in the distal lung airway epithelial cells are highly heterogenous. Further interrogation of secretory cells identified a subpopulation with potential for alveolar differentiation in vitro, implicating distal lung airway secretory cells as new candidates in alveolar repair and regeneration.

overall_design: Single cells were isolated via flow cytometry based on EPCAM and HTII-280 from an unidentified human donor lung tissue

first: Harold

last: Chapman


title: Differential gene expression in MCF10A cells upon stable co-upregulation of flotillins 1 and 2

status: Public on Dec 06 2021

city: Montpellier

first: Stéphane

last: Bodin

address: 1919 route de Mende

department: Montpellier Cell Biology Research Center

country: France

institute: CNRS - University of Montpellier

summary: The simultaneous overexpression of flotillins 1 and 2 is observed in many cancers and considered as a marker of poor prognosis, notably in breast cancer. Flotillin-overexpression was shown to participate in the invasive behavior of cancer cell leading to metastasis. To better characterize the specific contribution of flotillin upregulation in the acquisition of cellular invasive properties, we stably expressed at high level exogenous flotillin 1 (HA-tagged) and flotillin 2 (mCherry tagged) in the non-tumoral mammary epithelial MCF10A human cells. The obtained cell line was named MCF10AF1F2. As a control, we generated in parallel the MCF10AmCherry cell line, stably expressing mCherry alone. We compared by RNA-sequencing (RNA-seq) the expression profiles of MCF10AmCh cells and MCF10AF1F2 cells. This allows to identify the gene expression changes and the downstream signaling pathways associated with flotillin upregulation.  Using two differential gene expression analysis pipelines (Tuxedo and DSeq2), we identified 232 upregulated and 570 downregulated genes (802 genes in total, fold change 2.8, P<0.05) in MCF10AF1F2 cells compared with control cells. Gene ontology (GO) cluster analysis) revealed that flotillin upregulation was associated with deregulation of genes involved in extracellular matrix, cell adhesion, migration, differentiation, apoptosis and signaling pathways, particularly MAP kinases. Because these data suggested that MCF10AF1F2 cells underwent epithelio to mesenchymal transition (EMT), we compared the list of genes differentially in MCF10AF1F2 cells with the EMT transcriptional signature previously established by a meta-analysis (Gröger et al al. PloSOne 2012, https://doi.org/10.1371/journal.pone.0051136).  One third (22/67) of the upregulated genes and more than half (39/62) of the downregulated genes in this EMT signature overlapped with the genes deregulated upon flotillin overexpression in MCF10A cells. Using complementary approaches, we confirmed that upregulation of flotillins un non-tumoral mammary epithelial cells is sufficient to promote EMT.

overall_design: mRNA profiles from MCF10AmCh cells (stably expressing mCherry) and MCF10AF1F2 cells (stably co-expressing Flotillin1-HA and Flotillin2-mCherry) were generated by deep sequencing, in triplicate, using an Illumina HiSeq 4000

first: Cécile

last: Gauthier-Rouvière

first: Mallory

last: Genest

first: Franck

last: Comunale


title: RNA-Seq study of cartilage tissue regeneration in vivo using a biomimetic 3D scaffold

status: Public on Dec 07 2021

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

institute: Cardiff University

summary: Analysis of transcriptome changes in rabbit cartilage tissue following surgical induction of critical size defects on knee joints with or without collagen-chondroitin sulphate (CLCS) 3D scaffolds.

overall_design: Total RNA was obtained from cartilage tissue of rabbits that underwent surgical procedures to generate critical size defects in the knee joint. The regenerative effects of a collagen-chondroitin sulphate 3D scaffold were compared to untreated controls.

first: Guillermo

last: Bauza


title: Derivation of trophoblast stem cells (TSTerm cells) from term placentas (RNA-seq)

status: Public on Dec 21 2021

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

institute: Ming Chuan Univ

summary:
Purpose: To understand the regulatiory mechanisms of trophoblast stemness and differentiation gene expression.
Methods: Three trophoblast stem cell lines were derived from individual term placnta, TSTerm #1 and TSTerm #2 TSTerm #3. The three TSTerm cell lines were differentiated into syncytiotrophoblasts (STB：ST-TSTerm #1, ST-TSTerm #2, and ST-TSTerm #3) and extravillous trophoblasts (EVT：EVT-TSTerm #1, EVT-TSTerm #2 and EVT-TSTerm #3). TS#1GCM1-KO cell line was derived from TSTerm #1 cells by depletion of GCM1 gene. ST-TS#1GCM1-KO cells were differentiated from TS#1GCM1-KO cells. Additionally, CTBTerm #1, CTBTerm #2, and CTBTerm #3 were isolated from individual placentae. The mRNA profiles of tatal fourteen samples as mentioned above were generated by sequencing, using NovaSeq Sequencing System. The raw data were analyzed by CLC Genomics Workbench v10.
Conclusion: We elucidated reciprocal regulation of trophoblast stemness and differentiation gene expression, which facilitated the derivation of TS cells from term placentas.

overall_design: RNA-seq of fourteen cell lines

first: Liang-Jie

last: Wang

first: Hungwen

last: Chen


title: Next Generation Sequencing Facilitates Quantitative Analysis of the implication of autophagy in liver CD11c+ cells Transcriptomes

city: Los Angeles

first: Georges Doumet

last: HELOU

address: 1450 Biggy St, NRT5505, Keck School of Medicine

department: Molecular Microbiology and Immunology

institute: University of Southern California

summary: Autophagy is an essential mechanism involved in the degradation of cellular material and plays an important role in the maintenance of liver homeostasis. This study was designed to explore the effect of Autophagy-related 5 (Atg5) deficiency in liver CD11c+ cells in mice fed high-fat diet (HFD).

overall_design: mRNA profiles of isolated liver CD11c+ cells from WT and Atg5 CD11cKO mice were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.

first: D

middle: G

last: Helou

first: O

last: Akbari

first: L

last: Galle-Treger


title: Total RNA-Seq on control, Polycomb null and H3K27R mutant mESCs and EpiLCs

city: Copenhagen

first: Aditya

last: Sankar

email: cnj376@ku.dk, aditya.sankar@embl.de

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

summary: Here we report the results of total RNASeq derived transcriptomes from naïve pluripotent mouse embryonic stem cells (mESCs) and pre-gastrulation epilblast like cells (EpiLCs) derived from mESCs following a 48 hour treatment with activin, FGF and knockout serum replacement as described in Hayashi et al., Cell 2011 (PMID: 21820164). We observe a strong concordance between histone mutant (H3K27R) cell lines and Polycomb null (SUZ12 knockout) steady state mESCs, with the primary effect of mutation resulting in gene de-repression. H3K27me3 is found strongly correlated with gene repression while H3K27ac is found strongly correlative with gene expression. We also show the lack of requirement for H3K27ac for gene activation upon differentiation of promoter or enhancer mediated EpiLC gene markers, leading us to conclude that transcription occurs independently of the requirement of H3K27ac.

overall_design:
Transcriptomes of mESCs and EpiLCs in biological triplicates were assayed from total RNA isolated in control (ABE), SUZ12 knockout or different H3K27R mutant cell lines
Processed data are in Microsoft Excel worksheets with DeSeq2 comparisons between mutant and control mESC transcriptomes, mutant EpiLCs vs respective mESC transcriptomes and quantification of relevant ChIP signals of unchanged, down or upregulated genes at the transcriptomic levels.

first: Faizaan

last: Mohammad

first: Hua


title: Molecular signature predictive of long-term liver fibrosis progression to inform anti-fibrotic drug development

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

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

overall_design: Refer to individual Series


title: HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network [RNA-Seq]

city: Harbin

first: Yuhong

address: NO 23 Youzheng Street

country: China

institute: First Hospital of Harbin Medical University

summary:
Purpose: To explore the potential integrated molecular network by long non-coding RNA HOXA11-AS in keloid fibroblast
Methods:  Using primary cultured keloid-derived fibroblasts (sample 0), small interfering RNAs were designed and transfected into two keloid fibroblast samples (samples 1 and 2) to knockdown HOXA11-AS. One nonspecific transfection control (sample 3) and one blank control (sample 4) were used to remove nonspecific overlap from the studied group. The lncRNAs, messenger RNAs (mRNAs), and microRNAs (miRNAs) of five samples were sequenced to identify differentially expressed (DE) profiles in HOXA11-AS-knockdown keloid fibroblasts in samples 1 and 2, which facilitated removal of overlap with the nonspecific controls (samples 3 and 4). Using stepwise bioinformatic analysis, DE lncRNA and mRNAs characterized by close and natural antisense relationship were constructed into an interactive network by bioinformatic analysis. Based on this network, a lncRNA–mRNA–protein interaction network was extended by integration of the human protein–protein interaction (PPI) network. The Page Rank algorithm was used to score each mRNA in the extended LMN network to reveal significant functioning genes. Next, screened genes were validated by real-time PCR and western blot ting. Validated genes were used to construct a competing endogenous network based on DE miRNA profiles.
Results: SNED1, NIPAL3, and VTN were detected significantly changed in HOXA11-AS-knockdown keloid fibroblasts. Only NIPAL3 was predicted to be involved in an intergated network for HOXA11-AS via three competing endogenous miRNAs (hsa-miRNA-19a-3p, hsa-miR-141-3p, and hsa-miR-140- 5p).
Conclusion: An interactive molecular network of HOXA11-AS–three miRNAs–NIPAL3 was predicted in keloid fibroblasts

overall_design: Using primary cultured keloid-derived fibroblasts (sample 0), small interfering RNAs were designed and transfected into two keloid fibroblast samples (samples 1 and 2) to knockdown HOXA11-AS. One nonspecific transfection control (sample 3) and one blank control (sample 4) were used to remove nonspecific overlap from the studied group. Comparison between sample 1 and sample 0, sample 2 and sample 0,sample 3 and sample 0 as well as between sample 4 and sample 0 was respectively performed for differentially experessed (DE) profiles of lncRNA, mRNA or miRNA.

first: Xiaojie

last: Sun

first: Qiang

first: Wei